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

Biophysical Journal
Bruno L VictorCláudio M Soares

Abstract

Heme-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. Because the catalytic process occurs in the heme 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 modeled the structure of the quinol oxidase from Acidianus ambivalens using comparative modeling 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 modeling, 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 the...Continue Reading

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Citations

Apr 2, 2009·Journal of Biological Inorganic Chemistry : JBIC : a Publication of the Society of Biological Inorganic Chemistry·Bruno L VictorCláudio M Soares
Apr 2, 2016·Biochimica Et Biophysica Acta·A Sofia F OliveiraCláudio M Soares
Jun 3, 2008·Biochimica Et Biophysica Acta·Manuela M PereiraMiguel Teixeira
Oct 18, 2011·Biochimica Et Biophysica Acta·Filipa L SousaManuela M Pereira
Sep 20, 2005·Biophysical Journal·A Sofia F OliveiraCláudio M Soares
May 30, 2006·Biophysical Journal·Vitor H TeixeiraCláudio M Soares

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