Tuesday, May 20, 2008 - 10:20 AM
Medical Arts Building, Rm M-146 (Queensborough Community College)
394

The Transition State for Formation of the Peptide Bond in the Ribosome

Lou Massa, Hunter College, City University of New York, New York, NY

Using quantum mechanics and exploiting known crystallographic coordinates we have investigated the mechanism for peptide-bond formation in the ribosome. 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 calculated TS activation energy, Ea, is 35.5 kcal/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 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 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.