ArticleJournal of chemical theory and computation2009
Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles.
Article in Journal of chemical theory and computation, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 115 papers.
What it found
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The trial behind it
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Who cites it
115 citing papers in PubMed.
- Computational Identification of IL-17 a Small-Molecule Inhibitors as Potential Therapeutics for Plaque Psoriasis Through e-Pharmacophore Screening, Molecular Docking, and Molecular Dynamics Simulation.The protein journal · 2026Article
- Uncovering hidden druggable sites: computational approaches to allosteric and cryptic pocket discovery-from molecular dynamics to AI.Journal of computer-aided molecular design · 2026Review
- pH-Driven βACS omega · 2026Article
- MDPath: Unraveling Allosteric Communication Paths of Drug Targets through Molecular Dynamics Simulations.Journal of chemical information and modeling · 2025Article
- SARS-CoV-2 Mpro Dihedral Angles Reveal Allosteric Signaling.Proteins · 2025Article
- Mapping allosteric rewiring in related protein structures from collections of crystallographic multiconformer models.bioRxiv : the preprint server for biology · 2025Article
- Deep learning-guided design of dynamic proteins.Science (New York, N.Y.) · 2025Article
- Regulating IL-2 Immune Signaling Function Via A Core Allosteric Structural Network.Journal of molecular biology · 2025Article
- A hydrophobic funnel governs monovalent cation selectivity in the ion channel TRPM5.Biophysical journal · 2024Article
- SARS-CoV-2 3CLPro Dihedral Angles Reveal Allosteric Signaling.bioRxiv : the preprint server for biology · 2024Article
- Titratable residues that drive RND efflux: Insights from molecular simulations.QRB discovery · 2024Review
- Kinetic and thermodynamic allostery in the Ras protein family.Biophysical journal · 2023Article
- Combining structural and coevolution information to unveil allosteric sites.Chemical science · 2023Article
- Computational design of dynamic receptor-peptide signaling complexes applied to chemotaxis.Nature communications · 2023Article
- A cooperative knock-on mechanism underpins Ca2+-selective cation permeation in TRPV channels.The Journal of general physiology · 2023Article
- The "violin model": Looking at community networks for dynamic allostery.The Journal of chemical physics · 2023Review
- Conformational and Thermodynamic Differences Underlying Wild-Type and Mutant Eleven-Nineteen-Leukemia YEATS Domain Specificity for Epigenetic Marks.Journal of chemical information and modeling · 2023Article
- Temperature as a modulator of allosteric motions and crosstalk in mesophilic and thermophilic enzymes.Frontiers in molecular biosciences · 2023Review
- Allosteric Modulators of Dopamine DMolecules (Basel, Switzerland) · 2022Review
- Calculation of centralities in protein kinase A.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
55 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Allostery describes altered protein function at one site due to a perturbation at another site. One mechanism of allostery involves correlated motions, which can occur even in the absence of substantial conformational change. We present a novel method, "MutInf", to identify statistically significant correlated motions from equilibrium molecular dynamics simulations. Our approach analyzes both backbone and sidechain motions using internal coordinates to account for the gear-like twists that can take place even in the absence of the large conformational changes typical of traditional allosteric proteins. We quantify correlated motions using a mutual information metric, which we extend to incorporate data from multiple short simulations and to filter out correlations that are not statistically significant. Applying our approach to uncover mechanisms of cooperative small molecule binding in human interleukin-2, we identify clusters of correlated residues from 50 ns of molecular dynamics simulations. Interestingly, two of the clusters with the strongest correlations highlight known cooperative small-molecule binding sites and show substantial correlations between these sites. These cooperative binding sites on interleukin-2 are correlated not only through the hydrophobic core of the protein but also through a dynamic polar network of hydrogen bonding and electrostatic interactions. Since this approach identifies correlated conformations in an unbiased, statistically robust manner, it should be a useful tool for finding novel or "orphan" allosteric sites in proteins of biological and therapeutic importance.
Identifiers
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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.