title: A free-energy perturbation study of the binding of methotrexate to mutants of dihydrofolate reductase.
abstract: The importance of hydrophobic residues to the binding of methotrexate in the active site of dihydrofolate reductase (EC 1.5.1.3) was examined by a free-energy perturbation method. The replacement of a strictly conserved residue, Phe-31, by tyrosine or valine costs 1.8 and 5.1 kcal/mol, respectively, to the binding of the drug (1 cal = 4.184 J). In the case of the Phe31----Tyr mutation, the loss of the binding energy is due to the desolvation of the phenolic group; in the case of Phe31----Val mutation, it is mainly due to the loss of the interaction with the drug. The replacement of Leu-54 by glycine decreases the binding energy by 4.0 kcal/mol. A calculation on the mutation of Phe-31 to serine shows that the alteration could reduce the binding energy of methotrexate by 9.7 kcal/mol. The calculations clearly show that the hydrophobic interactions are as important as the hydrophilic ones in the binding of methotrexate.
authors.affiliation: Department of Molecular Biology, Scripps Clinic and Research Foundation, La Jolla, CA 92037.
authors.forename: U C
authors.initials: UC
authors.lastname: Singh
authors.forename: S J
authors.initials: SJ
authors.lastname: Benkovic
mesh_terms: D001665:Binding Sites; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D003198:Computer Simulation; D008727:Methotrexate / Q000378:metabolism*; D009154:Mutation; D010649:Phenylalanine; D013762:Tetrahydrofolate Dehydrogenase / Q000378:metabolism*; D014443:Tyrosine; D014633:Valine
chemical_list: D014443:Tyrosine; D010649:Phenylalanine; D013762:Tetrahydrofolate Dehydrogenase; D014633:Valine; D008727:Methotrexate