title: Close correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes.
abstract: 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.
authors.affiliation: Program 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.
authors.forename: Lei
authors.initials: L
authors.lastname: Yang
authors.forename: Guang
authors.initials: G
authors.lastname: Song
authors.forename: Alicia
authors.initials: A
authors.lastname: Carriquiry
authors.forename: Robert L
authors.initials: RL
authors.lastname: Jernigan
mesh_terms: D003198:Computer Simulation; D018360:Crystallography, X-Ray; D016333:HIV Protease / Q000737:chemistry*; D008958:Models, Molecular; D009038:Motion; D019906:Nuclear Magnetic Resonance, Biomolecular; D025341:Principal Component Analysis; D011487:Protein Conformation
chemical_list: D016333:HIV Protease; C514803:p16 protease, Human immunodeficiency virus 1