Biochemistry, Biophysics and Molecular Biology, Roy J. Carver Department of, Computer Science, Statistics, Bioinformatics and Computational Biology, Baker Center for Bioinformatics and Biological Statistics
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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.
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Yang, Lei; Song, Guang; Carriquiry, Alicia L.; and Jernigan, Robert L., "Close Correspondence between the Motions from Principal Component Analysis of Multiple HIV-1 Protease Structures and Elastic Network Modes" (2008). Biochemistry, Biophysics and Molecular Biology Publications. 304.