1
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Salveson PJ, Moyer AP, Said MY, Gӧkçe G, Li X, Kang A, Nguyen H, Bera AK, Levine PM, Bhardwaj G, Baker D. Expansive discovery of chemically diverse structured macrocyclic oligoamides. Science 2024; 384:420-428. [PMID: 38662830 DOI: 10.1126/science.adk1687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 03/22/2024] [Indexed: 05/03/2024]
Abstract
Small macrocycles with four or fewer amino acids are among the most potent natural products known, but there is currently no way to systematically generate such compounds. We describe a computational method for identifying ordered macrocycles composed of alpha, beta, gamma, and 17 other amino acid backbone chemistries, which we used to predict 14.9 million closed cycles composed of >42,000 monomer combinations. We chemically synthesized 18 macrocycles predicted to adopt single low-energy states and determined their x-ray or nuclear magnetic resonance structures; 15 of these were very close to the design models. We illustrate the therapeutic potential of these macrocycle designs by developing selective inhibitors of three protein targets of current interest. By opening up a vast space of readily synthesizable drug-like macrocycles, our results should considerably enhance structure-based drug design.
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Affiliation(s)
- Patrick J Salveson
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Adam P Moyer
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Meerit Y Said
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Gizem Gӧkçe
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Xinting Li
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Alex Kang
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Hannah Nguyen
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Asim K Bera
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Paul M Levine
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Gaurav Bhardwaj
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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2
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Krishna R, Wang J, Ahern W, Sturmfels P, Venkatesh P, Kalvet I, Lee GR, Morey-Burrows FS, Anishchenko I, Humphreys IR, McHugh R, Vafeados D, Li X, Sutherland GA, Hitchcock A, Hunter CN, Kang A, Brackenbrough E, Bera AK, Baek M, DiMaio F, Baker D. Generalized biomolecular modeling and design with RoseTTAFold All-Atom. Science 2024; 384:eadl2528. [PMID: 38452047 DOI: 10.1126/science.adl2528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 02/27/2024] [Indexed: 03/09/2024]
Abstract
Deep-learning methods have revolutionized protein structure prediction and design but are presently limited to protein-only systems. We describe RoseTTAFold All-Atom (RFAA), which combines a residue-based representation of amino acids and DNA bases with an atomic representation of all other groups to model assemblies that contain proteins, nucleic acids, small molecules, metals, and covalent modifications, given their sequences and chemical structures. By fine-tuning on denoising tasks, we developed RFdiffusion All-Atom (RFdiffusionAA), which builds protein structures around small molecules. Starting from random distributions of amino acid residues surrounding target small molecules, we designed and experimentally validated, through crystallography and binding measurements, proteins that bind the cardiac disease therapeutic digoxigenin, the enzymatic cofactor heme, and the light-harvesting molecule bilin.
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Affiliation(s)
- Rohith Krishna
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Jue Wang
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Woody Ahern
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98105, USA
| | - Pascal Sturmfels
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98105, USA
| | - Preetham Venkatesh
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
- Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA 98105, USA
| | - Indrek Kalvet
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98105, USA
| | - Gyu Rie Lee
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98105, USA
| | | | - Ivan Anishchenko
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Ian R Humphreys
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Ryan McHugh
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
- Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA 98105, USA
| | - Dionne Vafeados
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Xinting Li
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | | | - Andrew Hitchcock
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - C Neil Hunter
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Alex Kang
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Evans Brackenbrough
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Asim K Bera
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Minkyung Baek
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98105, USA
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3
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de Haas RJ, Brunette N, Goodson A, Dauparas J, Yi SY, Yang EC, Dowling Q, Nguyen H, Kang A, Bera AK, Sankaran B, de Vries R, Baker D, King NP. Rapid and automated design of two-component protein nanomaterials using ProteinMPNN. Proc Natl Acad Sci U S A 2024; 121:e2314646121. [PMID: 38502697 PMCID: PMC10990136 DOI: 10.1073/pnas.2314646121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 02/20/2024] [Indexed: 03/21/2024] Open
Abstract
The design of protein-protein interfaces using physics-based design methods such as Rosetta requires substantial computational resources and manual refinement by expert structural biologists. Deep learning methods promise to simplify protein-protein interface design and enable its application to a wide variety of problems by researchers from various scientific disciplines. Here, we test the ability of a deep learning method for protein sequence design, ProteinMPNN, to design two-component tetrahedral protein nanomaterials and benchmark its performance against Rosetta. ProteinMPNN had a similar success rate to Rosetta, yielding 13 new experimentally confirmed assemblies, but required orders of magnitude less computation and no manual refinement. The interfaces designed by ProteinMPNN were substantially more polar than those designed by Rosetta, which facilitated in vitro assembly of the designed nanomaterials from independently purified components. Crystal structures of several of the assemblies confirmed the accuracy of the design method at high resolution. Our results showcase the potential of deep learning-based methods to unlock the widespread application of designed protein-protein interfaces and self-assembling protein nanomaterials in biotechnology.
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Affiliation(s)
- Robbert J. de Haas
- Department of Physical Chemistry and Soft Matter, Wageningen University and Research, Wageningen6078 WE, The Netherlands
| | - Natalie Brunette
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Alex Goodson
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Justas Dauparas
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Sue Y. Yi
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Erin C. Yang
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Quinton Dowling
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Hannah Nguyen
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Asim K. Bera
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Renko de Vries
- Department of Physical Chemistry and Soft Matter, Wageningen University and Research, Wageningen6078 WE, The Netherlands
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
- HHMI, Seattle, WA98195
| | - Neil P. King
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
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4
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Sahtoe DD, Andrzejewska EA, Han HL, Rennella E, Schneider MM, Meisl G, Ahlrichs M, Decarreau J, Nguyen H, Kang A, Levine P, Lamb M, Li X, Bera AK, Kay LE, Knowles TPJ, Baker D. Design of amyloidogenic peptide traps. Nat Chem Biol 2024:10.1038/s41589-024-01578-5. [PMID: 38503834 DOI: 10.1038/s41589-024-01578-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 02/09/2024] [Indexed: 03/21/2024]
Abstract
Segments of proteins with high β-strand propensity can self-associate to form amyloid fibrils implicated in many diseases. We describe a general approach to bind such segments in β-strand and β-hairpin conformations using de novo designed scaffolds that contain deep peptide-binding clefts. The designs bind their cognate peptides in vitro with nanomolar affinities. The crystal structure of a designed protein-peptide complex is close to the design model, and NMR characterization reveals how the peptide-binding cleft is protected in the apo state. We use the approach to design binders to the amyloid-forming proteins transthyretin, tau, serum amyloid A1 and amyloid β1-42 (Aβ42). The Aβ binders block the assembly of Aβ fibrils as effectively as the most potent of the clinically tested antibodies to date and protect cells from toxic Aβ42 species.
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Affiliation(s)
- Danny D Sahtoe
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- HHMI, University of Washington, Seattle, WA, USA.
- Hubrecht Institute, Utrecht, the Netherlands.
| | - Ewa A Andrzejewska
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Hannah L Han
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Enrico Rennella
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Georg Meisl
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Maggie Ahlrichs
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Justin Decarreau
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Hannah Nguyen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Paul Levine
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Mila Lamb
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Xinting Li
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Asim K Bera
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Lewis E Kay
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- HHMI, University of Washington, Seattle, WA, USA.
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5
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Huddy TF, Hsia Y, Kibler RD, Xu J, Bethel N, Nagarajan D, Redler R, Leung PJY, Weidle C, Courbet A, Yang EC, Bera AK, Coudray N, Calise SJ, Davila-Hernandez FA, Han HL, Carr KD, Li Z, McHugh R, Reggiano G, Kang A, Sankaran B, Dickinson MS, Coventry B, Brunette TJ, Liu Y, Dauparas J, Borst AJ, Ekiert D, Kollman JM, Bhabha G, Baker D. Blueprinting extendable nanomaterials with standardized protein blocks. Nature 2024; 627:898-904. [PMID: 38480887 PMCID: PMC10972742 DOI: 10.1038/s41586-024-07188-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 02/09/2024] [Indexed: 03/26/2024]
Abstract
A wooden house frame consists of many different lumber pieces, but because of the regularity of these building blocks, the structure can be designed using straightforward geometrical principles. The design of multicomponent protein assemblies, in comparison, has been much more complex, largely owing to the irregular shapes of protein structures1. Here we describe extendable linear, curved and angled protein building blocks, as well as inter-block interactions, that conform to specified geometric standards; assemblies designed using these blocks inherit their extendability and regular interaction surfaces, enabling them to be expanded or contracted by varying the number of modules, and reinforced with secondary struts. Using X-ray crystallography and electron microscopy, we validate nanomaterial designs ranging from simple polygonal and circular oligomers that can be concentrically nested, up to large polyhedral nanocages and unbounded straight 'train track' assemblies with reconfigurable sizes and geometries that can be readily blueprinted. Because of the complexity of protein structures and sequence-structure relationships, it has not previously been possible to build up large protein assemblies by deliberate placement of protein backbones onto a blank three-dimensional canvas; the simplicity and geometric regularity of our design platform now enables construction of protein nanomaterials according to 'back of an envelope' architectural blueprints.
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Affiliation(s)
- Timothy F Huddy
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Yang Hsia
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Ryan D Kibler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Jinwei Xu
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Neville Bethel
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | | | - Rachel Redler
- Department of Cell Biology, NYU School of Medicine, New York, NY, USA
| | - Philip J Y Leung
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA
| | - Connor Weidle
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alexis Courbet
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Erin C Yang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Biological Physics, Structure and Design, University of Washington, Seattle, WA, USA
| | - Asim K Bera
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Nicolas Coudray
- Department of Cell Biology, NYU School of Medicine, New York, NY, USA
- Applied Bioinformatics Laboratories, NYU School of Medicine, New York, NY, USA
- Division of Precision Medicine, Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - S John Calise
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Fatima A Davila-Hernandez
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Hannah L Han
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Kenneth D Carr
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Zhe Li
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Ryan McHugh
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Gabriella Reggiano
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Miles S Dickinson
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Brian Coventry
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - T J Brunette
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Yulai Liu
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Justas Dauparas
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Andrew J Borst
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Damian Ekiert
- Department of Cell Biology, NYU School of Medicine, New York, NY, USA
- Applied Bioinformatics Laboratories, NYU School of Medicine, New York, NY, USA
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Gira Bhabha
- Applied Bioinformatics Laboratories, NYU School of Medicine, New York, NY, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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6
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Vázquez Torres S, Leung PJY, Venkatesh P, Lutz ID, Hink F, Huynh HH, Becker J, Yeh AHW, Juergens D, Bennett NR, Hoofnagle AN, Huang E, MacCoss MJ, Expòsit M, Lee GR, Bera AK, Kang A, De La Cruz J, Levine PM, Li X, Lamb M, Gerben SR, Murray A, Heine P, Korkmaz EN, Nivala J, Stewart L, Watson JL, Rogers JM, Baker D. De novo design of high-affinity binders of bioactive helical peptides. Nature 2024; 626:435-442. [PMID: 38109936 PMCID: PMC10849960 DOI: 10.1038/s41586-023-06953-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 12/07/2023] [Indexed: 12/20/2023]
Abstract
Many peptide hormones form an α-helix on binding their receptors1-4, and sensitive methods for their detection could contribute to better clinical management of disease5. De novo protein design can now generate binders with high affinity and specificity to structured proteins6,7. However, the design of interactions between proteins and short peptides with helical propensity is an unmet challenge. Here we describe parametric generation and deep learning-based methods for designing proteins to address this challenge. We show that by extending RFdiffusion8 to enable binder design to flexible targets, and to refining input structure models by successive noising and denoising (partial diffusion), picomolar-affinity binders can be generated to helical peptide targets by either refining designs generated with other methods, or completely de novo starting from random noise distributions without any subsequent experimental optimization. The RFdiffusion designs enable the enrichment and subsequent detection of parathyroid hormone and glucagon by mass spectrometry, and the construction of bioluminescence-based protein biosensors. The ability to design binders to conformationally variable targets, and to optimize by partial diffusion both natural and designed proteins, should be broadly useful.
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Affiliation(s)
- Susana Vázquez Torres
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA, USA
| | - Philip J Y Leung
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Molecular Engineering, University of Washington, Seattle, WA, USA
| | - Preetham Venkatesh
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA, USA
| | - Isaac D Lutz
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Fabian Hink
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Huu-Hien Huynh
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Jessica Becker
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Andy Hsien-Wei Yeh
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - David Juergens
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Molecular Engineering, University of Washington, Seattle, WA, USA
| | - Nathaniel R Bennett
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Molecular Engineering, University of Washington, Seattle, WA, USA
| | - Andrew N Hoofnagle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Eric Huang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Marc Expòsit
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Molecular Engineering, University of Washington, Seattle, WA, USA
| | - Gyu Rie Lee
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Asim K Bera
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Joshmyn De La Cruz
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Paul M Levine
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Xinting Li
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Mila Lamb
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Stacey R Gerben
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Analisa Murray
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Piper Heine
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Elif Nihal Korkmaz
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Jeff Nivala
- School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA
| | - Lance Stewart
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Joseph L Watson
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
| | - Joseph M Rogers
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark.
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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7
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Sumida K, Núñez-Franco R, Kalvet I, Pellock SJ, Wicky BIM, Milles LF, Dauparas J, Wang J, Kipnis Y, Jameson N, Kang A, De La Cruz J, Sankaran B, Bera AK, Jiménez-Osés G, Baker D. Improving Protein Expression, Stability, and Function with ProteinMPNN. J Am Chem Soc 2024; 146:2054-2061. [PMID: 38194293 PMCID: PMC10811672 DOI: 10.1021/jacs.3c10941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/03/2023] [Accepted: 12/05/2023] [Indexed: 01/10/2024]
Abstract
Natural proteins are highly optimized for function but are often difficult to produce at a scale suitable for biotechnological applications due to poor expression in heterologous systems, limited solubility, and sensitivity to temperature. Thus, a general method that improves the physical properties of native proteins while maintaining function could have wide utility for protein-based technologies. Here, we show that the deep neural network ProteinMPNN, together with evolutionary and structural information, provides a route to increasing protein expression, stability, and function. For both myoglobin and tobacco etch virus (TEV) protease, we generated designs with improved expression, elevated melting temperatures, and improved function. For TEV protease, we identified multiple designs with improved catalytic activity as compared to the parent sequence and previously reported TEV variants. Our approach should be broadly useful for improving the expression, stability, and function of biotechnologically important proteins.
