Structural ontogeny of protein-protein interactions.
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| Title: | Structural ontogeny of protein-protein interactions. |
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| Authors: | Yang, Aerin (AUTHOR), Jiang, Hanlun (AUTHOR), Jude, Kevin M. (AUTHOR), Akpinaroglu, Deniz (AUTHOR), Allenspach, Stephan (AUTHOR), Li, Alex Jie (AUTHOR), Bowden, James (AUTHOR), Perez, Carla Patricia (AUTHOR), Liu, Liu (AUTHOR), Huang, Po-Ssu (AUTHOR), Kortemme, Tanja (AUTHOR), Listgarten, Jennifer (AUTHOR), Garcia, K. Christopher (AUTHOR) |
| Source: | Science. 2/12/2026, Vol. 391 Issue 6786, p1-18. 18p. |
| Subjects: | Protein-protein interactions, Coevolution, Epistasis (Genetics), Binding sites, Machine learning, Molecular docking, Drug discovery |
| Abstract: | Understanding how protein binding sites evolve interactions with other proteins could hold clues to targeting "undruggable" surfaces. We used synthetic coevolution to engineer new interactions between naïve surfaces, simulating the de novo formation of protein complexes. We isolated seven distinct structural families of protein Z-domain complexes and found that synthetic complexes explore multiple shallow energy wells through ratchet-like docking modes, whereas complexes formed by natural binding sites converged in a deep energy well with a relatively fixed geometry. Epistasis analysis of a machine learning–estimated fitness landscape revealed "seed" contacts between binding partners that anchored the earliest stages of encounter complex formation. Our results suggest that "silent" surfaces have a shallower energy landscape than natural binding sites, disfavoring tight binding, likely owing to evolutionary counterselection. Editor's summary: A long-standing challenge in protein structure is understanding how protein surfaces enable interactions with other proteins, with the ultimate goal of predicting and designing such surfaces. However, we still do not fully understand how evolution shapes such interactions. Yang et al. used synthetic coevolution of artificial protein pairs to explore how protein-protein binding sites form and evolve. They identified seed contacts at a very early stage that could take several different paths as the binder pair coevolved. Natural interface surfaces appear to be preorganized to allow fast evolution of deep energy wells that support binding of new partner proteins. These insights will be important to consider when designing synthetic protein binders and may explain why antibodies and peptides often interact with natural protein binding interfaces. —Michael A. Funk INTRODUCTION: How proteins initiate and evolve interactions with other proteins to form binding sites and protein-protein interfaces remains poorly understood. Yet there appear to be distinctive properties of protein surfaces that have evolved to form protein-protein interfaces versus noninteracting surfaces of proteins. Natural protein binding sites are usually the most "druggable" sites on a given protein and tend to attract the majority of binders from combinatorial peptide or antibody libraries. Are there biophysical properties that distinguish regions of protein surfaces that have not evolved to bind to a ligand from natural binding sites? This question has implications for drug discovery. RATIONALE: In this study, we asked whether there are fundamental differences between surfaces of proteins that have evolved to bind to proteins versus surfaces that have not. To do this, we carried out a synthetic proxy of protein-protein coevolution by designing completely new interfaces between "silent" surfaces of proteins that have no ligand recognition history and do not normally interact. We experimentally simulated and then computationally deconstructed the process by which protein-protein interactions are initially formed and subsequently coevolve specificity and high affinity. This synthetic proxy of protein coevolution has also allowed us to gain a better insight into the differences between natural and nonnatural binding sites of proteins. RESULTS: By using a synthetic coevolution platform to design interactions between naïve surfaces unencumbered by a natural binding imprint, we captured previously unseen snapshots illustrating the formation of de novo protein complexes. We found that the type of epistasis and the structural adaptations that shape affinity, specificity, and orthogonality differ between complexes formed by surfaces that have naturally evolved to bind other proteins versus nonbinding surfaces. Remodeling an interface formed by natural surfaces led to high-affinity solutions with distinct specificities, but the docking mode stayed the same in a deep energy well. Selecting for completely new interfaces mediated by a "naïve" surface of a protein also led to distinct specificities, but these were mediated by a spectrum of lower-affinity, ratchet-like docking modes in shallow energy wells, demonstrating a notable plasticity within the same interface. To understand the formation of the new interfaces, we simulated evolutionary trajectories from a machine learning–estimated fitness function that, combined with epistasis analysis, revealed surface residues that act as initiating "seeds" at the earliest stages of an evolutionary path to a high-affinity complex. Our experimental data suggest a hypothesis wherein protein surfaces that have evolved to bind to other proteins have hard-wired biophysical properties conducive for ligand binding, versus other regions of proteins, which have likely been counterselected during evolution to avoid interactions. CONCLUSION: Our protein-protein coevolution platform has shown that there are differences between the surfaces of proteins that have evolved to bind to other proteins versus those of proteins that have not. Indeed, in the system studied, there appears to be a limit on the energetic fitness and affinity of complexes engineered between surfaces of proteins with no evolutionary binding imprint. These data suggest why natural binding sites attract binders: Alternative surfaces have a shallow energy landscape that disfavors tight binding, likely owing to evolutionary counterselection. This may explain, in part, the occurrence of "undruggable" protein surfaces and prompt new biophysically based strategies for overcoming this barrier. Schematic depiction of the initial encounter of a protein-protein complex mediated by seed contacts between phenylalanine residues, which propagates through epistasis to form the complete protein-protein interface.: FIGURE CREDIT: ERIC SMITH AND CHRIS GARCIA [ABSTRACT FROM AUTHOR] |
