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Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: the myoglobin case

Papaleo, Elena and Mereghetti, Paolo and Fantucci, Piercarlo and Grandori, Rita and De Gioia, Luca (2009) Free-energy landscape, principal component analysis, and structural clustering to identify representative conformations from molecular dynamics simulations: the myoglobin case. Journal of Molecular Graphics and Modelling, Vol. 27 (8), p. 889-899. ISSN 1093-3263. Article.

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DOI: 10.1016/j.jmgm.2009.01.006

Abstract

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 μs 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 PCA indicates that an accurate description of the Mb conformational space around the native state was achieved by multiple MD trajectories spanning at least 0.14 μs. 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.

Item Type:Article
ID Code:3524
Status:Published
Refereed:Yes
Uncontrolled Keywords:Molecular dynamics, conformational sampling, myoglobin, structural clustering, free-energy landscape
Subjects:Area 05 - Scienze biologiche > BIO/11 Biologia molecolare
Divisions:001 Università di Sassari > 01 Dipartimenti > Chimica
Publisher:Elsevier
ISSN:1093-3263
Deposited On:22 Jan 2010 19:21

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