LAUSR

Unmodified tRNAs provide essential insights into the structural and functional role of the extensive and diverse post-transcriptional modifications that naturally occur in tRNAs. The X-ray crystal structure of the completely unmodified Escherichia coli tRNAPhe showed preserved anticodon stem loop (ASL) conformation compared with that of the natively modified mature yeast tRNAPhe. On the other hand, NMR studies reveal that both unmodified E. coli and incompletely modified yeast tRNAPhe ASL structures differ from the canonical conformation by adopting altered conformations resembling extended stems and shorter loops. In the present work, we performed molecular dynamics simulation of the ASL domains of the unmodified counterparts of the yeast and E. coli tRNAPhe in explicit water with two recently revised AMBER force fields for RNA, ff99bsc0TORYIL and ff99bsc0χOL3, starting from the X-ray derived structures in the canonical conformation. For a single ASL system, five independent simulations of 200 ns each we...