1
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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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2
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Lee GR, Pellock SJ, Norn C, Tischer D, Dauparas J, Anischenko I, Mercer JAM, Kang A, Bera A, Nguyen H, Goreshnik I, Vafeados D, Roullier N, Han HL, Coventry B, Haddox HK, Liu DR, Yeh AHW, Baker D. Small-molecule binding and sensing with a designed protein family. bioRxiv 2023:2023.11.01.565201. [PMID: 37961294 PMCID: PMC10635051 DOI: 10.1101/2023.11.01.565201] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Despite transformative advances in protein design with deep learning, the design of small-molecule-binding proteins and sensors for arbitrary ligands remains a grand challenge. Here we combine deep learning and physics-based methods to generate a family of proteins with diverse and designable pocket geometries, which we employ to computationally design binders for six chemically and structurally distinct small-molecule targets. Biophysical characterization of the designed binders revealed nanomolar to low micromolar binding affinities and atomic-level design accuracy. The bound ligands are exposed at one edge of the binding pocket, enabling the de novo design of chemically induced dimerization (CID) systems; we take advantage of this to create a biosensor with nanomolar sensitivity for cortisol. Our approach provides a general method to design proteins that bind and sense small molecules for a wide range of analytical, environmental, and biomedical applications.
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Glasscock CJ, Pecoraro R, McHugh R, Doyle LA, Chen W, Boivin O, Lonnquist B, Na E, Politanska Y, Haddox HK, Cox D, Norn C, Coventry B, Goreshnik I, Vafeados D, Lee GR, Gordan R, Stoddard BL, DiMaio F, Baker D. Computational design of sequence-specific DNA-binding proteins. bioRxiv 2023:2023.09.20.558720. [PMID: 37790440 PMCID: PMC10542524 DOI: 10.1101/2023.09.20.558720] [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: 10/05/2023]
Abstract
Sequence-specific DNA-binding proteins (DBPs) play critical roles in biology and biotechnology, and there has been considerable interest in the engineering of DBPs with new or altered specificities for genome editing and other applications. While there has been some success in reprogramming naturally occurring DBPs using selection methods, the computational design of new DBPs that recognize arbitrary target sites remains an outstanding challenge. We describe a computational method for the design of small DBPs that recognize specific target sequences through interactions with bases in the major groove, and employ this method in conjunction with experimental screening to generate binders for 5 distinct DNA targets. These binders exhibit specificity closely matching the computational models for the target DNA sequences at as many as 6 base positions and affinities as low as 30-100 nM. The crystal structure of a designed DBP-target site complex is in close agreement with the design model, highlighting the accuracy of the design method. The designed DBPs function in both Escherichia coli and mammalian cells to repress and activate transcription of neighboring genes. Our method is a substantial step towards a general route to small and hence readily deliverable sequence-specific DBPs for gene regulation and editing.
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Affiliation(s)
- Cameron J. Glasscock
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Robert Pecoraro
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Physics, 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
| | - Lindsey A. Doyle
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Wei Chen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Olivier Boivin
- Program in Genetics and Genomic, Duke University, Durham, NC, USA
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
| | - Beau Lonnquist
- 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
| | - Emily Na
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Yuliya Politanska
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Hugh K. Haddox
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - David Cox
- Department of Biochemistry, Stanford University School of Medicine, Palo Alto, CA USA
- Department of Medicine, Division of Hematology, Stanford University, Stanford, CA, USA
| | - Christoffer Norn
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- BioInnovation Institute, DK2200 Copenhagen N, Denmark
| | - Brian Coventry
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, 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
| | - Dionne Vafeados
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, 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
- Howard Hughes Medical Institute, University of Washington, Seattle, WA USA
| | - Raluca Gordan
- Center for Advanced Genomic Technologies, Duke University, Durham, NC, USA
- Department of Biostatistics and Bioinformatics, Department of Computer Science, Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Barry L. Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Frank DiMaio
- 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
- BioInnovation Institute, DK2200 Copenhagen N, Denmark
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4
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Lutz ID, Wang S, Norn C, Courbet A, Borst AJ, Zhao YT, Dosey A, Cao L, Xu J, Leaf EM, Treichel C, Litvicov P, Li Z, Goodson AD, Rivera-Sánchez P, Bratovianu AM, Baek M, King NP, Ruohola-Baker H, Baker D. Top-down design of protein architectures with reinforcement learning. Science 2023; 380:266-273. [PMID: 37079676 DOI: 10.1126/science.adf6591] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [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: 11/05/2022] [Accepted: 03/21/2023] [Indexed: 04/22/2023]
Abstract
As a result of evolutionary selection, the subunits of naturally occurring protein assemblies often fit together with substantial shape complementarity to generate architectures optimal for function in a manner not achievable by current design approaches. We describe a "top-down" reinforcement learning-based design approach that solves this problem using Monte Carlo tree search to sample protein conformers in the context of an overall architecture and specified functional constraints. Cryo-electron microscopy structures of the designed disk-shaped nanopores and ultracompact icosahedra are very close to the computational models. The icosohedra enable very-high-density display of immunogens and signaling molecules, which potentiates vaccine response and angiogenesis induction. Our approach enables the top-down design of complex protein nanomaterials with desired system properties and demonstrates the power of reinforcement learning in protein design.
