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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