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Science 16 March 1984:
Vol. 223. no. 4641, pp. 1189 - 1191
DOI: 10.1126/science.6560785
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Articles

Science, Vol 223, Issue 4641, 1189-1191
Copyright © 1984 by American Association for the Advancement of Science

articles

Phenylalanine transfer RNA: molecular dynamics simulation

SC Harvey, M Prabhakaran, B Mao, and JA McCammon

Yeast phenylalanine transfer RNA was subjected to a 12-picosecond molecular dynamics simulation. The principal features of the x-ray crystallographic analysis are reproduced, and the amplitudes of atomic displacements appear to be determined by the degree of exposure of the atoms. An analysis of the hydrogen bonds shows a correlation between the average length of a bond and the fluctuation in that length and reveals a rocking motion of bases in Watson-Crick guanine X cytosine base pairs. The in-plane motions of the bases are generally of larger amplitude than the out-of-plane motions, and there are correlations in the motions of adjacent bases.




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Science. ISSN 0036-8075 (print), 1095-9203 (online)