MOLECULAR DYNAMIC SIMULATIONS OF LARGE RNA MOLECULES: THE YEAST tRNAPhe
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 we...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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Gdańsk University of Technology
1999-07-01
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| Series: | TASK Quarterly |
| Subjects: | |
| Online Access: | https://journal.mostwiedzy.pl/TASKQuarterly/article/view/2404 |
| _version_ | 1818264409641844736 |
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| author | BARTOSZ PLISZKA STANISŁAW OŁDZIEJ |
| author_facet | BARTOSZ PLISZKA STANISŁAW OŁDZIEJ |
| author_sort | BARTOSZ PLISZKA |
| collection | DOAJ |
| description |
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.
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| first_indexed | 2024-12-12T19:34:27Z |
| format | Article |
| id | doaj.art-bdca1be4d93540139bfa30908db6adb4 |
| institution | Directory Open Access Journal |
| issn | 1428-6394 |
| language | English |
| last_indexed | 2024-12-12T19:34:27Z |
| publishDate | 1999-07-01 |
| publisher | Gdańsk University of Technology |
| record_format | Article |
| series | TASK Quarterly |
| spelling | doaj.art-bdca1be4d93540139bfa30908db6adb42022-12-22T00:14:21ZengGdańsk University of TechnologyTASK Quarterly1428-63941999-07-0133MOLECULAR DYNAMIC SIMULATIONS OF LARGE RNA MOLECULES: THE YEAST tRNAPheBARTOSZ PLISZKA0STANISŁAW OŁDZIEJ1University of Gdansk, Faculty of ChemistryUniversity of Gdansk, Faculty of Chemistry 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. https://journal.mostwiedzy.pl/TASKQuarterly/article/view/2404tRNAPhemolecular dynamicsmodified basesnucleic acidselectrostatic interaction |
| spellingShingle | BARTOSZ PLISZKA STANISŁAW OŁDZIEJ MOLECULAR DYNAMIC SIMULATIONS OF LARGE RNA MOLECULES: THE YEAST tRNAPhe TASK Quarterly tRNAPhe molecular dynamics modified bases nucleic acids electrostatic interaction |
| title | MOLECULAR DYNAMIC SIMULATIONS OF LARGE RNA MOLECULES: THE YEAST tRNAPhe |
| title_full | MOLECULAR DYNAMIC SIMULATIONS OF LARGE RNA MOLECULES: THE YEAST tRNAPhe |
| title_fullStr | MOLECULAR DYNAMIC SIMULATIONS OF LARGE RNA MOLECULES: THE YEAST tRNAPhe |
| title_full_unstemmed | MOLECULAR DYNAMIC SIMULATIONS OF LARGE RNA MOLECULES: THE YEAST tRNAPhe |
| title_short | MOLECULAR DYNAMIC SIMULATIONS OF LARGE RNA MOLECULES: THE YEAST tRNAPhe |
| title_sort | molecular dynamic simulations of large rna molecules the yeast trnaphe |
| topic | tRNAPhe molecular dynamics modified bases nucleic acids electrostatic interaction |
| url | https://journal.mostwiedzy.pl/TASKQuarterly/article/view/2404 |
| work_keys_str_mv | AT bartoszpliszka moleculardynamicsimulationsoflargernamoleculestheyeasttrnaphe AT stanisławołdziej moleculardynamicsimulationsoflargernamoleculestheyeasttrnaphe |