We are interested in the study of reaction mechanisms in enzyme fields. Therefore it is necessary to interactively model build active sites and then visualize and compare minimized structures. We addressed again the triose phosphate isomerase (TIM) catalyzed isomerization of its ligands dihydroxy acetonephosphate (DHAP) and glyceraldehyde-3-phosphate, because recent results put forward a direct involvement of His95 in the reaction mechanism. In fact, they supposed that the proton transfer occurring in the enediolate is mediated by His95, that has a Lewis acid makes the enediolate of the substrate into an enediol. Evidence for this came from mechanistic studies on native and mutant TIM's and the considerable loss of catalytic activity upon replacement of His95 by Gln or Asn. This is in contrast to our previous result for this system that showed that the proton transfer of the hydroxyl hydrogen in the inediolate occurs intramolecularly. At that time, however, we made use of a very simple model of the substrate (the methylphosphate group was substituted with a mere hydrogen atom) and of the 4-31G basis set. Our present study follows two directions: First, we examine the intramolecular proton transfer of the hydroxyl hydrogen to the carbonyl oxygen in the enediolate of DHAP and show that it proceeds with a very small barrier even in vacuo. Secondly, we show that a simple model for the enediolate has no intrinsic tendency to accept a proton from an imidazole. We consider two models of the enzyme: one made up of just four residues and the other one of the residues (37) within 10 angstroms of the active site. Our results could, of course, change upon study of a different representation of the enzyme active site.
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