Phenylalanine transfer RNA: molecular dynamics simulation.
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.
D055598:Chemical Phenomena; D002621:Chemistry; D003201:Computers; D003596:Cytosine; D006147:Guanine; D006860:Hydrogen Bonding; D009690:Nucleic Acid Conformation; D012331:RNA, Fungal; D012346:RNA, Transfer, Amino Acyl; D015003:Yeasts / Q000032:analysis
D012331:RNA, Fungal; D012346:RNA, Transfer, Amino Acyl; D006147:Guanine; D003596:Cytosine