title: The transition state for formation of the peptide bond in the ribosome.
abstract: Using quantum mechanics and exploiting known crystallographic coordinates of tRNA substrate located in the ribosome peptidyl transferase center around the 2-fold axis, we have investigated the mechanism for peptide-bond formation. The calculation is based on a choice of 50 atoms assumed to be important in the mechanism. We used density functional theory to optimize the geometry and energy of the transition state (TS) for peptide-bond formation. The TS is formed simultaneously with the rotatory motion enabling the translocation of the A-site tRNA 3' end into the P site, and we estimated the magnitude of rotation angle between the A-site starting position and the place at which the TS occurs. The calculated TS activation energy, E(a), is 35.5 kcal (1 kcal = 4.18 kJ)/mol, and the increase in hydrogen bonding between the rotating A-site tRNA and ribosome nucleotides as the TS forms appears to stabilize it to a value qualitatively estimated to be approximately 18 kcal/mol. The optimized geometry corresponds to a structure in which the peptide bond is being formed as other bonds are being broken, in such a manner as to release the P-site tRNA so that it may exit as a free molecule and be replaced by the translocating A-site tRNA. At TS formation the 2' OH group of the P-site tRNA A76 forms a hydrogen bond with the oxygen atom of the carboxyl group of the amino acid attached to the A-site tRNA, which may be indicative of its catalytic role, consistent with recent biochemical experiments.
authors.affiliation: Hunter College and the Graduate School, City University of New York, New York, NY 10021, USA.
authors.forename: Asta
authors.initials: A
authors.lastname: Gindulyte
authors.forename: Anat
authors.initials: A
authors.lastname: Bashan
authors.forename: Ilana
authors.initials: I
authors.lastname: Agmon
authors.forename: Lou
authors.initials: L
authors.lastname: Massa
authors.forename: Ada
authors.initials: A
authors.lastname: Yonath
authors.forename: Jerome
authors.initials: J
authors.lastname: Karle
mesh_terms: D018360:Crystallography, X-Ray; D006860:Hydrogen Bonding; D008956:Models, Chemical; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism*; D010458:Peptidyl Transferases / Q000737:chemistry / Q000378:metabolism / Q000502:physiology; D011485:Protein Binding; D011487:Protein Conformation; D011789:Quantum Theory; D012343:RNA, Transfer / Q000737:chemistry / Q000378:metabolism; D012270:Ribosomes / Q000737:chemistry* / Q000378:metabolism*; D012399:Rotation
chemical_list: D010455:Peptides; D012343:RNA, Transfer; D010458:Peptidyl Transferases