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Internet Electronic Journal of Molecular Design - IEJMD, ISSN 1538-6414, CODEN IEJMAT
ABSTRACT - Internet Electron. J. Mol. Des. November 2003, Volume 2, Number 11, 732-740

Theoretical Study of Hydrogen-Bonded Network and Proton Transfer in the Active Site of Reduced Cytochrome c Oxidase
Yasunori Yoshioka and Masaki Mitani
Internet Electron. J. Mol. Des. 2003, 2, 732-740

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Abstract:
There are many proposals of reaction mechanisms of O2-reduction catalyzed by cytochrome c oxidase (CcO) and the mechanism is not still conclusive. We have previously proposed new 'water-proton transport' (WPT) mechanism in which H2O hydrogen-bonded to His290 and Tyr244 transports a proton to FeOO to yield FeOOH. The path through which a proton is transferred to this H2O molecule in the active site of CcO is investigated from theoretical viewpoint in this work. The moderate size of model of the active site in CcO was constructed based on the geometry of fully reduced form 1OCR in PDB. All histidines were modeled by imidazoles and Tyr244 by phenol. The key fragments concerned with the hydrogen-bonded network were geometrically optimized. The hybrid exchange-correlation functional B3LYP method was employed with double-zeta basis set. The H2O molecule exists between farnesylethyl and Thr316 by hydrogen bonds and the hydrogen-bonded network, which is connecting from Lys319 to the active site of O2-reduction, is formed in the reduced CcO. The proton necessary for O2-reduction is provided through this hydrogen-bonded network. The proton is trapped on farnesylethyl of heme a3, subsequently the proton is transferred to Tyr244 to give a proton to the H2O molecule between His290 and Tyr244. The energy barrier of the proton transfer is qualitatively estimated to be 12 kcal/mol. The proton path, which is necessary to perform the O2-reduction, was made clear from the theoretical viewpoint.

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