1
|
Vicente JJ, Wagenbach M, Decarreau J, Zelter A, MacCoss MJ, Davis TN, Wordeman L. The kinesin motor Kif9 regulates centriolar satellite positioning and mitotic progression. bioRxiv 2024:2024.04.03.587821. [PMID: 38617353 PMCID: PMC11014612 DOI: 10.1101/2024.04.03.587821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Centrosomes are the principal microtubule-organizing centers of the cell and play an essential role in mitotic spindle function. Centrosome biogenesis is achieved by strict control of protein acquisition and phosphorylation prior to mitosis. Defects in this process promote fragmentation of pericentriolar material culminating in multipolar spindles and chromosome missegregation. Centriolar satellites, membrane-less aggrupations of proteins involved in the trafficking of proteins toward and away from the centrosome, are thought to contribute to centrosome biogenesis. Here we show that the microtubule plus-end directed kinesin motor Kif9 localizes to centriolar satellites and regulates their pericentrosomal localization during interphase. Lack of Kif9 leads to aggregation of satellites closer to the centrosome and increased centrosomal protein degradation that disrupts centrosome maturation and results in chromosome congression and segregation defects during mitosis. Our data reveal roles for Kif9 and centriolar satellites in the regulation of cellular proteostasis and mitosis.
Collapse
|
2
|
Shen H, Lynch EM, Akkineni S, Watson JL, Decarreau J, Bethel NP, Benna I, Sheffler W, Farrell D, DiMaio F, Derivery E, De Yoreo JJ, Kollman J, Baker D. De novo design of pH-responsive self-assembling helical protein filaments. Nat Nanotechnol 2024:10.1038/s41565-024-01641-1. [PMID: 38570702 DOI: 10.1038/s41565-024-01641-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/26/2024] [Indexed: 04/05/2024]
Abstract
Biological evolution has led to precise and dynamic nanostructures that reconfigure in response to pH and other environmental conditions. However, designing micrometre-scale protein nanostructures that are environmentally responsive remains a challenge. Here we describe the de novo design of pH-responsive protein filaments built from subunits containing six or nine buried histidine residues that assemble into micrometre-scale, well-ordered fibres at neutral pH. The cryogenic electron microscopy structure of an optimized design is nearly identical to the computational design model for both the subunit internal geometry and the subunit packing into the fibre. Electron, fluorescent and atomic force microscopy characterization reveal a sharp and reversible transition from assembled to disassembled fibres over 0.3 pH units, and rapid fibre disassembly in less than 1 s following a drop in pH. The midpoint of the transition can be tuned by modulating buried histidine-containing hydrogen bond networks. Computational protein design thus provides a route to creating unbound nanomaterials that rapidly respond to small pH changes.
Collapse
Affiliation(s)
- Hao Shen
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
| | - Eric M Lynch
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Susrut Akkineni
- Department of Materials Science and Engineering, University of Washington, Seattle, WA, USA
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Joseph L Watson
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Justin Decarreau
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Neville P Bethel
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Issa Benna
- 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
| | - Daniel Farrell
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | | | - James J De Yoreo
- Department of Materials Science and Engineering, University of Washington, Seattle, WA, USA
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Justin Kollman
- 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.
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
Mout R, Bretherton RC, Decarreau J, Lee S, Gregorio N, Edman NI, Ahlrichs M, Hsia Y, Sahtoe DD, Ueda G, Sharma A, Schulman R, DeForest CA, Baker D. De novo design of modular protein hydrogels with programmable intra- and extracellular viscoelasticity. Proc Natl Acad Sci U S A 2024; 121:e2309457121. [PMID: 38289949 PMCID: PMC10861882 DOI: 10.1073/pnas.2309457121] [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: 12/26/2023] [Indexed: 02/01/2024] Open
Abstract
Relating the macroscopic properties of protein-based materials to their underlying component microstructure is an outstanding challenge. Here, we exploit computational design to specify the size, flexibility, and valency of de novo protein building blocks, as well as the interaction dynamics between them, to investigate how molecular parameters govern the macroscopic viscoelasticity of the resultant protein hydrogels. We construct gel systems from pairs of symmetric protein homo-oligomers, each comprising 2, 5, 24, or 120 individual protein components, that are crosslinked either physically or covalently into idealized step-growth biopolymer networks. Through rheological assessment, we find that the covalent linkage of multifunctional precursors yields hydrogels whose viscoelasticity depends on the crosslink length between the constituent building blocks. In contrast, reversibly crosslinking the homo-oligomeric components with a computationally designed heterodimer results in viscoelastic biomaterials exhibiting fluid-like properties under rest and low shear, but solid-like behavior at higher frequencies. Exploiting the unique genetic encodability of these materials, we demonstrate the assembly of protein networks within living mammalian cells and show via fluorescence recovery after photobleaching (FRAP) that mechanical properties can be tuned intracellularly in a manner similar to formulations formed extracellularly. We anticipate that the ability to modularly construct and systematically program the viscoelastic properties of designer protein-based materials could have broad utility in biomedicine, with applications in tissue engineering, therapeutic delivery, and synthetic biology.
