Molecular dynamic simulations of large RNA molecules: the yeast tRNA Phe

• Autorzy: Pliszka B. , Ołodziej S.
• Języki publikacji: EN

Abstrakty

EN

Molecular dynamics trajectories (700 ps) of the solvated and neutralized 75-residue yeast tRNA Phe 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.

Słowa kluczowe

EN

tRNA Phe; molecular dynamics; modified bases; nucleic acids; electrostatic interaction

• Wydawca: Politechnika Gdańska
• Czasopismo: TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk
• Rocznik: 1999
• Tom: Vol. 3, No 3
• Strony: 333--342
• Opis fizyczny: Bibliogr. 19 poz., rys.

Twórcy

autor

Pliszka B.

• Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland

autor

Ołodziej S.

• Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland

Bibliografia

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