Evolution of Conformation and Dynamics of Solvents in Hydration Shell along the Urea-induced Unfolding of Ubiquitin

Ke-Cheng Yang; Feng-Chao Cui; Ce Shi; Wen-Duo Chen; Yun-Qi Li

doi:10.1007/s10118-019-2238-8

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Evolution of Conformation and Dynamics of Solvents in Hydration Shell along the Urea-induced Unfolding of Ubiquitin

ARTICLE | Updated：2021-02-18

- Evolution of Conformation and Dynamics of Solvents in Hydration Shell along the Urea-induced Unfolding of Ubiquitin
- Evolution of Conformation and Dynamics of Solvents in Hydration Shell along the Urea-induced Unfolding of Ubiquitin
- Chinese Journal of Polymer Science 2019年37卷第7期页码：708-718
- Affiliations：
  
  a.Key Laboratory of Synthetic Rubber, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
  b.Smart City Research Institute, Zhengzhou University, Zhengzhou 450001, China
- Author bio：
  
  fccui@ciac.ac.cn (F.C.C.)
  yunqi@ciac.ac.cn (Y.Q.L.)
- Funds：
  
  This work was financially supported by the National Natural Science Foundation of China (Nos. 21504092 and U1832177), and One Hundred Person Project of the Chinese Academy of Sciences. We are also grateful to Computing Center of Jilin Province and Henan Province Supercomputer Center for essential support.
- DOI：10.1007/s10118-019-2238-8
  中图分类号：
- 收稿：2018-12-24，
  
  修回：2019-1-18，
  
  录用：2019-1-31，
  
  网络首发：2019-03-14，
  
  纸质出版：2019-07
- Accepted：
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Citation: Yang, K. C.; Cui, F. C.; Shi, C.; Chen, W. D.; Li, Y. Q. Evolution of conformation and dynamics of solvents in hydration shell along the urea-induced unfolding of ubiquitin. Chinese J. Polym. Sci. 2019, 37, 708–718

Ke-Cheng Yang, Feng-Chao Cui, Ce Shi, et al. Evolution of Conformation and Dynamics of Solvents in Hydration Shell along the Urea-induced Unfolding of Ubiquitin[J]. Chinese Journal of Polymer Science, 2019, 37(7): 708-718.
Citation: Yang, K. C.; Cui, F. C.; Shi, C.; Chen, W. D.; Li, Y. Q. Evolution of conformation and dynamics of solvents in hydration shell along the urea-induced unfolding of ubiquitin. Chinese J. Polym. Sci. 2019, 37, 708–718 DOI： 10.1007/s10118-019-2238-8.

Ke-Cheng Yang, Feng-Chao Cui, Ce Shi, et al. Evolution of Conformation and Dynamics of Solvents in Hydration Shell along the Urea-induced Unfolding of Ubiquitin[J]. Chinese Journal of Polymer Science, 2019, 37(7): 708-718. DOI： 10.1007/s10118-019-2238-8.

摘要

Abstract

A clear diagram for the unfolding of protein induced by denaturant is a classical but still unsolved challenge. To explore the unfolded conformations of ubiquitin under different urea concentrations

we performed hybrid Monte Carlo-molecular dynamics simulations (MC-MD) guided by small angle X-ray scattering (SAXS) structural information. Conformational ensembles sampled by the hybrid MC-MD algorithm exhibited typical 3D structures at different urea concentrations. These typical structures suggested that ubiquitin was subjected to a sequential unfolding

where the native contacts between adjacent

-sheets at first were disrupted together with the exposure of hydrophobic core

followed by the conversion of remaining

-strands and helices into random coils. Ubiquitin in 8 mol·L

−1

urea is almost a random coil. With the disruption of native structure

urea molecules are enriched at protein hydrated layer to stabilize newly exposed residues. Compared with water

urea molecules prefer to form hydrogen bonds with the backbone of ubiquitin

thus occupying nodes of the hydrogen bonding network that construct the secondary structure of proteins. Meanwhile

we also found that the slow dynamics of urea molecules was almost unchanged while the dynamics of water was accelerated in the hydration shell when more residues were unfolded and exposed. The former was also responsible for the stabilization of unfolded structures.

关键词

Keywords

references

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