Collapse
Affiliation(s)
- Rubul Mout
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
- Stem Cell Program at Boston Children’s Hospital, Harvard Medical School, Boston, MA02115
| | - Ross C. Bretherton
- Department of Bioengineering, University of Washington, Seattle, WA98195
- Department of Chemical Engineering, University of Washington, Seattle, WA98195
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA98195
- Department of Chemistry, University of Washington, Seattle, WA98195
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA98195
| | - Justin Decarreau
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Sangmin Lee
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Nicole Gregorio
- Department of Bioengineering, University of Washington, Seattle, WA98195
- Department of Chemical Engineering, University of Washington, Seattle, WA98195
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA98195
- Department of Chemistry, University of Washington, Seattle, WA98195
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA98195
| | - Natasha I. Edman
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA98195
- Medical Scientist Training Program, University of Washington, Seattle, WA98195
| | - Maggie Ahlrichs
- 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
| | - Danny D. Sahtoe
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
- HHMI, University of Washington, Seattle, WA98195
| | - George Ueda
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Alee Sharma
- College of Professional Studies, Northeastern University, Boston, MA02115
| | - Rebecca Schulman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD21218
- Department of Computer Science, Johns Hopkins University, Baltimore, MD21218
| | - Cole A. DeForest
- Institute for Protein Design, University of Washington, Seattle, WA98195
- Department of Bioengineering, University of Washington, Seattle, WA98195
- Department of Chemical Engineering, University of Washington, Seattle, WA98195
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA98195
- Department of Chemistry, University of Washington, Seattle, WA98195
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA98195
| | - 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
| |
Collapse
|
5
|
Olshefsky A, Benasutti H, Sylvestre M, Butterfield GL, Rocklin GJ, Richardson C, Hicks DR, Lajoie MJ, Song K, Leaf E, Treichel C, Decarreau J, Ke S, Kher G, Carter L, Chamberlain JS, Baker D, King NP, Pun SH. In vivo selection of synthetic nucleocapsids for tissue targeting. Proc Natl Acad Sci U S A 2023; 120:e2306129120. [PMID: 37939083 PMCID: PMC10655225 DOI: 10.1073/pnas.2306129120] [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: 04/15/2023] [Accepted: 09/21/2023] [Indexed: 11/10/2023] Open
Abstract
Controlling the biodistribution of protein- and nanoparticle-based therapeutic formulations remains challenging. In vivo library selection is an effective method for identifying constructs that exhibit desired distribution behavior; library variants can be selected based on their ability to localize to the tissue or compartment of interest despite complex physiological challenges. Here, we describe further development of an in vivo library selection platform based on self-assembling protein nanoparticles encapsulating their own mRNA genomes (synthetic nucleocapsids or synNCs). We tested two distinct libraries: a low-diversity library composed of synNC surface mutations (45 variants) and a high-diversity library composed of synNCs displaying miniproteins with binder-like properties (6.2 million variants). While we did not identify any variants from the low-diversity surface library that yielded therapeutically relevant changes in biodistribution, the high-diversity miniprotein display library yielded variants that shifted accumulation toward lungs or muscles in just two rounds of in vivo selection. Our approach should contribute to achieving specific tissue homing patterns and identifying targeting ligands for diseases of interest.
