Hydrolysis of Cyclic Phosphates by Ribonuclease A: A Computational Study Using a Simplified Ab Initio Quantum Model

Published

November 15, 2003

Author(s)

B Wladkowski, P Ostazeski, S A. Chenoweth, S J. Broadwater, Morris Krauss

Abstract

The second step in the enzyme-catalyzed hydrolysis of phosphate esters by Ribonuclease A (Rnase A) was studied using an ab initio quantum-based model of the active site including constrained parts of three critical residues, His-12, His-119, and Lys-41 and a model substrate. Specifically, the competition between release of the cyclic phosphate intermediate and subsequent hydrolysis following transphosphorylation was explored to determine the factors that contribute to the fact that intermediate product release is kinetically preferred. The structural and energetic results obtained at both the RHF and MP2 level reveal several contributing factors consistent with the experimental observation. Although the intrinsic electronic effects tends to favor hydrolysis slightly with an overall activation free energy of approximately 70 kJ mol-1, entropic and solvation effects favor release of the cyclic phosphate intermediate over hydrolysis consistent with the experimental observations. Exploration of the second, hydrolysis step also revealed interesting similarity with the transphosphorylation step including the fact that an important aspect of the reaction pathway in both cases involves autocatalysis by the substrate. Moreover, in both steps multiple pathways were found involving proton transfers to sites of similar proton affinities. The anionic phosphate in both steps can act as a stable proton binding site as protons are moved around the active site throughout the progress of the reaction. The aspect of autocatalysis in the case of RNase A may be representative of more general behavior of enzymes involving highly charged substrates, especially phosphates.

Citation

Journal of Computational Chemistry

Volume

24

Issue

14

Pub Type

Journals

Keywords

ab initio quantum chemistry, cyclic phosphate, hydrolysis, proton transfer, reaction path, ribonuclease A

Citation

Wladkowski, B. , Ostazeski, P. , Chenoweth, S. , Broadwater, S. and Krauss, M. (2003), Hydrolysis of Cyclic Phosphates by Ribonuclease A: A Computational Study Using a Simplified Ab Initio Quantum Model, Journal of Computational Chemistry (Accessed April 25, 2024)