COMPUTER-SIMULATION OF THE TRIOSEPHOSPHATE ISOMERASE CATALYZED REACTION

A major challenge for theoretical simulation methods is the calculatio n of enzymic reaction rates directly from the three-dimensional protei n structure together with some idea of the chemical reaction mechanism . Here, we report the evaluation of a complete free energy profile for all the elementary steps of the triosephosphate isomerase catalyzed r eaction using such an approach. The results are compatible with availa ble experimental data and also suggest which of the possible reaction intermediates is kinetically observable. In addition to previously ide ntified catalytic residues, the simulations show that a crystallograph ically observed active site water molecule plays an important role dur ing catalysis and an intersubunit interaction that could explain the l ow activity of the monomeric enzyme is also observed. The calculations clearly demonstrate the important catalytic effects associated with s tabilization of charged high energy intermediates and reduction of reo rganization energy, which are likely to be general principles of enzym e catalyzed charge transfer and separation reactions.