Chemical reaction mechanisms in vacuo, in solution and in enzyme fields: Isomerization catalyzed by triose phosphate isomerase (TIM)

The first step of the reversible isomerization of dihydroxyacetone phosphate (DHAP) to glyceraldehyde-3-phosphate catalyzed by triose phosphate isomerase has been studied in the past by us [J. Mol. Biol., 191 (1986) 23], making use of a very simple model of the enzyme field and not including the phosphate group. The effect of this group on the reaction energetics in vacuo, in solution (using the polarizable continuum model) and in the enzyme field is considered at the 4-31G/SCF level. The reliability of the phosphate description has been checked by computing reference points at the 6-31+G level; also, the effect of electron correlation has been taken into account including correlation corrections at the MP2 level. The enzyme active site around the reacting partners, modeled with AMBER4, has been included in the calculations at the 4-31G level as a rigid charge cloud made up of either the five key residues (Lys 13, His 95, Ser 96, Glu 97 and Arg 98) or the 37 residues within 10 Angstrom of Glu 165 and the substrate. The enediolate of DHAP (ENEP)... acetic acid (the latter as a model of protonated Glu 165) adduct turns out to be almost isoenergetic with the DHAP ... acetate complex in either environment compared to an energy gap of 33 kcal mol(-1) in vacuo. The reaction barrier located by constructing a potential energy surface in the presence of the enzyme field is only 20 kcal mol(-1), compared to a calculated barrier of 40 kcal mol(-1) in vacuo and 28 kcal mol(-1) in solution.