ReviewProtein science : a publication of the Protein Society2011
Pre-existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins.
Review in Protein science : a publication of the Protein Society, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed.
- A Minimalist Model for Navigating Conformational Landscape Uncovers the Activation Mechanism of βACS physical chemistry Au · 2026Article
- Adaptive Normal Mode Sampling (aMDeNM) Enhances Exploration of Protein Conformational Space and Reveals the Functional Role of Frequency Coupling.Journal of chemical theory and computation · 2026Article
- Arginine methylation of human DNA topoisomerase I by PRMT5 facilitates DNA relaxation.Nucleic acids research · 2026Article
- Small Molecule Activator of Phosphatase PP2A Remodels Scaffold PR65 Structural Dynamics To Promote Holoenzyme Assembly.JACS Au · 2026Article
- Synergistic Effects of Thymoquinone, 3-Hydrazinoquinoxaline-2-Thiol, and Amphotericin B Against Methicillin-ResistantInternational journal of general medicine · 2026Article
- Small molecule activator of phosphatase PP2A remodels scaffold PR65 structural dynamics to promote holoenzyme assembly.bioRxiv : the preprint server for biology · 2025Article
- A Computationally Efficient Method to Generate Plausible Conformers for Ensemble Docking and Binding Free Energy Calculations.Journal of chemical information and modeling · 2025Article
- Structural and pKa Estimation of the Amphipathic HR1 in SARS-CoV-2: Insights from Constant pH MD, Linear vs. Nonlinear Normal Mode Analysis.International journal of molecular sciences · 2023Article
- Cognate RNA-Binding Modes by the Alternative-Splicing Regulator MBNL1 Inferred from Molecular Dynamics.International journal of molecular sciences · 2022Article
- Review
- Why are large conformational changes well described by harmonic normal modes?Biophysical journal · 2021Article
- Different Single-Enzyme Conformational Dynamics upon Binding Hydrolyzable or Nonhydrolyzable Ligands.The journal of physical chemistry. B · 2021Article
- State-dependent sequential allostery exhibited by chaperonin TRiC/CCT revealed by network analysis of Cryo-EM maps.Progress in biophysics and molecular biology · 2021Article
- Intrinsic dynamics is evolutionarily optimized to enable allosteric behavior.Current opinion in structural biology · 2020Review
- Modulation of Toroidal Proteins Dynamics in Favor of Functional Mechanisms upon Ligand Binding.Biophysical journal · 2020Article
- Long-range correlation in protein dynamics: Confirmation by structural data and normal mode analysis.PLoS computational biology · 2020Article
- Near-field THz micropolarimetry.Optics express · 2019Article
- Shared Signature Dynamics Tempered by Local Fluctuations Enables Fold Adaptability and Specificity.Molecular biology and evolution · 2019Article
- Monoamine transporters: structure, intrinsic dynamics and allosteric regulation.Nature structural & molecular biology · 2019Review
- Allostery in Its Many Disguises: From Theory to Applications.Structure (London, England : 1993) · 2019Review
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4 authors.
Funding
Abstract
Modeling protein flexibility constitutes a major challenge in accurate prediction of protein-ligand and protein-protein interactions in docking simulations. The lack of a reliable method for predicting the conformational changes relevant to substrate binding prevents the productive application of computational docking to proteins that undergo large structural rearrangements. Here, we examine how coarse-grained normal mode analysis has been advantageously applied to modeling protein flexibility associated with ligand binding. First, we highlight recent studies that have shown that there is a close agreement between the large-scale collective motions of proteins predicted by elastic network models and the structural changes experimentally observed upon ligand binding. Then, we discuss studies that have exploited the predicted soft modes in docking simulations. Two general strategies are noted: pregeneration of conformational ensembles that are then utilized as input for standard fixed-backbone docking and protein structure deformation along normal modes concurrent to docking. These studies show that the structural changes apparently "induced" upon ligand binding occur selectively along the soft modes accessible to the protein prior to ligand binding. They further suggest that proteins offer suitable means of accommodating/facilitating the recognition and binding of their ligand, presumably acquired by evolutionary selection of the suitable three-dimensional structure.
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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.