ArticlePLoS computational biology2012
Collective dynamics differentiates functional divergence in protein evolution.
Article in PLoS computational biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Protein Catalysis Through Structural Dynamics: A Comprehensive Analysis of Energy Conversion in Enzymatic Systems and Its Computational Limitations.Pharmaceuticals (Basel, Switzerland) · 2025Review
- How enzyme functions evolve: genetic, structural, and kinetic perspectives.Biophysical reviews · 2025Review
- Dynamic energy conversion in protein catalysis: From brownian motion to enzymatic function.Computational and structural biotechnology journal · 2025Review
- Protein dynamics provide mechanistic insights about epistasis among common missense polymorphisms.Biophysical journal · 2023Article
- Dynamic coupling of residues within proteins as a mechanistic foundation of many enigmatic pathogenic missense variants.PLoS computational biology · 2022Article
- Hinge-shift mechanism as a protein design principle for the evolution of β-lactamases from substrate promiscuity to specificity.Nature communications · 2021Article
- Mutations Utilize Dynamic Allostery to Confer Resistance in TEM-1 β-lactamase.International journal of molecular sciences · 2018Article
- Ancient thioredoxins evolved to modern-day stability-function requirement by altering native state ensemble.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2018Article
- Patterns of coevolving amino acids unveil structural and dynamical domains.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Photoconvertible Fluorescent Proteins and the Role of Dynamics in Protein Evolution.International journal of molecular sciences · 2017Article
- Using THz Spectroscopy, Evolutionary Network Analysis Methods, and MD Simulation to Map the Evolution of Allosteric Communication Pathways in c-Type Lysozymes.Molecular biology and evolution · 2016Article
- Integration of structural dynamics and molecular evolution via protein interaction networks: a new era in genomic medicine.Current opinion in structural biology · 2015Review
- The Role of Conformational Dynamics and Allostery in the Disease Development of Human Ferritin.Biophysical journal · 2015Article
- Structure-Encoded Global Motions and Their Role in Mediating Protein-Substrate Interactions.Biophysical journal · 2015Review
- Conformational dynamics of nonsynonymous variants at protein interfaces reveals disease association.Proteins · 2015Article
- A hinge migration mechanism unlocks the evolution of green-to-red photoconversion in GFP-like proteins.Structure (London, England : 1993) · 2015Article
- Evol and ProDy for bridging protein sequence evolution and structural dynamics.Bioinformatics (Oxford, England) · 2014Article
- Structural dynamics flexibility informs function and evolution at a proteome scale.Evolutionary applications · 2013Article
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Authors and funding
5 authors.
Funding
Abstract
Protein evolution is most commonly studied by analyzing related protein sequences and generating ancestral sequences through Bayesian and Maximum Likelihood methods, and/or by resurrecting ancestral proteins in the lab and performing ligand binding studies to determine function. Structural and dynamic evolution have largely been left out of molecular evolution studies. Here we incorporate both structure and dynamics to elucidate the molecular principles behind the divergence in the evolutionary path of the steroid receptor proteins. We determine the likely structure of three evolutionarily diverged ancestral steroid receptor proteins using the Zipping and Assembly Method with FRODA (ZAMF). Our predictions are within ~2.7 Å all-atom RMSD of the respective crystal structures of the ancestral steroid receptors. Beyond static structure prediction, a particular feature of ZAMF is that it generates protein dynamics information. We investigate the differences in conformational dynamics of diverged proteins by obtaining the most collective motion through essential dynamics. Strikingly, our analysis shows that evolutionarily diverged proteins of the same family do not share the same dynamic subspace, while those sharing the same function are simultaneously clustered together and distant from those, that have functionally diverged. Dynamic analysis also enables those mutations that most affect dynamics to be identified. It correctly predicts all mutations (functional and permissive) necessary to evolve new function and ~60% of permissive mutations necessary to recover ancestral function.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.