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

• 作者: Hu Chen Ping Yu Qiushi Li Xiaofeng Zhang Xin Zhou Zilong Guo
• 来源期刊: 中国物理B（英文版）
• 关键词: protein folding molecular dynamics simulation umbrella sampling potential of mean force
• 年，卷（期）: 2020,（7）
• 页码范围: 109-114
• 页数: 6页
• 语种: 英文
• DOI: 10.1088/1674-1056/ab8daf

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 GB 1 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 GB 1,and the unfolding process of gpW has more variability than that of GB 1 according to their force-extension curves.The potential of mean force (PMF) of GB 1 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.