Jump to main content
Jump to site search

Issue 12, 2010
Previous Article Next Article

Consensus modes, a robust description of protein collective motions from multiple-minima normal mode analysis—application to the HIV-1 protease

Author affiliations

Abstract

Protein flexibility is essential for enzymatic function, ligand binding, and proteinprotein or proteinnucleic acid interactions. Normal mode analysis has increasingly been shown to be well suited for studying such flexibility, as it can be used to identify favorable structural deformations that correspond to functional motions. However, normal modes are strictly relevant to a single structure, reflecting a particular minimum on a complex energy surface, and are thus susceptible to artifacts. We describe a new theoretical framework for determining “consensus” normal modes from a set of related structures, such as those issuing from a short molecular dynamics simulation. This approach is more robust than standard normal mode analysis, and provides higher collectivity and symmetry properties. In an application to HIV-1 protease, the low-frequency consensus modes describe biologically relevant motions including flap opening and closing that can be used in interpreting structural changes accompanying the binding of widely differing inhibitors.

Graphical abstract: Consensus modes, a robust description of protein collective motions from multiple-minima normal mode analysis—application to the HIV-1 protease

Back to tab navigation

Supplementary files

Publication details

The article was received on 16 Sep 2009, accepted on 23 Dec 2009 and first published on 01 Feb 2010


Article type: Paper
DOI: 10.1039/B919148H
Citation: Phys. Chem. Chem. Phys., 2010,12, 2850-2859
  •   Request permissions

    Consensus modes, a robust description of protein collective motions from multiple-minima normal mode analysis—application to the HIV-1 protease

    P. R. Batista, C. H. Robert, J. Maréchal, M. B. Hamida-Rebaï, P. G. Pascutti, P. M. Bisch and D. Perahia, Phys. Chem. Chem. Phys., 2010, 12, 2850
    DOI: 10.1039/B919148H

Search articles by author

Spotlight

Advertisements