ArticleProtein science : a publication of the Protein Society2008
Correspondences between low-energy modes in enzymes: dynamics-based alignment of enzymatic functional families.
Article in Protein science : a publication of the Protein Society, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Explicit versus implicit consideration of binding partners in protein-protein complex to elucidate intrinsic dynamics.Biophysical reviews · 2022Review
- What the protein data bank tells us about the evolutionary conservation of protein conformational diversity.Protein science : a publication of the Protein Society · 2022Article
- Ligand-protein interactions in lysozyme investigated through a dual-resolution model.Proteins · 2020Article
- Dynamics-function relationship in the catalytic domains of N-terminal acetyltransferases.Computational and structural biotechnology journal · 2020Article
- Characterization of Differential Dynamics, Specificity, and Allostery of Lipoxygenase Family Members.Journal of chemical information and modeling · 2019Article
- A Biophysical Perspective on Enzyme Catalysis.Biochemistry · 2019Article
- Barnaba: software for analysis of nucleic acid structures and trajectories.RNA (New York, N.Y.) · 2019Article
- Optimal Coarse-Grained Site Selection in Elastic Network Models of Biomolecules.Journal of chemical theory and computation · 2019Article
- Dynamics based clustering of globin family members.PloS one · 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
- Similarity in Shape Dictates Signature Intrinsic Dynamics Despite No Functional Conservation in TIM Barrel Enzymes.PLoS computational biology · 2016Article
- Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments.Nucleic acids research · 2015Article
- Comparison of the Internal Dynamics of Metalloproteases Provides New Insights on Their Function and Evolution.PloS one · 2015Article
- WEBnm@ v2.0: Web server and services for comparing protein flexibility.BMC bioinformatics · 2014Article
- Biophysics of protein evolution and evolutionary protein biophysics.Journal of the Royal Society, Interface · 2014Article
- Specialized Dynamical Properties of Promiscuous Residues Revealed by Simulated Conformational Ensembles.Journal of chemical theory and computation · 2013Article
- Mechanical and assembly units of viral capsids identified via quasi-rigid domain decomposition.PLoS computational biology · 2013Article
- Sequence evolution correlates with structural dynamics.Molecular biology and evolution · 2012Article
- Exploring protein dynamics space: the dynasome as the missing link between protein structure and function.PloS one · 2012Article
- Corresponding functional dynamics across the Hsp90 Chaperone family: insights from a multiscale analysis of MD simulations.PLoS computational biology · 2012Article
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4 authors.
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Abstract
Proteins that show similarity in their equilibrium dynamics can be aligned by identifying regions that undergo similar concerted movements. These movements are computed from protein native structures using coarse-grained elastic network models. We show the existence of common large-scale movements in enzymes selected from the main functional and structural classes. Alignment via dynamics does not require prior detection of sequence or structural correspondence. Indeed, a third of the statistically significant dynamics-based alignments involve enzymes that lack substantial global or local structural similarities. The analysis of specific residue-residue correspondences of these structurally dissimilar enzymes in some cases suggests a functional relationship of the detected common dynamic features. Including dynamics-based criteria in protein alignment thus provides a promising avenue for relating and grouping enzymes in terms of dynamic aspects that often, though not always, assist or accompany biological function.
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