title: A mechanistic study supports a two-step mechanism for peptide bond formation on the ribosome.
abstract: We report the feasible pathways of the quaternary model system for the ribosome-catalyzed PT reaction obtained by density functional calculations. Our results indicate that the step from the reactant complex to the first six-membered TS involving a proton shuttle via the 2'-OH of the P-site A76 in the stepwise pathway is the most favored rate-limiting step in solution. It is found that the C-O3' bond-breaking of A76 is not significant but the C-N bond formation with a tetrahedral intermediate occurs in the rate-limiting step and that the fast breakdown of the C-O3' bond is followed in the second transition state. These are consistent with recent kinetic experiments.
authors.affiliation: Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea.
authors.forename: Byung Jin
authors.initials: BJ
authors.lastname: Byun
authors.forename: Young Kee
authors.initials: YK
authors.lastname: Kang
mesh_terms: D002384:Catalysis; D007700:Kinetics; D008958:Models, Molecular; D008968:Molecular Conformation; D010455:Peptides / Q000138:chemical synthesis* / Q000737:chemistry; D011789:Quantum Theory; D012270:Ribosomes / Q000737:chemistry*
chemical_list: D010455:Peptides