Collapse
Affiliation(s)
- Audrey Olshefsky
- Department of Bioengineering, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Halli Benasutti
- Department of Biochemistry, University of Washington, Seattle, WA98195
| | - Meilyn Sylvestre
- Department of Bioengineering, University of Washington, Seattle, WA98195
| | - Gabriel L. Butterfield
- Institute for Protein Design, University of Washington, Seattle, WA98195
- Department of Molecular and Cellular Biology, University of Washington, Seattle, WA98195
| | - Gabriel J. Rocklin
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Christian Richardson
- Department of Bioengineering, University of Washington, Seattle, WA98195
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Derrick R. Hicks
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Marc J. Lajoie
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Kefan Song
- Department of Bioengineering, University of Washington, Seattle, WA98195
| | - Elizabeth Leaf
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Catherine Treichel
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Justin Decarreau
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Sharon Ke
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Gargi Kher
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Lauren Carter
- Institute for Protein Design, University of Washington, Seattle, WA98195
| | - Jeffrey S. Chamberlain
- Department of Biochemistry, University of Washington, Seattle, WA98195
- Department of Neurology, University of Washington, Seattle, WA98195
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, WA98195
- Department of Biochemistry, University of Washington, Seattle, WA98195
| | - Neil P. King
- Institute for Protein Design, University of Washington, Seattle, WA98195
- Department of Biochemistry, University of Washington, Seattle, WA98195
| | - Suzie H. Pun
- Department of Bioengineering, University of Washington, Seattle, WA98195
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA98195
| |
Collapse
|
6
|
Mout R, Bretherton RC, Decarreau J, Lee S, Edman NI, Ahlrichs M, Hsia Y, Sahtoe DD, Ueda G, Gregorio N, Sharma A, Schulman R, DeForest CA, Baker D. De novo design of modular protein hydrogels with programmable intra- and extracellular viscoelasticity. bioRxiv 2023:2023.06.02.543449. [PMID: 37398067 PMCID: PMC10312586 DOI: 10.1101/2023.06.02.543449] [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: 07/04/2023]
Abstract
Relating the macroscopic properties of protein-based materials to their underlying component microstructure is an outstanding challenge. Here, we exploit computational design to specify the size, flexibility, and valency of de novo protein building blocks, as well as the interaction dynamics between them, to investigate how molecular parameters govern the macroscopic viscoelasticity of the resultant protein hydrogels. We construct gel systems from pairs of symmetric protein homo-oligomers, each comprising 2, 5, 24, or 120 individual protein components, that are crosslinked either physically or covalently into idealized step-growth biopolymer networks. Through rheological assessment and molecular dynamics (MD) simulation, we find that the covalent linkage of multifunctional precursors yields hydrogels whose viscoelasticity depends on the crosslink length between the constituent building blocks. In contrast, reversibly crosslinking the homo-oligomeric components with a computationally designed heterodimer results in non-Newtonian biomaterials exhibiting fluid-like properties under rest and low shear, but shear-stiffening solid-like behavior at higher frequencies. Exploiting the unique genetic encodability of these materials, we demonstrate the assembly of protein networks within living mammalian cells and show via fluorescence recovery after photobleaching (FRAP) that mechanical properties can be tuned intracellularly, in correlation with matching formulations formed extracellularly. We anticipate that the ability to modularly construct and systematically program the viscoelastic properties of designer protein-based materials could have broad utility in biomedicine, with applications in tissue engineering, therapeutic delivery, and synthetic biology.
Collapse
Affiliation(s)
- Rubul Mout
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Stem Cell Program at Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115
| | - Ross C. Bretherton
- Department of Bioengineering, University of Washington, Seattle, WA 98195
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98195
- Department of Chemistry, University of Washington, Seattle, WA 98195
- Molecular Engineering & Sciences Institute, 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
| | - Sangmin Lee
- 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 98195
- Medical Scientist Training Program, University of Washington, Seattle, WA 98195
| | - Maggie Ahlrichs
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, 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
| | - Danny D. Sahtoe
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195
| | - George Ueda
- Department of Biochemistry, University of Washington, Seattle, WA 98195
- Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Nicole Gregorio
- Department of Bioengineering, University of Washington, Seattle, WA 98195
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98195
- Department of Chemistry, University of Washington, Seattle, WA 98195
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA 98195
| | - Alee Sharma
- Stem Cell Program at Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115
| | - Rebecca Schulman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218
| | - Cole A. DeForest
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Department of Bioengineering, University of Washington, Seattle, WA 98195
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98195
- Department of Chemistry, University of Washington, Seattle, WA 98195
- Molecular Engineering & Sciences Institute, 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
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195
| |
Collapse
|
7
|
Yang EC, Divine R, Miranda MC, Borst AJ, Sheffler W, Zhang JZ, Decarreau J, Saragovi A, Abedi M, Goldbach N, Ahlrichs M, Dobbins C, Hand A, Cheng S, Lamb M, Levine PM, Chan S, Skotheim R, Fallas J, Ueda G, Lubner J, Somiya M, Khmelinskaia A, King NP, Baker D. Computational design of non-porous, pH-responsive antibody nanoparticles. bioRxiv 2023:2023.04.17.537263. [PMID: 37131615 PMCID: PMC10153164 DOI: 10.1101/2023.04.17.537263] [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: 05/04/2023]
Abstract
Programming protein nanomaterials to respond to changes in environmental conditions is a current challenge for protein design and important for targeted delivery of biologics. We describe the design of octahedral non-porous nanoparticles with the three symmetry axes (four-fold, three-fold, and two-fold) occupied by three distinct protein homooligomers: a de novo designed tetramer, an antibody of interest, and a designed trimer programmed to disassemble below a tunable pH transition point. The nanoparticles assemble cooperatively from independently purified components, and a cryo-EM density map reveals that the structure is very close to the computational design model. The designed nanoparticles can package a variety of molecular payloads, are endocytosed following antibody-mediated targeting of cell surface receptors, and undergo tunable pH-dependent disassembly at pH values ranging between to 5.9-6.7. To our knowledge, these are the first designed nanoparticles with more than two structural components and with finely tunable environmental sensitivity, and they provide new routes to antibody-directed targeted delivery.
