Abstract
In order to elucidate the energetics of RNA cleaving reactions, the reaction coordinate was simulated by ab initio molecular orbital calculations. The calculated energy profile was applied to explain mutagenesis results of RNase T1 and Barnase in which acids/bases play pivotal roles in catalysis. Enzyme kinetics were also analyzed in some detail putting emphasis on slopes in pH-rate profiles. Further calculations invotving Mg2+ reveal that, in ribozyme reactions, the actual catalyst may be Mg2+ and the RNA components may merely provide the proper binding site for the Mg2+ ion.
