Computer modeling studies of ribonuclease T₁-guanosine monophosphate complexes

Abstract

The three-dimensional structures of ribonuclease (RNase) T₁ complexes with the inhibitors 2'-guanylic acid (2'-GMP), 3'-guanylic acid (3'-GMP), and 5'-guanylic acid (5'-GMP) were predicted by energy minimization studies. It is shown that these inhibitors can bind to RNase T₁ in either of the ribose puckered conformations (C2'-endo and C3'-endo) in solid state and exist in significant amounts in both forms in solution. These studies are in agreement with the x-ray crystallographic studies of the 2'-GMP-Lys25-RNase T₁ complex, where the inhibitor binds in C2'-endo puckered conformation. These results are also in good agreement with the available ¹H-nmr results of Inagaki et al. [(1985) Biochemistry24, 1013-1020], but differ from their conclusions where the authors favor only the C3'-endo ribose conformation for all the three inhibitors. The calculations explain the apparent discrepancies in the conclusions drawn by x-ray crystallographic and spectroscopic studies. An extensive hydrogen-bonding scheme was predicted in all the three complexes. The hydrogen-bonding scheme predicted for the 2'-GMP (C2'-endo)-RNase T₁ complex agrees well with those reported from x-ray crystallographic studies. In all three complexes the base and the phosphate bind in nearly identical sites independent of the position of the phosphate or the ribose pucker. The glycosyl torsion angle favors a value in the +syn range in the 2'-GMP(C2'-endo)-RNase T₁, 3'-GMP(C2'-endo)-RNase T₁, and 3-GMP(C3'-endo)-RNase T₁ complexes; in the high-synrange in the 2'-GMP(C3'-endo)-RNase T₁ complex; and in the -syn range in the 5'-GMP(C2'-endo)-RNase T₁, and 5'-GMP(C3'-endo)-RNase T₁ complexes. These results are in agreement with experimental studies showing that the inhibitory power decreases in the order 2'-GMP > 3'-GMP > 5'-GMP, and they also explain the high pK_a value observed for Glu58 in the 2'-GMP-RNase T₁ complex.