Deploying synthetic coevolution and machine learning to engineer protein-protein interactions

Yang, Aerin; Jude, Kevin M.; Lai, Ben; Minot, Mason; Kocyla, Anna M.; Glassman, Caleb R.; Nishimiya, Daisuke; Kim, Yoon Seok; Reddy, Sai T.; Khan, Aly A.; Garcia, K. Christopher

doi:10.1126/science.adh1720

Deploying synthetic coevolution and machine learning to engineer protein-protein interactions

Journal Article · Fri Jul 28 00:00:00 EDT 2023 · Science

DOI:https://doi.org/10.1126/science.adh1720· OSTI ID:2471685

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Stanford Univ., CA (United States). School of Medicine
Toyota Technological Institute at Chicago, IL (United States)
Eidgenoessische Technische Hochschule (ETH), Zurich (Switzerland)
Toyota Technological Institute at Chicago, IL (United States); Univ. of Chicago, IL (United States)

Fine-tuning of protein-protein interactions occurs naturally through coevolution, but this process is difficult to recapitulate in the laboratory. We describe a platform for synthetic protein-protein coevolution that can isolate matched pairs of interacting muteins from complex libraries. This large dataset of coevolved complexes drove a systems-level analysis of molecular recognition between Z domain–affibody pairs spanning a wide range of structures, affinities, cross-reactivities, and orthogonalities, and captured a broad spectrum of coevolutionary networks. Furthermore, we harnessed pretrained protein language models to expand, in silico, the amino acid diversity of our coevolution screen, predicting remodeled interfaces beyond the reach of the experimental library. Further, the integration of these approaches provides a means of simulating protein coevolution and generating protein complexes with diverse molecular recognition properties for biotechnology and synthetic biology.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). Advanced Light Source (ALS); SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL)

Sponsoring Organization:: National Institute of General Medical Sciences (NIGMS); National Institutes of Health (NIH); USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231; AC02-76SF00515

OSTI ID:: 2471685

Journal Information:: Science, Journal Name: Science Journal Issue: 6656 Vol. 381; ISSN 0036-8075

Publisher:: AAASCopyright Statement

Country of Publication:: United States

Language:: English

References (62)