Collapse
Affiliation(s)
- Erin C Yang
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Graduate Program in Biological Physics, Structure & Design, University of Washington, Seattle, WA, USA
| | - Robby Divine
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Graduate Program in Biochemistry, University of Washington, Seattle, WA, USA
- Department of Chemistry, University of California, Davis, Davis, CA, USA
| | - Marcos C Miranda
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Medicine Solna, Division of Immunology and Allergy, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Andrew J Borst
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Will Sheffler
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Jason Z Zhang
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Justin Decarreau
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Amijai Saragovi
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Mohamad Abedi
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Nicolas Goldbach
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Technical University of Munich, Munich, Germany
| | - Maggie Ahlrichs
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Craig Dobbins
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Alexis Hand
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Suna Cheng
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Mila Lamb
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Paul M Levine
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Sidney Chan
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Rebecca Skotheim
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Jorge Fallas
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - George Ueda
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Joshua Lubner
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Masaharu Somiya
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- SANKEN, Osaka University, Osaka, Japan
| | - Alena Khmelinskaia
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Transdisciplinary Research Area "Building Blocks of Matter and Fundamental Interactions (TRA Matter)", University of Bonn, Bonn, Germany
- Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Neil P King
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| |
Collapse
|
8
|
Levy S, Somasundaram L, Raj IX, Ic-Mex D, Phal A, Schmidt S, Ng WI, Mar D, Decarreau J, Moss N, Alghadeer A, Honkanen H, Sarthy J, Vitanza N, Hawkins RD, Mathieu J, Wang Y, Baker D, Bomsztyk K, Ruohola-Baker H. dCas9 fusion to computer-designed PRC2 inhibitor reveals functional TATA box in distal promoter region. Cell Rep 2022; 38:110457. [PMID: 35235780 PMCID: PMC8984963 DOI: 10.1016/j.celrep.2022.110457] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 11/23/2021] [Accepted: 02/08/2022] [Indexed: 11/18/2022] Open
Abstract
Bifurcation of cellular fates, a critical process in development, requires histone 3 lysine 27 methylation (H3K27me3) marks propagated by the polycomb repressive complex 2 (PRC2). However, precise chromatin loci of functional H3K27me3 marks are not yet known. Here, we identify critical PRC2 functional sites at high resolution. We fused a computationally designed protein, EED binder (EB), which competes with EZH2 and thereby inhibits PRC2 function, to dCas9 (EBdCas9) to allow for PRC2 inhibition at a precise locus using gRNA. Targeting EBdCas9 to four different genes (TBX18, p16, CDX2, and GATA3) results in precise H3K27me3 and EZH2 reduction, gene activation, and functional outcomes in the cell cycle (p16) or trophoblast transdifferentiation (CDX2 and GATA3). In the case of TBX18, we identify a PRC2-controlled, functional TATA box >500 bp upstream of the TBX18 transcription start site (TSS) using EBdCas9. Deletion of this TATA box eliminates EBdCas9-dependent TATA binding protein (TBP) recruitment and transcriptional activation. EBdCas9 technology may provide a broadly applicable tool for epigenomic control of gene regulation. Levy et al. fused a computationally designed protein, EED binder (EB), which competes with EZH2 and thereby inhibits PRC2 function, to dCas9 (EBdCas9). EBdCas9 represses PRC2 action in precise loci, remodels epigenomic marks, exposes transcriptional elements, and induces transdifferentiation.
