Dynamics of 3′‐Cytidine Monophosphate Bound to Ribonuclease A — A Molecular Dynamic Simulation Study

Abstract

AbstractMolecular dynamic simulations of the 3′‐cytidine monophosphate (3′‐CMP)/RNase A complex were carried out at three temperatures, 273 K, 300 K and 323 K. The trajectories obtained allowed us to calculate the dynamics of 3′‐CMP in protein complex. The O‐P bond was found to exert angular fluctuations with an average magnitude of 20° 26°, and 30° at 273 K, 300 K, and 323 K, respectively. These values compare quite favorably with those obtained from lineshape simulation of the 31P NMR powder patterns. The magnitude of the translational fluctuation of the center of mass of the ligand was found to be in the range of 0.17 A to 0.21 Å. On the other hand, the phosphate atom was found to fluctuate with amplitude ranging from 0.22 Å to 0.42 Å, depending on orientation. Fluctuation of the dihedral angle, defined by P‐O3‐C3‐C4′ bonds of the ligand, was more restricted in the protein complex as compared to that in free form. The average number of hydrogen bonds formed between the phosphate group and the protein moiety was 1.6 at 273 K and 1.2 at 323 K.