Redesigning the hydrophobic core of a four-helix-bundle protein Munson, Mary; Regan, Lynne; O'Brien, Ronan Protein Science, Vol. 3, Issue 11 https://doi.org/10.1002/pro.5560031114	journal	November 1994
The response of T4 lysozyme to large-to-small substitutions within the core and its relation to the hydrophobic effect: Cavity-creating mutations in T4 lysozyme Xu, Jian; Baase, Walter A.; Baldwin, Enoch Protein Science, Vol. 7, Issue 1 https://doi.org/10.1002/pro.5560070117	journal	January 1998
RosettaHoles: Rapid assessment of protein core packing for structure prediction, refinement, design and validation Sheffler, Will; Baker, David Protein Science https://doi.org/10.1002/pro.8	journal	January 2008
Anti‐idiotypic protein domains selected from protein A‐based affibody libraries Eklund, Malin; Axelsson, Lars; Uhlén, Mathias Proteins: Structure, Function, and Bioinformatics, Vol. 48, Issue 3 https://doi.org/10.1002/prot.10169	journal	June 2002
Correlated mutations contain information about protein-protein interaction 1 1Edited by A. R. Fersht Pazos, Florencio; Helmer-Citterich, Manuela; Ausiello, Gabriele Journal of Molecular Biology, Vol. 271, Issue 4 https://doi.org/10.1006/jmbi.1997.1198	journal	August 1997
A heterodimeric coiled-coil peptide pair selected in vivo from a designed library- versus -library ensemble 1 1Edited by A. R. Fersht Arndt, Katja M.; Pelletier, Joelle N.; Müller, Kristian M. Journal of Molecular Biology, Vol. 295, Issue 3 https://doi.org/10.1006/jmbi.1999.3352	journal	January 2000
Dramatic Structural and Thermodynamic Consequences of Repacking a Protein's Hydrophobic Core Willis, Mark A.; Bishop, Barney; Regan, Lynne Structure, Vol. 8, Issue 12 https://doi.org/10.1016/S0969-2126(00)00544-X	journal	December 2000
Evolving New Protein-Protein Interaction Specificity through Promiscuous Intermediates Aakre, Christopher D.; Herrou, Julien; Phung, Tuyen N. Cell, Vol. 163, Issue 3 https://doi.org/10.1016/j.cell.2015.09.055	journal	October 2015
Programmable protein circuit design Chen, Zibo; Elowitz, Michael B. Cell, Vol. 184, Issue 9 https://doi.org/10.1016/j.cell.2021.03.007	journal	April 2021
Learning the protein language: Evolution, structure, and function Bepler, Tristan; Berger, Bonnie Cell Systems, Vol. 12, Issue 6 https://doi.org/10.1016/j.cels.2021.05.017	journal	June 2021
New genotype–phenotype linkages for directed evolution of functional proteins Leemhuis, H.; Stein, V.; Griffiths, A. Current Opinion in Structural Biology, Vol. 15, Issue 4 https://doi.org/10.1016/j.sbi.2005.07.006	journal	August 2005
Computational design of novel protein–protein interactions – An overview on methodological approaches and applications Marchand, Anthony; Van Hall-Beauvais, Alexandra K.; Correia, Bruno E. Current Opinion in Structural Biology, Vol. 74 https://doi.org/10.1016/j.sbi.2022.102370	journal	June 2022
Lysine Methylation as a Routine Rescue Strategy for Protein Crystallization Walter, Thomas S.; Meier, Christoph; Assenberg, Rene Structure, Vol. 14, Issue 11 https://doi.org/10.1016/j.str.2006.09.005	journal	November 2006
Synthetic Biological Circuits within an Orthogonal Central Dogma Costello, Alan; Badran, Ahmed H. Trends in Biotechnology, Vol. 39, Issue 1 https://doi.org/10.1016/j.tibtech.2020.05.013	journal	January 2021
Molecular mechanisms of epistasis within and between genes Lehner, Ben Trends in Genetics, Vol. 27, Issue 8 https://doi.org/10.1016/j.tig.2011.05.007	journal	August 2011
Mutual Information in Protein Multiple Sequence Alignments Reveals Two Classes of Coevolving Positions ^† Gloor, Gregory B.; Martin, Louise C.; Wahl, Lindi M. Biochemistry, Vol. 44, Issue 19 https://doi.org/10.1021/bi050293e	journal	May 2005
Design of a 4-helix bundle protein: synthesis of peptides which self-associate into a helical protein Ho, Siew Peng; DeGrado, William F. Journal of the American Chemical Society, Vol. 109, Issue 22, p. 6751-6758 https://doi.org/10.1021/ja00256a032	journal	October 1987
An in vivo library-versus-library selection of optimized protein–protein interactions Pelletier, Joelle N.; Arndt, Katja M.; Plückthun, Andreas Nature Biotechnology, Vol. 17, Issue 7 https://doi.org/10.1038/10897	journal	July 1999
Hydrophobic stabilization in T4 lysozyme determined directly by multiple substitutions of Ile 3 Matsumura, Masazumi; Becktel, Wayne J.; Matthews, Brian W. Nature, Vol. 334, Issue 6181 https://doi.org/10.1038/334406a0	journal	August 1988
