ArticleMethods in molecular biology (Clifton, N.J.)2012
Ensemble properties of network rigidity reveal allosteric mechanisms.
Article in Methods in molecular biology (Clifton, N.J.), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Probing Conformational Dynamics of Antibodies with Geometric Simulations.Methods in molecular biology (Clifton, N.J.) · 2023Article
- A Coarse-Grained Methodology Identifies Intrinsic Mechanisms That Dissociate Interacting Protein Pairs.Frontiers in molecular biosciences · 2020Article
- Chokepoints in Mechanical Coupling Associated with Allosteric Proteins: The Pyruvate Kinase Example.Biophysical journal · 2019Article
- Computational Tools for Allosteric Drug Discovery: Site Identification and Focus Library Design.Methods in molecular biology (Clifton, N.J.) · 2017Article
- Mutations in Antibody Fragments Modulate Allosteric Response Via Hydrogen-Bond Network Fluctuations.Biophysical journal · 2016Article
- Rigid Residue Scan Simulations Systematically Reveal Residue Entropic Roles in Protein Allostery.PLoS computational biology · 2016Article
- Rigidity Emerges during Antibody Evolution in Three Distinct Antibody Systems: Evidence from QSFR Analysis of Fab Fragments.PLoS computational biology · 2015Article
- Article
- Flexibility Correlation between Active Site Regions Is Conserved across Four AmpC β-Lactamase Enzymes.PloS one · 2015Article
- Thermodynamic stability and flexibility characteristics of antibody fragment complexes.Protein and peptide letters · 2014Article
- Redistribution of flexibility in stabilizing antibody fragment mutants follows Le Châtelier's principle.PloS one · 2014Article
- A case study comparing quantitative stability-flexibility relationships across five metallo-β-lactamases highlighting differences within NDM-1.Methods in molecular biology (Clifton, N.J.) · 2014Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
The distance constraint model (DCM) is a unique computational modeling paradigm that integrates mechanical and thermodynamic descriptions of macromolecular structure. That is, network rigidity calculations are used to account for nonadditivity within entropy components, thus restoring the utility of free-energy decomposition. The DCM outputs a large number of structural characterizations that collectively allow for quantified stability-flexibility relationships (QSFR) to be identified. In this review, we describe the theoretical underpinnings of the DCM and introduce several common QSFR metrics. Application of the DCM across protein families highlights the sensitivity within the set of protein structure residue-to-residue couplings. Further, we have developed a perturbation method to identify putative allosteric sites, where large changes in QSFR upon rigidification (mimicking ligand-binding) detect sites likely to invoke allosteric changes.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.