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Affiliation(s)
- 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
| | - Shunzhi Wang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Christoffer Norn
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- BioInnovation Institute, DK2200 Copenhagen N, Denmark
| | - 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
| | - Andrew J Borst
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Yan Ting Zhao
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Oral Health Sciences, University of Washington, Seattle, WA, USA
| | - Annie Dosey
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Longxing Cao
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Jinwei Xu
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Elizabeth M Leaf
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Catherine Treichel
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Patrisia Litvicov
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, 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
| | - Alexander D Goodson
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | | | | | - Minkyung Baek
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Neil P King
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Hannele Ruohola-Baker
- 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
- Oral Health Sciences, 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
- Department of Bioengineering, University of Washington, Seattle, WA, USA
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5
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Norn C, André I. Atomistic simulation of protein evolution reveals sequence covariation and time-dependent fluctuations of site-specific substitution rates. PLoS Comput Biol 2023; 19:e1010262. [PMID: 36961827 PMCID: PMC10075473 DOI: 10.1371/journal.pcbi.1010262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 04/05/2023] [Accepted: 03/01/2023] [Indexed: 03/25/2023] Open
Abstract
Thermodynamic stability is a crucial fitness constraint in protein evolution and is a central factor in shaping the sequence landscapes of proteins. The correlation between stability and molecular fitness depends on the mechanism that relates the biophysical property with biological function. In the simplest case, stability and fitness are related by the amount of folded protein. However, when proteins are toxic in the unfolded state, the fitness function shifts, resulting in higher stability under mutation-selection balance. Likewise, a higher population size results in a similar change in protein stability, as it magnifies the effect of the selection pressure in evolutionary dynamics. This study investigates how such factors affect the evolution of protein stability, site-specific mutation rates, and residue-residue covariation. To simulate evolutionary trajectories with realistic modeling of protein energetics, we develop an all-atom simulator of protein evolution, RosettaEvolve. By evolving proteins under different fitness functions, we can study how the fitness function affects the distribution of proposed and accepted mutations, site-specific rates, and the prevalence of correlated amino acid substitutions. We demonstrate that fitness pressure affects the proposal distribution of mutational effects, that changes in stability can largely explain variations in site-specific substitution rates in evolutionary trajectories, and that increased fitness pressure results in a stronger covariation signal. Our results give mechanistic insight into the evolutionary consequences of variation in protein stability and provide a basis to rationalize the strong covariation signal observed in natural sequence alignments.
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Affiliation(s)
- Christoffer Norn
- Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Ingemar André
- Biochemistry and Structural Biology, Lund University, Lund, Sweden
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6
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Yeh AHW, Norn C, Kipnis Y, Tischer D, Pellock SJ, Evans D, Ma P, Lee GR, Zhang JZ, Anishchenko I, Coventry B, Cao L, Dauparas J, Halabiya S, DeWitt M, Carter L, Houk KN, Baker D. De novo design of luciferases using deep learning. Nature 2023; 614:774-780. [PMID: 36813896 PMCID: PMC9946828 DOI: 10.1038/s41586-023-05696-3] [Citation(s) in RCA: 79] [Impact Index Per Article: 79.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 01/03/2023] [Indexed: 02/24/2023]
Abstract
De novo enzyme design has sought to introduce active sites and substrate-binding pockets that are predicted to catalyse a reaction of interest into geometrically compatible native scaffolds1,2, but has been limited by a lack of suitable protein structures and the complexity of native protein sequence-structure relationships. Here we describe a deep-learning-based 'family-wide hallucination' approach that generates large numbers of idealized protein structures containing diverse pocket shapes and designed sequences that encode them. We use these scaffolds to design artificial luciferases that selectively catalyse the oxidative chemiluminescence of the synthetic luciferin substrates diphenylterazine3 and 2-deoxycoelenterazine. The designed active sites position an arginine guanidinium group adjacent to an anion that develops during the reaction in a binding pocket with high shape complementarity. For both luciferin substrates, we obtain designed luciferases with high selectivity; the most active of these is a small (13.9 kDa) and thermostable (with a melting temperature higher than 95 °C) enzyme that has a catalytic efficiency on diphenylterazine (kcat/Km = 106 M-1 s-1) comparable to that of native luciferases, but a much higher substrate specificity. The creation of highly active and specific biocatalysts from scratch with broad applications in biomedicine is a key milestone for computational enzyme design, and our approach should enable generation of a wide range of luciferases and other enzymes.