Collapse
Affiliation(s)
- Shiri Levy
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA
| | - Logeshwaran Somasundaram
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA
| | - Infencia Xavier Raj
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA
| | - Diego Ic-Mex
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA
| | - Ashish Phal
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, School of Medicine, Seattle, WA 98105, USA
| | - Sven Schmidt
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA
| | - Weng I Ng
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA
| | - Daniel Mar
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, WA 98195, USA
| | - Justin Decarreau
- Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Nicholas Moss
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Division of Medical Genetics, Department of Medicine, University of Washington, School of Medicine, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Ammar Alghadeer
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Oral Health Sciences, University of Washington, School of Dentistry, Seattle, WA 98109, USA; Department of Biomedical Dental Sciences, Imam Abdulrahman Bin Faisal University, College of Dentistry, Dammam 31441, Saudi Arabia
| | - Henrik Honkanen
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA
| | - Jay Sarthy
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Cancer and Blood Disorder Center, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Nicholas Vitanza
- The Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA, USA; Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - R David Hawkins
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Division of Medical Genetics, Department of Medicine, University of Washington, School of Medicine, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Julie Mathieu
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Comparative Medicine, University of Washington, Seattle, WA 98195, USA
| | - Yuliang Wang
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA
| | - David Baker
- Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Karol Bomsztyk
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Medicine, Division of Allergy and Infectious Disease, University of Washington, Seattle, WA 98195, USA
| | - Hannele Ruohola-Baker
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA; Department of Bioengineering, University of Washington, School of Medicine, Seattle, WA 98105, USA; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Department of Oral Health Sciences, University of Washington, School of Dentistry, Seattle, WA 98109, USA.
| |
Collapse
|
9
|
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: 24] [Impact Index Per Article: 12.0] [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.
Collapse
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.
| |
Collapse
|
10
|
Ben-Sasson AJ, Watson JL, Sheffler W, Johnson MC, Bittleston A, Somasundaram L, Decarreau J, Jiao F, Chen J, Mela I, Drabek AA, Jarrett SM, Blacklow SC, Kaminski CF, Hura GL, De Yoreo JJ, Kollman JM, Ruohola-Baker H, Derivery E, Baker D. Author Correction: Design of biologically active binary protein 2D materials. Nature 2021; 591:E16. [PMID: 33654323 DOI: 10.1038/s41586-021-03331-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ariel J Ben-Sasson
- 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
| | | | | | - Logeshwaran Somasundaram
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA, USA
| | - Justin Decarreau
- Department of Biochemistry, University of Washington, Seattle, WA, USA.,Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Fang Jiao
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jiajun Chen
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.,Department of Materials Science and Engineering, University of Washington, Seattle, WA, USA
| | - Ioanna Mela
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Andrew A Drabek
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Sanchez M Jarrett
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Stephen C Blacklow
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Clemens F Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Greg L Hura
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - James J De Yoreo
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.,Department of Materials Science and Engineering, University of Washington, Seattle, WA, USA
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Hannele Ruohola-Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.,Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, 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.
| |
Collapse
|
11
|
Ben-Sasson AJ, Watson JL, Sheffler W, Johnson MC, Bittleston A, Somasundaram L, Decarreau J, Jiao F, Chen J, Mela I, Drabek AA, Jarrett SM, Blacklow SC, Kaminski CF, Hura GL, De Yoreo JJ, Ruohola-Baker H, Kollman JM, Derivery E, Baker D. Design of biologically active binary protein 2D materials. Nature 2021; 589:468-473. [PMID: 33408408 PMCID: PMC7855610 DOI: 10.1038/s41586-020-03120-8] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [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: 04/19/2019] [Accepted: 11/06/2020] [Indexed: 02/07/2023]
Abstract
Ordered two-dimensional arrays such as S-layers1,2 and designed analogues3-5 have intrigued bioengineers6,7, but with the exception of a single lattice formed with flexible linkers8, they are constituted from just one protein component. Materials composed of two components have considerable potential advantages for modulating assembly dynamics and incorporating more complex functionality9-12. Here we describe a computational method to generate co-assembling binary layers by designing rigid interfaces between pairs of dihedral protein building blocks, and use it to design a p6m lattice. The designed array components are soluble at millimolar concentrations, but when combined at nanomolar concentrations, they rapidly assemble into nearly crystalline micrometre-scale arrays nearly identical to the computational design model in vitro and in cells without the need for a two-dimensional support. Because the material is designed from the ground up, the components can be readily functionalized and their symmetry reconfigured, enabling formation of ligand arrays with distinguishable surfaces, which we demonstrate can drive extensive receptor clustering, downstream protein recruitment and signalling. Using atomic force microscopy on supported bilayers and quantitative microscopy on living cells, we show that arrays assembled on membranes have component stoichiometry and structure similar to arrays formed in vitro, and that our material can therefore impose order onto fundamentally disordered substrates such as cell membranes. In contrast to previously characterized cell surface receptor binding assemblies such as antibodies and nanocages, which are rapidly endocytosed, we find that large arrays assembled at the cell surface suppress endocytosis in a tunable manner, with potential therapeutic relevance for extending receptor engagement and immune evasion. Our work provides a foundation for a synthetic cell biology in which multi-protein macroscale materials are designed to modulate cell responses and reshape synthetic and living systems.
