A Molecular Mechanism of Hydrolysis of Peptide Bonds at Neutral pH Using a Model Compound

Abstract

The covalent stability of peptide bonds is a critical aspect of biological chemistry and therapeutic protein applications. In this computational study, the hydrolytic reaction of peptide bonds at neutral pH was studied using a model compound, N-MAA. The most probable reaction pathway and intermediate(s) involved are controversial in previous studies. In addition, most previous computational studies focus on the energetics of chemical species involved, rather than providing a dynamic picture of the reaction process in aqueous conditions. However, fluctuations at finite temperatures are quite important, as we show. Thus, a path sampling method was used to generate an ensemble of trajectories according to their statistical weights in trajectory space. An ab initio molecular dynamics technique was applied to advance the time of the reaction in order to collect trajectories. The likelihood maximization procedure and its modification were used in extracting dynamically relevant degrees of freedom in the system, and approximations of the reaction coordinate were compared. It was found that this hydrolytic reaction is very complex because it involves many degrees of freedom. The reaction coordinate C-O distance previously assumed was found to be inadequate in describing the dynamic progress of the reaction. In addition to affecting atoms directly involved in bond-making and -breaking processes, the water network also has determining effects on the hydrolytic reaction, a fact which is manifest in the expression of the best one-dimensional reaction coordinate that we found, which includes five geometric quantities. p(B) histograms were computed to verify the results of the likelihood maximization and to evaluate the accuracy of our best reaction coordinate to the "true" reaction coordinate. The relation with previous suggested reaction pathways and intermediate(s) is discussed in terms of computational system, method, and accuracy.