ArticleBiophysical journal2010
Manipulation of conformational change in proteins by single-residue perturbations.
Article in Biophysical journal, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed, 160 citations in OpenAlex.
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- Multiply Perturbed Response: A Computational Protocol to Identify Cooperative Allosteric Residue Combinations Driving Protein Conformational Transitions.Bio-protocol · 2026Article
- Topological metrics as evolutionary and dynamical descriptors of conformational landscapes within protein families.PLoS computational biology · 2026Article
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- Statistical Physics-Based Approaches to Model the Function and Complexation of Disordered Proteins.The journal of physical chemistry. B · 2025Article
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- Using deep learning and molecular dynamics simulations to unravel the regulation mechanism of peptides as noncompetitive inhibitor of xanthine oxidase.Scientific reports · 2024Article
- Engineering gain-of-function mutants of a WW domain by dynamics and structural analysis.Protein science : a publication of the Protein Society · 2023Article
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- Probing conformational landscapes of binding and allostery in the SARS-CoV-2 omicron variant complexes using microsecond atomistic simulations and perturbation-based profiling approaches: hidden role of omicron mutations as modulators of allosteric signaling and epistatic relationships.Physical chemistry chemical physics : PCCP · 2023Article
- Structural Dynamics Predominantly Determine the Adaptability of Proteins to Amino Acid Deletions.International journal of molecular sciences · 2023Article
- Exploring and Learning the Universe of Protein Allostery Using Artificial Intelligence Augmented Biophysical and Computational Approaches.Journal of chemical information and modeling · 2023Review
- The "violin model": Looking at community networks for dynamic allostery.The Journal of chemical physics · 2023Review
- Wordom update 2: A user-friendly program for the analysis of molecular structures and conformational ensembles.Computational and structural biotechnology journal · 2023Article
- Design of novel cyanovirin-N variants by modulation of binding dynamics through distal mutations.eLife · 2022Article
- Biophysical Insight into the SARS-CoV2 Spike-ACE2 Interaction and Its Modulation by Hepcidin through a Multifaceted Computational Approach.ACS omega · 2022Article
- Elastic network modeling of cellular networks unveils sensor and effector genes that control information flow.PLoS computational biology · 2022Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Using the perturbation-response scanning (PRS) technique, we study a set of 25 proteins that display a variety of conformational motions upon ligand binding (e.g., shear, hinge, allosteric). In most cases, PRS determines single residues that may be manipulated to achieve the resulting conformational change. PRS reveals that for some proteins, binding-induced conformational change may be achieved through the perturbation of residues scattered throughout the protein, whereas in others, perturbation of specific residues confined to a highly specific region is necessary. Overlaps between the experimental and PRS-calculated atomic displacement vectors are usually more descriptive of the conformational change than those obtained from a modal analysis of elastic network models. Furthermore, the largest overlaps obtained by the latter approach do not always appear in the most collective modes; there are cases where more than one mode yields comparable overlap sizes. We show that success of the modal analysis depends on an absence of redundant paths in the protein. PRS thus demonstrates that several relevant modes can be induced simultaneously by perturbing a single select residue on the protein. We also illustrate the biological relevance of applying PRS to the GroEL, adenylate kinase, myosin, and kinesin structures in detail by showing that the residues whose perturbation leads to precise conformational changes usually correspond to those experimentally determined to be functionally important.
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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.