Collapse
Affiliation(s)
- Ariel J. Ben-Sasson
- Department of Biochemistry, University of Washington,
Seattle, WA 98195, USA,Institute for Protein Design, University of Washington,
Seattle, WA 98195, USA
| | - Joseph L. Watson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue,
Cambridge, UK
| | - William Sheffler
- Department of Biochemistry, University of Washington,
Seattle, WA 98195, USA,Institute for Protein Design, University of Washington,
Seattle, WA 98195, USA
| | | | - Alice Bittleston
- MRC Laboratory of Molecular Biology, Francis Crick Avenue,
Cambridge, UK
| | - Logeshwaran Somasundaram
- Institute for Stem Cell and Regenerative Medicine,
University of Washington, School of Medicine, Seattle, WA 98109, USA
| | - Justin Decarreau
- Department of Biochemistry, University of Washington,
Seattle, WA 98195, USA,Institute for Protein Design, University of Washington,
Seattle, WA 98195, USA
| | - Fang Jiao
- Department of Materials Science and Engineering, University
of Washington, Seattle, WA 98195, USA
| | - Jiajun Chen
- Department of Materials Science and Engineering, University
of Washington, Seattle, WA 98195, USA,Physical Sciences Division, Pacific Northwest National
Laboratory, Richland, WA 99352, USA
| | - Ioanna Mela
- Department of Chemical Engineering and Biotechnology,
University of Cambridge, Cambridge, UK
| | - Andrew A. Drabek
- Department of Biological Chemistry and Molecular
Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Sanchez M. Jarrett
- Department of Biological Chemistry and Molecular
Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Stephen C. Blacklow
- Department of Biological Chemistry and Molecular
Pharmacology, Harvard Medical School, Boston, MA 02115, USA,Department of Cancer Biology, Dana-Farber Cancer Institute,
Boston, MA 02215, USA
| | - Clemens F. Kaminski
- Department of Chemical Engineering and Biotechnology,
University of Cambridge, Cambridge, UK
| | - Greg L. Hura
- Molecular Biophysics and Integrated Bioimaging, Lawrence
Berkeley National Lab, Berkeley, CA 94720, USA
| | - James J De Yoreo
- Department of Materials Science and Engineering, University
of Washington, Seattle, WA 98195, USA,Physical Sciences Division, Pacific Northwest National
Laboratory, Richland, WA 99352, USA
| | - Hannele Ruohola-Baker
- Department of Biochemistry, University of Washington,
Seattle, WA 98195, USA,Institute for Stem Cell and Regenerative Medicine,
University of Washington, School of Medicine, Seattle, WA 98109, USA
| | - Justin M. Kollman
- Department of Biochemistry, University of Washington,
Seattle, WA 98195, USA
| | - Emmanuel Derivery
- MRC Laboratory of Molecular Biology, Francis Crick Avenue,
Cambridge, UK
| | - David Baker
- Department of Biochemistry, University of Washington,
Seattle, WA 98195, USA,Institute for Protein Design, University of Washington,
Seattle, WA 98195, USA,Howard Hughes Medical Institute, University of
Washington, Seattle, WA 98195, USA
| |
Collapse
|
12
|
Shen H, Fallas JA, Lynch E, Sheffler W, Parry B, Jannetty N, Decarreau J, Wagenbach M, Vicente JJ, Chen J, Wang L, Dowling Q, Oberdorfer G, Stewart L, Wordeman L, De Yoreo J, Jacobs-Wagner C, Kollman J, Baker D. De novo design of self-assembling helical protein filaments. Science 2019; 362:705-709. [PMID: 30409885 DOI: 10.1126/science.aau3775] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 09/29/2018] [Indexed: 11/02/2022]
Abstract
We describe a general computational approach to designing self-assembling helical filaments from monomeric proteins and use this approach to design proteins that assemble into micrometer-scale filaments with a wide range of geometries in vivo and in vitro. Cryo-electron microscopy structures of six designs are close to the computational design models. The filament building blocks are idealized repeat proteins, and thus the diameter of the filaments can be systematically tuned by varying the number of repeat units. The assembly and disassembly of the filaments can be controlled by engineered anchor and capping units built from monomers lacking one of the interaction surfaces. The ability to generate dynamic, highly ordered structures that span micrometers from protein monomers opens up possibilities for the fabrication of new multiscale metamaterials.
