Effect of ligand binding on the flexibility of dihydrofolate reductase as revealed by compressibility

The partial specific volume, nu, and adiabatic compressibility, beta(s), of Escherichia coli dihydrofolate reductase were measured at 30 degrees C in the presence of various ligands (folate, dihydrofolate, tetrahydrofolate, N ADPH, NADP, methotrexate, and KCI). Binding of these ligands (binary and te rnary complexes) brought about large changes of nu (0.734-0.754 cm(3) g(-1) ) and beta(s) (6.6 x 10(-6)-9.8 x 10(-6) bar(-1)), keeping a linear relatio nship between the two parameters. The values of nu and beta(s) increased wi th an increase in internal cavity, V-cav, and a decrease in accessible surf ace area, ASA, which were calculated from the X-ray crystal structures of t he complexes. A large variation of V-cav relative to ASA by ligand binding suggested that the cavity is a dominant factor and the effect of hydration might be small for the ligand-induced changes of nu and beta(s). The beta(s ) values of the binary and ternary complexes suggested a characteristic con formational flexibility of the kinetic intermediates in the enzyme reaction coordinate. Comparison of beta(s) with the cavity distribution in the crys tal structures revealed that the flexibility of the intermediates was mainl y determined by the total cavity volume with minor contributions of the num ber, position, and size of cavities. These results demonstrate that the com pressibility is a useful measure of the conformational flexibility of the i ntermediates in the enzyme reaction and that the combined study of compress ibility and X-ray crystallography gives new insight into the protein dynami cs through the behavior of the cavities. (C) 2000 Elsevier Science B.V. All rights reserved.