دورية أكاديمية
EFFECT OF THE ION TREATMENT ON AN RNA HAIRPIN: MOLECULAR DYNAMICS STUDY
| العنوان: | EFFECT OF THE ION TREATMENT ON AN RNA HAIRPIN: MOLECULAR DYNAMICS STUDY |
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| المؤلفون: | Elisabeth Catherina Widjajakusuma, Alessandra Villa, Gerhard Stock |
| المصدر: | Indonesian Journal of Chemistry, Vol 12, Iss 1, Pp 1-11 (2012) |
| بيانات النشر: | Department of Chemistry, Universitas Gadjah Mada, 2012. |
| سنة النشر: | 2012 |
| المجموعة: | LCC:Chemistry |
| مصطلحات موضوعية: | RNA hairpin, md simulations, ion treatment, Coxsackievirus B3, Chemistry, QD1-999 |
| الوصف: | Molecular dynamics has been employed to study the effect of ion treatment on the stability of 14-nucleotide 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 Mg2+ 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+, 1,03 M Na+, and 0.08 M Mg2+ concentrations. However, the simulations revealed different ion occupations of Na+ and Mg2+. |
| نوع الوثيقة: | article |
| وصف الملف: | electronic resource |
| اللغة: | English |
| تدمد: | 1411-9420 2460-1578 |
| العلاقة: | https://jurnal.ugm.ac.id/ijc/article/view/21365Test; https://doaj.org/toc/1411-9420Test; https://doaj.org/toc/2460-1578Test |
| DOI: | 10.22146/ijc.21365 |
| الوصول الحر: | https://doaj.org/article/afd82bf91e9c410c857b09147ad16527Test |
| رقم الانضمام: | edsdoj.fd82bf91e9c410c857b09147ad16527 |
| قاعدة البيانات: | Directory of Open Access Journals |
| تدمد: | 14119420 24601578 |
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| DOI: | 10.22146/ijc.21365 |