Masami Uebayasi

Theoretical analyses on the role of Mg2+ ions in ribozyme reactions.

To elucidate the role of the Mg2+ ion in ribozyme reactions, we carried out ab initio molecular orbital investigations on dianionic trimethoxyphosphorane A and its Mg2+ complex (overall a neutral molecule) as a model system for the reaction center of Tetrahymena‐type ribozyme. Although dianionic oxyphosphorane A concentrates its negative charges on the equatorial phosphoryl oxygens, the coordination of the Mg2+ ion between these two oxygens is unlikely. Geometry optimizations of the complex and the electrostatic potential of A both suggest that Mg2+ coordination preferably occurs in the region between the axial oxygen and the equatorial phosphoryl oxygen. The considerations of electrostatic potential rationalize the geometries of carboxylate‐metal and phosphate‐metal interactions extracted from the Cambridge Structural Database as well. Consequently, the Mg2+ ion at the active site of Tetrahymena‐type ribozyme most likely lies in the regions between the axial and equatorial oxygens. The axial‐equatorial coordinations of Mg2+ ions conceivably increase the electronegativities of the axial oxygens and facilitate cleavage of the phosphodiester bond located at the junction of the intron and the exon. It is thus likely that the Mg2∗ ions play the key role in the phosphodiester cleavage reactions mediated by ribozymes.— Uchimaru, T., Uebayasi, M., Tanabe, K., Taira, K. Theoretical analyses of the role of Mg2+ ions in ribozyme reactions. FASEB J. 7: 137‐142; 1993.

RNA hydrolysis via an oxyphosphorane intermediate

From calculations of a model reaction scheme for base-catalyzed RNA hydrolysis, a pentacoodinate dianionic intermediate 2a (Storer, et al., J. Am. Chem. Soc., 1991, 113, 5216-5219) as well as two transition states, TS1 and TS2, to the intermediate have been located by ab initio calculations at the 3-21G* level. Although the intermediate, which has the well depth on the order of kBT, is unlikely to be kinetically significant, the overall rate-limiting transition state structure TS2 obtained at 3-21G* level is very close to the corresponding structure at the STO-3G level; it has an extended P-O(5) bond breaking character. These gas-phase calculation results are used to qualitatively interpret mutagenesis results of Barnase and RNase T1 where water molecules are absent from the active site.