ArticleProceedings of the National Academy of Sciences of the United States of America2016
Strain analysis of protein structures and low dimensionality of mechanical allosteric couplings.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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35 citing papers in PubMed.
- Time-Dependent Voronoi Analysis of Amino Acid Side-Chain Packing in Simulations.Journal of computational chemistry · 2026Article
- Directional information flow as a tool for analyzing protein allostery.bioRxiv : the preprint server for biology · 2026Article
- Simple biological controllers drive the evolution of soft modes.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Framework for Quantifying the Efficiency of Competing Signal Transmission Modes in Proteins.Journal of the American Chemical Society · 2026Article
- Global comparative structural analysis of responses to protein phosphorylation.Nature communications · 2025Article
- Elastic analysis bridges structure and dynamics of an AAA+ molecular motor.PLoS computational biology · 2025Article
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- Soft Modes as a Predictive Framework for Low-Dimensional Biological Systems Across Scales.Annual review of biophysics · 2025Review
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- Soft Modes as a Predictive Framework for Low Dimensional Biological Systems across Scales.ArXiv · 2024Article
- Mapping Protein Conformational Landscapes from Crystallographic Drug Fragment Screens.Journal of chemical information and modeling · 2024Article
- Exploring the unfolding pathways of protein families using Elastic Network Model.Scientific reports · 2024Article
- Mapping protein conformational landscapes from crystallographic drug fragment screens.bioRxiv : the preprint server for biology · 2024Article
- Perturbative diffraction methods resolve a conformational switch that facilitates a two-step enzymatic mechanism.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Molecular analysis of the type III interferon complex and its applications in protein engineering.Biophysical journal · 2023Article
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- Solvent accessibility of E1α and E1β residues with known missense mutations causing pyruvate dehydrogenase complex (PDC) deficiency: Impact on PDC-E1 structure and function.Journal of inherited metabolic disease · 2022Article
- Strain and rupture of HIV-1 capsids during uncoating.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Toward wide-spectrum antivirals against coronaviruses: Molecular characterization of SARS-CoV-2 NSP13 helicase inhibitors.Science advances · 2022Article
- Periodic training of creeping solids.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
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3 authors.
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Abstract
In many proteins, especially allosteric proteins that communicate regulatory states from allosteric to active sites, structural deformations are functionally important. To understand these deformations, dynamical experiments are ideal but challenging. Using static structural information, although more limited than dynamical analysis, is much more accessible. Underused for protein analysis, strain is the natural quantity for studying local deformations. We calculate strain tensor fields for proteins deformed by ligands or thermal fluctuations using crystal and NMR structure ensembles. Strains-primarily shears-show deformations around binding sites. These deformations can be induced solely by ligand binding at distant allosteric sites. Shears reveal quasi-2D paths of mechanical coupling between allosteric and active sites that may constitute a widespread mechanism of allostery. We argue that strain-particularly shear-is the most appropriate quantity for analysis of local protein deformations. This analysis can reveal mechanical and biological properties of many proteins.
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