We use quantum mechanics / molecular mechanics (QM/MM) simulations to study the roles of metal ions in the cleavage of the ribonucleic acid (RNA) backbone catalyzed by ribonuclease H. This protein is a prototypical member of a large family of enzymes that use two-metal ion catalysis to process nucleic acids. The specific functional role of the metal ions in catalysis is not well understood. By combining Hamiltonian replica exchange with a finite-temperature string method, we calculate the free energy surface underlying the RNA cleavage reaction with single metal ion substitutions from Mg2+ to Ca2+. We find that metal ion replacement of either metal ion A or B abolishes catalysis. Our results suggest that the proper function of metal ion A, as measured by the activation barrier for the RNA cleavage reaction, is highly sensitive to changes in the electronic character of the ion, with geometry changes playing a minor role.

On two-metal ion catalysis: Study in Ribonuclease H

243rd National Meeting (2012)

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