title: First-principles molecular dynamics study of proton transfer mechanism in bovine cytochrome c oxidase.
abstract: Density functional based first-principles molecular dynamics calculations, performed on a model system extracted from the bovine cytochrome c oxidase, have been performed in an attempt to inspect the proton transfer mechanism across a peptide group. Our model system includes the specific Tyr440-Ser441 peptide group involved in a novel proton transfer path and shows that the Y440-S441 enol peptide group [-C(OH) = N-], which is a structural isomer of a keto form [-CO-NH-], is the product of the deprotonation of an imidic acid [-C(OH)-NH-] occurring in the vicinity of the deprotonated aspartic acid residue. For the subsequent enol-to-keto tautomerization, a direct H(+) transfer path in the Y440-S441 peptide group has been identified, in which the transition state takes a distorted four-membered ring structure.
authors.affiliation: Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan. CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
authors.forename: Katsumasa
authors.initials: K
authors.lastname: Kamiya
authors.forename: Mauro
authors.initials: M
authors.lastname: Boero
authors.forename: Masaru
authors.initials: M
authors.lastname: Tateno
authors.forename: Kenji
authors.initials: K
authors.lastname: Shiraishi
authors.forename: Atsushi
authors.initials: A
authors.lastname: Oshiyama