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Affiliation(s)
- Kiera
H. Sumida
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Reyes Núñez-Franco
- Center
for Cooperative Research in Biosciences, Basque Research and Technology Alliance, Derio 48160, Spain
| | - Indrek Kalvet
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
- Howard
Hughes Medical Institute, University of
Washington, Seattle, Washington 98195, United States
| | - Samuel J. Pellock
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Basile I. M. Wicky
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Lukas F. Milles
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Justas Dauparas
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Jue Wang
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Yakov Kipnis
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
- Howard
Hughes Medical Institute, University of
Washington, Seattle, Washington 98195, United States
| | - Noel Jameson
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Alex Kang
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Joshmyn De La Cruz
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Banumathi Sankaran
- Berkeley
Center for Structural Biology, Molecular Biophysics, and Integrated
Bioimaging, Lawrence Berkeley Laboratory, Berkeley, California 94720, United States
| | - Asim K. Bera
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Gonzalo Jiménez-Osés
- Center
for Cooperative Research in Biosciences, Basque Research and Technology Alliance, Derio 48160, Spain
- Ikerbasque,
Basque Foundation for Science, Bilbao 48013, Spain
| | - David Baker
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States
- Howard
Hughes Medical Institute, University of
Washington, Seattle, Washington 98195, United States
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8
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An L, Said M, Tran L, Majumder S, Goreshnik I, Lee GR, Juergens D, Dauparas J, Anishchenko I, Coventry B, Bera AK, Kang A, Levine PM, Alvarez V, Pillai A, Norn C, Feldman D, Zorine D, Hicks DR, Li X, Sanchez MG, Vafeados DK, Salveson PJ, Vorobieva AA, Baker D. De novo design of diverse small molecule binders and sensors using Shape Complementary Pseudocycles. bioRxiv 2023:2023.12.20.572602. [PMID: 38187589 PMCID: PMC10769206 DOI: 10.1101/2023.12.20.572602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
A general method for designing proteins to bind and sense any small molecule of interest would be widely useful. Due to the small number of atoms to interact with, binding to small molecules with high affinity requires highly shape complementary pockets, and transducing binding events into signals is challenging. Here we describe an integrated deep learning and energy based approach for designing high shape complementarity binders to small molecules that are poised for downstream sensing applications. We employ deep learning generated psuedocycles with repeating structural units surrounding central pockets; depending on the geometry of the structural unit and repeat number, these pockets span wide ranges of sizes and shapes. For a small molecule target of interest, we extensively sample high shape complementarity pseudocycles to generate large numbers of customized potential binding pockets; the ligand binding poses and the interacting interfaces are then optimized for high affinity binding. We computationally design binders to four diverse molecules, including for the first time polar flexible molecules such as methotrexate and thyroxine, which are expressed at high levels and have nanomolar affinities straight out of the computer. Co-crystal structures are nearly identical to the design models. Taking advantage of the modular repeating structure of pseudocycles and central location of the binding pockets, we constructed low noise nanopore sensors and chemically induced dimerization systems by splitting the binders into domains which assemble into the original pseudocycle pocket upon target molecule addition.
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Affiliation(s)
- Linna An
- Department of Biochemistry, The University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Meerit Said
- Department of Biochemistry, The University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Long Tran
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
| | - Sagardip Majumder
- Department of Biochemistry, The University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Inna Goreshnik
- Department of Biochemistry, The University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Gyu Rie Lee
- Department of Biochemistry, The University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - David Juergens
- Department of Biochemistry, The University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Justas Dauparas
- Department of Biochemistry, The University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Ivan Anishchenko
- Department of Biochemistry, The University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Brian Coventry
- Department of Biochemistry, The University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Asim K. Bera
- Department of Biochemistry, The University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alex Kang
- Department of Biochemistry, The University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Paul M. Levine
- Department of Biochemistry, The University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Valentina Alvarez
- Department of Biochemistry, The University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Arvind Pillai
- Department of Biochemistry, The University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | | | - David Feldman
- BioInnovation Institute, DK2200 Copenhagen N, Denmark
| | - Dmitri Zorine
- Department of Biochemistry, The University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Derrick R. Hicks
- Department of Biochemistry, The University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Xinting Li
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | | | - Dionne K. Vafeados
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Patrick J. Salveson
- Department of Biochemistry, The University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | | | - David Baker
- Department of Biochemistry, The University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
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9
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Berhanu S, Majumder S, Müntener T, Whitehouse J, Berner C, Bera AK, Kang A, Liang B, Khan GN, Sankaran B, Tamm LK, Brockwell DJ, Hiller S, Radford SE, Baker D, Vorobieva AA. Sculpting conducting nanopore size and shape through de novo protein design. bioRxiv 2023:2023.12.20.572500. [PMID: 38187764 PMCID: PMC10769293 DOI: 10.1101/2023.12.20.572500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Transmembrane β-barrels (TMBs) are widely used for single molecule DNA and RNA sequencing and have considerable potential for a broad range of sensing and sequencing applications. Current engineering approaches for nanopore sensors are limited to naturally occurring channels such as CsgG, which have evolved to carry out functions very different from sensing, and hence provide sub-optimal starting points. In contrast, de novo protein design can in principle create an unlimited number of new nanopores with any desired properties. Here we describe a general approach to the design of transmembrane β-barrel pores with different diameter and pore geometry. NMR and crystallographic characterization shows that the designs are stably folded with structures close to the design models. We report the first examples of de novo designed TMBs with 10, 12 and 14 stranded β-barrels. The designs have distinct conductances that correlate with their pore diameter, ranging from 110 pS (~0.5 nm pore diameter) to 430 pS (~1.1 nm pore diameter), and can be converted into sensitive small-molecule sensors with high signal to noise ratio. The capability to generate on demand β-barrel pores of defined geometry opens up fundamentally new opportunities for custom engineering of sequencing and sensing technologies.
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Affiliation(s)
- Samuel Berhanu
- Department of Biochemistry, The University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Sagardip Majumder
- Department of Biochemistry, The University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | | | - James Whitehouse
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT
| | - Carolin Berner
- Structural Biology Brussel, Vrije Universiteit Brussel, Brussels, Belgium
- VUB-VIB Center for Structural Biology, Brussels, Belgium
| | - Asim K. Bera
- Department of Biochemistry, The University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alex Kang
- Department of Biochemistry, The University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Binyong Liang
- Department of Molecular Physiology and Biological Physics and Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22903, USA
| | - G Nasir Khan
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Lukas K. Tamm
- Department of Molecular Physiology and Biological Physics and Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22903, USA
| | - David J. Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT
| | | | - Sheena E. Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT
| | - David Baker
- Department of Biochemistry, The University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Anastassia A. Vorobieva
- Structural Biology Brussel, Vrije Universiteit Brussel, Brussels, Belgium
- VUB-VIB Center for Structural Biology, Brussels, Belgium
- VIB Center for AI and Computational Biology, Belgium
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10
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Davila-Hernandez FA, Jin B, Pyles H, Zhang S, Wang Z, Huddy TF, Bera AK, Kang A, Chen CL, De Yoreo JJ, Baker D. Directing polymorph specific calcium carbonate formation with de novo protein templates. Nat Commun 2023; 14:8191. [PMID: 38097544 PMCID: PMC10721895 DOI: 10.1038/s41467-023-43608-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/15/2023] [Indexed: 12/17/2023] Open
Abstract
Biomolecules modulate inorganic crystallization to generate hierarchically structured biominerals, but the atomic structure of the organic-inorganic interfaces that regulate mineralization remain largely unknown. We hypothesized that heterogeneous nucleation of calcium carbonate could be achieved by a structured flat molecular template that pre-organizes calcium ions on its surface. To test this hypothesis, we design helical repeat proteins (DHRs) displaying regularly spaced carboxylate arrays on their surfaces and find that both protein monomers and protein-Ca2+ supramolecular assemblies directly nucleate nano-calcite with non-natural {110} or {202} faces while vaterite, which forms first in the absence of the proteins, is bypassed. These protein-stabilized nanocrystals then assemble by oriented attachment into calcite mesocrystals. We find further that nanocrystal size and polymorph can be tuned by varying the length and surface chemistry of the designed protein templates. Thus, bio-mineralization can be programmed using de novo protein design, providing a route to next-generation hybrid materials.
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Affiliation(s)
- Fatima A Davila-Hernandez
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98105, USA
- Molecular Engineering Graduate Program, University of Washington, Seattle, WA, 98105, USA
| | - Biao Jin
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
- Department of Materials Science and Engineering, University of Washington, Seattle, WA, 98195, USA.
| | - Harley Pyles
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98105, USA
| | - Shuai Zhang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
- Department of Materials Science and Engineering, University of Washington, Seattle, WA, 98195, USA
| | - Zheming Wang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Timothy F Huddy
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98105, USA
| | - Asim K Bera
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98105, USA
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA, 98105, USA
| | - Chun-Long Chen
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
- Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA
| | - James J De Yoreo
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
- Department of Materials Science and Engineering, University of Washington, Seattle, WA, 98195, USA.
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, 98105, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98105, USA.
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11
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Bethel NP, Borst AJ, Parmeggiani F, Bick MJ, Brunette TJ, Nguyen H, Kang A, Bera AK, Carter L, Miranda MC, Kibler RD, Lamb M, Li X, Sankaran B, Baker D. Precisely patterned nanofibres made from extendable protein multiplexes. Nat Chem 2023; 15:1664-1671. [PMID: 37667012 PMCID: PMC10695826 DOI: 10.1038/s41557-023-01314-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/04/2023] [Indexed: 09/06/2023]
Abstract
Molecular systems with coincident cyclic and superhelical symmetry axes have considerable advantages for materials design as they can be readily lengthened or shortened by changing the length of the constituent monomers. Among proteins, alpha-helical coiled coils have such symmetric, extendable architectures, but are limited by the relatively fixed geometry and flexibility of the helical protomers. Here we describe a systematic approach to generating modular and rigid repeat protein oligomers with coincident C2 to C8 and superhelical symmetry axes that can be readily extended by repeat propagation. From these building blocks, we demonstrate that a wide range of unbounded fibres can be systematically designed by introducing hydrophilic surface patches that force staggering of the monomers; the geometry of such fibres can be precisely tuned by varying the number of repeat units in the monomer and the placement of the hydrophilic patches.
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Affiliation(s)
- Neville P Bethel
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Andrew J Borst
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Fabio Parmeggiani
- School of Chemistry, University of Bristol, Bristol, UK
- School of Biochemistry, University of Bristol, Bristol, UK
- Bristol Biodesign Institute, University of Bristol, Bristol, UK
| | - Matthew J Bick
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - T J Brunette
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Hannah Nguyen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Asim K Bera
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Marcos C Miranda
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Ryan D Kibler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Mila Lamb
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Xinting Li
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley Laboratory, Berkeley, CA, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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12
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Li Z, Wang S, Nattermann U, Bera AK, Borst AJ, Yaman MY, Bick MJ, Yang EC, Sheffler W, Lee B, Seifert S, Hura GL, Nguyen H, Kang A, Dalal R, Lubner JM, Hsia Y, Haddox H, Courbet A, Dowling Q, Miranda M, Favor A, Etemadi A, Edman NI, Yang W, Weidle C, Sankaran B, Negahdari B, Ross MB, Ginger DS, Baker D. Accurate computational design of three-dimensional protein crystals. Nat Mater 2023; 22:1556-1563. [PMID: 37845322 DOI: 10.1038/s41563-023-01683-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 09/07/2023] [Indexed: 10/18/2023]
Abstract
Protein crystallization plays a central role in structural biology. Despite this, the process of crystallization remains poorly understood and highly empirical, with crystal contacts, lattice packing arrangements and space group preferences being largely unpredictable. Programming protein crystallization through precisely engineered side-chain-side-chain interactions across protein-protein interfaces is an outstanding challenge. Here we develop a general computational approach for designing three-dimensional protein crystals with prespecified lattice architectures at atomic accuracy that hierarchically constrains the overall number of degrees of freedom of the system. We design three pairs of oligomers that can be individually purified, and upon mixing, spontaneously self-assemble into >100 µm three-dimensional crystals. The structures of these crystals are nearly identical to the computational design models, closely corresponding in both overall architecture and the specific protein-protein interactions. The dimensions of the crystal unit cell can be systematically redesigned while retaining the space group symmetry and overall architecture, and the crystals are extremely porous and highly stable. Our approach enables the computational design of protein crystals with high accuracy, and the designed protein crystals, which have both structural and assembly information encoded in their primary sequences, provide a powerful platform for biological materials engineering.
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Affiliation(s)
- Zhe Li
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Shunzhi Wang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Una Nattermann
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Biological Physics, Structure & Design, University of Washington, Seattle, WA, USA
| | - Asim K Bera
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Andrew J Borst
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Muammer Y Yaman
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Matthew J Bick
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Erin C Yang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Biological Physics, Structure & Design, University of Washington, Seattle, WA, USA
| | - William Sheffler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Byeongdu Lee
- X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL, USA
| | - Soenke Seifert
- X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL, USA
| | - Greg L Hura
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hannah Nguyen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Radhika Dalal
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Joshua M Lubner
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Yang Hsia
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Hugh Haddox
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alexis Courbet
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- HHMI, University of Washington, Seattle, WA, USA
| | - Quinton Dowling
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Marcos Miranda
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Andrew Favor
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA
| | - Ali Etemadi
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Medical Biotechnology Department, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Natasha I Edman
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Wei Yang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Connor Weidle
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Babak Negahdari
- Medical Biotechnology Department, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Michael B Ross
- Department of Chemistry, University of Massachusetts Lowell, Lowell, MA, USA
| | - David S Ginger
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- HHMI, University of Washington, Seattle, WA, USA.
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13
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Goldbach N, Benna I, Wicky BIM, Croft JT, Carter L, Bera AK, Nguyen H, Kang A, Sankaran B, Yang EC, Lee KK, Baker D. De novo design of monomeric helical bundles for pH-controlled membrane lysis. Protein Sci 2023; 32:e4769. [PMID: 37632837 PMCID: PMC10578055 DOI: 10.1002/pro.4769] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/10/2023] [Accepted: 08/24/2023] [Indexed: 08/28/2023]
Abstract
Targeted intracellular delivery via receptor-mediated endocytosis requires the delivered cargo to escape the endosome to prevent lysosomal degradation. This can in principle be achieved by membrane lysis tightly restricted to endosomal membranes upon internalization to avoid general membrane insertion and lysis. Here, we describe the design of small monomeric proteins with buried histidine containing pH-responsive hydrogen bond networks and membrane permeating amphipathic helices. Of the 30 designs that were experimentally tested, all expressed in Escherichia coli, 13 were monomeric with the expected secondary structure, and 4 designs disrupted artificial liposomes in a pH-dependent manner. Mutational analysis showed that the buried histidine hydrogen bond networks mediate pH-responsiveness and control lysis of model membranes within a very narrow range of pH (6.0-5.5) with almost no lysis occurring at neutral pH. These tightly controlled lytic monomers could help mediate endosomal escape in designed targeted delivery platforms.
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Affiliation(s)
- Nicolas Goldbach
- Institute for Protein DesignUniversity of WashingtonSeattleWashingtonUSA
- Molecular Life SciencesTechnical University of MunichMunichGermany
| | - Issa Benna
- Institute for Protein DesignUniversity of WashingtonSeattleWashingtonUSA
- Department of BioengineeringUniversity of WashingtonSeattleWashingtonUSA
| | - Basile I. M. Wicky
- Institute for Protein DesignUniversity of WashingtonSeattleWashingtonUSA
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Jacob T. Croft
- Department of Medicinal ChemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Lauren Carter
- Institute for Protein DesignUniversity of WashingtonSeattleWashingtonUSA
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Asim K. Bera
- Institute for Protein DesignUniversity of WashingtonSeattleWashingtonUSA
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Hannah Nguyen
- Institute for Protein DesignUniversity of WashingtonSeattleWashingtonUSA
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Alex Kang
- Institute for Protein DesignUniversity of WashingtonSeattleWashingtonUSA
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated BioimagingLawrence Berkeley National LaboratoryBerkeleyCaliforniaUSA
| | - Erin C. Yang
- Institute for Protein DesignUniversity of WashingtonSeattleWashingtonUSA
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
- Biological Physics, Structure and Design Graduate ProgramUniversity of WashingtonSeattleWashingtonUSA
| | - Kelly K. Lee
- Department of Medicinal ChemistryUniversity of WashingtonSeattleWashingtonUSA
- Biological Physics, Structure and Design Graduate ProgramUniversity of WashingtonSeattleWashingtonUSA
- Department of MicrobiologyUniversity of WashingtonSeattleWashingtonUSA
| | - David Baker
- Institute for Protein DesignUniversity of WashingtonSeattleWashingtonUSA
- Department of BiochemistryUniversity of WashingtonSeattleWashingtonUSA
- Howard Hughes Medical InstituteUniversity of WashingtonSeattleWashingtonUSA
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14
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An L, Hicks DR, Zorine D, Dauparas J, Wicky BIM, Milles LF, Courbet A, Bera AK, Nguyen H, Kang A, Carter L, Baker D. Hallucination of closed repeat proteins containing central pockets. Nat Struct Mol Biol 2023; 30:1755-1760. [PMID: 37770718 PMCID: PMC10643118 DOI: 10.1038/s41594-023-01112-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/28/2023] [Indexed: 09/30/2023]
Abstract
In pseudocyclic proteins, such as TIM barrels, β barrels, and some helical transmembrane channels, a single subunit is repeated in a cyclic pattern, giving rise to a central cavity that can serve as a pocket for ligand binding or enzymatic activity. Inspired by these proteins, we devised a deep-learning-based approach to broadly exploring the space of closed repeat proteins starting from only a specification of the repeat number and length. Biophysical data for 38 structurally diverse pseudocyclic designs produced in Escherichia coli are consistent with the design models, and the three crystal structures we were able to obtain are very close to the designed structures. Docking studies suggest the diversity of folds and central pockets provide effective starting points for designing small-molecule binders and enzymes.