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| Database: | Psychology and Behavioral Sciences Collection |
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| Abstract: | Understanding how protein binding sites evolve interactions with other proteins could hold clues to targeting "undruggable" surfaces. We used synthetic coevolution to engineer new interactions between naïve surfaces, simulating the de novo formation of protein complexes. We isolated seven distinct structural families of protein Z-domain complexes and found that synthetic complexes explore multiple shallow energy wells through ratchet-like docking modes, whereas complexes formed by natural binding sites converged in a deep energy well with a relatively fixed geometry. Epistasis analysis of a machine learning–estimated fitness landscape revealed "seed" contacts between binding partners that anchored the earliest stages of encounter complex formation. Our results suggest that "silent" surfaces have a shallower energy landscape than natural binding sites, disfavoring tight binding, likely owing to evolutionary counterselection. Editor's summary: A long-standing challenge in protein structure is understanding how protein surfaces enable interactions with other proteins, with the ultimate goal of predicting and designing such surfaces. However, we still do not fully understand how evolution shapes such interactions. Yang et al. used synthetic coevolution of artificial protein pairs to explore how protein-protein binding sites form and evolve. They identified seed contacts at a very early stage that could take several different paths as the binder pair coevolved. Natural interface surfaces appear to be preorganized to allow fast evolution of deep energy wells that support binding of new partner proteins. These insights will be important to consider when designing synthetic protein binders and may explain why antibodies and peptides often interact with natural protein binding interfaces. —Michael A. Funk INTRODUCTION: How proteins initiate and evolve interactions with other proteins to form binding sites and protein-protein interfaces remains poorly understood. Yet there appear to be distinctive properties of protein surfaces that have evolved to form protein-protein interfaces versus noninteracting surfaces of proteins. Natural protein binding sites are usually the most "druggable" sites on a given protein and tend to attract the majority of binders from combinatorial peptide or antibody libraries. Are there biophysical properties that distinguish regions of protein surfaces that have not evolved to bind to a ligand from natural binding sites? This question has implications for drug discovery. RATIONALE: In this study, we asked whether there are fundamental differences between surfaces of proteins that have evolved to bind to proteins versus surfaces that have not. To do this, we carried out a synthetic proxy of protein-protein coevolution by designing completely new interfaces between "silent" surfaces of proteins that have no ligand recognition history and do not normally interact. We experimentally simulated and then computationally deconstructed the process by which protein-protein interactions are initially formed and subsequently coevolve specificity and high affinity. This synthetic proxy of protein coevolution has also allowed us to gain a better insight into the differences between natural and nonnatural binding sites of proteins. RESULTS: By using a synthetic coevolution platform to design interactions between naïve surfaces unencumbered by a natural binding imprint, we captured previously unseen snapshots illustrating the formation of de novo protein complexes. We found that the type of epistasis and the structural adaptations that shape affinity, specificity, and orthogonality differ between complexes formed by surfaces that have naturally evolved to bind other proteins versus nonbinding surfaces. Remodeling an interface formed by natural surfaces led to high-affinity solutions with distinct specificities, but the docking mode stayed the same in a deep energy well. Selecting for completely new interfaces mediated by a "naïve" surface of a protein also led to distinct specificities, but these were mediated by a spectrum of lower-affinity, ratchet-like docking modes in shallow energy wells, demonstrating a notable plasticity within the same interface. To understand the formation of the new interfaces, we simulated evolutionary trajectories from a machine learning–estimated fitness function that, combined with epistasis analysis, revealed surface residues that act as initiating "seeds" at the earliest stages of an evolutionary path to a high-affinity complex. Our experimental data suggest a hypothesis wherein protein surfaces that have evolved to bind to other proteins have hard-wired biophysical properties conducive for ligand binding, versus other regions of proteins, which have likely been counterselected during evolution to avoid interactions. CONCLUSION: Our protein-protein coevolution platform has shown that there are differences between the surfaces of proteins that have evolved to bind to other proteins versus those of proteins that have not. Indeed, in the system studied, there appears to be a limit on the energetic fitness and affinity of complexes engineered between surfaces of proteins with no evolutionary binding imprint. These data suggest why natural binding sites attract binders: Alternative surfaces have a shallow energy landscape that disfavors tight binding, likely owing to evolutionary counterselection. This may explain, in part, the occurrence of "undruggable" protein surfaces and prompt new biophysically based strategies for overcoming this barrier. Schematic depiction of the initial encounter of a protein-protein complex mediated by seed contacts between phenylalanine residues, which propagates through epistasis to form the complete protein-protein interface.: FIGURE CREDIT: ERIC SMITH AND CHRIS GARCIA [ABSTRACT FROM AUTHOR] |
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| ISSN: | 00368075 |
| DOI: | 10.1126/science.adx6931 |
