ArticlePLoS computational biology2016
Rigid Residue Scan Simulations Systematically Reveal Residue Entropic Roles in Protein Allostery.
Article in PLoS computational biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Directional information flow as a tool for analyzing protein allostery.bioRxiv : the preprint server for biology · 2026Article
- Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development.ACS omega · 2024Review
- Anti-HIV Potential of Beesioside I Derivatives as Maturation Inhibitors: Synthesis, 3D-QSAR, Molecular Docking and Molecular Dynamics Simulations.International journal of molecular sciences · 2023Article
- Investigating the allosteric response of the PICK1 PDZ domain to different ligands with all-atom simulations.Protein science : a publication of the Protein Society · 2022Article
- Sparse group selection and analysis of function-related residue for protein-state recognition.Journal of computational chemistry · 2022Article
- Allosterism in the PDZ Family.International journal of molecular sciences · 2022Review
- SenseNet, a tool for analysis of protein structure networks obtained from molecular dynamics simulations.PloS one · 2022Article
- Computational study on the allosteric mechanism ofComputational and structural biotechnology journal · 2021Article
- Allosteric Regulation at the Crossroads of New Technologies: Multiscale Modeling, Networks, and Machine Learning.Frontiers in molecular biosciences · 2020Review
- Gibbs Free Energy Calculation of Mutation in PncA and RpsA Associated With Pyrazinamide Resistance.Frontiers in molecular biosciences · 2020Article
- Directed kinetic transition network model.The Journal of chemical physics · 2019Article
- Why Proteins are Big: Length Scale Effects on Equilibria and Kinetics.The protein journal · 2019Review
- Allosteric mechanism of the circadian protein Vivid resolved through Markov state model and machine learning analysis.PLoS computational biology · 2019Article
- REDAN: Relative Entropy-Based Dynamical Allosteric Network Model.Molecular physics · 2019Article
- Seeking allosteric networks in PDZ domains.Protein engineering, design & selection : PEDS · 2018Review
- Decomposing Dynamical Couplings in Mutated scFv Antibody Fragments into Stabilizing and Destabilizing Effects.Journal of the American Chemical Society · 2017Article
- Energetic redistribution in allostery to execute protein function.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Optimal allosteric stabilization sites using contact stabilization analysis.Journal of computational chemistry · 2017Article
- Revealing Hidden Conformational Space of LOV Protein VIVID Through Rigid Residue Scan Simulations.Scientific reports · 2017Article
- Migration of small ligands in globins: Xe diffusion in truncated hemoglobin N.PLoS computational biology · 2017Article
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4 authors.
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Abstract
Intra-protein information is transmitted over distances via allosteric processes. This ubiquitous protein process allows for protein function changes due to ligand binding events. Understanding protein allostery is essential to understanding protein functions. In this study, allostery in the second PDZ domain (PDZ2) in the human PTP1E protein is examined as model system to advance a recently developed rigid residue scan method combining with configurational entropy calculation and principal component analysis. The contributions from individual residues to whole-protein dynamics and allostery were systematically assessed via rigid body simulations of both unbound and ligand-bound states of the protein. The entropic contributions of individual residues to whole-protein dynamics were evaluated based on covariance-based correlation analysis of all simulations. The changes of overall protein entropy when individual residues being held rigid support that the rigidity/flexibility equilibrium in protein structure is governed by the La Châtelier's principle of chemical equilibrium. Key residues of PDZ2 allostery were identified with good agreement with NMR studies of the same protein bound to the same peptide. On the other hand, the change of entropic contribution from each residue upon perturbation revealed intrinsic differences among all the residues. The quasi-harmonic and principal component analyses of simulations without rigid residue perturbation showed a coherent allosteric mode from unbound and bound states, respectively. The projection of simulations with rigid residue perturbation onto coherent allosteric modes demonstrated the intrinsic shifting of ensemble distributions supporting the population-shift theory of protein allostery. Overall, the study presented here provides a robust and systematic approach to estimate the contribution of individual residue internal motion to overall protein dynamics and allostery.
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