ReviewBiophysical journal2015
Structure-Encoded Global Motions and Their Role in Mediating Protein-Substrate Interactions.
Review in Biophysical journal, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Topological metrics as evolutionary and dynamical descriptors of conformational landscapes within protein families.PLoS computational biology · 2026Article
- Comparative Dynamics Enables Discovery of Embedded Bacterial Ferredoxin Domains in Large Redox Enzymes.Proteins · 2025Article
- A Computationally Efficient Method to Generate Plausible Conformers for Ensemble Docking and Binding Free Energy Calculations.Journal of chemical information and modeling · 2025Article
- Computational elucidation ofIn silico pharmacology · 2025Article
- Exploration of Cryptic Pockets Using Enhanced Sampling Along Normal Modes: A Case Study of KRASJournal of chemical information and modeling · 2024Article
- Allosteric modulation of serotonin and dopamine transporters: New insights from computations and experiments.Current research in physiology · 2024Article
- Glycosylation and Crowded Membrane Effects on Influenza Neuraminidase Stability and Dynamics.The journal of physical chemistry letters · 2023Article
- Molecular Dynamics Mappings of the CCT/TRiC Complex-Mediated Protein Folding Cycle Using Diffracted X-ray Tracking.International journal of molecular sciences · 2023Article
- Scipion-EM-ProDy: A Graphical Interface for the ProDy Python Package within the Scipion Workflow Engine Enabling Integration of Databases, Simulations and Cryo-Electron Microscopy Image Processing.International journal of molecular sciences · 2023Article
- Statistical learning of protein elastic network from positional covariance matrix.Computational and structural biotechnology journal · 2023Article
- Article
- Structural deformability induced in proteins of potential interest associated with COVID-19 by binding of homologues present in ivermectin: Comparative study based in elastic networks models.Journal of molecular liquids · 2021Article
- Structural insight into host plasma membrane association and assembly of HIV-1 matrix protein.Scientific reports · 2021Article
- Free Energy Analysis of a Conformational Change of Heme ABC Transporter BhuUV-T.The journal of physical chemistry letters · 2020Article
- Characterizing and Predicting Protein Hinges for Mechanistic Insight.Journal of molecular biology · 2020Article
- Dynamics-function relationship in the catalytic domains of N-terminal acetyltransferases.Computational and structural biotechnology journal · 2020Article
- Both intra and inter-domain interactions define the intrinsic dynamics and allosteric mechanism in DNMT1s.Computational and structural biotechnology journal · 2020Article
- Activation and desensitization of ionotropic glutamate receptors by selectively triggering pre-existing motions.Neuroscience letters · 2019Review
- Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy.Acta crystallographica. Section F, Structural biology communications · 2019Review
- Coarse-Grained Protein Dynamics Studies Using Elastic Network Models.International journal of molecular sciences · 2018Review
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Recent structure-based computational studies suggest that, in contrast to the classical description of equilibrium fluctuations as wigglings and jigglings, proteins have access to well-defined spectra of collective motions, called intrinsic dynamics, encoded by their structure under native state conditions. In particular, the global modes of motions (at the low frequency end of the spectrum) are shown by multiple studies to be highly robust to minor differences in the structure or to detailed interactions at the atomic level. These modes, encoded by the overall fold, usually define the mechanisms of interactions with substrates. They can be estimated by low-resolution models such as the elastic network models (ENMs) exclusively based on interresidue contact topology. The ability of ENMs to efficiently assess the global motions intrinsically favored by the overall fold as well as the relevance of these predictions to the dominant changes in structure experimentally observed for a given protein in the presence of different substrates suggest that the intrinsic dynamics plays a role in mediating protein-substrate interactions. These observations underscore the functional significance of structure-encoded dynamics, or the importance of the predisposition to favor functional global modes in the evolutionary selection of structures.
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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.