title: An uncharged amine in the transition state of the ribosomal peptidyl transfer reaction.
abstract: The ribosome has an active site comprised of RNA that catalyzes peptide bond formation. To understand how RNA promotes this reaction requires a detailed understanding of the chemical transition state. Here, we report the Brønsted coefficient of the alpha-amino nucleophile with a series of puromycin derivatives. Both 50S subunit- and 70S ribosome-catalyzed reactions displayed linear free-energy relationships with slopes close to zero under conditions where chemistry is rate limiting. These results indicate that, at the transition state, the nucleophile is neutral in the ribosome-catalyzed reaction, in contrast to the substantial positive charge reported for typical uncatalyzed aminolysis reactions. This suggests that the ribosomal transition state involves deprotonation to a degree commensurate with nitrogen-carbon bond formation. Such a transition state is significantly different from that of uncatalyzed aminolysis reactions in solution.
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
authors.forename: David A
authors.initials: DA
authors.lastname: Kingery
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Pfund
authors.forename: Rebecca M
authors.initials: RM
authors.lastname: Voorhees
authors.forename: Kensuke
authors.initials: K
authors.lastname: Okuda
authors.forename: Ingo
authors.initials: I
authors.lastname: Wohlgemuth
authors.forename: David E
authors.initials: DE
authors.lastname: Kitchen
authors.forename: Marina V
authors.initials: MV
authors.lastname: Rodnina
authors.forename: Scott A
authors.initials: SA
authors.lastname: Strobel
mesh_terms: D000588:Amines / Q000737:chemistry*; D012269:Ribosomal Proteins / Q000737:chemistry*
chemical_list: D000588:Amines; D012269:Ribosomal Proteins