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Affiliation(s)
- Linna An
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
| | - Derrick R Hicks
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Dmitri Zorine
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Justas Dauparas
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Basile I M Wicky
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Lukas F Milles
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alexis Courbet
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Asim K Bera
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Hannah Nguyen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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15
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Roy A, Shi L, Chang A, Dong X, Fernandez A, Kraft JC, Li J, Le VQ, Winegar RV, Cherf GM, Slocum D, Poulson PD, Casper GE, Vallecillo-Zúniga ML, Valdoz JC, Miranda MC, Bai H, Kipnis Y, Olshefsky A, Priya T, Carter L, Ravichandran R, Chow CM, Johnson MR, Cheng S, Smith M, Overed-Sayer C, Finch DK, Lowe D, Bera AK, Matute-Bello G, Birkland TP, DiMaio F, Raghu G, Cochran JR, Stewart LJ, Campbell MG, Van Ry PM, Springer T, Baker D. De novo design of highly selective miniprotein inhibitors of integrins αvβ6 and αvβ8. Nat Commun 2023; 14:5660. [PMID: 37704610 PMCID: PMC10500007 DOI: 10.1038/s41467-023-41272-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 08/18/2023] [Indexed: 09/15/2023] Open
Abstract
The RGD (Arg-Gly-Asp)-binding integrins αvβ6 and αvβ8 are clinically validated cancer and fibrosis targets of considerable therapeutic importance. Compounds that can discriminate between homologous αvβ6 and αvβ8 and other RGD integrins, stabilize specific conformational states, and have high thermal stability could have considerable therapeutic utility. Existing small molecule and antibody inhibitors do not have all these properties, and hence new approaches are needed. Here we describe a generalized method for computationally designing RGD-containing miniproteins selective for a single RGD integrin heterodimer and conformational state. We design hyperstable, selective αvβ6 and αvβ8 inhibitors that bind with picomolar affinity. CryoEM structures of the designed inhibitor-integrin complexes are very close to the computational design models, and show that the inhibitors stabilize specific conformational states of the αvβ6 and the αvβ8 integrins. In a lung fibrosis mouse model, the αvβ6 inhibitor potently reduced fibrotic burden and improved overall lung mechanics, demonstrating the therapeutic potential of de novo designed integrin binding proteins with high selectivity.
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Affiliation(s)
- Anindya Roy
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Lei Shi
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Encodia Inc, 5785 Oberlin Drive, San Diego, CA, 92121, USA
| | - Ashley Chang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
| | - Xianchi Dong
- Program in Cellular and Molecular Medicine, Children's Hospital Boston, and Departments of Biological Chemistry and Molecular Pharmacology and of Medicine, Harvard Medical School, Boston, MA, USA
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
- Engineering Research Center of Protein and Peptide Medicine, Ministry of Education, Nanjing, China
| | - Andres Fernandez
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - John C Kraft
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Jing Li
- Program in Cellular and Molecular Medicine, Children's Hospital Boston, and Departments of Biological Chemistry and Molecular Pharmacology and of Medicine, Harvard Medical School, Boston, MA, USA
| | - Viet Q Le
- Program in Cellular and Molecular Medicine, Children's Hospital Boston, and Departments of Biological Chemistry and Molecular Pharmacology and of Medicine, Harvard Medical School, Boston, MA, USA
| | - Rebecca Viazzo Winegar
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
| | - Gerald Maxwell Cherf
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- Denali Therapeutics, South San Francisco, CA, USA
| | - Dean Slocum
- Program in Cellular and Molecular Medicine, Children's Hospital Boston, and Departments of Biological Chemistry and Molecular Pharmacology and of Medicine, Harvard Medical School, Boston, MA, USA
| | - P Daniel Poulson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
| | - Garrett E Casper
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
| | | | - Jonard Corpuz Valdoz
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
| | - Marcos C Miranda
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Department of Medicine Solna, Division of Immunology and Allergy, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Hua Bai
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Yakov Kipnis
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
| | - Audrey Olshefsky
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA
| | - Tanu Priya
- Department of Materials Science and Engineering, University of Washington, Seattle, WA, 98195, USA
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Lauren Carter
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Rashmi Ravichandran
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Cameron M Chow
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Max R Johnson
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Suna Cheng
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - McKaela Smith
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Catherine Overed-Sayer
- Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
- Bioscience COPD/IPF, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Donna K Finch
- Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
- Alchemab Therapeutics Ltd, Cambridge, UK
| | - David Lowe
- Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
- Evox Therapeutics Limited, Oxford Science Park, Medawar Centre, East Building, Robert Robinson Avenue, Oxford, OX4 4HG, England
| | - Asim K Bera
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Gustavo Matute-Bello
- Center for Lung Biology, Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, USA
| | - Timothy P Birkland
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Frank DiMaio
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Ganesh Raghu
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
- Dept of Medicine, University of Washington, Seattle, WA, USA
| | - Jennifer R Cochran
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Lance J Stewart
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Melody G Campbell
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA.
| | - Pam M Van Ry
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA.
| | - Timothy Springer
- Program in Cellular and Molecular Medicine, Children's Hospital Boston, and Departments of Biological Chemistry and Molecular Pharmacology and of Medicine, Harvard Medical School, Boston, MA, USA.
| | - David Baker
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA.
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16
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Praetorius F, Leung PJY, Tessmer MH, Broerman A, Demakis C, Dishman AF, Pillai A, Idris A, Juergens D, Dauparas J, Li X, Levine PM, Lamb M, Ballard RK, Gerben SR, Nguyen H, Kang A, Sankaran B, Bera AK, Volkman BF, Nivala J, Stoll S, Baker D. Design of stimulus-responsive two-state hinge proteins. Science 2023; 381:754-760. [PMID: 37590357 PMCID: PMC10697137 DOI: 10.1126/science.adg7731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 07/11/2023] [Indexed: 08/19/2023]
Abstract
In nature, proteins that switch between two conformations in response to environmental stimuli structurally transduce biochemical information in a manner analogous to how transistors control information flow in computing devices. Designing proteins with two distinct but fully structured conformations is a challenge for protein design as it requires sculpting an energy landscape with two distinct minima. Here we describe the design of "hinge" proteins that populate one designed state in the absence of ligand and a second designed state in the presence of ligand. X-ray crystallography, electron microscopy, double electron-electron resonance spectroscopy, and binding measurements demonstrate that despite the significant structural differences the two states are designed with atomic level accuracy and that the conformational and binding equilibria are closely coupled.
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Affiliation(s)
- Florian Praetorius
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Philip J. Y. Leung
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Molecular Engineering, University of Washington, Seattle, WA, USA
| | - Maxx H. Tessmer
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Adam Broerman
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Chemical Engineering, University of Washington, Seattle, WA, USA
| | - Cullen Demakis
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Biological Physics, Structure, and Design, University of Washington, Seattle, Washington, USA
| | - Acacia F. Dishman
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
- Medical Scientist Training Program, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Arvind Pillai
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Abbas Idris
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - David Juergens
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Molecular Engineering, University of Washington, Seattle, WA, USA
| | - Justas Dauparas
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Xinting Li
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Paul M. Levine
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Mila Lamb
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Ryanne K. Ballard
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Stacey R. Gerben
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Hannah Nguyen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Asim K. Bera
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Brian F. Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jeff Nivala
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA
| | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA,USA
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17
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de Haas RJ, Brunette N, Goodson A, Dauparas J, Yi SY, Yang EC, Dowling Q, Nguyen H, Kang A, Bera AK, Sankaran B, de Vries R, Baker D, King NP. Rapid and automated design of two-component protein nanomaterials using ProteinMPNN. bioRxiv 2023:2023.08.04.551935. [PMID: 37577478 PMCID: PMC10418170 DOI: 10.1101/2023.08.04.551935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
The design of novel protein-protein interfaces using physics-based design methods such as Rosetta requires substantial computational resources and manual refinement by expert structural biologists. A new generation of deep learning methods promises to simplify protein-protein interface design and enable its application to a wide variety of problems by researchers from various scientific disciplines. Here we test the ability of a deep learning method for protein sequence design, ProteinMPNN, to design two-component tetrahedral protein nanomaterials and benchmark its performance against Rosetta. ProteinMPNN had a similar success rate to Rosetta, yielding 13 new experimentally confirmed assemblies, but required orders of magnitude less computation and no manual refinement. The interfaces designed by ProteinMPNN were substantially more polar than those designed by Rosetta, which facilitated in vitro assembly of the designed nanomaterials from independently purified components. Crystal structures of several of the assemblies confirmed the accuracy of the design method at high resolution. Our results showcase the potential of deep learning-based methods to unlock the widespread application of designed protein-protein interfaces and self-assembling protein nanomaterials in biotechnology.
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18
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de Haas RJ, Tas RP, van den Broek D, Zheng C, Nguyen H, Kang A, Bera AK, King NP, Voets IK, de Vries R. De novo designed ice-binding proteins from twist-constrained helices. Proc Natl Acad Sci U S A 2023; 120:e2220380120. [PMID: 37364125 PMCID: PMC10319034 DOI: 10.1073/pnas.2220380120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 05/02/2023] [Indexed: 06/28/2023] Open
Abstract
Attaining molecular-level control over solidification processes is a crucial aspect of materials science. To control ice formation, organisms have evolved bewildering arrays of ice-binding proteins (IBPs), but these have poorly understood structure-activity relationships. We propose that reverse engineering using de novo computational protein design can shed light on structure-activity relationships of IBPs. We hypothesized that the model alpha-helical winter flounder antifreeze protein uses an unusual undertwisting of its alpha-helix to align its putative ice-binding threonine residues in exactly the same direction. We test this hypothesis by designing a series of straight three-helix bundles with an ice-binding helix projecting threonines and two supporting helices constraining the twist of the ice-binding helix. Our findings show that ice-recrystallization inhibition by the designed proteins increases with the degree of designed undertwisting, thus validating our hypothesis, and opening up avenues for the computational design of IBPs.
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Affiliation(s)
- Robbert J. de Haas
- Department of Physical Chemistry and Soft Matter, Wageningen University and Research, Wageningen, WE6708, The Netherlands
| | - Roderick P. Tas
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, MB5600, The Netherlands
| | - Daniëlle van den Broek
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, MB5600, The Netherlands
| | - Chuanbao Zheng
- Department of Physical Chemistry and Soft Matter, Wageningen University and Research, Wageningen, WE6708, The Netherlands
| | - Hannah Nguyen
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Asim K. Bera
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Neil P. King
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Ilja K. Voets
- Laboratory of Self-Organizing Soft Matter, Department of Chemical Engineering and Chemistry and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, MB5600, The Netherlands
| | - Renko de Vries
- Department of Physical Chemistry and Soft Matter, Wageningen University and Research, Wageningen, WE6708, The Netherlands
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19
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Roy A, Shi L, Chang A, Dong X, Fernandez A, Kraft JC, Li J, Le VQ, Winegar RV, Cherf GM, Slocum D, Daniel Poulson P, Casper GE, Vallecillo-Zúniga ML, Valdoz JC, Miranda MC, Bai H, Kipnis Y, Olshefsky A, Priya T, Carter L, Ravichandran R, Chow CM, Johnson MR, Cheng S, Smith M, Overed-Sayer C, Finch DK, Lowe D, Bera AK, Matute-Bello G, Birkland TP, DiMaio F, Raghu G, Cochran JR, Stewart LJ, Campbell MG, Van Ry PM, Springer T, Baker D. De novo design of highly selective miniprotein inhibitors of integrins αvβ6 and αvβ8. bioRxiv 2023:2023.06.12.544624. [PMID: 37398153 PMCID: PMC10312613 DOI: 10.1101/2023.06.12.544624] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The RGD (Arg-Gly-Asp)-binding integrins αvβ6 and αvβ8 are clinically validated cancer and fibrosis targets of considerable therapeutic importance. Compounds that can discriminate between the two closely related integrin proteins and other RGD integrins, stabilize specific conformational states, and have sufficient stability enabling tissue restricted administration could have considerable therapeutic utility. Existing small molecules and antibody inhibitors do not have all of these properties, and hence there is a need for new approaches. Here we describe a method for computationally designing hyperstable RGD-containing miniproteins that are highly selective for a single RGD integrin heterodimer and conformational state, and use this strategy to design inhibitors of αvβ6 and αvβ8 with high selectivity. The αvβ6 and αvβ8 inhibitors have picomolar affinities for their targets, and >1000-fold selectivity over other RGD integrins. CryoEM structures are within 0.6-0.7Å root-mean-square deviation (RMSD) to the computational design models; the designed αvβ6 inhibitor and native ligand stabilize the open conformation in contrast to the therapeutic anti-αvβ6 antibody BG00011 that stabilizes the bent-closed conformation and caused on-target toxicity in patients with lung fibrosis, and the αvβ8 inhibitor maintains the constitutively fixed extended-closed αvβ8 conformation. In a mouse model of bleomycin-induced lung fibrosis, the αvβ6 inhibitor potently reduced fibrotic burden and improved overall lung mechanics when delivered via oropharyngeal administration mimicking inhalation, demonstrating the therapeutic potential of de novo designed integrin binding proteins with high selectivity.
