ArticleProceedings of the National Academy of Sciences of the United States of America2007
Functional residues serve a dominant role in mediating the cooperativity of the protein ensemble.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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42 citing papers in PubMed, 67 citations in OpenAlex.
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- Ancient thioredoxins evolved to modern-day stability-function requirement by altering native state ensemble.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2018Article
- Sequence-based prediction of physicochemical interactions at protein functional sites using a function-and-interaction-annotated domain profile database.BMC bioinformatics · 2018Article
- Site-to-site interdomain communication may mediate different loss-of-function mechanisms in a cancer-associated NQO1 polymorphism.Scientific reports · 2017Article
- Steric trapping reveals a cooperativity network in the intramembrane protease GlpG.Nature chemical biology · 2016Article
- Energetic Coupling between Ligand Binding and Dimerization in Escherichia coli Phosphoglycerate Mutase.Biochemistry · 2016Article
- Mutation near the binding interfaces at α-hemoglobin stabilizing protein is highly pathogenic.American journal of translational research · 2016Article
- When the Scaffold Cannot Be Ignored: The Role of the Hydrophobic Core in Ligand Binding and Specificity.Journal of molecular biology · 2015Article
- Dynamic Transmission of Protein Allostery without Structural Change: Spatial Pathways or Global Modes?Biophysical journal · 2015Article
- Thermodynamic mechanism for the evasion of antibody neutralization in flaviviruses.Journal of the American Chemical Society · 2014Article
- Using the COREX/BEST server to model the native-state ensemble.Methods in molecular biology (Clifton, N.J.) · 2014Article
- Modulation of global low-frequency motions underlies allosteric regulation: demonstration in CRP/FNR family transcription factors.PLoS biology · 2013Article
- Conformational heterogeneity within the LID domain mediates substrate binding to Escherichia coli adenylate kinase: function follows fluctuations.Topics in current chemistry · 2013Review
- Perturbation centrality and turbine: a novel centrality measure obtained using a versatile network dynamics tool.PloS one · 2013Article
- Nodes having a major influence to break cooperation define a novel centrality measure: game centrality.PloS one · 2013Article
- A host-guest relationship in bone morphogenetic protein receptor-II defines specificity in ligand-receptor recognition.Biochemistry · 2012Article
- Quantitative assessment of protein structural models by comparison of H/D exchange MS data with exchange behavior accurately predicted by DXCOREX.Journal of the American Society for Mass Spectrometry · 2012Article
- HotRegion: a database of predicted hot spot clusters.Nucleic acids research · 2012Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Conformational fluctuations in proteins have emerged as a potentially important aspect of biological function, although the precise relationship and the implications have yet to be fully explored. Numerous studies have reported that the binding of ligand can influence fluctuations. However, the role of the binding site in mediating these fluctuations is not known. Of particular interest is whether in addition to serving as structural scaffolds for recognition and catalysis, active-site residues may also play a role in modulating the cooperative network. To address this question, we employ an experimentally validated ensemble-based description of proteins to elucidate the extent to which perturbations at different sites can influence the cooperative network in the protein. Applying this method to a database of test proteins, it is found statistically that binding sites are located in regions most able to affect the cooperative network, even for cooperative interactions between residues distant to the binding sites. This indicates that the conformational manifold under native conditions is determined by the network of cooperative interactions within the protein and suggests that proteins have evolved to use these conformational fluctuations in carrying out their functions. Furthermore, because the energetic coupling pattern calculated for each protein is robust and relatively insensitive to sequence, these studies further suggest that binding sites evolved in regions of the protein that are inherently poised to take advantage of the fluctuations in the native structure.
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