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Affiliation(s)
- Andy Hsien-Wei Yeh
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA.
| | - Christoffer Norn
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Yakov Kipnis
- 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
| | - Doug Tischer
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Samuel J Pellock
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Declan Evans
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Pengchen Ma
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
- School of Chemistry, Xi'an Key Laboratory of Sustainable Energy Materials Chemistry, MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, Xi'an Jiaotong University, Xi'an, China
| | - Gyu Rie Lee
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Jason Z Zhang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Ivan Anishchenko
- 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
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Longxing Cao
- 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
| | - Samer Halabiya
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Michelle DeWitt
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Lauren Carter
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, 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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7
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Norn C, André I, Theobald DL. A thermodynamic model of protein structure evolution explains empirical amino acid substitution matrices. Protein Sci 2021; 30:2057-2068. [PMID: 34218472 PMCID: PMC8442976 DOI: 10.1002/pro.4155] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 03/17/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 12/30/2022]
Abstract
Proteins evolve under a myriad of biophysical selection pressures that collectively control the patterns of amino acid substitutions. These evolutionary pressures are sufficiently consistent over time and across protein families to produce substitution patterns, summarized in global amino acid substitution matrices such as BLOSUM, JTT, WAG, and LG, which can be used to successfully detect homologs, infer phylogenies, and reconstruct ancestral sequences. Although the factors that govern the variation of amino acid substitution rates have received much attention, the influence of thermodynamic stability constraints remains unresolved. Here we develop a simple model to calculate amino acid substitution matrices from evolutionary dynamics controlled by a fitness function that reports on the thermodynamic effects of amino acid mutations in protein structures. This hybrid biophysical and evolutionary model accounts for nucleotide transition/transversion rate bias, multi‐nucleotide codon changes, the number of codons per amino acid, and thermodynamic protein stability. We find that our theoretical model accurately recapitulates the complex yet universal pattern observed in common global amino acid substitution matrices used in phylogenetics. These results suggest that selection for thermodynamically stable proteins, coupled with nucleotide mutation bias filtered by the structure of the genetic code, is the primary driver behind the global amino acid substitution patterns observed in proteins throughout the tree of life.
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Affiliation(s)
- Christoffer Norn
- Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Ingemar André
- Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Douglas L Theobald
- Biochemistry Department, Brandeis University, Waltham, Massachusetts, USA
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8
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Norn C, Wicky BIM, Juergens D, Liu S, Kim D, Tischer D, Koepnick B, Anishchenko I, Baker D, Ovchinnikov S. Protein sequence design by conformational landscape optimization. Proc Natl Acad Sci U S A 2021; 118:e2017228118. [PMID: 33712545 PMCID: PMC7980421 DOI: 10.1073/pnas.2017228118] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [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] [Indexed: 12/17/2022] Open
Abstract
The protein design problem is to identify an amino acid sequence that folds to a desired structure. Given Anfinsen's thermodynamic hypothesis of folding, this can be recast as finding an amino acid sequence for which the desired structure is the lowest energy state. As this calculation involves not only all possible amino acid sequences but also, all possible structures, most current approaches focus instead on the more tractable problem of finding the lowest-energy amino acid sequence for the desired structure, often checking by protein structure prediction in a second step that the desired structure is indeed the lowest-energy conformation for the designed sequence, and typically discarding a large fraction of designed sequences for which this is not the case. Here, we show that by backpropagating gradients through the transform-restrained Rosetta (trRosetta) structure prediction network from the desired structure to the input amino acid sequence, we can directly optimize over all possible amino acid sequences and all possible structures in a single calculation. We find that trRosetta calculations, which consider the full conformational landscape, can be more effective than Rosetta single-point energy estimations in predicting folding and stability of de novo designed proteins. We compare sequence design by conformational landscape optimization with the standard energy-based sequence design methodology in Rosetta and show that the former can result in energy landscapes with fewer alternative energy minima. We show further that more funneled energy landscapes can be designed by combining the strengths of the two approaches: the low-resolution trRosetta model serves to disfavor alternative states, and the high-resolution Rosetta model serves to create a deep energy minimum at the design target structure.
