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Dynamics of 3′‐Cytidine Monophosphate Bound to Ribonuclease A — A Molecular Dynamic Simulation Study
Author(s) -
Lee KueiJen,
Huang TaiHuang
Publication year - 1995
Publication title -
journal of the chinese chemical society
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.329
H-Index - 45
eISSN - 2192-6549
pISSN - 0009-4536
DOI - 10.1002/jccs.199500123
Subject(s) - chemistry , cytidine , dihedral angle , molecular dynamics , ligand (biochemistry) , hydrogen bond , crystallography , moiety , ribonuclease , rnase p , protein dynamics , bond length , stereochemistry , computational chemistry , molecule , rna , crystal structure , enzyme , biochemistry , organic chemistry , receptor , gene
Molecular 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 31 P 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‐O 3 ‐C 3 ‐C 4 ′ 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.