Biochemical reactions can be guided by mechanical stress. An external force has been previously shown both experimentally and theoretically to act as a catalyst for the scission of a disulfide bond in thiol/disulfide exchange reactions. How the dynamics of peptide hydrolysis, one of the most prevalent biochemical reactions, is influenced by a stretching force was investigated here using combined quantum and molecular mechanical (QM/MM) simulations together with transition path sampling. Our simulations predict mechanical force to only marginally enhance the reactivity of the rate-limiting step, the nucleophilic attack of hydroxide to the peptide moiety, and not to alter the reaction mechanism, even though the peptide bond and its π-electron conjugation is weakened by force. We describe a previously unidentified hydrogen bonded intermediate state, which is likely to play a role in general in base-catalyzed and analogous enzymatic reactions. Our predictions can be directly tested by single molecule stretching experiments.
© 2011 American Chemical Society