EFFECTOF THE IONTREATMENTONAN RNA HAIRPIN: MOLECULAR DYNAMICS STUDY
| Main Author: | Perpustakaan UGM, i-lib |
|---|---|
| Format: | Article NonPeerReviewed |
| Terbitan: |
[Yogyakarta] : Universitas Gadjah Mada
, 2011
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| Subjects: | |
| Online Access: |
https://repository.ugm.ac.id/28538/ http://i-lib.ugm.ac.id/jurnal/download.php?dataId=11601 |
Daftar Isi:
- 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