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CO escape from myoglobin with metadynamics simulations (Articolo in rivista)

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CO escape from myoglobin with metadynamics simulations (Articolo in rivista) (literal)

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Ceccarelli, M; Anedda, R; Casu, M; Ruggerone, P (2008)
CO escape from myoglobin with metadynamics simulations
in Proteins (Online)
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\"[Ceccarelli, Matteo; Ruggerone, Paolo] Univ Cagliari, CNR, INFM, I-09042 Monserrato, Italy; [Anedda, Roberto; Casu, Mariano] Univ Cagliari, Dept Chem Sci, I-09042 Monserrato, Italy; [Ruggerone, Paolo] CNR INFM Democritos Modeling Ctr, I-34014 Trieste, Italy (literal)

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Abstract

The relatively small size of myoglobin makes it suitable for the investigation of the ligand escape process in respiratory proteins and, in general, an ideal model system for the study of the more general structure-function paradigm. In this work, we use Molecular Dynamics simulations combined with an accelerated algorithm, the metadynamics, to probe the escape of CO from myoglobin. Our approach permits to quantitatively describe the escape process via the reconstruction of the associated free energy surface. Additionally, hints on the involvement of a larger numbers of residues than hitherto assumed in the gating process are extracted from our data. (literal)

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