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Conformation and flexibility of the 3′‐end of trna
Author(s) -
Kumar N. Vasanth,
Govil Girjesh
Publication year - 2009
Publication title -
international journal of quantum chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.484
H-Index - 105
eISSN - 1097-461X
pISSN - 0020-7608
DOI - 10.1002/qua.560180710
Subject(s) - dihedral angle , flexibility (engineering) , crystal structure , chemistry , crystallography , transfer rna , energy minimization , acceptor , stereochemistry , terminal (telecommunication) , molecule , physics , computational chemistry , computer science , mathematics , rna , hydrogen bond , statistics , biochemistry , organic chemistry , gene , condensed matter physics , telecommunications
A close examination of the crystal structure of tRNA Phe proposed by various groups reveals a great deal of discrepancy in the secondary structure of its acceptor end. The technique of energy minimization has been employed to study the preferred conformations and the flexibility of the pCpCpA fragment. Starting from various structures proposed for the —C—C—A end in tRNA Phe , the energy has been minimized as a function of 17 dihedral angles. A conformation where the terminal adenine is not stacked over the other two bases is found to be the most preferred conformation. This geometry is close to the refined structure proposed by the DUK group. Our results suggest a high degree of flexibility for the terminal adenosine unit in the —C—C—A segment. These findings are compared with the structure of —C—C—A in solution, as observed by nuclear magnetic resonance.