Possible mechanism of proton transfer through peptide groups in the H-pathway of the bovine cytochrome c oxidase

J Am Chem Soc. 2007 Aug 8;129(31):9663-73. doi: 10.1021/ja070464y. Epub 2007 Jul 18.

Abstract

The peptide group connecting Tyr440 and Ser441 of the bovine cytochrome c oxidase is involved in a recently proposed proton-transfer path (H-path) where, at variance with other pathways (D- and K-paths), a usual hydrogen-bond network is interrupted, thus making this proton propagation rather unconventional. Our density-functional based molecular dynamics simulations show that, despite this anomaly and provided that a proton can reach a nearby water, a multistep proton-transfer pathway can become a viable pathway for such a reaction: a proton is initially transferred to the carbonyl oxygen of a keto form of the Tyr440-Ser441 peptide group [-CO-NH-], producing an imidic acid [-C(OH)-NH-] as a metastable state; the amide proton of the imidic acid is then transferred, spontaneously to the deprotonated carboxyl group of the Asp51 side chain, leading to the formation of an enol form [-C(OH)=N-] of the Tyr440-Ser441 peptide group. Then a subsequent enol-to-keto tautomerization occurs via a double proton-transfer path realized in the two adjacent Tyr440-Ser441 and Ser441-Asp442 peptide groups. An analysis of this multistep proton-transfer pathway shows that each elementary process occurs through the shortest distance, no permanent conformational changes are induced, thus preserving the X-ray crystal structure, and the reaction path is characterized by a reasonable activation barrier.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acids / genetics
  • Amino Acids / metabolism
  • Animals
  • Cattle
  • Computer Simulation
  • Electron Transport Complex IV / chemistry*
  • Electron Transport Complex IV / genetics
  • Electron Transport Complex IV / metabolism*
  • Electrons
  • Isomerism
  • Models, Molecular
  • Mutation / genetics
  • Peptides / chemistry*
  • Peptides / metabolism*
  • Protein Structure, Quaternary
  • Protein Structure, Tertiary
  • Protein Subunits / chemistry
  • Protein Subunits / genetics
  • Protein Subunits / metabolism
  • Protons*

Substances

  • Amino Acids
  • Peptides
  • Protein Subunits
  • Protons
  • Electron Transport Complex IV