Send to

Choose Destination
See comment in PubMed Commons below
Structure. 2008 Feb;16(2):321-30. doi: 10.1016/j.str.2007.12.011.

Close correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes.

Author information

  • 1Program of Bioinformatics and Computational Biology, Department of Biochemistry, Biophysics, and Molecular Biology, L.H. Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011, USA.


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 the dynamics of the HIV-1 protease. After structure matching, we apply principal component analysis (PCA) to obtain the important apparent motions for both 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.

[PubMed - indexed for MEDLINE]
Free PMC Article
PubMed Commons home

PubMed Commons

How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for Elsevier Science Icon for PubMed Central
    Loading ...
    Write to the Help Desk