Structure-based simulations complemented by conventional all-atom simulations to provide new insights into the folding dynamics of human telomeric G-quadruplex

doi:10.1088/1674-1056/abe1a7

中国物理B ›› 2021, Vol. 30 ›› Issue (7): 78702-078702.doi: 10.1088/1674-1056/abe1a7

Structure-based simulations complemented by conventional all-atom simulations to provide new insights into the folding dynamics of human telomeric G-quadruplex

Yun-Qiang Bian(边运强)^†, Feng Song(宋峰), Zan-Xia Cao(曹赞霞), Jia-Feng Yu(于家峰), and Ji-Hua Wang(王吉华)^‡

Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China

收稿日期:2020-11-06 修回日期:2021-01-01 接受日期:2021-02-01 出版日期:2021-06-22 发布日期:2021-06-22
通讯作者: Yun-Qiang Bian, Ji-Hua Wang E-mail:bianyunqiang@gmail.com;jhw25336@126.com
基金资助:
Project supported by the National Natural Science Foundation of China (Grant Nos. 11504043, 61671107, 31670727, and 61771093), the Science Foundation of Shandong Province of China (Grant No. ZR2016JL027), the Taishan Young Scholars Program of Shandong Province of China (Grant No. tsqn20161049), and the Youth Science and Technology Innovation Plan of Universities in Shandong, China (Grant No. 2019KJE007).

Structure-based simulations complemented by conventional all-atom simulations to provide new insights into the folding dynamics of human telomeric G-quadruplex

Yun-Qiang Bian(边运强)^†, Feng Song(宋峰), Zan-Xia Cao(曹赞霞), Jia-Feng Yu(于家峰), and Ji-Hua Wang(王吉华)^‡

Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China

Received:2020-11-06 Revised:2021-01-01 Accepted:2021-02-01 Online:2021-06-22 Published:2021-06-22
Contact: Yun-Qiang Bian, Ji-Hua Wang E-mail:bianyunqiang@gmail.com;jhw25336@126.com
Supported by:
Project supported by the National Natural Science Foundation of China (Grant Nos. 11504043, 61671107, 31670727, and 61771093), the Science Foundation of Shandong Province of China (Grant No. ZR2016JL027), the Taishan Young Scholars Program of Shandong Province of China (Grant No. tsqn20161049), and the Youth Science and Technology Innovation Plan of Universities in Shandong, China (Grant No. 2019KJE007).

1. 2021-078702-SI.pdf(1075KB)

摘要/Abstract

摘要： The hybrid atomistic structure-based model has been validated to be effective in investigation of G-quadruplex folding. In this study, we performed large-scale conventional all-atom simulations to complement the folding mechanism of human telomeric sequence Htel24 revealed by a multi-basin hybrid atomistic structure-based model. Firstly, the real time-scale of folding rate, which cannot be obtained from the structure-based simulations, was estimated directly by constructing a Markov state model. The results show that Htel24 may fold as fast as on the order of milliseconds when only considering the competition between the hybrid-1 and hybrid-2 G-quadruplex conformations. Secondly, in comparison with the results of structure-based simulations, more metastable states were identified to participate in the formation of hybrid-1 and hybrid-2 conformations. These findings suggest that coupling the hybrid atomistic structure-based model and the conventional all-atom model can provide more insights into the folding dynamics of DNA G-quadruplex. As a result, the multiscale computational framework adopted in this study may be useful to study complex processes of biomolecules involving large conformational changes.

关键词: molecular dynamics simulation, structure-based model, all-atom model, DNA G-quadruplex

Abstract: The hybrid atomistic structure-based model has been validated to be effective in investigation of G-quadruplex folding. In this study, we performed large-scale conventional all-atom simulations to complement the folding mechanism of human telomeric sequence Htel24 revealed by a multi-basin hybrid atomistic structure-based model. Firstly, the real time-scale of folding rate, which cannot be obtained from the structure-based simulations, was estimated directly by constructing a Markov state model. The results show that Htel24 may fold as fast as on the order of milliseconds when only considering the competition between the hybrid-1 and hybrid-2 G-quadruplex conformations. Secondly, in comparison with the results of structure-based simulations, more metastable states were identified to participate in the formation of hybrid-1 and hybrid-2 conformations. These findings suggest that coupling the hybrid atomistic structure-based model and the conventional all-atom model can provide more insights into the folding dynamics of DNA G-quadruplex. As a result, the multiscale computational framework adopted in this study may be useful to study complex processes of biomolecules involving large conformational changes.

Key words: molecular dynamics simulation, structure-based model, all-atom model, DNA G-quadruplex

中图分类号: (Large-scale biological processes and integrative biophysics)

87.18.Nq

Yun-Qiang Bian(边运强), Feng Song(宋峰), Zan-Xia Cao(曹赞霞), Jia-Feng Yu(于家峰), and Ji-Hua Wang(王吉华). Structure-based simulations complemented by conventional all-atom simulations to provide new insights into the folding dynamics of human telomeric G-quadruplex[J]. 中国物理B, 2021, 30(7): 78702-078702.

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Structure-based simulations complemented by conventional all-atom simulations to provide new insights into the folding dynamics of human telomeric G-quadruplex

Structure-based simulations complemented by conventional all-atom simulations to provide new insights into the folding dynamics of human telomeric G-quadruplex

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