EFFECTOF THE IONTREATMENTONAN RNA HAIRPIN: MOLECULAR DYNAMICS STUDY
Molecular dynamics has been employed to study the effect of ion treatment on the stability of 14-nucleQtide RNA hairpin of Coxsackievirus B3. Three AMBER force fields were used: AMBER94, AMBER98, and AMBER99, which showed no significant structural difference of the hairpin. Thereafter, we applied tw...
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[Yogyakarta] : Universitas Gadjah Mada
2011
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| _version_ | 1826033246023974912 |
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| author | Perpustakaan UGM, i-lib |
| author_facet | Perpustakaan UGM, i-lib |
| author_sort | Perpustakaan UGM, i-lib |
| collection | UGM |
| description | Molecular dynamics has been employed to study the effect of ion treatment on the stability of 14-nucleQtide RNA hairpin of Coxsackievirus B3. Three AMBER force fields were used: AMBER94, AMBER98, and AMBER99, which showed no significant structural difference of the hairpin. Thereafter, we applied two different long-range
electrostatic treatments that were reaction field and PME methods, and calculated the distribution of ions around the hairpin. Although the structural stabilities of the MD simulations using both methods were similar in 0.14 M Na+,ion environment around the hairpin was notably different. In particular, structural stabilition of the hairpin with increasing ion concentration and with ion Mi+ cannot be accommodated by simulations using reaction field method. Furthermore, the MD simulations using PME method suggested the strong similarity in structural and dynamical
properties of the hairpin with 0.14 M Na+,0.50 M Na+, 1.03M Na+,and 0.08 M Mi+ concentrations. However, the simulations ravea/eddifferent ion occupations of Na+and Mg2 |
| first_indexed | 2024-03-05T23:12:41Z |
| format | Article |
| id | oai:generic.eprints.org:28538 |
| institution | Universiti Gadjah Mada |
| last_indexed | 2024-03-05T23:12:41Z |
| publishDate | 2011 |
| publisher | [Yogyakarta] : Universitas Gadjah Mada |
| record_format | dspace |
| spelling | oai:generic.eprints.org:285382014-06-18T00:23:26Z https://repository.ugm.ac.id/28538/ EFFECTOF THE IONTREATMENTONAN RNA HAIRPIN: MOLECULAR DYNAMICS STUDY Perpustakaan UGM, i-lib Jurnal i-lib UGM Molecular dynamics has been employed to study the effect of ion treatment on the stability of 14-nucleQtide RNA hairpin of Coxsackievirus B3. Three AMBER force fields were used: AMBER94, AMBER98, and AMBER99, which showed no significant structural difference of the hairpin. Thereafter, we applied two different long-range electrostatic treatments that were reaction field and PME methods, and calculated the distribution of ions around the hairpin. Although the structural stabilities of the MD simulations using both methods were similar in 0.14 M Na+,ion environment around the hairpin was notably different. In particular, structural stabilition of the hairpin with increasing ion concentration and with ion Mi+ cannot be accommodated by simulations using reaction field method. Furthermore, the MD simulations using PME method suggested the strong similarity in structural and dynamical properties of the hairpin with 0.14 M Na+,0.50 M Na+, 1.03M Na+,and 0.08 M Mi+ concentrations. However, the simulations ravea/eddifferent ion occupations of Na+and Mg2 [Yogyakarta] : Universitas Gadjah Mada 2011 Article NonPeerReviewed Perpustakaan UGM, i-lib (2011) EFFECTOF THE IONTREATMENTONAN RNA HAIRPIN: MOLECULAR DYNAMICS STUDY. Jurnal i-lib UGM. http://i-lib.ugm.ac.id/jurnal/download.php?dataId=11601 |
| spellingShingle | Jurnal i-lib UGM Perpustakaan UGM, i-lib EFFECTOF THE IONTREATMENTONAN RNA HAIRPIN: MOLECULAR DYNAMICS STUDY |
| title | EFFECTOF THE IONTREATMENTONAN RNA HAIRPIN: MOLECULAR DYNAMICS STUDY |
| title_full | EFFECTOF THE IONTREATMENTONAN RNA HAIRPIN: MOLECULAR DYNAMICS STUDY |
| title_fullStr | EFFECTOF THE IONTREATMENTONAN RNA HAIRPIN: MOLECULAR DYNAMICS STUDY |
| title_full_unstemmed | EFFECTOF THE IONTREATMENTONAN RNA HAIRPIN: MOLECULAR DYNAMICS STUDY |
| title_short | EFFECTOF THE IONTREATMENTONAN RNA HAIRPIN: MOLECULAR DYNAMICS STUDY |
| title_sort | effectof the iontreatmentonan rna hairpin molecular dynamics study |
| topic | Jurnal i-lib UGM |
| work_keys_str_mv | AT perpustakaanugmilib effectoftheiontreatmentonanrnahairpinmoleculardynamicsstudy |