Molecular Dynamics and Free Energy Perturbation Calculations on the Mutation of Tyrosine 45 to Tryptophan in Ribonuclease T₁

Abstract

The mutation of tyrosine 45 to tryptophan in ribonuclease T₁ enhances uncleolytic and binding abilities to its ligands [S. Nishikawa et al., Eur. J. Biochem., 173, 389 (1988)]. To examine the energetic and structural influence of this mutation in ribonuclease T₁, we made molecular dynamics and free energy perturbation calculations by converting the wild-type enzyme to the mutant one. The calculated difference of free energy changes following binding to 2'-guanylic acid (2'-GMP) molecule well agreed with experimental value. Between the mutant-2'-GMP complex and the wild-type-2'-GMP complex, subtle structural changes in stacking and hydrogen bonding interactions were found. Enhanced activity was almost entirely attributable to increased hydrophobic interaction between the ligand and the mutant enzyme. in the vicinity of ligand binding site, distributed water molecules revealed typical unordered structure around apolar atoms.