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Title: Heme cavity dynamics of photodissociated CO from ba3-Cytochrome c oxidase : the role of ring-D propionate
Authors: Porrini, Massimiliano 
Varotsis, Constantinos 
Daskalakis, Evangelos 
Porrini, Massimiliano 
Keywords: Porphyrins
Carbon monoxide
Density functionals
Infrared spectroscopy
Molecular dynamics
Spectroscopic analysis
Issue Date: 2009
Publisher: ACS Publications
Source: Journal of physical chemistry B, 2009, volume 113, issue 35, pages 12129-12135
Abstract: Intracavity molecular dynamics studies of photodissociated carbon monoxide from ba3-cytochrome c oxidase have been performed by sampling the phase space with several hundreds of trajectories each integrated up to 100 ps time interval. It is shown that the cis conformation of protonated ring-D propionate of heme a3 and its trans conformation for the deprotonated species control the CO location by creating two distinct equilibrium states for CO confined in a cavity internal to the distal heme pocket. Thus, these cis (closed gate) and trans (open gate) conformations of heme a3 propionate D play the role of a switch, opening or closing a gate for confining CO in a cavity internal to the heme pocket or releasing it to a bigger outer cavity. The geometry of the inner cavity and the validity of the potential function employed are further investigated by Density Functional Theory calculations for the active site, potential of mean force curves along the copper-CO bond, as well as with Quantum Mechanics/Molecular Mechanics calculations. In the light of the present study, trajectory scenarios for the dissociation of CO previously suggested from time-resolved infrared spectroscopy are re-examined
ISSN: 15206106
DOI: 10.1021/jp904466n
Rights: © 2009 American Chemical Society
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