Combined Quantum and Molecular Mechanics (QM/MM) Study of the Ionization State of 8-Methylpterin Substrate Bound to Dihydrofolate Reductase

Abstract

The prediction of stabilities of ion pairs relative to the corresponding neutral pairs is a challenging computational problem but very important in biological systems where the occurrence of such pairs is often mechanistically significant. Here we have computed the relative free energy for the protonated and neutral forms of the mechanism-based substrate 8-methylpterin bound to dihydrofolate reductase (DHFR) in a ternary complex with cofactor nicotinamide adenine dinucleotide phosphate (NADPH). The free energy components required to calculate relative affinities of the protonated substrate hydrogen (H) bonded to the unprotonated form of the conserved active-site carboxylate residue (Glu30 for chicken DHFR) and neutral substrate H bonded to the neutral (carboxylic acid) form of Glu30 were obtained using both ab initio QM methods and combined semiempirical (AM1) QM and MM (QM/MM) methods. The energy difference for the H-bonded systems was first calculated in a vacuum using ab initio QM methods for a model s...