Collapse
Affiliation(s)
- Hao Shen
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.,Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Molecular Engineering Ph.D. Program, University of Washington, Seattle, WA 98195, USA
| | - Jorge A Fallas
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA. .,Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Eric Lynch
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - William Sheffler
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.,Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Bradley Parry
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA.,Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA
| | - Nicholas Jannetty
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA.,Howard Hughes Medical Institute, Yale University, West Haven, CT 06516, USA
| | - Justin Decarreau
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
| | - Michael Wagenbach
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
| | - Juan Jesus Vicente
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
| | - Jiajun Chen
- Department of Materials Science and Engineering, University of Washington, Seattle, WA 98195, USA.,Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Lei Wang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.,State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, China
| | - Quinton Dowling
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.,Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Gustav Oberdorfer
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.,Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Lance Stewart
- Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Linda Wordeman
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
| | - James De Yoreo
- Department of Materials Science and Engineering, University of Washington, Seattle, WA 98195, USA.,Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Christine Jacobs-Wagner
- Microbial Sciences Institute, Yale University, West Haven, CT 06516, USA.,Howard Hughes Medical Institute, Yale University, West Haven, CT 06516, USA.,Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06510, USA
| | - Justin Kollman
- Department of Biochemistry, 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.,Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| |
Collapse
|
13
|
Decarreau J, Wagenbach M, Lynch E, Halpern AR, Vaughan JC, Kollman J, Wordeman L. Corrigendum: The tetrameric kinesin Kif25 suppresses pre-mitotic centrosome separation to establish proper spindle orientation. Nat Cell Biol 2017; 19:740. [PMID: 28561052 DOI: 10.1038/ncb3546] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
14
|
Decarreau J, Wagenbach M, Lynch E, Halpern AR, Vaughan JC, Kollman J, Wordeman L. The tetrameric kinesin Kif25 suppresses pre-mitotic centrosome separation to establish proper spindle orientation. Nat Cell Biol 2017; 19:384-390. [PMID: 28263957 PMCID: PMC5376238 DOI: 10.1038/ncb3486] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [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: 10/02/2016] [Accepted: 02/03/2017] [Indexed: 12/17/2022]
Abstract
Microtubules tether centrosomes together during interphase. How this is accomplished and what benefit it provides to the cell is not known. We have identified a bipolar, minus-end-directed kinesin, Kif25, that suppresses centrosome separation. Kif25 is required to prevent premature centrosome separation during interphase. We show that premature centrosome separation leads to microtubule-dependent nuclear translocation, culminating in eccentric nuclear positioning that disrupts the cortical spindle positioning machinery. The activity of Kif25 during interphase is required to maintain a centred nucleus to ensure the spindle is stably oriented at the onset of mitosis.
