Combined ab initio and Free Energy Calculations To Study Reactions in Enzymes and Solution:  Amide Hydrolysis in Trypsin and Aqueous Solution

Abstract

We present a new more general way to combine ab initio quantum mechanical calculations with classical mechanical free energy perturbation approach to calculate the energetics of enzyme-catalyzed reactions and the same reaction in solution. This approach, which enables enzyme and solution reactions to be compared without the use of empirical parameters, is applied to the formation of the tetrahedral intermediate in trypsin, but it should be generally applicable to any enzymatic reaction. Critical to the accurate calculation of the reaction energetics in solution is the estimate of the free energy to assemble the reacting groups, where the approach recently published by Hermans and Wang (J. Am. Chem. Soc. 1997, 119, 2707) was used. A central aspect of this new approach is the use of the RESP protocol to calculate the charge distribution of structures along the reaction pathway, which enables us to circumvent problems in partitioning the charge across a residue that is being divided into QM and MM parts. The classical mechanical free energy calculations are implemented with two different approaches, “Cartesian mapping” and “flexible FEP”. The similarity of the results found by using these two approaches supports the robustness of the calculated free energies. The calculated free energies are in quite good agreement with available experimental data for the activation free energies in the enzyme and aqueous phase reactions.

Communication: Constructing an implicit quantum mechanical/molecular mechanics solvent model by coarse-graining explicit solvent

“…This has traditionally been done by computing point charges or more elaborate representations of the solute. [7][8][9][10][11][12][13][14][15] The approach used here is similar to the mean-field ASEP model in that it obtains a set of averaged solvent properties for use in a single quantum calculation. However, it uses a mathematically rigorous coarse-graining that does not rely on statistical data fitting, and it includes electrostatics, polarization, and dispersion effects, all of which prove important.…”

Factors determining the relative stability of anionic tetrahedral complexes in serine protease catalysis and inhibition

“…1 Recently, in agreement with Warshel and Russell's assumption, 21 Kollman and coworkers demonstrated, in ab initio quantum mechanical modeling combined with the MD FEP simulations, 52 that the TC formation in serine protease active site is a two-step process. Proton transfer form Ser195 O ␥ to His57 N ⑀ precedes the nucleophilic attack on the carbonyl group.…”

“…51 Several other studies were involved in the development of various QM and MM approaches and their application to serine protease catalysis. Stanton et al 52 studied amide hydrolysis in trypsin and aqueous solution. Free energy difference between two states on the reaction coordinate was calculated as a sum of two contributions.…”

Simulating enzyme reactions: Challenges and perspectives

“…However, to give readers a flavor of what has been done, recent work (among much other) has been performed on the reactions catalyzed by acetyl cholinesterase, 93 aldose reductase, 94 121 and trypsin. 122,123 Additional references, to pre-1999 work on enzymes using hybrid potentials, may be found in ref. 46.…”