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Molecular‐dynamics simulation of phenylalanine transfer RNA. II. Amplitudes, anisotropies, and anharmonicities of atomic motions
Author(s) -
Prabhakaran M.,
Harvey Stephen C.,
McCammon J. Andrew
Publication year - 1985
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360240707
Subject(s) - anharmonicity , chemistry , molecular dynamics , transfer rna , amplitude , anisotropy , nucleic acid , chemical physics , molecule , molecular physics , computational chemistry , crystallography , rna , physics , quantum mechanics , biochemistry , organic chemistry , gene
The atomic motions from a molecular‐dynamics simulation of yeast tRNA Phe are analyzed and compared with those observed in protein simulations. In general, the tRNA motions are of larger amplitude, they are more anisotropic, and they arise from potentials of mean force that are more anharmonic than in the protein case. In both cases, the amplitudes are largest for atoms on the surface of the molecules. On the other hand, the most anisotropic and anharmonic atomic motions are generally found in the interior of the tRNA, while they are found on the surface of the protein. These differences are discussed in terms of the differences in structure between nucleic acids and proteins.