ArticlePLoS computational biology2009
Computation of conformational coupling in allosteric proteins.
Article in PLoS computational biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 63 citations in OpenAlex.
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- Rigid Residue Scan Simulations Systematically Reveal Residue Entropic Roles in Protein Allostery.PLoS computational biology · 2016Article
- DIRECT-ID: An automated method to identify and quantify conformational variations--application to β2 -adrenergic GPCR.Journal of computational chemistry · 2016Article
- Dehydration and Cognition in Geriatrics: A Hydromolecular Hypothesis.Frontiers in molecular biosciences · 2016Article
- AlloPred: prediction of allosteric pockets on proteins using normal mode perturbation analysis.BMC bioinformatics · 2015Article
- Using kernelized partial canonical correlation analysis to study directly coupled side chains and allostery in small G proteins.Bioinformatics (Oxford, England) · 2015Article
- Local packing modulates diversity of iron pathways and cooperative behavior in eukaryotic and prokaryotic ferritins.The Journal of chemical physics · 2014Article
- An allosteric signaling pathway of human 3-phosphoglycerate kinase from force distribution analysis.PLoS computational biology · 2014Article
- The designability of protein switches by chemical rescue of structure: mechanisms of inactivation and reactivation.Journal of the American Chemical Society · 2013Article
- Automated identification of functional dynamic contact networks from X-ray crystallography.Nature methods · 2013Article
- SPACER: Server for predicting allosteric communication and effects of regulation.Nucleic acids research · 2013Article
- Ensemble-based characterization of unbound and bound states on protein energy landscape.Protein science : a publication of the Protein Society · 2013Article
- Rational design of a ligand-controlled protein conformational switch.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Impact of mutations on the allosteric conformational equilibrium.Journal of molecular biology · 2013Article
- Force distribution reveals signal transduction in E. coli Hsp90.Biophysical journal · 2012Article
- Exploiting protein flexibility to predict the location of allosteric sites.BMC bioinformatics · 2012Article
- Designing allosteric control into enzymes by chemical rescue of structure.Journal of the American Chemical Society · 2012Article
- Structure-based model of allostery predicts coupling between distant sites.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
In allosteric regulation, an effector molecule binding a protein at one site induces conformational changes, which alter structure and function at a distant active site. Two key challenges in the computational modeling of allostery are the prediction of the structure of one allosteric state starting from the structure of the other, and elucidating the mechanisms underlying the conformational coupling of the effector and active sites. Here we approach these two challenges using the Rosetta high-resolution structure prediction methodology. We find that the method can recapitulate the relaxation of effector-bound forms of single domain allosteric proteins into the corresponding ligand-free states, particularly when sampling is focused on regions known to change conformation most significantly. Analysis of the coupling between contacting pairs of residues in large ensembles of conformations spread throughout the landscape between and around the two allosteric states suggests that the transitions are built up from blocks of tightly coupled interacting sets of residues that are more loosely coupled to one another.
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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.