Probing the salt bridge in the dihydrofolate reductase-methotrexate complex by using the coordinate-coupled free-energy perturbation method.

The importance of the ionic interaction due to the formation of the salt bridge between the Asp-27 and the pteridine ring in Escherichia coli dihydrofolate reductase-methotrexate complex has been studied by using the free-energy perturbation method. The calculation suggests that the ion-pair contribution to the binding energy is insignificant, as the enzyme surroundings do not stabilize the salt bridge to the extent of the desolvation of the charged groups. The activation barrier for the proton exchange between the pteridine ring and the Asp-27 is calculated to be 20.1 kcal/mol (1 cal = 4.184 J) by using the coordinate-coupled perturbation method, implying that this may be a channel to the proton exchange from the pteridine ring to the solvent. The Gibbs-energy difference of binding between the Asn-27 and Ser-27 is calculated to be 3.2 kcal/mol and is mainly due to the electrostatic interactions.