ArticleProceedings of the National Academy of Sciences of the United States of America2018
Green function of correlated genes in a minimal mechanical model of protein evolution.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- Distinguishing direct interactions from global epistasis using rank statistics.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Exploring the unfolding pathways of protein families using Elastic Network Model.Scientific reports · 2024Article
- A linear reciprocal relationship between robustness and plasticity in homeostatic biological networks.PloS one · 2023Article
- General Theory of Specific Binding: Insights from a Genetic-Mechano-Chemical Protein Model.Molecular biology and evolution · 2022Article
- The Statistical Trends of Protein Evolution: A Lesson from AlphaFold Database.Molecular biology and evolution · 2022Article
- Allostery and Epistasis: Emergent Properties of Anisotropic Networks.Entropy (Basel, Switzerland) · 2020Article
- Allosteric communication in molecular machines via information exchange: what can be learned from dynamical modeling.Biophysical reviews · 2020Review
- Direct coupling analysis of epistasis in allosteric materials.PLoS computational biology · 2020Article
- Mechanics of Allostery: Contrasting the Induced Fit and Population Shift Scenarios.Biophysical journal · 2019Article
- Simple mechanics of protein machines.Journal of the Royal Society, Interface · 2019Article
- Revealing evolutionary constraints on proteins through sequence analysis.PLoS computational biology · 2019Article
- Catalytic enzymes are active matter.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Designed Elastic Networks: Models of Complex Protein Machinery.International journal of molecular sciences · 2018Review
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4 authors.
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Abstract
The function of proteins arises from cooperative interactions and rearrangements of their amino acids, which exhibit large-scale dynamical modes. Long-range correlations have also been revealed in protein sequences, and this has motivated the search for physical links between the observed genetic and dynamic cooperativity. We outline here a simplified theory of protein, which relates sequence correlations to physical interactions and to the emergence of mechanical function. Our protein is modeled as a strongly coupled amino acid network with interactions and motions that are captured by the mechanical propagator, the Green function. The propagator describes how the gene determines the connectivity of the amino acids and thereby, the transmission of forces. Mutations introduce localized perturbations to the propagator that scatter the force field. The emergence of function is manifested by a topological transition when a band of such perturbations divides the protein into subdomains. We find that epistasis-the interaction among mutations in the gene-is related to the nonlinearity of the Green function, which can be interpreted as a sum over multiple scattering paths. We apply this mechanical framework to simulations of protein evolution and observe long-range epistasis, which facilitates collective functional modes.
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