Publication:
Folding dynamics of proteins from denatured to native state: principal component analysis

dc.contributor.coauthorN/A
dc.contributor.departmentDepartment of Computer Engineering
dc.contributor.departmentDepartment of Chemical and Biological Engineering
dc.contributor.kuauthorArkun, Yaman
dc.contributor.kuauthorErman, Burak
dc.contributor.kuauthorGürsoy, Attila
dc.contributor.kuauthorPalazoğlu, Ahmet
dc.contributor.schoolcollegeinstituteCollege of Engineering
dc.date.accessioned2024-11-09T23:00:49Z
dc.date.issued2004
dc.description.abstractSeveral trajectories starting from random configurations and ending in the native state for chymotrypsin inhibitor 2, CI2, are generated using a Go-type model where the backbone torsional angles execute random jumps on which a drift towards their native values is superposed. Bond lengths and bond angles are kept fixed, and the size of the backbone atoms and side groups are recognized. The large datasets obtained are analyzed using a particular type of principal component analysis known as Karhunen - Loeve expansion (KLE). Trajectories are decomposed separately into modes in residue space and time space. General features of different folding trajectories are compared in the modal space and relationships between the structure of CI2 and its folding dynamics are obtained. Dynamic scaling and order reduction of the folding trajectories are discussed. A continuous wavelet transform is used to decompose the nonstationary folding trajectories into windows exhibiting different features of folding dynamics. Analysis of correlations confirms the known two-state nature of folding of CI2. All of the conserved residues of the protein are shown to be stationary in the small modes of the residue space. The sequential nature of folding is shown by examining the slow modes of the trajectories. The present model of protein folding dynamics is compared with the simple Rouse model of polymer dynamics. Principal component analysis is shown to be a very effective tool for the characterization of the general folding features of proteins.
dc.description.indexedbyWOS
dc.description.indexedbyScopus
dc.description.indexedbyPubMed
dc.description.issue6
dc.description.openaccessNO
dc.description.sponsoredbyTubitakEuN/A
dc.description.volume11
dc.identifier.doi10.1089/cmb.2004.11.1149
dc.identifier.eissn1557-8666
dc.identifier.issn1066-5277
dc.identifier.scopus2-s2.0-12844268201
dc.identifier.urihttps://doi.org/10.1089/cmb.2004.11.1149
dc.identifier.urihttps://hdl.handle.net/20.500.14288/8131
dc.identifier.wos226750300009
dc.keywordsFolding trajectories
dc.keywordsGo-type model
dc.keywordsChymotrypsyn inhibitor
dc.keywordsPrincipal component analysis
dc.keywordsKarhunen-loeve expansion
dc.keywordsContinuous wavelet transform
dc.keywordsConserved residues
dc.keywordsRouse model
dc.keywordsSequential folding
dc.keywordsDynamic scaling
dc.keywordsCoarse-grained model of proteins
dc.keywordsChymotrypsin inhibitor-2
dc.keywordsMolecular-dynamics
dc.keywordsFluctuations
dc.keywordsIdentification
dc.keywordsPathways
dc.keywordsModels
dc.language.isoeng
dc.publisherMary Ann Liebert, Inc
dc.relation.ispartofJournal of Computational Biology
dc.subjectBiochemical research methods
dc.subjectBiotechnology
dc.subjectApplied microbiology
dc.subjectComputer science
dc.subjectMathematical and computational biology
dc.subjectStatistics
dc.subjectProbability
dc.titleFolding dynamics of proteins from denatured to native state: principal component analysis
dc.typeJournal Article
dspace.entity.typePublication
local.contributor.kuauthorPalazoğlu, Ahmet
local.contributor.kuauthorGürsoy, Attila
local.contributor.kuauthorArkun, Yaman
local.contributor.kuauthorErman, Burak
local.publication.orgunit1College of Engineering
local.publication.orgunit2Department of Chemical and Biological Engineering
local.publication.orgunit2Department of Computer Engineering
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relation.isOrgUnitOfPublicationc747a256-6e0c-4969-b1bf-3b9f2f674289
relation.isOrgUnitOfPublication.latestForDiscovery89352e43-bf09-4ef4-82f6-6f9d0174ebae
relation.isParentOrgUnitOfPublication8e756b23-2d4a-4ce8-b1b3-62c794a8c164
relation.isParentOrgUnitOfPublication.latestForDiscovery8e756b23-2d4a-4ce8-b1b3-62c794a8c164

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