ArticleMolecular biology and evolution2019
Shared Signature Dynamics Tempered by Local Fluctuations Enables Fold Adaptability and Specificity.
Article in Molecular biology and evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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30 citing papers in PubMed.
- AI-guided epitope engineering of a SARS-CoV-2 spike antigen for broad sarbecovirus neutralization.Frontiers in immunology · 2026Article
- Comparative Dynamics Enables Discovery of Embedded Bacterial Ferredoxin Domains in Large Redox Enzymes.Proteins · 2025Article
- Global comparative structural analysis of responses to protein phosphorylation.Nature communications · 2025Article
- InSty: A ProDy Module for Evaluating Protein Interactions and Stability.Journal of molecular biology · 2025Article
- Exploring the Intrinsic Structural Plasticity and Conformational Dynamics of Human Beta Coronavirus Spike Glycoproteins.Journal of chemical information and modeling · 2025Article
- Identifying a non-conserved site for achieving allosteric covalent inhibition of CECR2.Acta pharmacologica Sinica · 2025Article
- Global hinge sites of proteins as target sites for drug binding.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Genome structural dynamics: insights from Gaussian network analysis of Hi-C data.Briefings in functional genomics · 2024Article
- WatFinder: a ProDy tool for protein-water interactions.Bioinformatics (Oxford, England) · 2024Article
- Scipion-EM-ProDy: A Graphical Interface for the ProDy Python Package within the Scipion Workflow Engine Enabling Integration of Databases, Simulations and Cryo-Electron Microscopy Image Processing.International journal of molecular sciences · 2023Article
- Scipion Flexibility Hub: an integrative framework for advanced analysis of conformational heterogeneity in cryoEM.Acta crystallographica. Section D, Structural biology · 2023Article
- Structural Dynamics Predominantly Determine the Adaptability of Proteins to Amino Acid Deletions.International journal of molecular sciences · 2023Article
- Activation and Speciation Mechanisms in Class A GPCRs.Journal of molecular biology · 2022Article
- Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0.Acta crystallographica. Section D, Structural biology · 2022Review
- A Comparative Evaluation of the Structural and Dynamic Properties of Insect Odorant Binding Proteins.Biomolecules · 2022Article
- Sampling of Protein Conformational Space Using Hybrid Simulations: A Critical Assessment of Recent Methods.Frontiers in molecular biosciences · 2022Article
- Structural dynamics in the evolution of a bilobed protein scaffold.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Evolution of dynamical networks enhances catalysis in a designer enzyme.Nature chemistry · 2021Article
- Article
- State-dependent sequential allostery exhibited by chaperonin TRiC/CCT revealed by network analysis of Cryo-EM maps.Progress in biophysics and molecular biology · 2021Article
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4 authors.
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Abstract
Recent studies have drawn attention to the evolution of protein dynamics, in addition to sequence and structure, based on the premise structure-encodes-dynamics-encodes-function. Of interest is to understand how functional differentiation is accomplished while maintaining the fold, or how intrinsic dynamics plays out in the evolution of structural variations and functional specificity. We performed a systematic computational analysis of 26,899 proteins belonging to 116 CATH superfamilies. Characterizing cooperative mechanisms and convergent/divergent features that underlie the shared/differentiated dynamics of family members required a methodology that lends itself to efficient analyses of large ensembles of proteins. We therefore introduced, SignDy, an integrated pipeline for evaluating the signature dynamics of families based on elastic network models. Our analysis confirmed that family members share conserved, highly cooperative (global) modes of motion. Importantly, our analysis discloses a subset of motions that sharply distinguishes subfamilies, which lie in a low-to-intermediate frequency regime of the mode spectrum. This regime has maximal impact on functional differentiation of families into subfamilies, while being evolutionarily conserved among subfamily members. Notably, the high-frequency end of the spectrum also reveals evolutionary conserved features across and within subfamilies; but in sharp contrast to global motions, high-frequency modes are minimally collective. Modulation of robust/conserved global dynamics by low-to-intermediate frequency fluctuations thus emerges as a versatile mechanism ensuring the adaptability of selected folds and the specificity of their subfamilies. SignDy further allows for dynamics-based categorization as a new layer of information relevant to distinctive mechanisms of action of subfamilies, beyond sequence or structural classifications.
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