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Affiliation(s)
- Christoffer Norn
- Department of Biochemistry, University of Washington, Seattle, WA 98105
- Institute for Protein Design, University of Washington, Seattle, WA 98105
| | - Basile I M Wicky
- Department of Biochemistry, University of Washington, Seattle, WA 98105
- Institute for Protein Design, University of Washington, Seattle, WA 98105
| | - David Juergens
- Department of Biochemistry, University of Washington, Seattle, WA 98105
- Institute for Protein Design, University of Washington, Seattle, WA 98105
- Graduate Program in Molecular Engineering, University of Washington, Seattle, WA 98105
| | - Sirui Liu
- Faculty of Arts and Sciences, Division of Science, Harvard University, Cambridge, MA 02138
| | - David Kim
- Department of Biochemistry, University of Washington, Seattle, WA 98105
- Institute for Protein Design, University of Washington, Seattle, WA 98105
| | - Doug Tischer
- Department of Biochemistry, University of Washington, Seattle, WA 98105
- Institute for Protein Design, University of Washington, Seattle, WA 98105
| | - Brian Koepnick
- Department of Biochemistry, University of Washington, Seattle, WA 98105
- Institute for Protein Design, University of Washington, Seattle, WA 98105
| | - Ivan Anishchenko
- Department of Biochemistry, University of Washington, Seattle, WA 98105
- Institute for Protein Design, University of Washington, Seattle, WA 98105
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98105;
- Institute for Protein Design, University of Washington, Seattle, WA 98105
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98105
| | - Sergey Ovchinnikov
- Faculty of Arts and Sciences, Division of Science, Harvard University, Cambridge, MA 02138;
- John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA 02138
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9
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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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10
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Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, Bradley P, Bystroff C, Conway P, Cooper S, Correia BE, Coventry B, Das R, De Jong RM, DiMaio F, Dsilva L, Dunbrack R, Ford AS, Frenz B, Fu DY, Geniesse C, Goldschmidt L, Gowthaman R, Gray JJ, Gront D, Guffy S, Horowitz S, Huang PS, Huber T, Jacobs TM, Jeliazkov JR, Johnson DK, Kappel K, Karanicolas J, Khakzad H, Khar KR, Khare SD, Khatib F, Khramushin A, King IC, Kleffner R, Koepnick B, Kortemme T, Kuenze G, Kuhlman B, Kuroda D, Labonte JW, Lai JK, Lapidoth G, Leaver-Fay A, Lindert S, Linsky T, London N, Lubin JH, Lyskov S, Maguire J, Malmström L, Marcos E, Marcu O, Marze NA, Meiler J, Moretti R, Mulligan VK, Nerli S, Norn C, Ó'Conchúir S, Ollikainen N, Ovchinnikov S, Pacella MS, Pan X, Park H, Pavlovicz RE, Pethe M, Pierce BG, Pilla KB, Raveh B, Renfrew PD, Burman SSR, Rubenstein A, Sauer MF, Scheck A, Schief W, Schueler-Furman O, Sedan Y, Sevy AM, Sgourakis NG, Shi L, Siegel JB, Silva DA, Smith S, Song Y, Stein A, Szegedy M, Teets FD, Thyme SB, Wang RYR, Watkins A, Zimmerman L, Bonneau R. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nat Methods 2020; 17:665-680. [PMID: 32483333 PMCID: PMC7603796 DOI: 10.1038/s41592-020-0848-2] [Citation(s) in RCA: 373] [Impact Index Per Article: 93.3] [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: 04/29/2019] [Accepted: 04/22/2020] [Indexed: 12/12/2022]
Abstract
The Rosetta software for macromolecular modeling, docking and design is extensively used in laboratories worldwide. During two decades of development by a community of laboratories at more than 60 institutions, Rosetta has been continuously refactored and extended. Its advantages are its performance and interoperability between broad modeling capabilities. Here we review tools developed in the last 5 years, including over 80 methods. We discuss improvements to the score function, user interfaces and usability. Rosetta is available at http://www.rosettacommons.org.
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Affiliation(s)
- Julia Koehler Leman
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA.
- Department of Biology, New York University, New York, New York, USA.
| | - Brian D Weitzner
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Lyell Immunopharma Inc., Seattle, WA, USA
| | - Steven M Lewis
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biochemistry, Duke University, Durham, NC, USA
- Cyrus Biotechnology, Seattle, WA, USA
| | - Jared Adolf-Bryfogle
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Nawsad Alam
- Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Rebecca F Alford
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Melanie Aprahamian
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Kyle A Barlow
- Graduate Program in Bioinformatics, University of California San Francisco, San Francisco, CA, USA
| | - Patrick Barth
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Baylor College of Medicine, Department of Pharmacology, Houston, TX, USA
| | - Benjamin Basanta
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Biological Physics Structure and Design PhD Program, University of Washington, Seattle, WA, USA
| | - Brian J Bender
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
| | - Kristin Blacklock
- Institute of Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Jaume Bonet
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Scott E Boyken
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Lyell Immunopharma Inc., Seattle, WA, USA
| | - Phil Bradley
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Chris Bystroff
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Patrick Conway
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Seth Cooper
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Bruno E Correia
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Brian Coventry
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Rhiju Das
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Lorna Dsilva
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Roland Dunbrack
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Alexander S Ford
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Brandon Frenz
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Cyrus Biotechnology, Seattle, WA, USA
| | - Darwin Y Fu
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - Caleb Geniesse
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Ragul Gowthaman
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Jeffrey J Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Dominik Gront
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Sharon Guffy
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Scott Horowitz
- Department of Chemistry & Biochemistry, University of Denver, Denver, CO, USA
- The Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA
| | - Po-Ssu Huang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Tim M Jacobs
- Program in Bioinformatics and Computational Biology, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - David K Johnson
- Center for Computational Biology, University of Kansas, Lawrence, KS, USA
| | - Kalli Kappel
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - John Karanicolas
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Hamed Khakzad
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Institute for Computational Science, University of Zurich, Zurich, Switzerland
- S3IT, University of Zurich, Zurich, Switzerland
| | - Karen R Khar
- Cyrus Biotechnology, Seattle, WA, USA
- Center for Computational Biology, University of Kansas, Lawrence, KS, USA
| | - Sagar D Khare
