Computational and NMR analyses for the identification of bound water molecules in ribonuclease T1

A structural characterization of bound water molecules in ribonuclease T1 (RNase T1) was carried out by nuclear magnetic resonance spectroscopy and molecular dynamics simulation. Amide protons of residues Trp59, Leu62, Tyr68 and Phe100 were found to cross-relax with protons of bound waters. Molecular dynamics simulations of the 120 water molecules observed in the free form of the crystal structure indicate that these amide protons donate hydrogen bonds to the less mobile water molecules. Hydrogen-bonded chains of the water molecules that are identified in the simulation study are located in the hairpin-like loop of RNase T1, comprising residues 62 to 76. The temperature factors of the observed water molecules in the crystal structure are very low, indicating that these bound waters are intrinsic components of RNase T1.