Structural Stability of the Anticodon Stem Loop Domains of the Unmodified Yeast and Escherichia coli tRNA ^Phe:Differing Views from Different Force Fields

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 tRNA Phe showed preserved anticodon stem loop (ASL) conformation compared with that of the natively modified mature yeast tRNA Phe . On the other hand, NMR studies reveal that both unmodified E. coli and incompletely modified yeast tRNA Phe 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 tRNA Phe in explicit water with two recently revised AMBER force fields for RNA, ff99bsc0TOR YIL and ff99bsc0χ OL3 , starting from the X-ray derived structures in the canonical conformation. For a single ASL system, five independent simulations of 200 ns each were performed yielding 4000 ns (or 4 μs) of simulation time in total. The ff99bsc0χ OL3 force field was found to retain the X-ray-like conformational features during the entire course of simulations of both the ASLs in the absence of natural modifications. In the case of the ff99bsc0TOR YIL force field, the observed deviations from the initial structures, conformational flexibility, and destabilization in the canonical U-turn structure and in the A-RNA-like conformational preferences for the backbone torsion angles were noticeably larger compared with those obtained with the ff99bsc0χ OL3 force field. The observed destabilization in the canonical anticodon stair-stepped conformation was larger for the unmodified ASLs of yeast tRNA Phe compared with that of E. coli. However, none of the force fields could reproduce the conformational characteristics reported in the solution NMR studies of unmodified E. coli and incompletely modified yeast tRNA Phe ASL structures.