- Institute of Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, The State University of New Jersey, Piscataway, NJ, USA
- Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Computational Biology and Molecular Biophysics Program, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Firas Khatib
- Department of Computer and Information Science, University of Massachusetts Dartmouth, Dartmouth, MA, USA
| | - Alisa Khramushin
- Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Indigo C King
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Cyrus Biotechnology, Seattle, WA, USA
| | - Robert Kleffner
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Brian Koepnick
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Georg Kuenze
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Daisuke Kuroda
- Medical Device Development and Regulation Research Center, School of Engineering, University of Tokyo, Tokyo, Japan
- Department of Bioengineering, School of Engineering, University of Tokyo, Tokyo, Japan
| | - Jason W Labonte
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA, USA
| | - Jason K Lai
- Baylor College of Medicine, Department of Pharmacology, Houston, TX, USA
| | - Gideon Lapidoth
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Andrew Leaver-Fay
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA
| | - Thomas Linsky
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Nir London
- Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Joseph H Lubin
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Sergey Lyskov
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jack Maguire
- Program in Bioinformatics and Computational Biology, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lars Malmström
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Institute for Computational Science, University of Zurich, Zurich, Switzerland
- S3IT, University of Zurich, Zurich, Switzerland
- Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden
| | - Enrique Marcos
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Orly Marcu
- Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nicholas A Marze
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jens Meiler
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
- Departments of Chemistry, Pharmacology and Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
- Institute for Chemical Biology, Vanderbilt University, Nashville, TN, USA
| | - Rocco Moretti
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - Vikram Khipple Mulligan
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Santrupti Nerli
- Department of Computer Science, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Christoffer Norn
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Shane Ó'Conchúir
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Noah Ollikainen
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Sergey Ovchinnikov
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Michael S Pacella
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Xingjie Pan
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Hahnbeom Park
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Ryan E Pavlovicz
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Cyrus Biotechnology, Seattle, WA, USA
| | - Manasi Pethe
- Department of Chemistry and Chemical Biology, The State University of New Jersey, Piscataway, NJ, USA
- Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Brian G Pierce
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Kala Bharath Pilla
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Barak Raveh
- Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - P Douglas Renfrew
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Shourya S Roy Burman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Aliza Rubenstein
- Institute of Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Computational Biology and Molecular Biophysics Program, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Marion F Sauer
- Chemical and Physical Biology Program, Vanderbilt Vaccine Center, Vanderbilt University, Nashville, TN, USA
| | - Andreas Scheck
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - William Schief
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yuval Sedan
- Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Alexander M Sevy
- Chemical and Physical Biology Program, Vanderbilt Vaccine Center, Vanderbilt University, Nashville, TN, USA
| | - Nikolaos G Sgourakis
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Lei Shi
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Justin B Siegel
- Department of Chemistry, University of California, Davis, Davis, CA, USA
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, California, USA
- Genome Center, University of California, Davis, Davis, CA, USA
| | | | - Shannon Smith
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - Yifan Song
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Cyrus Biotechnology, Seattle, WA, USA
| | - Amelie Stein
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Maria Szegedy
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Frank D Teets
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Summer B Thyme
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Ray Yu-Ruei Wang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Andrew Watkins
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Lior Zimmerman
- Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Richard Bonneau
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA.
- Department of Biology, New York University, New York, New York, USA.
- Department of Computer Science, New York University, New York, NY, USA.
- Center for Data Science, New York University, New York, NY, USA.
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11
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Amon R, Grant OC, Leviatan Ben-Arye S, Makeneni S, Nivedha AK, Marshanski T, Norn C, Yu H, Glushka JN, Fleishman SJ, Chen X, Woods RJ, Padler-Karavani V. A combined computational-experimental approach to define the structural origin of antibody recognition of sialyl-Tn, a tumor-associated carbohydrate antigen. Sci Rep 2018; 8:10786. [PMID: 30018351 PMCID: PMC6050261 DOI: 10.1038/s41598-018-29209-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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: 02/28/2018] [Accepted: 07/06/2018] [Indexed: 12/16/2022] Open
Abstract
Anti-carbohydrate monoclonal antibodies (mAbs) hold great promise as cancer therapeutics and diagnostics. However, their specificity can be mixed, and detailed characterization is problematic, because antibody-glycan complexes are challenging to crystallize. Here, we developed a generalizable approach employing high-throughput techniques for characterizing the structure and specificity of such mAbs, and applied it to the mAb TKH2 developed against the tumor-associated carbohydrate antigen sialyl-Tn (STn). The mAb specificity was defined by apparent KD values determined by quantitative glycan microarray screening. Key residues in the antibody combining site were identified by site-directed mutagenesis, and the glycan-antigen contact surface was defined using saturation transfer difference NMR (STD-NMR). These features were then employed as metrics for selecting the optimal 3D-model of the antibody-glycan complex, out of thousands plausible options generated by automated docking and molecular dynamics simulation. STn-specificity was further validated by computationally screening of the selected antibody 3D-model against the human sialyl-Tn-glycome. This computational-experimental approach would allow rational design of potent antibodies targeting carbohydrates.
