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Biophys. J. BioFAST: First Published September 17, 2004. doi:10.1529/biophysj.104.049353
© 2004 by the Biophysical Society.

A more recent version of this article appeared on December 1, 2004.
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BIOENERGETICS

Theoretical identification of proton channels in the quinol oxidase aa3 from Acidianus ambivalens

Bruno L Victor 1, António M. Baptista 1 and Claudio M. Soares 1*

1 Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa

* To whom correspondence should be addressed. E-mail: claudio{at}itqb.unl.pt.

Submitted on July 9, 2004
Revised on August 27, 2004
Accepted on 8 September 2004


  Abstract
Haem-copper oxidases are membrane proteins found in the respiratory chain of aerobic organisms. They are the terminal electron acceptors coupling the translocation of protons across the membrane with the reduction of oxygen to water. Since the catalytic process occurs in the haem cofactors positioned well inside the protein matrix, proton channels must exist. However, due to the high structural divergence among this kind of proteins, the proton channels previously described are not necessarily conserved. In this work we modelled the structure of the quinol oxidase from Acidianus ambivalens using comparative modelling techniques for identifying proton channels. Additionally, given the high importance that water molecules may have in this process, we have developed a methodology, within the context of comparative modelling, to identify high water probability zones and to deconvolute them into chains of ordered water molecules. From our results, and from the existent information from other proteins from the same superfamily, we were able to suggest three possible proton channels: one K-, one D- and one Q-spatial homologous proton channels. This methodology can be applied to other systems where water molecules are important for their biological function.

Key Words: Comparative modelling, Monte Carlo simulated annealing, heme-copper quinol oxidase, proton channels, structural waters




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Copyright © 2004 by the Biophysical Society.