Conformational change of the methionine 20 loop of Escherichia coli dihydrofolate reductase modulates pKa of the bound dihydrofolate

• DOI: 10.1110/ps.062724307
• Publication Date: 2007-05-02T14:01:58Z
• Authors: Ilja V. Khavrutskii; Daniel J. Price; Jinhyuk Lee; Charles L. Brooks
• Keywords: Dihydrofolate reductase; Ternary complex; Conformational change

We evaluate the pK(a) of dihydrofolate (H(2)F) at N(5) position in three ternary complexes with Escherichia coli reductase (ecDHFR), namely ecDHFR(NADP(+):H(2)F) closed form (1), and Michaelis ecDHFR(NADPH:H(2)F) (2) occluded (3) forms, by performing free energy perturbation molecular dynamics simulations (FEP/MD). Our suggest that complex is modulated Met20 loop fluctuations, providing largest shift substates a "tightly closed" conformation; "partially closed/open" substates, similar to complex. Conducive protonation, tightly closing enhances interactions cofactor substrate side chain aligns nicotinamide ring coplanar pterin substrate. Overall, present study favors hypothesis protonated directly from solution provides further insights into mechanism protonation.