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Affiliation(s)
- Ron Amon
- Department of Cell Research and Immunology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Oliver C Grant
- Complex Carbohydrate Research Center, University of Georgia, Athens, 30606, GA, USA
| | - Shani Leviatan Ben-Arye
- Department of Cell Research and Immunology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Spandana Makeneni
- Complex Carbohydrate Research Center, University of Georgia, Athens, 30606, GA, USA
| | - Anita K Nivedha
- Complex Carbohydrate Research Center, University of Georgia, Athens, 30606, GA, USA
| | - Tal Marshanski
- Department of Cell Research and Immunology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Christoffer Norn
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Hai Yu
- Department of Chemistry, University of California-Davis, Davis, CA, USA
| | - John N Glushka
- Complex Carbohydrate Research Center, University of Georgia, Athens, 30606, GA, USA
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Xi Chen
- Department of Chemistry, University of California-Davis, Davis, CA, USA
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, Athens, 30606, GA, USA.
| | - Vered Padler-Karavani
- Department of Cell Research and Immunology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel.
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12
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Boelt SG, Norn C, Rasmussen MI, André I, Čiplys E, Slibinskas R, Houen G, Højrup P. Mapping the Ca(2+) induced structural change in calreticulin. J Proteomics 2016; 142:138-48. [PMID: 27195812 DOI: 10.1016/j.jprot.2016.05.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [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: 01/12/2016] [Revised: 05/09/2016] [Accepted: 05/14/2016] [Indexed: 01/04/2023]
Abstract
UNLABELLED Calreticulin is a highly conserved multifunctional protein implicated in many different biological systems and has therefore been the subject of intensive research. It is primarily present in the endoplasmatic reticulum where its main functions are to regulate Ca(2+) homeostasis, act as a chaperone and stabilize the MHC class I peptide-loading complex. Although several high-resolution structures of calreticulin exist, these only cover three-quarters of the entire protein leaving the extended structures unsolved. Additionally, the structure of calreticulin is influenced by the presence of Ca(2+). The conformational changes induced by Ca(2+) have not been determined yet as they are hard to study with traditional approaches. Here, we investigated the Ca(2+)-induced conformational changes with a combination of chemical cross-linking, mass spectrometry, bioinformatics analysis and modelling in Rosetta. Using a bifunctional linker, we found a large Ca(2+)-induced change to the cross-linking pattern in calreticulin. Our results are consistent with a high flexibility in the P-loop, a stabilization of the acidic C-terminal and a relatively close interaction of the P-loop and the acidic C-terminal. BIOLOGICAL SIGNIFICANCE The function of calreticulin, an endoplasmatic reticulin chaperone, is affected by fluctuations in Ca(2+)concentration, but the structural mechanism is unknown. The present work suggests that Ca(2+)-dependent regulation is caused by different conformations of a long proline-rich loop that changes the accessibility to the peptide/lectin-binding site. Our results indicate that the binding of Ca(2+) to calreticulin may thus not only just be a question of Ca(2+) storage but is likely to have an impact on the chaperone activity.
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Affiliation(s)
- Sanne Grundvad Boelt
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230 Odense, Denmark; Department of Autoimmunology and Biomarkers, Statens Serum Institut, Artillerivej 5, DK 2300 Copenhagen, Denmark
| | - Christoffer Norn
- Department of Biochemistry and Structural Biology, Lund University, Paradisgatan 2, SE 221 00 Lund, Sweden
| | - Morten Ib Rasmussen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230 Odense, Denmark
| | - Ingemar André
- Department of Biochemistry and Structural Biology, Lund University, Paradisgatan 2, SE 221 00 Lund, Sweden
| | - Evaldas Čiplys
- Department of Eukayote Gene Engineering, Institute of Biotechnology, Vilnius University, V. Graičiūno St, LT 02241 Vilnius, Lithuania
| | - Rimantas Slibinskas
- Department of Eukayote Gene Engineering, Institute of Biotechnology, Vilnius University, V. Graičiūno St, LT 02241 Vilnius, Lithuania
| | - Gunnar Houen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230 Odense, Denmark; Department of Autoimmunology and Biomarkers, Statens Serum Institut, Artillerivej 5, DK 2300 Copenhagen, Denmark
| | - Peter Højrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230 Odense, Denmark.
