MOLECULAR DYNAMIC SIMULATIONS OF LARGE RNA MOLECULES: THE YEAST tRNAPhe

TASK Quarterly

BARTOSZ PLISZKA¹  STANISŁAW OŁDZIEJ¹ 

[1] University of Gdansk, Faculty of Chemistry;

关键词: tRNAPhe;    molecular dynamics;    modified bases;    nucleic acids;    electrostatic interaction;   

DOI  :  

来源: DOAJ

【 摘 要 】

Molecular dynamics trajectories (700 ps) of the solvated and neutralized 75-residue yeast tRNAPhe were generated using the AMBER 5.0 molecular dynamics software package. The cut-off scheme was used to treat electrostatic interactions; consequently, all long-range interactions beyond 12 angstroms were neglected. The equilibration procedure and conditions during simulations led to a dynamically stable model of the tRNA molecule. During the simulations all base-base interactions (which determine the secondary and the tertiary structure of the molecule) were well preserved. Consequently, the global shape of the molecule was preserved well and the RMS deviation calculated between the starting x-ray structure and the final structure after 700 ps of simulations was 3.25 angstroms. The biggest deviation is observed in the region of the anticodon hairpin loop; this high mobility is associated with the presence of a very unusual Y-base and a binding site of a magnesium ion in this region.

【 授权许可】

Unknown