Close Correspondence between the Motions from Principal Component Analysis of Multiple HIV-1 Protease Structures and Elastic Network Modes

dc.contributor.author Yang, Lei
dc.contributor.author Song, Guang
dc.contributor.author Carriquiry, Alicia
dc.contributor.author Jernigan, Robert
dc.contributor.department Biochemistry, Biophysics and Molecular Biology
dc.contributor.department Computer Science
dc.contributor.department Statistics
dc.contributor.department Bioinformatics and Computational Biology
dc.contributor.department Biochemistry, Biophysics and Molecular Biology, Roy J. Carver Department of
dc.contributor.department Baker Center for Bioinformatics and Biological Statistics
dc.date 2021-03-15T12:26:59.000
dc.date.accessioned 2021-04-29T23:57:46Z
dc.date.available 2021-04-29T23:57:46Z
dc.date.copyright Tue Jan 01 00:00:00 UTC 2008
dc.date.issued 2008-02-12
dc.description.abstract <p>The large number of available HIV-1 protease structures provides a remarkable sampling of conformations of the different conformational states, which can be viewed as direct structural information about its dynamics. After structure matching, we apply principal component analysis (PCA) to obtain the important apparent motions, including bound and unbound structures. There are significant similarities between the first few key motions and the first few low-frequency normal modes calculated from a static representative structure with an elastic network model (ENM), strongly suggesting that the variations among the observed structures and the corresponding conformational changes are facilitated by the low-frequency, global motions intrinsic to the structure. Similarities are also found when the approach is applied to an NMR ensemble, as well as to molecular dynamics (MD) trajectories. Thus, a sufficiently large number of experimental structures can directly provide important information about protein dynamics, but ENM can also provide similar sampling of conformations.</p>
dc.description.comments <p>This is a manuscript of an article published as Yang, Lei, Guang Song, Alicia Carriquiry, and Robert L. Jernigan. "Close correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes." <em>Structure</em> 16, no. 2 (2008): 321-330. doi: <a href="https://doi.org/10.1016/j.str.2007.12.011" target="_blank" title="Persistent link using digital object identifier">10.1016/j.str.2007.12.011</a>. Posted with permission.</p>
dc.format.mimetype application/pdf
dc.identifier archive/lib.dr.iastate.edu/bbmb_ag_pubs/304/
dc.identifier.articleid 1306
dc.identifier.contextkey 22037287
dc.identifier.s3bucket isulib-bepress-aws-west
dc.identifier.submissionpath bbmb_ag_pubs/304
dc.identifier.uri https://dr.lib.iastate.edu/handle/20.500.12876/104634
dc.language.iso en
dc.source.bitstream archive/lib.dr.iastate.edu/bbmb_ag_pubs/304/2008_Jernigan_CloseCorrespondenceManuscript.pdf|||Fri Jan 14 23:28:51 UTC 2022
dc.source.uri 10.1016/j.str.2007.12.011
dc.subject.disciplines Biochemistry, Biophysics, and Structural Biology
dc.subject.disciplines Computer Sciences
dc.subject.disciplines Molecular Biology
dc.subject.disciplines Statistical Models
dc.title Close Correspondence between the Motions from Principal Component Analysis of Multiple HIV-1 Protease Structures and Elastic Network Modes
dc.type article
dc.type.genre article
dspace.entity.type Publication
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