کد مقاله | کد نشریه | سال انتشار | مقاله انگلیسی | نسخه تمام متن |
---|---|---|---|---|
6370024 | 1623845 | 2015 | 5 صفحه PDF | دانلود رایگان |
عنوان انگلیسی مقاله ISI
Folding of SAM-II riboswitch explored by replica-exchange molecular dynamics simulation
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کلمات کلیدی
موضوعات مرتبط
علوم زیستی و بیوفناوری
علوم کشاورزی و بیولوژیک
علوم کشاورزی و بیولوژیک (عمومی)
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چکیده انگلیسی
Riboswitches are cis-acting RNA fragments that function via a conformational transition mechanism when a specific target molecule binds to its binding pocket, representing an inviting new class of biomolecular target for the development of antibiotics. To understand the folding mechanism of SAM-II riboswitch, occurring predominantly in proteobacteria, a 100Â ns replica-exchange molecular dynamics simulation in explicit solvent is performed. Our results show that this RNA pseudoknot has multiple folding pathways, and various intermediate structures. The resultant riboswitch conformational transition map is well consistent with the recent fluorescence measurement, which confirms the dynamical properties of this pseudoknot. Moreover, a novel transition pathway is predicted. The global folding dynamics is mainly coupled with the helix rather than the loop region. The potential folding pathways of the riboswitch presented here should lead to a deeper understanding of the folding mechanism of the riboswitch, as well as the conformational change of RNA pseudoknot.
ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Journal of Theoretical Biology - Volume 365, 21 January 2015, Pages 265-269
Journal: Journal of Theoretical Biology - Volume 365, 21 January 2015, Pages 265-269
نویسندگان
Xu Xue, Wang Yongjun, Li Zhihong,