Collapse
Affiliation(s)
- Justin Decarreau
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington 98195, USA
| | - Michael Wagenbach
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington 98195, USA
| | - Eric Lynch
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Aaron R Halpern
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Joshua C Vaughan
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington 98195, USA.,Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Justin Kollman
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Linda Wordeman
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington 98195, USA
| |
Collapse
|
15
|
Wordeman L, Decarreau J, Vicente JJ, Wagenbach M. Divergent microtubule assembly rates after short- versus long-term loss of end-modulating kinesins. Mol Biol Cell 2016; 27:1300-9. [PMID: 26912793 PMCID: PMC4831883 DOI: 10.1091/mbc.e15-11-0803] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [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: 11/24/2015] [Accepted: 02/16/2016] [Indexed: 11/11/2022] Open
Abstract
Depletion of microtubule (MT) regulators can initiate stable alterations in MT assembly rates that affect chromosome instability and mitotic spindle function, but the manner by which cellular MT assembly rates can stably increase or decrease is not understood. To investigate this phenomenon, we measured the response of microtubule assembly to both rapid and long-term loss of MT regulators MCAK/Kif2C and Kif18A. Depletion of MCAK/Kif2C by siRNA stably decreases MT assembly rates in mitotic spindles, whereas depletion of Kif18A stably increases rates of assembly. Surprisingly, this is not phenocopied by rapid rapamycin-dependent relocalization of MCAK/Kif2C and Kif18A to the plasma membrane. Instead, this treatment yields opposite affects on MT assembly. Rapidly increased MT assembly rates are balanced by a decrease in nucleated microtubules, whereas nucleation appears to be maximal and limiting for decreased MT assembly rates and also for long-term treatments. We measured amplified tubulin synthesis during long-term depletion of MT regulators and hypothesize that this is the basis for different phenotypes arising from long-term versus rapid depletion of MT regulators.
Collapse
Affiliation(s)
- Linda Wordeman
- Department of Physiology and Biophysics, University of Washington School of Medicine, Seattle, WA 98195
| | - Justin Decarreau
- Department of Physiology and Biophysics, University of Washington School of Medicine, Seattle, WA 98195
| | - Juan Jesus Vicente
- Department of Physiology and Biophysics, University of Washington School of Medicine, Seattle, WA 98195
| | - Michael Wagenbach
- Department of Physiology and Biophysics, University of Washington School of Medicine, Seattle, WA 98195
| |
Collapse
|
16
|
Affiliation(s)
- Linda Wordeman
- Department of Physiology & Biophysics, University of Washington School of Medicine, Seattle, WA, USA
| | - Justin Decarreau
- Department of Physiology & Biophysics, University of Washington School of Medicine, Seattle, WA, USA
| |
Collapse
|
17
|
Abstract
Factors that influence the orientation of the mitotic spindle are important for the maintenance of stem cell populations and in cancer development. However, screening for these factors requires rapid quantification of alterations of the angle of the mitotic spindle in cultured cell lines. Here we describe a method to image mitotic cells and rapidly score the angle of the mitotic spindle using a simple MATLAB application to analyze a stack of Z-images.
Collapse
Affiliation(s)
- Justin Decarreau
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | | | | | | |
Collapse
|
18
|
Domnitz SB, Wagenbach M, Decarreau J, Wordeman L. MCAK activity at microtubule tips regulates spindle microtubule length to promote robust kinetochore attachment. ACTA ACUST UNITED AC 2012; 197:231-7. [PMID: 22492725 PMCID: PMC3328376 DOI: 10.1083/jcb.201108147] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [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: 11/30/2022]
Abstract
The kinesin MCAK binds to end-binding proteins and antagonizes centrosome separation and promotes robust kinetochore attachments to spindle microtubules. Mitotic centromere-associated kinesin (MCAK) is a microtubule-depolymerizing kinesin-13 member that can track with polymerizing microtubule tips (hereafter referred to as tip tracking) during both interphase and mitosis. MCAK tracks with microtubule tips by binding to end-binding proteins (EBs) through the microtubule tip localization signal SKIP, which lies N terminal to MCAK’s neck and motor domain. The functional significance of MCAK’s tip-tracking behavior during mitosis has never been explained. In this paper, we identify and define a mitotic function specific to the microtubule tip–associated population of MCAK: negative regulation of microtubule length within the assembling bipolar spindle. This function depends on MCAK’s ability to bind EBs and track with polymerizing nonkinetochore microtubule tips. Although this activity antagonizes centrosome separation during bipolarization, it ultimately benefits the dividing cell by promoting robust kinetochore attachments to the spindle microtubules.
Collapse
Affiliation(s)
- Sarah B Domnitz
- Department of Physiology and Biophysics, University of Washington School of Medicine, Seattle, WA 98195, USA
| | | | | | | |
Collapse
|
19
|
Decarreau J, Chrin L, Berger C. Loop 1's Role in a Novel Step on the ADP Release Pathway of Smooth Muscle. Biophys J 2010. [DOI: 10.1016/j.bpj.2009.12.2936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
|
20
|
Decarreau J, Chrin L, Berger C. A Glimpse at Loop 1 Movement in Smooth Muscle Using Intrinsic Tryptophan Fluorescence. Biophys J 2009. [DOI: 10.1016/j.bpj.2008.12.2546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
|