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Affiliation(s)
- Anindya Roy
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Lei Shi
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Current Address: Encodia Inc, 5785 Oberlin Drive, San Diego, CA 92121
| | - Ashley Chang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | - Xianchi Dong
- Program in Cellular and Molecular Medicine, Children’s Hospital Boston, and Departments of Biological Chemistry and Molecular Pharmacology and of Medicine, Harvard Medical School, Boston, United States
- Current address: State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China; Engineering Research Center of Protein and Peptide Medicine,Ministry of Education
| | - Andres Fernandez
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - John C. Kraft
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Jing Li
- Program in Cellular and Molecular Medicine, Children’s Hospital Boston, and Departments of Biological Chemistry and Molecular Pharmacology and of Medicine, Harvard Medical School, Boston, United States
| | - Viet Q. Le
- Program in Cellular and Molecular Medicine, Children’s Hospital Boston, and Departments of Biological Chemistry and Molecular Pharmacology and of Medicine, Harvard Medical School, Boston, United States
| | - Rebecca Viazzo Winegar
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | - Gerald Maxwell Cherf
- Department of Bioengineering, Stanford University, Stanford CA 94305
- Current Address: Denali Therapeutics, South San Francisco, CA, USA
| | - Dean Slocum
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | - P. Daniel Poulson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | - Garrett E. Casper
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | | | - Jonard Corpuz Valdoz
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | - Marcos C. Miranda
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Current Address: Department of Medicine Solna, Division of Immunology and Allergy, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Hua Bai
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Yakov Kipnis
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington
| | - Audrey Olshefsky
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Tanu Priya
- Department of Materials Science and Engineering, University of Washington, Seattle, WA 98195, USA
- Current Address: Department of Pharmacology, Northwestern University Feinberg School of Medicine; Chicago, IL 60611, USA
| | - Lauren Carter
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Rashmi Ravichandran
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Cameron M. Chow
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Max R. Johnson
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Suna Cheng
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - McKaela Smith
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Catherine Overed-Sayer
- Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
- Current Address: Bioscience COPD/IPF, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Donna K. Finch
- Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
- Current Address: Alchemab Therapeutics Ltd, Cambridge, United Kingdom
| | - David Lowe
- Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
- Current Address: Evox Therapeutics Limited, Oxford Science Park, Medawar Centre, East Building, Robert Robinson Avenue, Oxford, OX4 4HG
| | - Asim K. Bera
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Gustavo Matute-Bello
- Center for Lung Biology, Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington
| | - Timothy P Birkland
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington
| | - Frank DiMaio
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Ganesh Raghu
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington
| | | | - Lance J. Stewart
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Melody G. Campbell
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Pam M. Van Ry
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
| | - Timothy Springer
- Program in Cellular and Molecular Medicine, Children’s Hospital Boston, and Departments of Biological Chemistry and Molecular Pharmacology and of Medicine, Harvard Medical School, Boston, United States
| | - David Baker
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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20
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Huddy TF, Hsia Y, Kibler RD, Xu J, Bethel N, Nagarajan D, Redler R, Leung PJY, Courbet A, Yang EC, Bera AK, Coudray N, Calise SJ, Davila-Hernandez FA, Weidle C, Han HL, Li Z, McHugh R, Reggiano G, Kang A, Sankaran B, Dickinson MS, Coventry B, Brunette TJ, Liu Y, Dauparas J, Borst AJ, Ekiert D, Kollman JM, Bhabha G, Baker D. Blueprinting expandable nanomaterials with standardized protein building blocks. bioRxiv 2023:2023.06.09.544258. [PMID: 37333359 PMCID: PMC10274926 DOI: 10.1101/2023.06.09.544258] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
A wooden house frame consists of many different lumber pieces, but because of the regularity of these building blocks, the structure can be designed using straightforward geometrical principles. The design of multicomponent protein assemblies in comparison has been much more complex, largely due to the irregular shapes of protein structures 1 . Here we describe extendable linear, curved, and angled protein building blocks, as well as inter-block interactions that conform to specified geometric standards; assemblies designed using these blocks inherit their extendability and regular interaction surfaces, enabling them to be expanded or contracted by varying the number of modules, and reinforced with secondary struts. Using X-ray crystallography and electron microscopy, we validate nanomaterial designs ranging from simple polygonal and circular oligomers that can be concentrically nested, up to large polyhedral nanocages and unbounded straight "train track" assemblies with reconfigurable sizes and geometries that can be readily blueprinted. Because of the complexity of protein structures and sequence-structure relationships, it has not been previously possible to build up large protein assemblies by deliberate placement of protein backbones onto a blank 3D canvas; the simplicity and geometric regularity of our design platform now enables construction of protein nanomaterials according to "back of an envelope" architectural blueprints.
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21
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Wang JY(J, Khmelinskaia A, Sheffler W, Miranda MC, Antanasijevic A, Borst AJ, Torres SV, Shu C, Hsia Y, Nattermann U, Ellis D, Walkey C, Ahlrichs M, Chan S, Kang A, Nguyen H, Sydeman C, Sankaran B, Wu M, Bera AK, Carter L, Fiala B, Murphy M, Baker D, Ward AB, King NP. Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains. Proc Natl Acad Sci U S A 2023; 120:e2214556120. [PMID: 36888664 PMCID: PMC10089191 DOI: 10.1073/pnas.2214556120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 02/03/2023] [Indexed: 03/09/2023] Open
Abstract
Computationally designed protein nanoparticles have recently emerged as a promising platform for the development of new vaccines and biologics. For many applications, secretion of designed nanoparticles from eukaryotic cells would be advantageous, but in practice, they often secrete poorly. Here we show that designed hydrophobic interfaces that drive nanoparticle assembly are often predicted to form cryptic transmembrane domains, suggesting that interaction with the membrane insertion machinery could limit efficient secretion. We develop a general computational protocol, the Degreaser, to design away cryptic transmembrane domains without sacrificing protein stability. The retroactive application of the Degreaser to previously designed nanoparticle components and nanoparticles considerably improves secretion, and modular integration of the Degreaser into design pipelines results in new nanoparticles that secrete as robustly as naturally occurring protein assemblies. Both the Degreaser protocol and the nanoparticles we describe may be broadly useful in biotechnological applications.
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Affiliation(s)
- Jing Yang (John) Wang
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA98195
| | - Alena Khmelinskaia
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
- Transdisciplinary Research Area “Building Blocks of Matter and Fundamental Interactions”, University of Bonn, 53113Bonn, Germany
- Life and Medical Sciences Institute, University of Bonn, 53121Bonn, Germany
| | - William Sheffler
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Marcos C. Miranda
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Aleksandar Antanasijevic
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA92037
- Scripps Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA92037
| | - Andrew J. Borst
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Susana V. Torres
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Chelsea Shu
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Yang Hsia
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Una Nattermann
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
- Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA98195
| | - Daniel Ellis
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
- Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA98195
| | - Carl Walkey
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Maggie Ahlrichs
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Sidney Chan
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Hannah Nguyen
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Claire Sydeman
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley Laboratory, Berkeley, CA94720
- Berkeley Center for Structural Biology, Lawrence Berkeley Laboratory, Berkeley, CA94720
| | - Mengyu Wu
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Asim K. Bera
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Brooke Fiala
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Michael Murphy
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Andrew B. Ward
- Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA92037
- Scripps Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA92037
| | - Neil P. King
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
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22
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Kim DE, Jensen DR, Feldman D, Tischer D, Saleem A, Chow CM, Li X, Carter L, Milles L, Nguyen H, Kang A, Bera AK, Peterson FC, Volkman BF, Ovchinnikov S, Baker D. De novo design of small beta barrel proteins. Proc Natl Acad Sci U S A 2023; 120:e2207974120. [PMID: 36897987 PMCID: PMC10089152 DOI: 10.1073/pnas.2207974120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 01/27/2023] [Indexed: 03/12/2023] Open
Abstract
Small beta barrel proteins are attractive targets for computational design because of their considerable functional diversity despite their very small size (<70 amino acids). However, there are considerable challenges to designing such structures, and there has been little success thus far. Because of the small size, the hydrophobic core stabilizing the fold is necessarily very small, and the conformational strain of barrel closure can oppose folding; also intermolecular aggregation through free beta strand edges can compete with proper monomer folding. Here, we explore the de novo design of small beta barrel topologies using both Rosetta energy-based methods and deep learning approaches to design four small beta barrel folds: Src homology 3 (SH3) and oligonucleotide/oligosaccharide-binding (OB) topologies found in nature and five and six up-and-down-stranded barrels rarely if ever seen in nature. Both approaches yielded successful designs with high thermal stability and experimentally determined structures with less than 2.4 Å rmsd from the designed models. Using deep learning for backbone generation and Rosetta for sequence design yielded higher design success rates and increased structural diversity than Rosetta alone. The ability to design a large and structurally diverse set of small beta barrel proteins greatly increases the protein shape space available for designing binders to protein targets of interest.
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Affiliation(s)
- David E. Kim
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
- HHMI, University of Washington, Seattle, WA98195
| | - Davin R. Jensen
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI53226
| | - David Feldman
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Doug Tischer
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Ayesha Saleem
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Cameron M. Chow
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Xinting Li
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Lukas Milles
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Hannah Nguyen
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Asim K. Bera
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Francis C. Peterson
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI53226
| | - Brian F. Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI53226
| | - Sergey Ovchinnikov
- Division of Science, Faculty of Arts and Sciences, Harvard University, Cambridge, MA02138
- John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA02138
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
- HHMI, University of Washington, Seattle, WA98195
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23
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Rettie SA, Campbell KV, Bera AK, Kang A, Kozlov S, De La Cruz J, Adebomi V, Zhou G, DiMaio F, Ovchinnikov S, Bhardwaj G. Cyclic peptide structure prediction and design using AlphaFold. bioRxiv 2023:2023.02.25.529956. [PMID: 36865323 PMCID: PMC9980166 DOI: 10.1101/2023.02.25.529956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
Abstract
Deep learning networks offer considerable opportunities for accurate structure prediction and design of biomolecules. While cyclic peptides have gained significant traction as a therapeutic modality, developing deep learning methods for designing such peptides has been slow, mostly due to the small number of available structures for molecules in this size range. Here, we report approaches to modify the AlphaFold network for accurate structure prediction and design of cyclic peptides. Our results show this approach can accurately predict the structures of native cyclic peptides from a single sequence, with 36 out of 49 cases predicted with high confidence (pLDDT > 0.85) matching the native structure with root mean squared deviation (RMSD) less than 1.5 Å. Further extending our approach, we describe computational methods for designing sequences of peptide backbones generated by other backbone sampling methods and for de novo design of new macrocyclic peptides. We extensively sampled the structural diversity of cyclic peptides between 7-13 amino acids, and identified around 10,000 unique design candidates predicted to fold into the designed structures with high confidence. X-ray crystal structures for seven sequences with diverse sizes and structures designed by our approach match very closely with the design models (root mean squared deviation < 1.0 Å), highlighting the atomic level accuracy in our approach. The computational methods and scaffolds developed here provide the basis for custom-designing peptides for targeted therapeutic applications.
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Affiliation(s)
- Stephen A. Rettie
- Molecular and Cell Biology program, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Katelyn V. Campbell
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Asim K. Bera
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alex Kang
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Simon Kozlov
- FAS Division of Science, Harvard University, Cambridge, MA, USA
| | - Joshmyn De La Cruz
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Victor Adebomi
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - Guangfeng Zhou
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Frank DiMaio
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Sergey Ovchinnikov
- John Harvard Distinguished Science Fellowship, Harvard University, Cambridge, MA, USA
- FAS Division of Science, Harvard University, Cambridge, MA, USA
| | - Gaurav Bhardwaj
- Molecular and Cell Biology program, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
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24
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Gerben S, Borst AJ, Hicks DR, Moczygemba I, Feldman D, Coventry B, Yang W, Bera AK, Miranda M, Kang A, Nguyen H, Baker D. Design of Diverse Asymmetric Pockets in De Novo Homo-oligomeric Proteins. Biochemistry 2023; 62:358-368. [PMID: 36627259 PMCID: PMC9850923 DOI: 10.1021/acs.biochem.2c00497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A challenge for design of protein-small-molecule recognition is that incorporation of cavities with size, shape, and composition suitable for specific recognition can considerably destabilize protein monomers. This challenge can be overcome through binding pockets formed at homo-oligomeric interfaces between folded monomers. Interfaces surrounding the central homo-oligomer symmetry axes necessarily have the same symmetry and so may not be well suited to binding asymmetric molecules. To enable general recognition of arbitrary asymmetric substrates and small molecules, we developed an approach to designing asymmetric interfaces at off-axis sites on homo-oligomers, analogous to those found in native homo-oligomeric proteins such as glutamine synthetase. We symmetrically dock curved helical repeat proteins such that they form pockets at the asymmetric interface of the oligomer with sizes ranging from several angstroms, appropriate for binding a single ion, to up to more than 20 Å across. Of the 133 proteins tested, 84 had soluble expression in E. coli, 47 had correct oligomeric states in solution, 35 had small-angle X-ray scattering (SAXS) data largely consistent with design models, and 8 had negative-stain electron microscopy (nsEM) 2D class averages showing the structures coming together as designed. Both an X-ray crystal structure and a cryogenic electron microscopy (cryoEM) structure are close to the computational design models. The nature of these proteins as homo-oligomers allows them to be readily built into higher-order structures such as nanocages, and the asymmetric pockets of these structures open rich possibilities for small-molecule binder design free from the constraints associated with monomer destabilization.
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Affiliation(s)
- Stacey
R Gerben
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States,Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Andrew J Borst
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States,Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Derrick R Hicks
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States,Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Isabelle Moczygemba
- Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - David Feldman
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States,Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Brian Coventry
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States,Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Wei Yang
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States,Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Asim K. Bera
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States,Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Marcos Miranda
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States,Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Alex Kang
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States,Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Hannah Nguyen
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States,Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - David Baker
- Department
of Biochemistry, University of Washington, Seattle, Washington 98195, United States,Institute
for Protein Design, University of Washington, Seattle, Washington 98195, United States,Howard
Hughes Medical Institute, University of
Washington, Seattle, Washington 98195, United States,Mailing address: David Baker, University
of Washington, Molecular Engineering and Sciences, Box 351655, Seattle,
Washington 98195-1655, United States;
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25
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Said M, Kang CS, Wang S, Sheffler W, Salveson PJ, Bera AK, Kang A, Nguyen H, Ballard R, Li X, Bai H, Stewart L, Levine P, Baker D. Exploration of Structured Symmetric Cyclic Peptides as Ligands for Metal-Organic Frameworks. Chem Mater 2022; 34:9736-9744. [PMID: 36397834 PMCID: PMC9648172 DOI: 10.1021/acs.chemmater.2c02597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Despite remarkable advances in the assembly of highly structured coordination polymers and metal-organic frameworks, the rational design of such materials using more conformationally flexible organic ligands such as peptides remains challenging. In an effort to make the design of such materials fully programmable, we first developed a computational design method for generating metal-mediated 3D frameworks using rigid and symmetric peptide macrocycles with metal-coordinating sidechains. We solved the structures of six crystalline networks involving conformationally constrained 6 to 12 residue cyclic peptides with C2, C3, and S2 internal symmetry and three different types of metals (Zn2+, Co2+, or Cu2+) by single-crystal X-ray diffraction, which reveals how the peptide sequences, backbone symmetries, and metal coordination preferences drive the assembly of the resulting structures. In contrast to smaller ligands, these peptides associate through peptide-peptide interactions without full coordination of the metals, contrary to one of the assumptions underlying our computational design method. The cyclic peptides are the largest peptidic ligands reported to form crystalline coordination polymers with transition metals to date, and while more work is required to develop methods for fully programming their crystal structures, the combination of high chemical diversity with synthetic accessibility makes them attractive building blocks for engineering a broader set of new crystalline materials for use in applications such as sensing, asymmetric catalysis, and chiral separation.
