Computational Methods for the Study of Enzymic Reaction Mechanisms. 1. Application to the Hydride Transfer Step in the Catalysis of Dihydrofolate Reductase

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We report results and assessment from the use of several “state-of-the-art” computational methods to investigate the effect of the Asp27 ionization state on the hydride-ion transfer step in the enzymic reduction of folate and dihydrofolate (DHF) by DHFR from Escherichia coli (E. coli). The active forms of the DHFR complex are assumed protonated on the pterin/dihydropterin ring of the folate/dihydrofolate molecule prior to transfer of the hydride ion from the nicotinamide adenine dinucleotide phosphate (NADPH) cofactor. The calculations have been carried out for both protonated (neutral) and unprotonated (negatively charged) states of the conserved active-site Asp27 (E. coli) residue in the DHFR complexes. First, geometry optimizations at the semiempirical (PM3), density functional (DFT) and ab initio levels were performed on reaction-analogue clusters to obtain reactant, transition state (TS), and product complexes. The DFT and ab initio reaction energies obtained for the unprotonated Asp complexes were e...