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13
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Lapidoth GD, Baran D, Pszolla GM, Norn C, Alon A, Tyka MD, Fleishman SJ. AbDesign: An algorithm for combinatorial backbone design guided by natural conformations and sequences. Proteins 2015; 83:1385-406. [PMID: 25670500 PMCID: PMC4881815 DOI: 10.1002/prot.24779] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [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: 11/12/2014] [Revised: 01/13/2015] [Accepted: 01/26/2015] [Indexed: 12/20/2022]
Abstract
Computational design of protein function has made substantial progress, generating new enzymes, binders, inhibitors, and nanomaterials not previously seen in nature. However, the ability to design new protein backbones for function--essential to exert control over all polypeptide degrees of freedom--remains a critical challenge. Most previous attempts to design new backbones computed the mainchain from scratch. Here, instead, we describe a combinatorial backbone and sequence optimization algorithm called AbDesign, which leverages the large number of sequences and experimentally determined molecular structures of antibodies to construct new antibody models, dock them against target surfaces and optimize their sequence and backbone conformation for high stability and binding affinity. We used the algorithm to produce antibody designs that target the same molecular surfaces as nine natural, high-affinity antibodies; in five cases interface sequence identity is above 30%, and in four of those the backbone conformation at the core of the antibody binding surface is within 1 Å root-mean square deviation from the natural antibodies. Designs recapitulate polar interaction networks observed in natural complexes, and amino acid sidechain rigidity at the designed binding surface, which is likely important for affinity and specificity, is high compared to previous design studies. In designed anti-lysozyme antibodies, complementarity-determining regions (CDRs) at the periphery of the interface, such as L1 and H2, show greater backbone conformation diversity than the CDRs at the core of the interface, and increase the binding surface area compared to the natural antibody, potentially enhancing affinity and specificity.
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Affiliation(s)
- Gideon D. Lapidoth
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Dror Baran
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Gabriele M. Pszolla
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Christoffer Norn
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Assaf Alon
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Michael D. Tyka
- Google Inc., 1600 Amphitheatre Pkwy, Mountain View, CA 94043
| | - Sarel J. Fleishman
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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Engelstoft MS, Norn C, Hauge M, Holliday ND, Elster L, Lehmann J, Jones RM, Frimurer TM, Schwartz TW. Structural basis for constitutive activity and agonist-induced activation of the enteroendocrine fat sensor GPR119. Br J Pharmacol 2015; 171:5774-89. [PMID: 25117266 DOI: 10.1111/bph.12877] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 08/04/2014] [Accepted: 08/06/2014] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND AND PURPOSE GPR119 is a Gαs-coupled 7TM receptor activated by endogenous lipids such as oleoylethanolamide (OEA) and by the dietary triglyceride metabolite 2-monoacylglycerol. GPR119 stimulates enteroendocrine hormone and insulin secretion. But despite massive drug discovery efforts in the field, very little is known about the basic molecular pharmacology of GPR119. EXPERIMENTAL APPROACH GPR119 receptor signalling was studied in transfected cells. Mutational mapping (30 mutations in 23 positions) was performed on residues required for ligand-independent and agonist-induced GPR119 activation (AR231453 and OEA). Novel Rosetta-based receptor modelling was applied, using a composite template approach with segments from different X-ray structures and fully flexible ligand docking. KEY RESULTS The increased signalling induced by increasing the cell surface expression of GPR119 in the absence of agonist and the inhibitory effect of two synthetic inverse agonists demonstrated that GRP119 signals with a high degree of constitutive activity through the Gαs pathway. The mutational maps for AR231453 and OEA were very similar and, surprisingly, also similar to the mutational map for residues affecting the constitutive signalling - albeit with key differences. Surprisingly, almost all residues in extracellular loop-2b were important for the constitutive activity. The molecular modelling and docking demonstrated that AR231453 binds in a 'vertical' pocket in between mutational hits reaching from the centre of the receptor out to extracellular loop-2b. CONCLUSIONS AND IMPLICATIONS The high constitutive activity of GPR119 should be taken into account in future drug discovery efforts, which can now be guided by the detailed knowledge of the physiochemical properties of the extended ligand-binding pocket.
