ArticleBMC structural biology2009
Large-scale evaluation of dynamically important residues in proteins predicted by the perturbation analysis of a coarse-grained elastic model.
Article in BMC structural biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed.
- Article
- Modeling and Simulation of the NMDA Receptor at Coarse-Grained and Atomistic Levels.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Insight into the Nucleotide Based Modulation of the Grp94 Molecular Chaperone Using Multiscale Dynamics.The journal of physical chemistry. B · 2023Article
- Article
- Integrated Computational Approaches and Tools forAllosteric Drug Discovery.International journal of molecular sciences · 2020Review
- Dynamics-function relationship in the catalytic domains of N-terminal acetyltransferases.Computational and structural biotechnology journal · 2020Article
- Investigating the structural dynamics of the PIEZO1 channel activation and inactivation by coarse-grained modeling.Proteins · 2017Article
- Probing the Structural Dynamics of the NMDA Receptor Activation by Coarse-Grained Modeling.Biophysical journal · 2017Article
- Directional Force Originating from ATP Hydrolysis Drives the GroEL Conformational Change.Biophysical journal · 2017Article
- Evaluating the effect of mutations and ligand binding on transthyretin homotetramer dynamics.PloS one · 2017Article
- Evolutionary Conserved Positions Define Protein Conformational Diversity.PLoS computational biology · 2016Article
- Biophysical and computational methods to analyze amino acid interaction networks in proteins.Computational and structural biotechnology journal · 2016Review
- The Intrinsic Dynamics and Unfolding Process of an Antibody Fab Fragment Revealed by Elastic Network Model.International journal of molecular sciences · 2015Article
- Cutoff lensing: predicting catalytic sites in enzymes.Scientific reports · 2015Article
- Conformational Motions and Functionally Key Residues for Vitamin B12 Transporter BtuCD-BtuF Revealed by Elastic Network Model with a Function-Related Internal Coordinate.International journal of molecular sciences · 2015Article
- Study, by use of coarse-grained models, of the functionally crucial residues and allosteric pathway of anesthetic regulation of the Gloeobacter violaceus ligand-gated ion channel.European biophysics journal : EBJ · 2014Article
- Structure-based simulations of the translocation mechanism of the hepatitis C virus NS3 helicase along single-stranded nucleic acid.Biophysical journal · 2012Article
- Probing molecular mechanisms of the Hsp90 chaperone: biophysical modeling identifies key regulators of functional dynamics.PloS one · 2012Article
- Computational modeling of allosteric communication reveals organizing principles of mutation-induced signaling in ABL and EGFR kinases.PLoS computational biology · 2011Article
- Dynamical basis for drug resistance of HIV-1 protease.BMC structural biology · 2011Article
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2 authors.
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Abstract
backgroundIt is increasingly recognized that protein functions often require intricate conformational dynamics, which involves a network of key amino acid residues that couple spatially separated functional sites. Tremendous efforts have been made to identify these key residues by experimental and computational means.
resultsWe have performed a large-scale evaluation of the predictions of dynamically important residues by a variety of computational protocols including three based on the perturbation and correlation analysis of a coarse-grained elastic model. This study is performed for two lists of test cases with >500 pairs of protein structures. The dynamically important residues predicted by the perturbation and correlation analysis are found to be strongly or moderately conserved in >67% of test cases. They form a sparse network of residues which are clustered both in 3D space and along protein sequence. Their overall conservation is attributed to their dynamic role rather than ligand binding or high network connectivity.
conclusionBy modeling how the protein structural fluctuations respond to residue-position-specific perturbations, our highly efficient perturbation and correlation analysis can be used to dissect the functional conformational changes in various proteins with a residue level of detail. The predictions of dynamically important residues serve as promising targets for mutational and functional studies.
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