Molecular-dynamics simulation of phenylalanine transfer RNA. I. Methods and general results

✍ Scribed by Stephen C. Harvey; M. Prabhakaran; J. Andrew McCammon

• Publisher: Wiley (John Wiley & Sons)
• Year: 1985
• Tongue: English
• Weight: 885 KB
• Volume: 24
• Category: Article
• ISSN: 0006-3525
• DOI: 10.1002/bip.360240706

✦ Synopsis

Abstract

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.