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

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.

Keywords: molecular dynamics simulation structure-based model all-atom model DNA G-quadruplex

Received: 06 November 2020
Revised: 01 January 2021
Accepted manuscript online: 01 February 2021

PACS:

87.18.Nq

(Large-scale biological processes and integrative biophysics)

Fund: 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).

Corresponding Authors: Yun-Qiang Bian, Ji-Hua Wang
E-mail: bianyunqiang@gmail.com;jhw25336@126.com

Cite this article:

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 2021 Chin. Phys. B 30 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

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