Computer Simulation of Enzymatic Reactions

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Gaining a quantitative description of enzyme action is one of the most important challenges of molecular biology. Thus, we propose a continuation of our research projects aimed at the development, refinement, and implementation of computational models for simulations of enzymatic reactions. During previous grant periods we have demonstrated the general applicability of our empirical valence bond (EVB) approach. In recent years we started to develop more rigorous ab initio approaches that exploit the increasing availability of computer power. Our new strategies include: (a) quantum mechanical (ab initio)/Langevin dipole (QM(ai)/LD) model which provide crucial information about potential surfaces of reactions in solution. This allows us to calibrate EVB surfaces for studies of enzymes; (b) an ab initio free energy perturbation (QM(ai)/FEP) which uses EVB surfaces as reference potentials and thus allows us to start evaluating ab initio free energies of enzymatic reactions; and (c) a constrain density functional theory (CDFT) approach, which allows us to represent large parts of the protein at the ab initio level. Although these approaches still require further validation, we are ready to use them in studies of enzymatic catalysis. In addition to the method development projects, we have made significant progress in studying different classes of enzymatic reactions and in exploring the feasibility of different catalytic mechanisms. In order to exploit our advanced we propose to advance in the following three directions: (a) we will conduct method development studies that will include: (i) improving our ab initio approaches for constructing reference solution reactions. In particular, we will focus on transition state search and evaluation of entropic corrections for solution reactions; (ii) using solution surfaces in automated refined of EVB surfaces; (iii) using the EVB surfaces as reference potentials in automated refinement of EVB surfaces; (iii) using the EVB surfaces as reference potentials for QM(ai)/FEP studies of enzymes; (iv) CDFT studies of metalloenzyme. (b) We will conduct systematic studies of several important classes of enzymatic reactions including: (i) serine and cysteine proteases; (ii) DNA polymerase; and (iii) ribonuclease. (c) We will conduct studies of the relative importance of different catalytic proposals, including (i) entropic effects; (ii) low barrier hydrogen bond; (iii) near attack conformers; and (iv) pre-organization of enzyme active sites.