Isolating and engineering human antibodies using yeast surface display Chao, Ginger; Lau, Wai L.; Hackel, Benjamin J. Nature Protocols, Vol. 1, Issue 2 https://doi.org/10.1038/nprot.2006.94	journal	July 2006
Emerging methods in protein co-evolution de Juan, David; Pazos, Florencio; Valencia, Alfonso Nature Reviews Genetics, Vol. 14, Issue 4 https://doi.org/10.1038/nrg3414	journal	March 2013
Methods for the directed evolution of proteins Packer, Michael S.; Liu, David R. Nature Reviews Genetics, Vol. 16, Issue 7 https://doi.org/10.1038/nrg3927	journal	June 2015
Rapid screening of TCR-pMHC interactions by the YAMTAD system Wang, Lihui; Lan, Xun Cell Discovery, Vol. 8, Issue 1 https://doi.org/10.1038/s41421-022-00386-2	journal	April 2022
Structure-based protein function prediction using graph convolutional networks Gligorijević, Vladimir; Renfrew, P. Douglas; Kosciolek, Tomasz Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-021-23303-9	journal	May 2021
Single-sequence protein structure prediction using a language model and deep learning Chowdhury, Ratul; Bouatta, Nazim; Biswas, Surojit Nature Biotechnology, Vol. 40, Issue 11 https://doi.org/10.1038/s41587-022-01432-w	journal	October 2022
Selection platforms for directed evolution in synthetic biology Tizei, Pedro A. G.; Csibra, Eszter; Torres, Leticia Biochemical Society Transactions, Vol. 44, Issue 4 https://doi.org/10.1042/BST20160076	journal	August 2016
Anchor residues in protein–protein interactions Rajamani, Deepa; Thiel, Spencer; Vajda, Sandor Proceedings of the National Academy of Sciences, Vol. 101, Issue 31 https://doi.org/10.1073/pnas.0401942101	journal	July 2004
Structural basis for recognition by an in vitro evolved affibody Hogbom, M.; Eklund, M.; Nygren, P. -A. Proceedings of the National Academy of Sciences, Vol. 100, Issue 6 https://doi.org/10.1073/pnas.0436100100	journal	February 2003
Libraries against libraries for combinatorial selection of replicating antigen–antibody pairs Bowley, Diana R.; Jones, Teresa M.; Burton, Dennis R. Proceedings of the National Academy of Sciences, Vol. 106, Issue 5 https://doi.org/10.1073/pnas.0812291106	journal	February 2009
Protein-protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces Ma, B.; Elkayam, T.; Wolfson, H. Proceedings of the National Academy of Sciences, Vol. 100, Issue 10 https://doi.org/10.1073/pnas.1030237100	journal	May 2003
High-throughput characterization of protein–protein interactions by reprogramming yeast mating Younger, David; Berger, Stephanie; Baker, David Proceedings of the National Academy of Sciences, Vol. 114, Issue 46 https://doi.org/10.1073/pnas.1705867114	journal	October 2017
Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences Rives, Alexander; Meier, Joshua; Sercu, Tom Proceedings of the National Academy of Sciences, Vol. 118, Issue 15 https://doi.org/10.1073/pnas.2016239118	journal	April 2021
Additivity of mutant effects assessed by binomial mutagenesis. Gregoret, L. M.; Sauer, R. T. Proceedings of the National Academy of Sciences, Vol. 90, Issue 9 https://doi.org/10.1073/pnas.90.9.4246	journal	May 1993
PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments Jones, David T.; Buchan, Daniel W. A.; Cozzetto, Domenico Bioinformatics, Vol. 28, Issue 2 https://doi.org/10.1093/bioinformatics/btr638	journal	November 2011
circlize implements and enhances circular visualization in R Gu, Zuguang; Gu, Lei; Eils, Roland Bioinformatics, Vol. 30, Issue 19 https://doi.org/10.1093/bioinformatics/btu393	journal	June 2014
Directed co-evolution of interacting protein–peptide pairs by compartmentalized two-hybrid replication (C2HR) Siau, Jia Wei; Nonis, Samuel; Chee, Sharon Nucleic Acids Research, Vol. 48, Issue 22 https://doi.org/10.1093/nar/gkaa933	journal	October 2020
Development and application of a recombination-based library versus library high- throughput yeast two-hybrid (RLL-Y2H) screening system Yang, Fang; Lei, Yingying; Zhou, Meiling Nucleic Acids Research, Vol. 46, Issue 3 https://doi.org/10.1093/nar/gkx1173	journal	November 2017
High-affinity binding to staphylococcal protein A by an engineered dimeric Affibody molecule Lindborg, M.; Dubnovitsky, A.; Olesen, K. Protein Engineering Design and Selection, Vol. 26, Issue 10 https://doi.org/10.1093/protein/gzt038	journal	August 2013
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
Graphical tools for macromolecular crystallography in PHENIX Echols, Nathaniel; Grosse-Kunstleve, Ralf W.; Afonine, Pavel V. Journal of Applied Crystallography, Vol. 45, Issue 3 https://doi.org/10.1107/S0021889812017293	journal	May 2012
Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard Terwilliger, Thomas C.; Grosse-Kunstleve, Ralf W.; Afonine, Pavel V. Acta Crystallographica Section D Biological Crystallography, Vol. 64, Issue 1 https://doi.org/10.1107/S090744490705024X	journal	December 2007
MolProbity : all-atom structure validation for macromolecular crystallography Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1 https://doi.org/10.1107/S0907444909042073	journal	December 2009
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	journal	January 2010
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
An introduction to data reduction: space-group determination, scaling and intensity statistics Evans, Philip R. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S090744491003982X	journal	March 2011
Overview of the CCP 4 suite and current developments Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444910045749	journal	March 2011
Towards automated crystallographic structure refinement with phenix.refine Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4 https://doi.org/10.1107/S0907444912001308	journal	March 2012
How good are my data and what is the resolution? Evans, Philip R.; Murshudov, Garib N. Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 7 https://doi.org/10.1107/S0907444913000061	journal	June 2013
Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement Headd, Jeffrey J.; Echols, Nathaniel; Afonine, Pavel V. Acta Crystallographica Section D Biological Crystallography, Vol. 70, Issue 5 https://doi.org/10.1107/S1399004714003277	journal	April 2014
DIALS : implementation and evaluation of a new integration package Winter, Graeme; Waterman, David G.; Parkhurst, James M. Acta Crystallographica Section D Structural Biology, Vol. 74, Issue 2 https://doi.org/10.1107/S2059798317017235	journal	February 2018
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix Liebschner, Dorothee; Afonine, Pavel V.; Baker, Matthew L. Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 10 https://doi.org/10.1107/S2059798319011471	journal	October 2019
Linking Crystallographic Model and Data Quality Karplus, P. A.; Diederichs, K. Science, Vol. 336, Issue 6084 https://doi.org/10.1126/science.1218231	journal	May 2012
High thermodynamic stability of parametrically designed helical bundles Huang, Po-Ssu; Oberdorfer, Gustav; Xu, Chunfu Science, Vol. 346, Issue 6208 https://doi.org/10.1126/science.1257481	journal	October 2014
Sequence Requirements for Coiled-Coils: Analysis with λ Repressor-GCN4 Leucine Zipper Fusions Hu, James C.; O'Shea, Erin K.; Kim, Peter S. Science, Vol. 250, Issue 4986 https://doi.org/10.1126/science.2147779	journal	December 1990
Influence of Interior Packing and Hydrophobicity on the Stability of a Protein Sandberg, Warren S.; Terwilliger, Thomas C. Science, Vol. 245, Issue 4913 https://doi.org/10.1126/science.2787053	journal	July 1989
Evolutionarily Conserved Pathways of Energetic Connectivity in Protein Families Lockless, S. W. Science, Vol. 286, Issue 5438 https://doi.org/10.1126/science.286.5438.295	journal	October 1999
Characterization of a helical protein designed from first principles Regan, L.; DeGrado, W. F. Science, Vol. 241, Issue 4868, p. 976-978 https://doi.org/10.1126/science.3043666	journal	August 1988
Evolutionary-scale prediction of atomic-level protein structure with a language model Lin, Zeming; Akin, Halil; Rao, Roshan Science, Vol. 379, Issue 6637 https://doi.org/10.1126/science.ade2574	journal	March 2023
Engineered Protein Scaffolds as Next-Generation Therapeutics Gebauer, Michaela; Skerra, Arne Annual Review of Pharmacology and Toxicology, Vol. 60, Issue 1 https://doi.org/10.1146/annurev-pharmtox-010818-021118	journal	January 2020
Using Sequence Similarity Networks for Visualization of Relationships Across Diverse Protein Superfamilies Atkinson, Holly J.; Morris, John H.; Ferrin, Thomas E. PLoS ONE, Vol. 4, Issue 2 https://doi.org/10.1371/journal.pone.0004345	journal	February 2009
Collaboration gets the most out of software Morin, Andrew; Eisenbraun, Ben; Key, Jason eLife, Vol. 2 https://doi.org/10.7554/eLife.01456	journal	September 2013
Sequence co-evolution gives 3D contacts and structures of protein complexes Hopf, Thomas A.; Schärfe, Charlotta P. I.; Rodrigues, João P. G. L. M. eLife, Vol. 3 https://doi.org/10.7554/eLife.03430	journal	September 2014

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