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Affiliation(s)
- M S Engelstoft
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section for Metabolic Receptology and Enteroendocrinology, University of Copenhagen, Copenhagen, Denmark; Laboratory for Molecular Pharmacology, Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark
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15
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Nguyen ED, Norn C, Frimurer TM, Meiler J. Assessment and challenges of ligand docking into comparative models of G-protein coupled receptors. PLoS One 2013; 8:e67302. [PMID: 23844000 PMCID: PMC3699586 DOI: 10.1371/journal.pone.0067302] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [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: 02/17/2013] [Accepted: 05/16/2013] [Indexed: 01/09/2023] Open
Abstract
The rapidly increasing number of high-resolution X-ray structures of G-protein coupled receptors (GPCRs) creates a unique opportunity to employ comparative modeling and docking to provide valuable insight into the function and ligand binding determinants of novel receptors, to assist in virtual screening and to design and optimize drug candidates. However, low sequence identity between receptors, conformational flexibility, and chemical diversity of ligands present an enormous challenge to molecular modeling approaches. It is our hypothesis that rapid Monte-Carlo sampling of protein backbone and side-chain conformational space with Rosetta can be leveraged to meet this challenge. This study performs unbiased comparative modeling and docking methodologies using 14 distinct high-resolution GPCRs and proposes knowledge-based filtering methods for improvement of sampling performance and identification of correct ligand-receptor interactions. On average, top ranked receptor models built on template structures over 50% sequence identity are within 2.9 Å of the experimental structure, with an average root mean square deviation (RMSD) of 2.2 Å for the transmembrane region and 5 Å for the second extracellular loop. Furthermore, these models are consistently correlated with low Rosetta energy score. To predict their binding modes, ligand conformers of the 14 ligands co-crystalized with the GPCRs were docked against the top ranked comparative models. In contrast to the comparative models themselves, however, it remains difficult to unambiguously identify correct binding modes by score alone. On average, sampling performance was improved by 103 fold over random using knowledge-based and energy-based filters. In assessing the applicability of experimental constraints, we found that sampling performance is increased by one order of magnitude for every 10 residues known to contact the ligand. Additionally, in the case of DOR, knowledge of a single specific ligand-protein contact improved sampling efficiency 7 fold. These findings offer specific guidelines which may lead to increased success in determining receptor-ligand complexes.
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Affiliation(s)
- Elizabeth Dong Nguyen
- Center for Structural Biology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Christoffer Norn
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Thomas M. Frimurer
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Jens Meiler
- Center for Structural Biology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Department of Pharmacology, Vanderbilt Program in Drug Discovery, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Department of Chemistry and the Institute for Chemical Biology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- * E-mail:
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16
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Benned-Jensen T, Norn C, Laurent S, Madsen CM, Larsen HM, Arfelt KN, Wolf RM, Frimurer T, Sailer AW, Rosenkilde MM. Molecular characterization of oxysterol binding to the Epstein-Barr virus-induced gene 2 (GPR183). J Biol Chem 2012; 287:35470-35483. [PMID: 22875855 PMCID: PMC3471686 DOI: 10.1074/jbc.m112.387894] [Citation(s) in RCA: 35] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Indexed: 11/06/2022] Open
Abstract
Oxysterols are oxygenated cholesterol derivates that are emerging as a physiologically important group of molecules. Although they regulate a range of cellular processes, only few oxysterol-binding effector proteins have been identified, and the knowledge of their binding mode is limited. Recently, the family of G protein-coupled seven transmembrane-spanning receptors (7TM receptors) was added to this group. Specifically, the Epstein-Barr virus-induced gene 2 (EBI2 or GPR183) was shown to be activated by several oxysterols, most potently by 7α,25-dihydroxycholesterol (7α,25-OHC). Nothing is known about the binding mode, however. Using mutational analysis, we identify here four key residues for 7α,25-OHC binding: Arg-87 in TM-II (position II:20/2.60), Tyr-112 and Tyr-116 (positions III:09/3.33 and III:13/3.37) in TM-III, and Tyr-260 in TM-VI (position VI:16/6.51). Substituting these residues with Ala and/or Phe results in a severe decrease in agonist binding and receptor activation. Docking simulations suggest that Tyr-116 interacts with the 3β-OH group in the agonist, Tyr-260 with the 7α-OH group, and Arg-87, either directly or indirectly, with the 25-OH group, although nearby residues likely also contribute. In addition, Tyr-112 is involved in 7α,25-OHC binding but via hydrophobic interactions. Finally, we show that II:20/2.60 constitutes an important residue for ligand binding in receptors carrying a positively charged residue at this position. This group is dominated by lipid- and nucleotide-activated receptors, here exemplified by the CysLTs, P2Y12, and P2Y14. In conclusion, we present the first molecular characterization of oxysterol binding to a 7TM receptor and identify position II:20/2.60 as a generally important residue for ligand binding in certain 7TM receptors.
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Affiliation(s)
- Tau Benned-Jensen
- Laboratory for Molecular Pharmacology, Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Christoffer Norn
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Stephane Laurent
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, 4056 Basel, Switzerland
| | - Christian M Madsen
- Laboratory for Molecular Pharmacology, Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Hjalte M Larsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Kristine N Arfelt
- Laboratory for Molecular Pharmacology, Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Romain M Wolf
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 4056 Basel, Switzerland
| | - Thomas Frimurer
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Andreas W Sailer
- Developmental and Molecular Pathways, Novartis Institutes for BioMedical Research, 4056 Basel, Switzerland
| | - Mette M Rosenkilde
- Laboratory for Molecular Pharmacology, Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark.
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