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Molecular‐dynamics simulation of phenylalanine transfer RNA. I. Methods and general results
Author(s) -
Harvey Stephen C.,
Prabhakaran M.,
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.360240706
Subject(s) - chemistry , stacking , ribose , hydrogen bond , molecular dynamics , crystallography , transfer rna , molecule , stereochemistry , rna , base pair , computational chemistry , dna , biochemistry , organic chemistry , enzyme , gene
A 24‐ps molecular‐dynamics simulation of motions in yeast tRNA Phe has been completed. The overall structure of the molecule is well preserved, for the motions represent fluctuations about an average structure that is very much like the crystallographic structure. The four helical stems remain intact, the structures of the loop regions do not deteriorate, and even the base stacking in the single‐stranded amino acid acceptor terminus is maintained. With two exceptions, none of the sugar puckers is significantly changed. The unconstrained floppy motions of base A76 are responsible for the repuckering of ribose 76. The other sugar that repuckers is ribose, 46, and this is the result of a very small structural change in the center of the molecule that is also responsible for the breakage of one tertiary hydrogen bond. This change in local structure does not seriously distort the base‐stacking and intercalation patterns where the variable loop and the D‐stem interact.