A THEORETICAL INVESTIGATION OF MECHANISM OF THE ADENOSINE DEAMINASE MODIFICATION: REACTION OF GLUTAMATE RESIDUE WITH WOODWARD REAGENT K

Abstract

The kinetics and mechanism of the modification of adenosine deaminase with N-ethyl-5-phenyl isoxazoliom-3′-sulfonate (WR-K) are investigated using molecular dynamics simulations, QM and QM/MM minimization methods. Two methodological algorithms are employed. In the first algorithm, a glutamate residue is dissected from ADA and its reaction with WR-K is studied by employing minimization and frequency calculations under the B3LYP method. Results obtained show that ketoketenimine is produced from the interaction of WR-K with OH-in an exergonic two-step reaction. In this process, an intermediate is consumed in the rate-determining step. Next, the dissected residue is modified using ketoketenimine in a three-step reaction. This reaction is accompanied by the production of two intermediates, with the first intermediate produced in the rate-determining step.For the second algorithm, modification of glutamate residue in the presence of water molecules and ions is investigated using conformational sampling, MM and QM/MM minimization. Stability of species in the reaction is evaluated using a combination of the B3LYP method and the WASA model. It is proved that the stability of an intermediate which is initially produced in the reaction of glutamate residue with ketoketenimine must be considered crucial when the reactivity of the different residues is compared. Results obtained indicate that these reactions have energetic features qualitatively similar to the glutamate-dissected case. It is also clear that protein structure plays a basic role in the formation of the product that arises from the reaction of ADA with ketoketenimine.