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Affiliation(s)
- Meerit
Y. Said
- Institute
for Protein Design, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
| | - Christine S. Kang
- Institute
for Protein Design, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
| | - Shunzhi Wang
- Institute
for Protein Design, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
| | - William Sheffler
- Institute
for Protein Design, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
| | - Patrick J. Salveson
- Institute
for Protein Design, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
| | - Asim K. Bera
- Institute
for Protein Design, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
| | - Alex Kang
- Institute
for Protein Design, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
| | - Hannah Nguyen
- Institute
for Protein Design, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
| | - Ryanne Ballard
- Institute
for Protein Design, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
| | - Xinting Li
- Institute
for Protein Design, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
| | - Hua Bai
- Institute
for Protein Design, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
| | - Lance Stewart
- Institute
for Protein Design, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
| | - Paul Levine
- Institute
for Protein Design, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
| | - David Baker
- Institute
for Protein Design, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
- Department
of Biochemistry, University of Washington, 4000 15th Avenue NE, Seattle, Washington 98195, United States
- Howard
Hughes Medical Institute, University of
Washington, Seattle, Washington 98195, United States
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26
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Bhardwaj G, O'Connor J, Rettie S, Huang YH, Ramelot TA, Mulligan VK, Alpkilic GG, Palmer J, Bera AK, Bick MJ, Di Piazza M, Li X, Hosseinzadeh P, Craven TW, Tejero R, Lauko A, Choi R, Glynn C, Dong L, Griffin R, van Voorhis WC, Rodriguez J, Stewart L, Montelione GT, Craik D, Baker D. Accurate de novo design of membrane-traversing macrocycles. Cell 2022; 185:3520-3532.e26. [PMID: 36041435 PMCID: PMC9490236 DOI: 10.1016/j.cell.2022.07.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 05/01/2022] [Accepted: 07/21/2022] [Indexed: 01/26/2023]
Abstract
We use computational design coupled with experimental characterization to systematically investigate the design principles for macrocycle membrane permeability and oral bioavailability. We designed 184 6-12 residue macrocycles with a wide range of predicted structures containing noncanonical backbone modifications and experimentally determined structures of 35; 29 are very close to the computational models. With such control, we show that membrane permeability can be systematically achieved by ensuring all amide (NH) groups are engaged in internal hydrogen bonding interactions. 84 designs over the 6-12 residue size range cross membranes with an apparent permeability greater than 1 × 10-6 cm/s. Designs with exposed NH groups can be made membrane permeable through the design of an alternative isoenergetic fully hydrogen-bonded state favored in the lipid membrane. The ability to robustly design membrane-permeable and orally bioavailable peptides with high structural accuracy should contribute to the next generation of designed macrocycle therapeutics.
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Affiliation(s)
- Gaurav Bhardwaj
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA; Biological Physics, Structure and Design program, University of Washington, Seattle, WA 98195, USA.
| | - Jacob O'Connor
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Biological Physics, Structure and Design program, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Stephen Rettie
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Molecular Cell and Biology program, University of Washington, Seattle, WA 98195, USA
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Theresa A Ramelot
- Department of Chemistry and Chemical Biology and Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | | | - Gizem Gokce Alpkilic
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA; Molecular Engineering and Sciences Program, University of Washington, Seattle, WA 98195, USA
| | - Jonathan Palmer
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Asim K Bera
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Matthew J Bick
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Maddalena Di Piazza
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Xinting Li
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Parisa Hosseinzadeh
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Timothy W Craven
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Roberto Tejero
- Departamento de Quίmica Fίsica, Universidad de Valencia, Avenida Dr. Moliner 50, Burjassot, 46100 Valencia, Spain
| | - Anna Lauko
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Biological Physics, Structure and Design program, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Ryan Choi
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, WA, USA
| | - Calina Glynn
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA, USA
| | - Linlin Dong
- Takeda Pharmaceuticals Inc., Cambridge, MA, USA
| | | | - Wesley C van Voorhis
- Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, WA, USA
| | - Jose Rodriguez
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA, USA
| | - Lance Stewart
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Gaetano T Montelione
- Department of Chemistry and Chemical Biology and Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - David Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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27
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Dutta D, Bera AK, Maheshwari P, Kolay S, Yusuf SM, Pujari PK. High cubicity of D 2O ice inside spherical nanopores of MIL-101(Cr) framework: a neutron diffraction study. Phys Chem Chem Phys 2022; 24:11872-11881. [PMID: 35510632 DOI: 10.1039/d2cp00609j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Although cubic ice (ice Ic) is considered to be an important phase of water that impacts ice cloud formation in the Earth's upper atmosphere, its properties have not been studied to the same extent as those of hexagonal ice (ice Ih). This is because pristine ice Ic is not formed in simple laboratory conditions. Ice Ic formed in ambient conditions has a stacking disordered array of both hexagonal and cubic-structured hydrogen-bonded water molecules. It is therefore an active area of research to find ways of developing stacking disorder-free pure ice Ic. We demonstrate the evolution of almost pure ice Ic structure within the spherical nanopores of a hydrostable Cr-based metal-organic framework MIL-101(Cr) with an average pore size of 1 nm by low-temperature neutron diffraction study on D2O. It is observed that at temperatures below 230 K a fraction of liquid D2O transforms into ice and more than 94% of ice crystals evolved inside the pore are cubic in shape. This is a significantly high fraction of ice Ic formed under simple conditions inside the spherical pores of a Cr-based MOF. It is also observed that upon increasing the temperature, ice Ic remains stable until its melting point, without being transformed into ice Ih. This observation is in contrast to our previous observation of ice structure in the 2D cylindrical nanopores of MCM-41, where H2O ice after creeping out from the cylindrical channel was seen to be dominated by hexagonal shape. In the present study, the D2O molecules were confined into well-defined spherical nanopores, which hindered the growth of crystals above a certain size, thus minimizing the stacking disordered array. Nanoconfinement of water inside uniform spherical pores is therefore a promising method for the evolution of a significantly large fraction of cubic ice by minimizing the stacking disorder. This finding may open up the possibility of forming ice Ic with 100% cubicity under simple laboratory conditions, which will help in exploring the microphysics of ice cloud formation in the upper atmosphere.
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Affiliation(s)
- Dhanadeep Dutta
- Radiochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai-400085, India. .,Homi Bhabha National Institute, Anushaktinagar, Mumbai-400094, India
| | - A K Bera
- Homi Bhabha National Institute, Anushaktinagar, Mumbai-400094, India.,Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai-400085, India
| | - Priya Maheshwari
- Radiochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai-400085, India. .,Homi Bhabha National Institute, Anushaktinagar, Mumbai-400094, India
| | - Siddhartha Kolay
- Chemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai-400085, India
| | - S M Yusuf
- Homi Bhabha National Institute, Anushaktinagar, Mumbai-400094, India.,Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai-400085, India
| | - P K Pujari
- Radiochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai-400085, India. .,Homi Bhabha National Institute, Anushaktinagar, Mumbai-400094, India
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28
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Cao L, Coventry B, Goreshnik I, Huang B, Sheffler W, Park JS, Jude KM, Marković I, Kadam RU, Verschueren KHG, Verstraete K, Walsh STR, Bennett N, Phal A, Yang A, Kozodoy L, DeWitt M, Picton L, Miller L, Strauch EM, DeBouver ND, Pires A, Bera AK, Halabiya S, Hammerson B, Yang W, Bernard S, Stewart L, Wilson IA, Ruohola-Baker H, Schlessinger J, Lee S, Savvides SN, Garcia KC, Baker D. Design of protein-binding proteins from the target structure alone. Nature 2022; 605:551-560. [PMID: 35332283 PMCID: PMC9117152 DOI: 10.1038/s41586-022-04654-9] [Citation(s) in RCA: 125] [Impact Index Per Article: 62.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 03/15/2022] [Indexed: 12/03/2022]
Abstract
The design of proteins that bind to a specific site on the surface of a target protein using no information other than the three-dimensional structure of the target remains a challenge1-5. Here we describe a general solution to this problem that starts with a broad exploration of the vast space of possible binding modes to a selected region of a protein surface, and then intensifies the search in the vicinity of the most promising binding modes. We demonstrate the broad applicability of this approach through the de novo design of binding proteins to 12 diverse protein targets with different shapes and surface properties. Biophysical characterization shows that the binders, which are all smaller than 65 amino acids, are hyperstable and, following experimental optimization, bind their targets with nanomolar to picomolar affinities. We succeeded in solving crystal structures of five of the binder-target complexes, and all five closely match the corresponding computational design models. Experimental data on nearly half a million computational designs and hundreds of thousands of point mutants provide detailed feedback on the strengths and limitations of the method and of our current understanding of protein-protein interactions, and should guide improvements of both. Our approach enables the targeted design of binders to sites of interest on a wide variety of proteins for therapeutic and diagnostic applications.
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Affiliation(s)
- Longxing Cao
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Brian Coventry
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Molecular Engineering Graduate Program, University of Washington, Seattle, WA, USA
| | - Inna Goreshnik
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Buwei Huang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - William Sheffler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Joon Sung Park
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
| | - Kevin M Jude
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Iva Marković
- VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Rameshwar U Kadam
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Koen H G Verschueren
- VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Kenneth Verstraete
- VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Scott Thomas Russell Walsh
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
- J.A.M.E.S. Farm, Clarksville, MD, USA
| | - Nathaniel Bennett
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Molecular Engineering Graduate Program, University of Washington, Seattle, WA, USA
| | - Ashish Phal
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Aerin Yang
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lisa Kozodoy
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Michelle DeWitt
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Lora Picton
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lauren Miller
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Eva-Maria Strauch
- Deptartment of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, USA
| | - Nicholas D DeBouver
- UCB Pharma, Bainbridge Island, WA, USA
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA
| | - Allison Pires
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA
- Seattle Children's Center for Global Infectious Disease Research, Seattle, WA, USA
| | - Asim K Bera
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Samer Halabiya
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, USA
| | - Bradley Hammerson
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA
| | - Wei Yang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Steffen Bernard
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Lance Stewart
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Hannele Ruohola-Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Joseph Schlessinger
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
| | - Sangwon Lee
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
| | - Savvas N Savvides
- VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - K Christopher Garcia
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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29
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Singer JM, Novotney S, Strickland D, Haddox HK, Leiby N, Rocklin GJ, Chow CM, Roy A, Bera AK, Motta FC, Cao L, Strauch EM, Chidyausiku TM, Ford A, Ho E, Zaitzeff A, Mackenzie CO, Eramian H, DiMaio F, Grigoryan G, Vaughn M, Stewart LJ, Baker D, Klavins E. Large-scale design and refinement of stable proteins using sequence-only models. PLoS One 2022; 17:e0265020. [PMID: 35286324 PMCID: PMC8920274 DOI: 10.1371/journal.pone.0265020] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/18/2022] [Indexed: 12/25/2022] Open
Abstract
Engineered proteins generally must possess a stable structure in order to achieve their designed function. Stable designs, however, are astronomically rare within the space of all possible amino acid sequences. As a consequence, many designs must be tested computationally and experimentally in order to find stable ones, which is expensive in terms of time and resources. Here we use a high-throughput, low-fidelity assay to experimentally evaluate the stability of approximately 200,000 novel proteins. These include a wide range of sequence perturbations, providing a baseline for future work in the field. We build a neural network model that predicts protein stability given only sequences of amino acids, and compare its performance to the assayed values. We also report another network model that is able to generate the amino acid sequences of novel stable proteins given requested secondary sequences. Finally, we show that the predictive model—despite weaknesses including a noisy data set—can be used to substantially increase the stability of both expert-designed and model-generated proteins.
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Affiliation(s)
- Jedediah M. Singer
- Two Six Technologies, Arlington, Virginia, United States of America
- * E-mail:
| | - Scott Novotney
- Two Six Technologies, Arlington, Virginia, United States of America
| | - Devin Strickland
- Department of Electrical and Computer Engineering, University of Washington, Seattle, Washington, United States of America
| | - Hugh K. Haddox
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington, United States of America
| | - Nicholas Leiby
- Two Six Technologies, Arlington, Virginia, United States of America
| | - Gabriel J. Rocklin
- Department of Pharmacology and Center for Synthetic Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Cameron M. Chow
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington, United States of America
| | - Anindya Roy
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington, United States of America
| | - Asim K. Bera
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington, United States of America
| | - Francis C. Motta
- Department of Mathematical Sciences, Florida Atlantic University, Boca Raton, Florida, United States of America
| | - Longxing Cao
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington, United States of America
| | - Eva-Maria Strauch
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, Georgia, United States of America
| | - Tamuka M. Chidyausiku
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington, United States of America
| | - Alex Ford
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington, United States of America
| | - Ethan Ho
- Texas Advanced Computing Center, Austin, Texas, United States of America
| | | | - Craig O. Mackenzie
- Quantitative Biomedical Sciences Graduate Program, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Hamed Eramian
- Netrias, Cambridge, Massachusetts, United States of America
| | - Frank DiMaio
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington, United States of America
| | - Gevorg Grigoryan
- Departments of Computer Science and Biological Sciences, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Matthew Vaughn
- Texas Advanced Computing Center, Austin, Texas, United States of America
| | - Lance J. Stewart
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington, United States of America
| | - David Baker
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington, United States of America
| | - Eric Klavins
- Department of Electrical and Computer Engineering, University of Washington, Seattle, Washington, United States of America
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30
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Sahtoe DD, Praetorius F, Courbet A, Hsia Y, Wicky BI, Edman NI, Miller LM, Timmermans BJR, Decarreau J, Morris HM, Kang A, Bera AK, Baker D. Reconfigurable asymmetric protein assemblies through implicit negative design. Science 2022; 375:eabj7662. [PMID: 35050655 PMCID: PMC9881579 DOI: 10.1126/science.abj7662] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Asymmetric multiprotein complexes that undergo subunit exchange play central roles in biology but present a challenge for design because the components must not only contain interfaces that enable reversible association but also be stable and well behaved in isolation. We use implicit negative design to generate β sheet-mediated heterodimers that can be assembled into a wide variety of complexes. The designs are stable, folded, and soluble in isolation and rapidly assemble upon mixing, and crystal structures are close to the computational models. We construct linearly arranged hetero-oligomers with up to six different components, branched hetero-oligomers, closed C4-symmetric two-component rings, and hetero-oligomers assembled on a cyclic homo-oligomeric central hub and demonstrate that such complexes can readily reconfigure through subunit exchange. Our approach provides a general route to designing asymmetric reconfigurable protein systems.
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Affiliation(s)
- Danny D. Sahtoe
- Department of Biochemistry, University of Washington, Seattle, WA 98195,Institute for Protein Design, University of Washington, Seattle, WA 98195,HHMI, University of Washington, Seattle, WA 98195
| | - Florian Praetorius
- Department of Biochemistry, University of Washington, Seattle, WA 98195,Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Alexis Courbet
- Department of Biochemistry, University of Washington, Seattle, WA 98195,Institute for Protein Design, University of Washington, Seattle, WA 98195,HHMI, University of Washington, Seattle, WA 98195
| | - Yang Hsia
- Department of Biochemistry, University of Washington, Seattle, WA 98195,Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Basile I.M. Wicky
- Department of Biochemistry, University of Washington, Seattle, WA 98195,Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Natasha I. Edman
- Department of Biochemistry, University of Washington, Seattle, WA 98195,Institute for Protein Design, University of Washington, Seattle, WA 98195,Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA.,Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Lauren M. Miller
- Department of Biochemistry, University of Washington, Seattle, WA 98195,Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Bart J. R. Timmermans
- Department of Biochemistry, University of Washington, Seattle, WA 98195,Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Justin Decarreau
- Department of Biochemistry, University of Washington, Seattle, WA 98195,Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Hana M. Morris
- Department of Biochemistry, University of Washington, Seattle, WA 98195,Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA 98195,Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Asim K. Bera
- Department of Biochemistry, University of Washington, Seattle, WA 98195,Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195,Institute for Protein Design, University of Washington, Seattle, WA 98195,HHMI, University of Washington, Seattle, WA 98195,Corresponding author.
