QM/MM Simulation (B3LYP) of the RNase A Cleavage-Transesterification Reaction Supports a Triester A_N + D_N Associative Mechanism with an O2′ H Internal Proton Transfer

Abstract

The mechanism of the backbone cleavage-transesterification step of the RNase A enzyme remains controversial even after 60 years of study. We report quantum mechanics/molecule mechanics (QM/MM) free energy calculations for two optimized reaction paths based on an analysis of all structural data and identified by a search for reaction coordinates using a reliable quantum chemistry method (B3LYP), equilibrated structural optimizations, and free energy estimations. Both paths are initiated by nucleophilic attack of the ribose O2′ oxygen on the neighboring diester phosphate bond, and both reach the same product state (PS) (a O3′–O2′ cyclic phosphate and a O5′ hydroxyl terminated fragment). Path 1, resembles the widely accepted dianionic transition-state (TS) general acid (His119)/base (His12) classical mechanism. However, this path has a barrier (25 kcal/mol) higher than that of the rate-limiting hydrolysis step and a very loose TS. In Path 2, the proton initially coordinating the O2′ migrates to the nonbridging O1P in the initial reaction path rather than directly to the general base resulting in a triester (substrate as base) A_N + D_N mechanism with a monoanionic weakly stable intermediate. The structures in the transition region are associative with low barriers (TS1 10, TS2 7.5 kcal/mol). The Path 2 mechanism is consistent with the many results from enzyme and buffer catalyzed and uncatalyzed analog reactions and leads to a PS consistent with the reactive state for the following hydrolysis step. The differences between the consistently estimated barriers in Path 1 and 2 lead to a 10¹¹ difference in rate strongly supporting the less accepted triester mechanism