DC Field | Value | Language |
---|---|---|
dc.contributor.author | Park, Keun-Wan | ko |
dc.contributor.author | Kim, Dong-Sup | ko |
dc.date.accessioned | 2013-03-13T04:24:49Z | - |
dc.date.available | 2013-03-13T04:24:49Z | - |
dc.date.created | 2012-12-26 | - |
dc.date.created | 2012-12-26 | - |
dc.date.issued | 2012-12 | - |
dc.identifier.citation | BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, v.1824, no.12, pp.1484 - 1489 | - |
dc.identifier.issn | 1570-9639 | - |
dc.identifier.uri | http://hdl.handle.net/10203/104457 | - |
dc.description.abstract | Correlated mutation analysis (CMA) has been used to investigate protein functional sites. However, CMA has suffered from low signal-to-noise ratio caused by meaningless phylogenetic signals or structural constraints. We present a new method, Structure-based Correlated Mutation Analysis (SCMA), which encodes coevolution scores into a protein structure network. A path-based network model is adapted to describe information transfer between residues, and the statistical significance is estimated by network shuffling. This model intrinsically assumes that residues in physical contact have a more reliable coevolution score than distant residues, and that coevolution in distant residues likely arises from a series of contacting and coevolving residues. In addition, coevolutionary coupling is statistically controlled to remove the structural effects. When applied to the rhodopsin structure, the SCMA method identified a much higher percentage of functional residues than the typical coevolution score (61% vs. 22%). In addition, statistically significant residues are used to construct the coevolved residue-residue subnetwork. The network has one highly connected node (retinal bound Lys296). indicating that Lys296 can induce and regulate most other coevolved residues in a variety of locations. The coevolved network consists of a few modular clusters which have distinct functional roles. This article is part of a Special Issue entitled: Computational Methods for Protein Interaction and Structural Prediction. (C) 2012 Elsevier B.V. All rights reserved. | - |
dc.language | English | - |
dc.publisher | ELSEVIER SCIENCE BV | - |
dc.subject | DOMINANT RETINITIS-PIGMENTOSA | - |
dc.subject | PROTEIN-COUPLED-RECEPTORS | - |
dc.subject | CONSTITUTIVELY ACTIVE MUTANTS | - |
dc.subject | TRANSDUCIN ACTIVATION | - |
dc.subject | CORRELATED MUTATIONS | - |
dc.subject | IMPORTANT RESIDUES | - |
dc.subject | AMINO-ACIDS | - |
dc.subject | OPSIN | - |
dc.subject | SEQUENCE | - |
dc.subject | CONSERVATION | - |
dc.title | Structure-based rebuilding of coevolutionary information reveals functional modules in rhodopsin structure | - |
dc.type | Article | - |
dc.identifier.wosid | 000310761700022 | - |
dc.identifier.scopusid | 2-s2.0-84867666852 | - |
dc.type.rims | ART | - |
dc.citation.volume | 1824 | - |
dc.citation.issue | 12 | - |
dc.citation.beginningpage | 1484 | - |
dc.citation.endingpage | 1489 | - |
dc.citation.publicationname | BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS | - |
dc.identifier.doi | 10.1016/j.bbapap.2012.05.015 | - |
dc.embargo.liftdate | 9999-12-31 | - |
dc.embargo.terms | 9999-12-31 | - |
dc.contributor.localauthor | Kim, Dong-Sup | - |
dc.type.journalArticle | Article | - |
dc.subject.keywordAuthor | Correlated mutation analysis | - |
dc.subject.keywordAuthor | Coevolution | - |
dc.subject.keywordAuthor | Conservation | - |
dc.subject.keywordAuthor | Rhodopsin | - |
dc.subject.keywordAuthor | Functional site | - |
dc.subject.keywordAuthor | Functional module | - |
dc.subject.keywordPlus | DOMINANT RETINITIS-PIGMENTOSA | - |
dc.subject.keywordPlus | PROTEIN-COUPLED-RECEPTORS | - |
dc.subject.keywordPlus | CONSTITUTIVELY ACTIVE MUTANTS | - |
dc.subject.keywordPlus | TRANSDUCIN ACTIVATION | - |
dc.subject.keywordPlus | CORRELATED MUTATIONS | - |
dc.subject.keywordPlus | IMPORTANT RESIDUES | - |
dc.subject.keywordPlus | AMINO-ACIDS | - |
dc.subject.keywordPlus | OPSIN | - |
dc.subject.keywordPlus | SEQUENCE | - |
dc.subject.keywordPlus | CONSERVATION | - |
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