COMBINED AB-INITIO AND FREE-ENERGY CALCULATIONS TO STUDY REACTIONS INENZYMES AND SOLUTION - AMIDE HYDROLYSIS IN TRYPSIN AND AQUEOUS-SOLUTION

We present a new more general way to combine ab initio quantum mechani cal calculations with classical mechanical free energy perturbation ap proach to calculate the energetics of enzyme-catalyzed reactions and t he same reaction in solution. This approach, which enables enzyme and solution reactions to be compared without the use of empirical paramet ers, is applied to the formation of the tetrahedral intermediate in tr ypsin, but it should be generally applicable to any enzymatic reaction . Critical to the accurate calculation of the reaction energetics in s olution is the estimate of the free energy to assemble the reacting gr oups, where the approach recently published by Hermans and Wang (J. Am . Chem. Sec. 1997, 119, 2707) was used. A central aspect of this new a pproach is the use of the RESP protocol to calculate the charge distri bution of structures along the reaction pathway, which enables us to c ircumvent problems in partitioning the charge across a residue that is being divided into QM and MM parts. The classical mechanical free ene rgy calculations an implemented with two different approaches, ''Carte sian mapping'' and ''flexible FEP''. The similarity of the results fou nd by using these two approaches supports the robustness of the calcul ated free energies. The calculated free energies are in quite good agr eement with available experimental data for the activation free energi es in the enzyme and aqueous phase reactions.