期刊
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
卷 10, 期 18, 页码 5667-5673出版社
AMER CHEMICAL SOC
DOI: 10.1021/acs.jpclett.9b01556
关键词
-
类别
资金
- National Institutes of Health [R01 GM116961]
- Department of Chemistry, University of Illinois at Urbana Champaign
- NSF [MCB 1803786]
Proteins in vivo are immersed in a crowded environment of water, ions, metabolites, and macromolecules. In-cell experiments highlight how transient weak protein-protein interactions promote (via functional quinary structure) or hinder (via competitive binding or sticking) complex formation. Computational models of the cytoplasm are expensive. We tackle this challenge with an all-atom model of a small volume of the E. coli cytoplasm to simulate protein-protein contacts up to the 5 mu s time scale on the special-purpose supercomputer Anton 2. We use three CHARMM-derived force fields: C22*, C36m, and C36mCU (with CUFIX corrections). We find that both C36m and C36mCU form smaller contact surfaces than C22*. Although CUFIX was developed to reduce protein-protein sticking, larger contacts are observed with C36mCU than C36m. We show that the lifespan Delta t of protein-protein contacts obeys a power law distribution between 0.03 and 3 mu s, with similar to 90% of all contacts lasting <1 mu s (similar to the time scale for downhill folding).
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据