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dc.contributor.authorFokas, Alexander S
dc.contributor.authorCole, Daniel J
dc.contributor.authorAhnert, Sebastian
dc.contributor.authorChin, Alex
dc.date.accessioned2016-09-30T11:21:54Z
dc.date.available2016-09-30T11:21:54Z
dc.date.issued2016-09-14
dc.identifier.issn2045-2322
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/260599
dc.description.abstractAmino acid networks (AANs) abstract the protein structure by recording the amino acid contacts and can provide insight into protein function. Herein, we describe a novel AAN construction technique that employs the rigidity analysis tool, FIRST, to build the AAN, which we refer to as the residue geometry network (RGN). We show that this new construction can be combined with network theory methods to include the effects of allowed conformal motions and local chemical environments. Importantly, this is done without costly molecular dynamics simulations required by other AAN-related methods, which allows us to analyse large proteins and/or data sets. We have calculated the centrality of the residues belonging to 795 proteins. The results display a strong, negative correlation between residue centrality and the evolutionary rate. Furthermore, among residues with high closeness, those with low degree were particularly strongly conserved. Random walk simulations using the RGN were also successful in identifying allosteric residues in proteins involved in GPCR signalling. The dynamic function of these residues largely remain hidden in the traditional distance-cutoff construction technique. Despite being constructed from only the crystal structure, the results in this paper suggests that the RGN can identify residues that fulfil a dynamical function.
dc.description.sponsorshipA.S.F. is supported by a Doctoral Research Award from Microsoft Research. S.E.A. is supported by The Royal Society (UK). D.J.C. is supported by a Marie Curie International Outgoing Fellowship within the 7th European Community Framework Programme. A.W.C. is supported by the Winton Programme for the Physics of Sustainability.
dc.languageEnglish
dc.language.isoen
dc.publisherSpringer Science and Business Media LLC
dc.rightsAttribution 4.0 International
dc.rightsAttribution 4.0 International
dc.rightsAttribution 4.0 International
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.titleResidue Geometry Networks: A Rigidity-Based Approach to the Amino Acid Network and Evolutionary Rate Analysis.
dc.typeArticle
dc.description.versionThis is the final version of the article. It first appeared from Nature Publishing Group at http://dx.doi.org/10.1038/srep33213.
prism.number33213
prism.publicationDate2016
prism.publicationNameSci Rep
prism.volume6
dc.identifier.doi10.17863/CAM.4833
dcterms.dateAccepted2016-08-12
rioxxterms.versionofrecord10.1038/srep33213
rioxxterms.versionVoR
rioxxterms.licenseref.urihttp://creativecommons.org/licenses/by/4.0/
rioxxterms.licenseref.startdate2016-09-14
dc.identifier.eissn2045-2322
rioxxterms.typeJournal Article/Review
cam.issuedOnline2016-09-14


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Attribution 4.0 International
Except where otherwise noted, this item's licence is described as Attribution 4.0 International