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31
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Park JM, Yang SW, Zhuang W, Bera AK, Liu Y, Gurbani D, von Hoyningen-Huene SJ, Sakurada SM, Gan H, Pruett-Miller SM, Westover KD, Potts MB. The nonreceptor tyrosine kinase SRMS inhibits autophagy and promotes tumor growth by phosphorylating the scaffolding protein FKBP51. PLoS Biol 2021; 19:e3001281. [PMID: 34077419 PMCID: PMC8202955 DOI: 10.1371/journal.pbio.3001281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 06/14/2021] [Accepted: 05/10/2021] [Indexed: 01/18/2023] Open
Abstract
Nutrient-responsive protein kinases control the balance between anabolic growth and catabolic processes such as autophagy. Aberrant regulation of these kinases is a major cause of human disease. We report here that the vertebrate nonreceptor tyrosine kinase Src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristylation sites (SRMS) inhibits autophagy and promotes growth in a nutrient-responsive manner. Under nutrient-replete conditions, SRMS phosphorylates the PHLPP scaffold FK506-binding protein 51 (FKBP51), disrupts the FKBP51-PHLPP complex, and promotes FKBP51 degradation through the ubiquitin-proteasome pathway. This prevents PHLPP-mediated dephosphorylation of AKT, causing sustained AKT activation that promotes growth and inhibits autophagy. SRMS is amplified and overexpressed in human cancers where it drives unrestrained AKT signaling in a kinase-dependent manner. SRMS kinase inhibition activates autophagy, inhibits cancer growth, and can be accomplished using the FDA-approved tyrosine kinase inhibitor ibrutinib. This illuminates SRMS as a targetable vulnerability in human cancers and as a new target for pharmacological induction of autophagy in vertebrates. This study describes the discovery and characterization of a nutrient-sensitive signaling pathway that drives growth and inhibits autophagy in mammalian cells. This pathway, which involves the non-receptor tyrosine kinase SRMS and the PHLPP scaffold protein FKBP51, promotes tumor growth and is amenable to pharmacological inhibition.
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Affiliation(s)
- Jung Mi Park
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
- Department of Oncology Research, Amgen Research, Thousand Oaks, California, United States of America
| | - Seung Wook Yang
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Wei Zhuang
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Asim K. Bera
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Yan Liu
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Deepak Gurbani
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Sergei J. von Hoyningen-Huene
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Sadie Miki Sakurada
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Haiyun Gan
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Shondra M. Pruett-Miller
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Kenneth D. Westover
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Malia B. Potts
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
- Department of Oncology Research, Amgen Research, Thousand Oaks, California, United States of America
- * E-mail:
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32
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Hsia Y, Mout R, Sheffler W, Edman NI, Vulovic I, Park YJ, Redler RL, Bick MJ, Bera AK, Courbet A, Kang A, Brunette TJ, Nattermann U, Tsai E, Saleem A, Chow CM, Ekiert D, Bhabha G, Veesler D, Baker D. Design of multi-scale protein complexes by hierarchical building block fusion. Nat Commun 2021; 12:2294. [PMID: 33863889 PMCID: PMC8052403 DOI: 10.1038/s41467-021-22276-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 02/08/2021] [Indexed: 12/13/2022] Open
Abstract
A systematic and robust approach to generating complex protein nanomaterials would have broad utility. We develop a hierarchical approach to designing multi-component protein assemblies from two classes of modular building blocks: designed helical repeat proteins (DHRs) and helical bundle oligomers (HBs). We first rigidly fuse DHRs to HBs to generate a large library of oligomeric building blocks. We then generate assemblies with cyclic, dihedral, and point group symmetries from these building blocks using architecture guided rigid helical fusion with new software named WORMS. X-ray crystallography and cryo-electron microscopy characterization show that the hierarchical design approach can accurately generate a wide range of assemblies, including a 43 nm diameter icosahedral nanocage. The computational methods and building block sets described here provide a very general route to de novo designed protein nanomaterials.
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Affiliation(s)
- Yang Hsia
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Biological Physics, Structure and Design Graduate Program, University of Washington, Seattle, WA, USA
| | - Rubul Mout
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - William Sheffler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Natasha I Edman
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Ivan Vulovic
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Molecular Engineering Graduate Program, University of Washington, Seattle, WA, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Rachel L Redler
- Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
| | - Matthew J Bick
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Asim K Bera
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alexis Courbet
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - T J Brunette
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Una Nattermann
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Biological Physics, Structure and Design Graduate Program, University of Washington, Seattle, WA, USA
| | - Evelyn Tsai
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Ayesha Saleem
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Cameron M Chow
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Damian Ekiert
- Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Gira Bhabha
- Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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33
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Vorobieva AA, White P, Liang B, Horne JE, Bera AK, Chow CM, Gerben S, Marx S, Kang A, Stiving AQ, Harvey SR, Marx DC, Khan GN, Fleming KG, Wysocki VH, Brockwell DJ, Tamm LK, Radford SE, Baker D. De novo design of transmembrane β barrels. Science 2021; 371:eabc8182. [PMID: 33602829 PMCID: PMC8064278 DOI: 10.1126/science.abc8182] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 12/07/2020] [Indexed: 12/12/2022]
Abstract
Transmembrane β-barrel proteins (TMBs) are of great interest for single-molecule analytical technologies because they can spontaneously fold and insert into membranes and form stable pores, but the range of pore properties that can be achieved by repurposing natural TMBs is limited. We leverage the power of de novo computational design coupled with a "hypothesis, design, and test" approach to determine TMB design principles, notably, the importance of negative design to slow β-sheet assembly. We design new eight-stranded TMBs, with no homology to known TMBs, that insert and fold reversibly into synthetic lipid membranes and have nuclear magnetic resonance and x-ray crystal structures very similar to the computational models. These advances should enable the custom design of pores for a wide range of applications.
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Affiliation(s)
- Anastassia A Vorobieva
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Paul White
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, USA
| | - Binyong Liang
- Department of Molecular Physiology and Biological Physics and Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22903, USA
| | - Jim E Horne
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, USA
| | - Asim K Bera
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Cameron M Chow
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Stacey Gerben
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Sinduja Marx
- Department of Molecular Engineering and Sciences, University of Washington, Seattle, WA 98195, USA
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Alyssa Q Stiving
- Department of Chemistry and Biochemistry, Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Sophie R Harvey
- Department of Chemistry and Biochemistry, Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Dagan C Marx
- TC Jenkins Department of Biophysics Johns Hopkins University, Baltimore, MD 21218, USA
| | - G Nasir Khan
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, USA
| | - Karen G Fleming
- TC Jenkins Department of Biophysics Johns Hopkins University, Baltimore, MD 21218, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, USA
| | - Lukas K Tamm
- Department of Molecular Physiology and Biological Physics and Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22903, USA
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
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34
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Basanta B, Bick MJ, Bera AK, Norn C, Chow CM, Carter LP, Goreshnik I, Dimaio F, Baker D. An enumerative algorithm for de novo design of proteins with diverse pocket structures. Proc Natl Acad Sci U S A 2020; 117:22135-22145. [PMID: 32839327 PMCID: PMC7486743 DOI: 10.1073/pnas.2005412117] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To create new enzymes and biosensors from scratch, precise control over the structure of small-molecule binding sites is of paramount importance, but systematically designing arbitrary protein pocket shapes and sizes remains an outstanding challenge. Using the NTF2-like structural superfamily as a model system, we developed an enumerative algorithm for creating a virtually unlimited number of de novo proteins supporting diverse pocket structures. The enumerative algorithm was tested and refined through feedback from two rounds of large-scale experimental testing, involving in total the assembly of synthetic genes encoding 7,896 designs and assessment of their stability on yeast cell surface, detailed biophysical characterization of 64 designs, and crystal structures of 5 designs. The refined algorithm generates proteins that remain folded at high temperatures and exhibit more pocket diversity than naturally occurring NTF2-like proteins. We expect this approach to transform the design of small-molecule sensors and enzymes by enabling the creation of binding and active site geometries much more optimal for specific design challenges than is accessible by repurposing the limited number of naturally occurring NTF2-like proteins.
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Affiliation(s)
- Benjamin Basanta
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Biochemistry Department, School of Medicine, University of Washington, Seattle, WA 98195
| | - Matthew J Bick
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Biochemistry Department, School of Medicine, University of Washington, Seattle, WA 98195
| | - Asim K Bera
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Biochemistry Department, School of Medicine, University of Washington, Seattle, WA 98195
| | - Christoffer Norn
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Biochemistry Department, School of Medicine, University of Washington, Seattle, WA 98195
| | - Cameron M Chow
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Biochemistry Department, School of Medicine, University of Washington, Seattle, WA 98195
| | - Lauren P Carter
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Biochemistry Department, School of Medicine, University of Washington, Seattle, WA 98195
| | - Inna Goreshnik
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Biochemistry Department, School of Medicine, University of Washington, Seattle, WA 98195
| | - Frank Dimaio
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Biochemistry Department, School of Medicine, University of Washington, Seattle, WA 98195
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, WA 98195;
- Biochemistry Department, School of Medicine, University of Washington, Seattle, WA 98195
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195
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35
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Thangswamy M, Maheshwari P, Dutta D, Bera AK, Singh MN, Sinha AK, Yusuf SM, Pujari PK. Evolution of confined ice nano structures at different levels of pore filling: a synchrotron based X-ray diffraction study. Phys Chem Chem Phys 2020; 22:14309-14317. [PMID: 32567617 DOI: 10.1039/d0cp01988g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We have thoroughly investigated the crystal structure of ice evolved from super cooled water confined in MCM-41 cylindrical nano pores through a synchrotron-based X-ray diffraction (XRD) technique for two different levels of pore filling. A rigorous analysis of XRD data shows that the nucleation dynamics and the structure of nucleated ice highly depend on the level of pore filling. In the nearly fully hydrated pores, ice crystallites start nucleating inside the pores below 240 K and creep out of the pores to form bulk crystals having crystalline structure of a mixed phase of hexagonal and cubic forms. In the partially hydrated pores, on the other hand, ice crystals cannot creep out of the pore crossing the energy barrier. The crystalline ice particles remaining inside the cylindrical pore show a short range "cubic rich" structure. The "pure cubic" phase has not been identified at either of the pore fillings in these 2.5 nm average size pores. A large fraction of water inside the pores remains in the super cooled liquid phase even at 180 K. This observation is relevant for understanding the ice nucleation through the pore condensation and freezing mechanism, which is a major pathway for the formation of cirrus clouds in the upper atmosphere.
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Affiliation(s)
| | - Priya Maheshwari
- Radiochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai-400085, India. and Homi Bhabha National Institute, Bhabha Atomic Research Centre, Mumbai-400085, India
| | - Dhanadeep Dutta
- Radiochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai-400085, India. and Homi Bhabha National Institute, Bhabha Atomic Research Centre, Mumbai-400085, India
| | - A K Bera
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai-400085, India
| | - M N Singh
- Synchrotron Utilization Section, Raja Ramanna Centre for Advanced Technology, Indore-452013, India
| | - Anil K Sinha
- Synchrotron Utilization Section, Raja Ramanna Centre for Advanced Technology, Indore-452013, India
| | - S M Yusuf
- Homi Bhabha National Institute, Bhabha Atomic Research Centre, Mumbai-400085, India and Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai-400085, India
| | - Pradeep K Pujari
- Radiochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai-400085, India. and Homi Bhabha National Institute, Bhabha Atomic Research Centre, Mumbai-400085, India
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36
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Zhou ZW, Ambrogio C, Bera AK, Li Q, Li XX, Li L, Son J, Gondi S, Li J, Campbell E, Jin H, Okoro JJ, Xu CX, Janne PA, Westover KD. KRAS Q61H Preferentially Signals through MAPK in a RAF Dimer-Dependent Manner in Non-Small Cell Lung Cancer. Cancer Res 2020; 80:3719-3731. [PMID: 32605999 DOI: 10.1158/0008-5472.can-20-0448] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/21/2020] [Accepted: 06/24/2020] [Indexed: 11/16/2022]
Abstract
Assembly of RAS molecules into complexes at the cell membrane is critical for RAS signaling. We previously showed that oncogenic KRAS codon 61 mutations increase its affinity for RAF, raising the possibility that KRASQ61H, the most common KRAS mutation at codon 61, upregulates RAS signaling through mechanisms at the level of RAS assemblies. We show here that KRASQ61H exhibits preferential binding to RAF relative to PI3K in cells, leading to enhanced MAPK signaling in in vitro models and human NSCLC tumors. X-ray crystallography of KRASQ61H:GTP revealed that a hyperdynamic switch 2 allows for a more stable interaction with switch 1, suggesting that enhanced RAF activity arises from a combination of absent intrinsic GTP hydrolysis activity and increased affinity for RAF. Disruption of KRASQ61H assemblies by the RAS oligomer-disrupting D154Q mutation impaired RAF dimerization and altered MAPK signaling but had little effect on PI3K signaling. However, KRASQ61H oligomers but not KRASG12D oligomers were disrupted by RAF mutations that disrupt RAF-RAF interactions. KRASQ61H cells show enhanced sensitivity to RAF and MEK inhibitors individually, whereas combined treatment elicited synergistic growth inhibition. Furthermore, KRASQ61H tumors in mice exhibited high vulnerability to MEK inhibitor, consistent with cooperativity between KRASQ61H and RAF oligomerization and dependence on MAPK signaling. These findings support the notion that KRASQ61H and functionally similar mutations may serve as predictive biomarkers for targeted therapies against the MAPK pathway. SIGNIFICANCE: These findings show that oncogenic KRASQ61H forms a cooperative RAS-RAF ternary complex, which renders RAS-driven tumors vulnerable to MEKi and RAFi, thus establishing a framework for evaluating RAS biomarker-driven targeted therapies.
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Affiliation(s)
- Zhi-Wei Zhou
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Chiara Ambrogio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Molecular Biotechnology and Health Science, Molecular Biotechnology Center, University of Torino, Torino, Italy
| | - Asim K Bera
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Qing Li
- Cancer Center, Daping Hospital and Research Institute of Surgery, Third Military Medical University, Chongqing, China
| | - Xing-Xiao Li
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Lianbo Li
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Jieun Son
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Sudershan Gondi
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Jiaqi Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Emily Campbell
- Department of Physiology and Developmental Biology, Brigham Young University, Provo, Utah
| | - Hua Jin
- Department of Thoracic Surgery, Daping Hospital and Research Institute of Surgery, Third Military Medical University, Chongqing, China
| | - Jeffrey J Okoro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Cheng-Xiong Xu
- Cancer Center, Daping Hospital and Research Institute of Surgery, Third Military Medical University, Chongqing, China.
| | - Pasi A Janne
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. .,Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kenneth D Westover
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas.
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37
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Bera AK, Lu J, Lu C, Li L, Gondi S, Yan W, Nelson A, Zhang G, Westover KD. GTP hydrolysis is modulated by Arg34 in the RASopathy-associated KRAS P34R. Birth Defects Res 2020; 112:708-717. [PMID: 32187889 PMCID: PMC7495839 DOI: 10.1002/bdr2.1647] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 01/08/2020] [Indexed: 01/07/2023]
Abstract
RAS proteins are commonly mutated in cancerous tumors, but germline RAS mutations are also found in RASopathy syndromes such as Noonan syndrome (NS) and cardiofaciocutaneous (CFC) syndrome. Activating RAS mutations can be subclassified based on their activating mechanisms. Understanding the structural basis for these mechanisms may provide clues for how to manage associated health conditions. We determined high-resolution X-ray structures of the RASopathy mutant KRASP34R seen in NS and CFCS. GTP and GDP-bound KRASP34R crystallized in multiple forms, with each lattice consisting of multiple protein conformations. In all GTP-bound conformations, the switch regions are not compatible with GAP binding, suggesting a structural mechanism for the GAP insensitivity of this RAS mutant. However, GTP-bound conformations are compatible with intrinsic nucleotide hydrolysis, including one that places R34 in a position analogous to the GAP arginine finger or intrinsic arginine finger found in heterotrimeric G proteins, which may support intrinsic GTP hydrolysis. We also note that the affinity between KRASP34R and RAF-RBD is decreased, suggesting another possible mechanism for dampening of RAS signaling. These results may provide a foothold for development of new mutation-specific strategies to address KRASP34R -driven diseases.
