NDLI: Theoretical Identification of Proton Channels in the Quinol Oxidase aa 3 from Acidianus ambivalens

Content Provider	PubMed Central
Author	Victor, Bruno L. Baptista, António M. Soares, Cláudio M.
Copyright Year	2004
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 their biological function.
Related Links	http://dx.doi.org/10.1529/biophysj.104.049353
Ending Page	4325
Page Count	10
Starting Page	4316
File Format	PDF
ISSN	00063495
e-ISSN	15420086
Journal	Biophysical Journal
Issue Number	6
Volume Number	87
Language	English
Publisher	Biophysical Society
Publisher Date	2004-12-01
Access Restriction	Open
Rights Holder	Biophysical Society
Subject Keyword	Biophysics Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Biophysics

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