ArticleBiophysical journal2009
Coarse-grained description of protein internal dynamics: an optimal strategy for decomposing proteins in rigid subunits.
Article in Biophysical journal, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Mapping cryptic phosphorylation sites in the human proteome.The EMBO journal · 2025Article
- Fast, Accurate, and System-Specific Variable-Resolution Modeling of Proteins.Journal of chemical information and modeling · 2023Article
- Assignment of structural domains in proteins using diffusion kernels on graphs.BMC bioinformatics · 2022Article
- A journey through mapping space: characterising the statistical and metric properties of reduced representations of macromolecules.The European physical journal. B · 2021Article
- From System Modeling to System Analysis: The Impact of Resolution Level and Resolution Distribution in the Computer-Aided Investigation of Biomolecules.Frontiers in molecular biosciences · 2021Review
- An Information-Theory-Based Approach for Optimal Model Reduction of Biomolecules.Journal of chemical theory and computation · 2020Article
- Ligand-protein interactions in lysozyme investigated through a dual-resolution model.Proteins · 2020Article
- A deep learning approach to the structural analysis of proteins.Interface focus · 2019Article
- Optimal Coarse-Grained Site Selection in Elastic Network Models of Biomolecules.Journal of chemical theory and computation · 2019Article
- Large-Scale Conformational Changes and Protein Function: Breaking theFrontiers in molecular biosciences · 2019Review
- Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models.International journal of molecular sciences · 2018Review
- Protein dynamic communities from elastic network models align closely to the communities defined by molecular dynamics.PloS one · 2018Article
- Unifying view of mechanical and functional hotspots across class A GPCRs.PLoS computational biology · 2017Article
- Article
- Similarity in Shape Dictates Signature Intrinsic Dynamics Despite No Functional Conservation in TIM Barrel Enzymes.PLoS computational biology · 2016Article
- DNA Polymerase Conformational Dynamics and the Role of Fidelity-Conferring Residues: Insights from Computational Simulations.Frontiers in molecular biosciences · 2016Article
- Molecular dynamics simulations identify time scale of conformational changes responsible for conformational selection in molecular recognition of HIV-1 transactivation responsive RNA.Journal of the American Chemical Society · 2014Article
- Enhancing the activity of Bacillus circulans xylanase by modulating the flexibility of the hinge region.Journal of industrial microbiology & biotechnology · 2014Article
- Molecular dynamics studies on the conformational transitions of adenylate kinase: a computational evidence for the conformational selection mechanism.BioMed research international · 2013Article
- Elucidating the interacting domains of chandipura virus nucleocapsid protein.Advances in virology · 2013Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The possibility of accurately describing the internal dynamics of proteins, in terms of movements of a few approximately-rigid subparts, is an appealing biophysical problem with important implications for the analysis and interpretation of data from experiments or numerical simulations. The problem is tackled here by means of a novel variational approach that exploits information about equilibrium fluctuations of interresidues distances, provided, e.g., by atomistic molecular dynamics simulations or coarse-grained models. No contiguity in primary sequence or in space is enforced a priori for amino acids grouped in the same rigid unit. The identification of the rigid protein moduli, or dynamical domains, provides valuable insight into functionally oriented aspects of protein internal dynamics. To illustrate this point, we first discuss the decomposition of adenylate kinase and HIV-1 protease and then extend the investigation to several representatives of the hydrolase enzymatic class. The known catalytic site of these enzymes is found to be preferentially located close to the boundary separating the two primary dynamical subdomains.
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