Ab Initio and Molecular Dynamics Study of the Active Site of the Reaction between Ribonuclease A and Cytidyl-3‘,5‘-Adenosine

Abstract

In this ab initio study of the reaction mechanism of ribonuclease A with cytidyl-3',5'-adenosine, the geometry of the active site has been optimized using the Hartree-Fock method. The active site model contains the complete substrate, interacting water molecules, and fragments of eight amino acids that are involved in functional and structural interactions with the substrate. The refined conformations revealed an interesting hydrogen-bonding network that allows the prediction of the conformation of the active site in the initial step of the reaction mechanism. Based on the results of the calculations, a new mechanism is proposed: A proton is transferred from the 02'C-H2'C group to a phosphate oxygen through a water molecule. The developing charge on the phosphate group is stabilized through strong interactions with the enzyme. 02'C is hydrogen-bonded to the side chain of Lys41 as a precursor to catalysis and the two free phosphate oxygen atoms form strong hydrogen bonds with the side chain of Lys7 and the backbone of Phe 120. In contrast to earlier reaction proposals, it is shown here that His 12 is not directly involved in the initial step.