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Affiliation(s)
- Asim K. Bera
- Department of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Jia Lu
- Department of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Chunya Lu
- Department of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Lianbo Li
- Department of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Sudershan Gondi
- Department of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Wei Yan
- Department of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | | | - Goujun Zhang
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Kenneth D. Westover
- Department of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
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38
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Gurbani D, Du G, Henning NJ, Rao S, Bera AK, Zhang T, Gray NS, Westover KD. Structure and Characterization of a Covalent Inhibitor of Src Kinase. Front Mol Biosci 2020; 7:81. [PMID: 32509799 PMCID: PMC7248381 DOI: 10.3389/fmolb.2020.00081] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 04/08/2020] [Indexed: 12/11/2022] Open
Abstract
Unregulated Src activity promotes malignant processes in cancer, but no Src-directed targeted therapies are used clinically, possibly because early Src inhibitors produce off-target effects leading to toxicity. Improved selective Src inhibitors may enable Src-directed therapies. Previously, we reported an irreversible Src inhibitor, DGY-06-116, based on the hybridization of dasatinib and a promiscuous covalent kinase probe SM1-71. Here, we report biochemical and biophysical characterization of this compound. An x-ray co-crystal structure of DGY-06-116: Src shows a covalent interaction with the kinase p-loop and occupancy of the back hydrophobic kinase pocket, explaining its high potency, and selectivity. However, a reversible analog also shows similar potency. Kinetic analysis shows a slow inactivation rate compared to other clinically approved covalent kinase inhibitors, consistent with a need for p-loop movement prior to covalent bond formation. Overall, these results suggest that a strong reversible interaction is required to allow sufficient time for the covalent reaction to occur. Further optimization of the covalent linker may improve the kinetics of covalent bond formation.
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Affiliation(s)
- Deepak Gurbani
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX, United States
| | - Guangyan Du
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, United States
| | - Nathaniel J. Henning
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, United States
| | - Suman Rao
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, United States
- Harvard Program in Therapeutic Science (HiTS), Harvard Medical School, Boston, MA, United States
| | - Asim K. Bera
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX, United States
| | - Tinghu Zhang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, United States
| | - Nathanael S. Gray
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, United States
| | - Kenneth D. Westover
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX, United States
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39
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Singh B, Kumar D, Manna K, Bera AK, Cansever GA, Maljuk A, Wurmehl S, Büchner B, Kumar P. Correlated paramagnetism and interplay of magnetic and phononic degrees of freedom in 3d-5d coupled La 2CuIrO 6. J Phys Condens Matter 2019; 31:485803. [PMID: 31422956 DOI: 10.1088/1361-648x/ab3c14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Conventional paramagnetism-a state with finite magnetic moment per ion sans long range magnetic ordering, but with lowering temperature the moment each ion picks up a particular direction, breaking spin rotational symmetry, and results into long-range magnetic ordering. However, in systems with competing multiple degrees of freedom this conventional notion may easily break and results into short range correlation much above the global magnetic transition temperature. La2CuIrO6 with complex interplay of spins (s = 1/2) on Cu site and pseudo-spin (j = 1/2) on Ir site owing to strong spin-orbit coupling provides fertile ground to observe such correlated phenomena. By a comprehensive temperature dependent Raman study, we have shown the presence of such a correlated paramagnetic state in La2CuIrO6 much above the long-range magnetic ordering temperature (T N ). Our observation of strong interactions of phonons, associated with Cu/Ir octahedra, with underlying magnetic degrees of freedom mirrored in the observed Fano asymmetry, which remarkably persists as high as ~3.5T N clearly signals the existence of correlated paramagnetism hence broken spin rotational symmetry. Our detailed analysis also reveals anomalous changes in the self-energy parameters of the phonon modes, i.e. mode frequencies and linewidth, below T N , providing a useful gauge for monitoring the strong coupling between phonons and magnetic degrees of freedom.
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Affiliation(s)
- Birender Singh
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi 175005, India
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Bera AK, Lu J, Wales TE, Gondi S, Gurbani D, Nelson A, Engen JR, Westover KD. Structural basis of the atypical activation mechanism of KRAS V14I. J Biol Chem 2019; 294:13964-13972. [PMID: 31341022 PMCID: PMC6755796 DOI: 10.1074/jbc.ra119.009131] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/18/2019] [Indexed: 01/20/2023] Open
Abstract
RAS regulation and signaling are largely accomplished by direct protein-protein interactions, making RAS protein dynamics a critical determinant of RAS function. Here, we report a crystal structure of GDP-bound KRASV14I, a mutated KRAS variant associated with the developmental RASopathy disorder Noonan syndrome (NS), at 1.5-1.6 Å resolution. The structure is notable for revealing a marked extension of switch 1 away from the G-domain and nucleotide-binding site of the KRAS protein. We found that this extension is associated with a loss of the magnesium ion and a tilt in the position of the guanine base because of the additional carbon introduced by the isoleucine substitution. Hydrogen-deuterium exchange MS analysis confirmed that this conformation occurs in solution, but also disclosed a difference in kinetics when compared with KRASA146T, another RAS mutant that displays a nearly identical conformation in previously reported crystal structures. This conformational change contributed to a high rate of guanine nucleotide-exchange factor (GEF)-dependent and -independent nucleotide exchange and to an increase in affinity for SOS Ras/Rac GEF 1 (SOS1), which appears to be the major mode of activation for this RAS variant. These results highlight a mechanistic connection between KRASA146T and KRASV14I that may have implications for the regulation of these variants and for the development of therapeutic strategies to manage KRAS variant-associated disorders.
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Affiliation(s)
- Asim K Bera
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390
| | - Jia Lu
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Masachusetts 02115
| | - Sudershan Gondi
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390
| | - Deepak Gurbani
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390
| | - Andrew Nelson
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Masachusetts 02115
| | - Kenneth D Westover
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390
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Shi K, Cho S, Aukema KG, Lee T, Bera AK, Seffernick JL, Wackett LP, Aihara H. Crystal structures of Moorella thermoacetica cyanuric acid hydrolase reveal conformational flexibility and asymmetry important for catalysis. PLoS One 2019; 14:e0216979. [PMID: 31181074 PMCID: PMC6557486 DOI: 10.1371/journal.pone.0216979] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 05/02/2019] [Indexed: 01/07/2023] Open
Abstract
An ancient enzyme family responsible for the catabolism of the prebiotic chemical cyanuric acid (1,3,5-triazine-2,4,6-triol) was recently discovered and is undergoing proliferation in the modern world due to industrial synthesis and dissemination of 1,3,5-triazine compounds. Cyanuric acid has a highly stabilized ring system such that bacteria require a unique enzyme with a novel fold and subtle active site construction to open the ring. Each cyanuric acid hydrolase monomer consists of three isostructural domains that coordinate and activate the three-fold symmetric substrate cyanuric acid for ring opening. We have now solved a series of X-ray structures of an engineered, thermostable cyanuric acid ring-opening enzyme at 1.51 ~ 2.25 Å resolution, including various complexes with the substrate, a tight-binding inhibitor, or an analog of the reaction intermediate. These structures reveal asymmetric interactions between the enzyme and bound ligands, a metal ion binding coupled to conformational changes and substrate binding important for enzyme stability, and distinct roles of the isostructural domains of the enzyme. The multiple conformations of the enzyme observed across a series of structures and corroborating biochemical data suggest importance of the structural dynamics in facilitating the substrate entry and the ring-opening reaction, catalyzed by a conserved Ser-Lys dyad.
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Affiliation(s)
- Ke Shi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Seunghee Cho
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Kelly G. Aukema
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Thomas Lee
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Asim K. Bera
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Jennifer L. Seffernick
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Lawrence P. Wackett
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, United States of America
- Microbial and Plant Genomics Institute, University of Minnesota, St. Paul, Minnesota, United States of America
- * E-mail: (HA); (LPW)
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
- * E-mail: (HA); (LPW)
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Poulin EJ, Bera AK, Lu J, Lin YJ, Strasser SD, Paulo JA, Huang TQ, Morales C, Yan W, Cook J, Nowak JA, Brubaker DK, Joughin BA, Johnson CW, DeStefanis RA, Ghazi PC, Gondi S, Wales TE, Iacob RE, Bogdanova L, Gierut JJ, Li Y, Engen JR, Perez-Mancera PA, Braun BS, Gygi SP, Lauffenburger DA, Westover KD, Haigis KM. Tissue-Specific Oncogenic Activity of KRAS A146T. Cancer Discov 2019; 9:738-755. [PMID: 30952657 PMCID: PMC6548671 DOI: 10.1158/2159-8290.cd-18-1220] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 03/06/2019] [Accepted: 04/02/2019] [Indexed: 12/16/2022]
Abstract
KRAS is the most frequently mutated oncogene. The incidence of specific KRAS alleles varies between cancers from different sites, but it is unclear whether allelic selection results from biological selection for specific mutant KRAS proteins. We used a cross-disciplinary approach to compare KRASG12D, a common mutant form, and KRASA146T, a mutant that occurs only in selected cancers. Biochemical and structural studies demonstrated that KRASA146T exhibits a marked extension of switch 1 away from the protein body and nucleotide binding site, which activates KRAS by promoting a high rate of intrinsic and guanine nucleotide exchange factor-induced nucleotide exchange. Using mice genetically engineered to express either allele, we found that KRASG12D and KRASA146T exhibit distinct tissue-specific effects on homeostasis that mirror mutational frequencies in human cancers. These tissue-specific phenotypes result from allele-specific signaling properties, demonstrating that context-dependent variations in signaling downstream of different KRAS mutants drive the KRAS mutational pattern seen in cancer. SIGNIFICANCE: Although epidemiologic and clinical studies have suggested allele-specific behaviors for KRAS, experimental evidence for allele-specific biological properties is limited. We combined structural biology, mass spectrometry, and mouse modeling to demonstrate that the selection for specific KRAS mutants in human cancers from different tissues is due to their distinct signaling properties.See related commentary by Hobbs and Der, p. 696.This article is highlighted in the In This Issue feature, p. 681.
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Affiliation(s)
- Emily J Poulin
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Asim K Bera
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Jia Lu
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Yi-Jang Lin
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Samantha Dale Strasser
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts
| | - Tannie Q Huang
- Department of Pediatrics and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Carolina Morales
- Department of Pediatrics and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Wei Yan
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Joshua Cook
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Jonathan A Nowak
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Douglas K Brubaker
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Brian A Joughin
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Christian W Johnson
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Rebecca A DeStefanis
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Phaedra C Ghazi
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Sudershan Gondi
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts
| | - Roxana E Iacob
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts
| | - Lana Bogdanova
- Department of Pediatrics and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Jessica J Gierut
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Yina Li
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts
| | - Pedro A Perez-Mancera
- Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Benjamin S Braun
- Department of Pediatrics and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Kenneth D Westover
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas.
| | - Kevin M Haigis
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts.
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Harvard Digestive Disease Center, Harvard Medical School, Boston, Massachusetts
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Sreevatsava V, De S, Bandyopadhyay S, Chaudhury P, Bera AK, Muthiyan R, De AK, Perumal P, Sunder J, Chakraborty G, Bhattacharya D. Variability of the EG95 antigen-coding gene of Echinococcus granulosus in animal and human origin: implications for vaccine development. J Genet 2019; 98:53. [PMID: 31204707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In the present study, the genetic variability of the EG95 protein-coding gene in several animal and human isolates of Echinococcus granulosus was investigated. A total of 24 isolates collected from cattle, buffalo, sheep, goat, dog and man were amplified by Eg95-coding gene-specific primers. From the generated sequence information, a conceptual amino acid sequence was deduced. Phylogenetically, the Eg95 coding gene belongs to the Eg95-1/Eg95-2/Eg95-3/Eg95-4 cluster. Further confirmation on the maximum composite likelihood analysis revealed that the overall transition/transversion bias was 2.913. This finding indicated thatthere is bias towards transitional and transversional substitution. Using artificial neural networks, a B-cell epitope was predicted on primary sequence information. Stretches of amino acid residues varied between animal and human isolates when hydrophobicity was considered. Flexibility also varied between larval and adult stages of the organism. This observation is important to develop vaccines. However, cytotoxic T-lymphocyte epitopes on primary sequence data remained constant in all isolates. In this study, agretope identification started with hydrophobic amino acids. Amino acids with the same physico-chemical properties were present in the middle. The conformational propensity of the Eg95-coding gene of 156 amino acid residues had α-turns and β-turns, and α-amphipathic regions up to 129, 138-156 and 151-155 residues, respectively. The results indicated potential T-cell antigenic sites. The overall Tajima's D value was negative (-2.404165), indicative of negative selection pressure.
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Affiliation(s)
- V Sreevatsava
- Eastern Regional Station, Indian Veterinary Research Institute, Kolkata 700 037, India.
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Abstract
KRAS switch loop movements play a crucial role in regulating RAS signaling, and alteration of these sensitive dynamics is a principal mechanism through which disease-associated RAS mutations lead to aberrant RAS activation. Prior studies suggest that despite a high degree of sequence similarity, the switches in KRAS are more dynamic than those in HRAS. We determined X-ray crystal structures of the rare tumorigenic KRAS mutants KRASD33E, in switch 1 (SW1), and KRASA59G, in switch 2 (SW2), bound to GDP and found these adopt nearly identical, open SW1 conformations as well as altered SW2 conformations. KRASA59G bound to a GTP analogue crystallizes in the same conformation. This open conformation is consistent with the inactive "state 1" previously observed for HRAS bound to GTP. For KRASA59G, switch rearrangements may be regulated by increased flexibility in the 57DXXGQ61 motif at codon 59. However, loss of interactions between side chains at codons 33 and 35 in the SW1 33DPT35 motif drives changes for KRASD33E. The 33DPT35 motif is conserved for multiple members of the RAS subfamily but is not found in RAB, RHO, ARF, or Gα families, suggesting that dynamics mediated by this motif may be important for determining the selectivity of RAS-effector interactions. Biochemically, the consequence of altered switch dynamics is the same, showing impaired interaction with the guanine exchange factor SOS and loss of GAP-dependent GTPase activity. However, interactions with the RBD of RAF are preserved. Overall, these observations add to a body of evidence suggesting that HRAS and KRAS show meaningful differences in functionality stemming from differential protein dynamics independent of the hypervariable region.
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Affiliation(s)
- Jia Lu
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas , Dallas, Texas 75390, United States
| | - Asim K Bera
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas , Dallas, Texas 75390, United States
| | - Sudershan Gondi
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas , Dallas, Texas 75390, United States
| | - Kenneth D Westover
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas , Dallas, Texas 75390, United States
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Totzke J, Gurbani D, Raphemot R, Hughes PF, Bodoor K, Carlson DA, Loiselle DR, Bera AK, Eibschutz LS, Perkins MM, Eubanks AL, Campbell PL, Fox DA, Westover KD, Haystead TAJ, Derbyshire ER. Takinib, a Selective TAK1 Inhibitor, Broadens the Therapeutic Efficacy of TNF-α Inhibition for Cancer and Autoimmune Disease. Cell Chem Biol 2017; 24:1029-1039.e7. [PMID: 28820959 DOI: 10.1016/j.chembiol.2017.07.011] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 05/22/2017] [Accepted: 07/25/2017] [Indexed: 12/20/2022]
Abstract
Tumor necrosis factor alpha (TNF-α) has both positive and negative roles in human disease. In certain cancers, TNF-α is infused locally to promote tumor regression, but dose-limiting inflammatory effects limit broader utility. In autoimmune disease, anti-TNF-α antibodies control inflammation in most patients, but these benefits are offset during chronic treatment. TAK1 acts as a key mediator between survival and cell death in TNF-α-mediated signaling. Here, we describe Takinib, a potent and selective TAK1 inhibitor that induces apoptosis following TNF-α stimulation in cell models of rheumatoid arthritis and metastatic breast cancer. We demonstrate that Takinib is an inhibitor of autophosphorylated and non-phosphorylated TAK1 that binds within the ATP-binding pocket and inhibits by slowing down the rate-limiting step of TAK1 activation. Overall, Takinib is an attractive starting point for the development of inhibitors that sensitize cells to TNF-α-induced cell death, with general implications for cancer and autoimmune disease treatment.
