Journal
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
Volume 27, Issue 8, Pages 889-899Publisher
ELSEVIER SCIENCE INC
DOI: 10.1016/j.jmgm.2009.01.006
Keywords
Molecular dynamics; Conformational sampling; Myoglobin; Structural clustering; Free-energy landscape
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Funding
- CINECA [696-2008]
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Several molecular dynamics (MD) simulations were used to sample conformations in the neighborhood of the native structure of holo-myoglobin (holo-Mb), collecting trajectories spanning 0.22 mu s at 300 K. Principal component (PCA) and free-energy landscape (FEL) analyses, integrated by cluster analysis, which was performed considering the position and structures of the individual helices of the globin fold, were carried out. The coherence between the different structural clusters and the basins of the FEL, together with the convergence of parameters derived by PICA indicates that an accurate description of the Mb conformational space around the native state was achieved by multiple MID trajectories spanning at least 0.14 mu s. The integration of FEL, PCA, and structural clustering was shown to be a very useful approach to gain an overall view of the conformational landscape accessible to a protein and to identify representative protein substates. This method could be also used to investigate the conformational and dynamical properties of Mb apo-, mutant, or delete versions, in which greater conformational variability is expected and, therefore identification of representative substates from the simulations is relevant to disclose structure-function relationship. (C) 2009 Elsevier Inc. All rights reserved.
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