Different potential of mean force of two-state protein GB1 and downhill protein gpW revealed by molecular dynamics simulation

doi:10.1088/1674-1056/ab8daf

中国物理B ›› 2020, Vol. 29 ›› Issue (7): 78701-078701.doi: 10.1088/1674-1056/ab8daf

所属专题： SPECIAL TOPIC — Modeling and simulations for the structures and functions of proteins and nucleic acids

Different potential of mean force of two-state protein GB1 and downhill protein gpW revealed by molecular dynamics simulation

Xiaofeng Zhang(张晓峰), Zilong Guo(郭子龙), Ping Yu(余平), Qiushi Li(李秋实), Xin Zhou(周昕), Hu Chen(陈虎)

1 Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Laboratory for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, China;
2 School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100190, China

收稿日期:2020-03-30 修回日期:2020-04-20 出版日期:2020-07-05 发布日期:2020-07-05
通讯作者: Xin Zhou, Hu Chen E-mail:xzhou@ucas.ac.cn;chenhu@xmu.edu.cn
基金资助:
Project supported by the National Natural Science Foundation of China (Grant Nos. 11874309, 11474237, and 11574310) and the 111 Project, China (Grant No. B16029).

Different potential of mean force of two-state protein GB1 and downhill protein gpW revealed by molecular dynamics simulation

Xiaofeng Zhang(张晓峰)¹, Zilong Guo(郭子龙)¹, Ping Yu(余平)¹, Qiushi Li(李秋实)², Xin Zhou(周昕)², Hu Chen(陈虎)¹

1 Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Laboratory for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, China;
2 School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100190, China

Received:2020-03-30 Revised:2020-04-20 Online:2020-07-05 Published:2020-07-05
Contact: Xin Zhou, Hu Chen E-mail:xzhou@ucas.ac.cn;chenhu@xmu.edu.cn
Supported by:
Project supported by the National Natural Science Foundation of China (Grant Nos. 11874309, 11474237, and 11574310) and the 111 Project, China (Grant No. B16029).

摘要/Abstract

摘要： Two-state folding and down-hill folding are two kinds of protein folding dynamics for small single domain proteins. Here we apply molecular dynamics (MD) simulation to the two-state protein GB1 and down-hill folding protein gpW to reveal the relationship of their free energy landscape and folding/unfolding dynamics. Results from the steered MD simulations show that gpW is much less mechanical resistant than GB1, and the unfolding process of gpW has more variability than that of GB1 according to their force-extension curves. The potential of mean force (PMF) of GB1 and gpW obtained by the umbrella sampling simulations shows apparent difference: PMF of GB1 along the coordinate of extension exhibits a kink transition point where the slope of PMF drops suddenly, while PMF of gpW increases with extension smoothly, which are consistent with two-state folding dynamics of GB1 and downhill folding dynamics of gpW, respectively. Our results provide insight to understand the fundamental mechanism of different folding dynamics of two-state proteins and downhill folding proteins.

关键词: protein folding, molecular dynamics simulation, umbrella sampling, potential of mean force

Abstract: Two-state folding and down-hill folding are two kinds of protein folding dynamics for small single domain proteins. Here we apply molecular dynamics (MD) simulation to the two-state protein GB1 and down-hill folding protein gpW to reveal the relationship of their free energy landscape and folding/unfolding dynamics. Results from the steered MD simulations show that gpW is much less mechanical resistant than GB1, and the unfolding process of gpW has more variability than that of GB1 according to their force-extension curves. The potential of mean force (PMF) of GB1 and gpW obtained by the umbrella sampling simulations shows apparent difference: PMF of GB1 along the coordinate of extension exhibits a kink transition point where the slope of PMF drops suddenly, while PMF of gpW increases with extension smoothly, which are consistent with two-state folding dynamics of GB1 and downhill folding dynamics of gpW, respectively. Our results provide insight to understand the fundamental mechanism of different folding dynamics of two-state proteins and downhill folding proteins.

Key words: protein folding, molecular dynamics simulation, umbrella sampling, potential of mean force

中图分类号: (Proteins)

87.14.E-

87.10.Tf (Molecular dynamics simulation) 87.15.A- (Theory, modeling, and computer simulation)

张晓峰, 郭子龙, 余平, 李秋实, 周昕, 陈虎. Different potential of mean force of two-state protein GB1 and downhill protein gpW revealed by molecular dynamics simulation[J]. 中国物理B, 2020, 29(7): 78701-078701.

Xiaofeng Zhang(张晓峰), Zilong Guo(郭子龙), Ping Yu(余平), Qiushi Li(李秋实), Xin Zhou(周昕), Hu Chen(陈虎). Different potential of mean force of two-state protein GB1 and downhill protein gpW revealed by molecular dynamics simulation[J]. Chin. Phys. B, 2020, 29(7): 78701-078701.

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Different potential of mean force of two-state protein GB1 and downhill protein gpW revealed by molecular dynamics simulation

Different potential of mean force of two-state protein GB1 and downhill protein gpW revealed by molecular dynamics simulation

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