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Affiliation(s)
- Juliane Totzke
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA
| | - Deepak Gurbani
- Departments of Biochemistry and Radiation Oncology, University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Rene Raphemot
- Department of Chemistry, Duke University, Durham, NC 27710, USA
| | - Philip F Hughes
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA
| | - Khaldon Bodoor
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA; Department of Applied Biology, Jordan University of Science and Technology, PO Box 3030, Irbid 22110, Jordan
| | - David A Carlson
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA
| | - David R Loiselle
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA
| | - Asim K Bera
- Departments of Biochemistry and Radiation Oncology, University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Liesl S Eibschutz
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA
| | | | - Amber L Eubanks
- Department of Chemistry, Duke University, Durham, NC 27710, USA
| | - Phillip L Campbell
- University of Michigan, Division of Rheumatology and Clinical Autoimmunity Center of Excellence, Ann Arbor, MI 48109, USA
| | - David A Fox
- University of Michigan, Division of Rheumatology and Clinical Autoimmunity Center of Excellence, Ann Arbor, MI 48109, USA
| | - Kenneth D Westover
- Departments of Biochemistry and Radiation Oncology, University of Texas, Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA.
| | - Timothy A J Haystead
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA.
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Bera AK, Aukema KG, Elias M, Wackett LP. Structure of the Cyanuric Acid Hydrolase TrzD Reveals Product Exit Channel. Sci Rep 2017; 7:45277. [PMID: 28345631 PMCID: PMC5366886 DOI: 10.1038/srep45277] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 02/23/2017] [Indexed: 11/09/2022] Open
Abstract
Cyanuric acid hydrolases are of industrial importance because of their use in aquatic recreational facilities to remove cyanuric acid, a stabilizer for the chlorine. Degradation of excess cyanuric acid is necessary to maintain chlorine disinfection in the waters. Cyanuric acid hydrolase opens the cyanuric acid ring hydrolytically and subsequent decarboxylation produces carbon dioxide and biuret. In the present study, we report the X-ray structure of TrzD, a cyanuric acid hydrolase from Acidovorax citrulli. The crystal structure at 2.19 Å resolution shows a large displacement of the catalytic lysine (Lys163) in domain 2 away from the active site core, whereas the two other active site lysines from the two other domains are not able to move. The lysine displacement is proposed here to open up a channel for product release. Consistent with that, the structure also showed two molecules of the co-product, carbon dioxide, one in the active site and another trapped in the proposed exit channel. Previous data indicated that the domain 2 lysine residue plays a role in activating an adjacent serine residue carrying out nucleophilic attack, opening the cyanuric acid ring, and the mobile lysine guides products through the exit channel.
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Affiliation(s)
- Asim K Bera
- BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA
| | - Kelly G Aukema
- BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA
| | - Mikael Elias
- BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN 55108, USA
| | - Lawrence P Wackett
- BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN 55108, USA
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Aukema KG, Escalante DE, Maltby MM, Bera AK, Aksan A, Wackett LP. In Silico Identification of Bioremediation Potential: Carbamazepine and Other Recalcitrant Personal Care Products. Environ Sci Technol 2017; 51:880-888. [PMID: 27977154 DOI: 10.1021/acs.est.6b04345] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Emerging contaminants are principally personal care products not readily removed by conventional wastewater treatment and, with an increasing reliance on water recycling, become disseminated in drinking water supplies. Carbamazepine, a widely used neuroactive pharmaceutical, increasingly escapes wastewater treatment and is found in potable water. In this study, a mechanism is proposed by which carbamazepine resists biodegradation, and a previously unknown microbial biodegradation was predicted computationally. The prediction identified biphenyl dioxygenase from Paraburkholderia xenovorans LB400 as the best candidate enzyme for metabolizing carbamazepine. The rate of degradation described here is 40 times greater than the best reported rates. The metabolites cis-10,11-dihydroxy-10,11-dihydrocarbamazepine and cis-2,3-dihydroxy-2,3-dihydrocarbamazepine were demonstrated with the native organism and a recombinant host. The metabolites are considered nonharmful and mitigate the generation of carcinogenic acridine products known to form when advanced oxidation methods are used in water treatment. Other recalcitrant personal care products were subjected to prediction by the Pathway Prediction System and tested experimentally with P. xenovorans LB400. It was shown to biodegrade structurally diverse compounds. Predictions indicated hydrolase or oxygenase enzymes catalyzed the initial reactions. This study highlights the potential for using the growing body of enzyme-structural and genomic information with computational methods to rapidly identify enzymes and microorganisms that biodegrade emerging contaminants.
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Affiliation(s)
- Kelly G Aukema
- Department of Biochemistry, Molecular Biology and Biophysics, ‡BioTechnology Institute, and §Department of Mechanical Engineering, University of Minnesota-Twin Cities , Minneapolis, Minnesota 55455, United States
| | - Diego E Escalante
- Department of Biochemistry, Molecular Biology and Biophysics, ‡BioTechnology Institute, and §Department of Mechanical Engineering, University of Minnesota-Twin Cities , Minneapolis, Minnesota 55455, United States
| | - Meghan M Maltby
- Department of Biochemistry, Molecular Biology and Biophysics, ‡BioTechnology Institute, and §Department of Mechanical Engineering, University of Minnesota-Twin Cities , Minneapolis, Minnesota 55455, United States
| | - Asim K Bera
- Department of Biochemistry, Molecular Biology and Biophysics, ‡BioTechnology Institute, and §Department of Mechanical Engineering, University of Minnesota-Twin Cities , Minneapolis, Minnesota 55455, United States
| | - Alptekin Aksan
- Department of Biochemistry, Molecular Biology and Biophysics, ‡BioTechnology Institute, and §Department of Mechanical Engineering, University of Minnesota-Twin Cities , Minneapolis, Minnesota 55455, United States
| | - Lawrence P Wackett
- Department of Biochemistry, Molecular Biology and Biophysics, ‡BioTechnology Institute, and §Department of Mechanical Engineering, University of Minnesota-Twin Cities , Minneapolis, Minnesota 55455, United States
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Chaudhuri A, Bera AK, Sarkar I, Chakraborty S. Insights from Analysis of Binding Sites of Human Meprins: Screening of Inhibitors by Molecular Dynamics Simulation Study. Comb Chem High Throughput Screen 2016; 19:246-58. [PMID: 26875789 DOI: 10.2174/1386207319666160215161731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 01/28/2015] [Accepted: 02/12/2016] [Indexed: 11/22/2022]
Abstract
Human meprin-α and-β are important regulators of angiogenesis, cancer, inflammation, fibrosis, and neurodegenerative diseases and hence important therapeutic targets. Meprins are the only astacin proteases that are expressed in membrane-bound and secreted form. The cleavage specificity of human meprins is similar in certain cases but differs markedly in others. The inhibitor selectivity of human meprins is controlled by the specific residues involved in binding at the active-site cleft of the proteases. Meprins are inhibited by various small molecular inhibitors as well as macromolecular endogenous inhibitors, making them good drug targets. In the current study, molecular dynamics simulation was performed for 10 ns on ten systems consisting of two apoenzymes of meprin -α/β and eight complexes of human meprin-α and -β complexed to four inhibitors with different metal binding moieties and comparable Ki values. These simulation studies helped to elucidate the molecular details of how several parameters influence protein-inhibitor binding affinity. Analysis of the interaction energies of the protein-inhibitor complexes revealed the diverse binding nature of this series of inhibitors. Several structural segments of human meprins exhibited certain conformational changes during the simulation time course. Among the inhibitors studied captopril had a different disposition in the meprin-bound complexes compared to the other three inhibitors, namely Pro- Leu-Gly-hydroxamate, galardin and EDTA. Comparison of the interaction energies for each system helped us to conclude that the hydroxamic acid-based inhibitors are the most potent inhibitors of meprins.
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Affiliation(s)
| | | | | | - Sibani Chakraborty
- Department of Microbiology, West Bengal State University, Barasat, Berunanpukuria, P.O. Malikapur, North 24 Parganas, Kolkata 700126, West Bengal, India.
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Rathnakumar K, Savant S, Giri H, Ghosh A, Fisslthaler B, Fleming I, Ram U, Bera AK, Augustin HG, Dixit M. Angiopoietin-2 mediates thrombin-induced monocyte adhesion and endothelial permeability. J Thromb Haemost 2016; 14:1655-67. [PMID: 27241812 DOI: 10.1111/jth.13376] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 05/04/2016] [Indexed: 02/03/2023]
Abstract
UNLABELLED Essentials Mechanism of thrombin-induced inflammation is not fully understood. Thrombin induced monocyte adhesion and barrier loss require Angiopoietin-2 (Ang-2). Ang-2 mediates vessel leakage and monocyte adhesion through SHP-2/p38MAPK pathway. Calcium dependent SHP2/p38MAPK activation regulates Ang-2 expression through a feedback loop. SUMMARY Background Thrombin imparts an inflammatory phenotype to the endothelium by promoting increased monocyte adhesion and vascular permeability. However, the molecular players that govern these events are incompletely understood. Objective The aim of this study was to determine whether Angiopoietin-2 (Ang-2) has a role, if any, in regulating inflammatory signals initiated by thrombin. Methods Assessment of vascular leakage by Miles assay was performed by intra-dermal injection on the foot paw. Surface levels of intercellular adhesion molecule-1 (ICAM-1) were determined by flow cytometry. Overexpression, knockdown and phosphorylation of proteins were determined by Western blotting. Results In time-course experiments, thrombin-stimulated Ang-2 up-regulation, peaked prior to the expression of adhesion molecule ICAM-1 in human umbilical vein-derived endothelial cells (HUVECs). Knockdown of Ang-2 blocked both thrombin-induced monocyte adhesion and ICAM-1 expression. In addition, Ang-2(-/-) mice displayed defective vascular leakage when treated with thrombin. Introducing Ang-2 protein in Ang-2(-/-) mice failed to recover a wild-type phenotype. Mechanistically, Ang-2 appears to regulate the thrombin-activated calcium spike that is required for tyrosine phosphatase SHP2 and p38 MAPK activation. Further, down-regulation of SHP2 attenuated both thrombin-induced Ang-2 expression and monocyte adhesion. Down-regulation of the adaptor protein Gab1, a co-activator of SHP2, as well as overexpression of the Gab1 mutant incapable of interacting with SHP2 (YFGab1), inhibited thrombin-mediated effects, including downstream activation of p38 MAPK, which in turn was required for Ang-2 expression. Conclusions The data establish an essential role of the Gab1/SHP2/p38MAPK signaling pathway and Ang-2 in regulating thrombin-induced monocyte adhesion and vascular leakage.
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Affiliation(s)
- K Rathnakumar
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences and Bioengineering, Indian Institute of Technology Madras, Chennai, India
| | - S Savant
- Division of Vascular Oncology and Metastasis, German Cancer Research Center Heidelberg (DKFZ-ZMBH Alliance), Heidelberg, Germany
| | - H Giri
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences and Bioengineering, Indian Institute of Technology Madras, Chennai, India
| | - A Ghosh
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences and Bioengineering, Indian Institute of Technology Madras, Chennai, India
| | - B Fisslthaler
- Institute for Vascular Signalling, Centre for Molecular Medicine, Goethe University, Frankfurt, Germany
| | - I Fleming
- Institute for Vascular Signalling, Centre for Molecular Medicine, Goethe University, Frankfurt, Germany
| | - U Ram
- Seethapathy Clinic and Hospital, Chennai, India
| | - A K Bera
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences and Bioengineering, Indian Institute of Technology Madras, Chennai, India
| | - H G Augustin
- Division of Vascular Oncology and Metastasis, German Cancer Research Center Heidelberg (DKFZ-ZMBH Alliance), Heidelberg, Germany
- Vascular Biology and Tumor Angiogenesis, Medical Faculty Mannheim (CBTM), Heidelberg University, Heidelberg, Germany
| | - M Dixit
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences and Bioengineering, Indian Institute of Technology Madras, Chennai, India
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50
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Kesavan R, Chandel S, Upadhyay S, Bendre R, Ganugula R, Potunuru UR, Giri H, Sahu G, Kumar PU, Reddy GB, Joksic G, Bera AK, Dixit M. Gentiana lutea exerts anti-atherosclerotic effects by preventing endothelial inflammation and smooth muscle cell migration. Nutr Metab Cardiovasc Dis 2016; 26:293-301. [PMID: 26868432 DOI: 10.1016/j.numecd.2015.12.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Revised: 11/16/2015] [Accepted: 12/23/2015] [Indexed: 12/16/2022]
Abstract
BACKGROUND AND AIMS Studies suggest that Gentiana lutea (GL), and its component isovitexin, may exhibit anti-atherosclerotic properties. In this study we sought to investigate the protective mechanism of GL aqueous root extract and isovitexin on endothelial inflammation, smooth muscle cell migation, and on the onset and progression of atherosclerosis in streptozotocin (STZ)-induced diabetic rats. METHODS AND RESULTS Our results show that both GL extract and isovitexin, block leukocyte adhesion and generation of reactive oxygen species in human umbilical vein endothelial cells (HUVECs) and rat aortic smooth muscle cells (RASMCs), following TNF-alpha and platelet derived growth factor-BB (PDGF-BB) challenges respectively. Both the extract and isovitexin blocked TNF-α induced expression of ICAM-1 and VCAM-1 in HUVECs. PDGF-BB induced migration of RASMCs and phospholipase C-γ activation, were also abrogated by GL extract and isovitexin. Fura-2 based ratiometric measurements demonstrated that, both the extact, and isovitexin, inhibit PDGF-BB mediated intracellular calcium rise in RASMCs. Supplementation of regular diet with 2% GL root powder for STZ rats, reduced total cholesterol in blood. Oil Red O staining demonstrated decreased lipid accumulation in aortic wall of diabetic animals upon treatment with GL. Medial thickness and deposition of collagen in the aortic segment of diabetic rats were also reduced upon supplementation. Immunohistochemistry demonstrated reduced expression of vascular cell adhesion molecule-1 (VCAM-1), inducible nitric oxide synthase (iNOS), and vascular endothelial cadherin (VE-cadherin) in aortic segments of diabetic rats following GL treatment. CONCLUSIONS Thus, our results support that GL root extract/powder and isovitexin exhibit anti-atherosclerotic activities.
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Affiliation(s)
- R Kesavan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences and Bioengineering Building, Indian Institute of Technology Madras, Chennai 600036, India
| | - S Chandel
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences and Bioengineering Building, Indian Institute of Technology Madras, Chennai 600036, India
| | - S Upadhyay
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences and Bioengineering Building, Indian Institute of Technology Madras, Chennai 600036, India
| | - R Bendre
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences and Bioengineering Building, Indian Institute of Technology Madras, Chennai 600036, India
| | - R Ganugula
- National Institute of Nutrition, Hyderabad, India
| | - U R Potunuru
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences and Bioengineering Building, Indian Institute of Technology Madras, Chennai 600036, India
| | - H Giri
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences and Bioengineering Building, Indian Institute of Technology Madras, Chennai 600036, India
| | - G Sahu
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences and Bioengineering Building, Indian Institute of Technology Madras, Chennai 600036, India
| | - P Uday Kumar
- National Institute of Nutrition, Hyderabad, India
| | | | - G Joksic
- Department of Physical Chemistry, VINCA Institute of Nuclear Sciences, Belgrade, Serbia
| | - A K Bera
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences and Bioengineering Building, Indian Institute of Technology Madras, Chennai 600036, India
| | - Madhulika Dixit
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences and Bioengineering Building, Indian Institute of Technology Madras, Chennai 600036, India.
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