Theoretical identification of proton channels in the quinol oxidase aa 3 from Acidianus ambivalens

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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.

Original languageEnglish
Pages (from-to)4316-4325
Number of pages10
JournalBiophysical Journal
Volume87
Issue number6
DOIs
Publication statusPublished - Dec 2004

Fingerprint

Acidianus
Protons
Water
Heme
Proteins
Electron Transport
duroquinol oxidase
Membrane Proteins
Electrons
Oxygen
Membranes

Keywords

  • ubiquinol cytochrome c reductase
  • unclassified drug
  • cytochrome c oxidase
  • heme copper oxidase
  • heme derivative
  • membrane protein

Cite this

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title = "Theoretical identification of proton channels in the quinol oxidase aa 3 from Acidianus ambivalens",
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.",
keywords = "ubiquinol cytochrome c reductase, unclassified drug, cytochrome c oxidase, heme copper oxidase, heme derivative, membrane protein",
author = "Victor, {Bruno L.} and Baptista, {Ant{\'o}nio M.} and Soares, {Cl{\'a}udio M.}",
year = "2004",
month = "12",
doi = "10.1529/biophysj.104.049353",
language = "English",
volume = "87",
pages = "4316--4325",
journal = "Biophysical Journal",
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publisher = "CELL PRESS",
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TY - JOUR

T1 - Theoretical identification of proton channels in the quinol oxidase aa 3 from Acidianus ambivalens

AU - Victor, Bruno L.

AU - Baptista, António M.

AU - Soares, Cláudio M.

PY - 2004/12

Y1 - 2004/12

N2 - 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.

AB - 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.

KW - ubiquinol cytochrome c reductase

KW - unclassified drug

KW - cytochrome c oxidase

KW - heme copper oxidase

KW - heme derivative

KW - membrane protein

UR - http://www.scopus.com/inward/record.url?scp=10044240740&partnerID=8YFLogxK

U2 - 10.1529/biophysj.104.049353

DO - 10.1529/biophysj.104.049353

M3 - Article

VL - 87

SP - 4316

EP - 4325

JO - Biophysical Journal

JF - Biophysical Journal

SN - 0006-3495

IS - 6

ER -