Influence of Lipid Bilayer on the GPCR Structure: Comparison of All-Atom Lipid Force Fields

被引：8

作者：

Mahmood, Md Iqbal ^{[1
,2
]}

Yamashita, Takefumi ^{[1
]}

机构：

[1] Univ Tokyo, Res Ctr Adv Sci & Technol, Lab Syst Biol & Med, Meguro Ku, 4-6-1 Komaba, Tokyo 1538904, Japan

[2] Nagoya Univ, Grad Sch Sci, Dept Phys, Nagoya, Aichi 4648602, Japan

来源：

BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN | 2021年 / 94卷 / 10期

关键词：

GPCR; Molecular dynamics; Force field; MOLECULAR-DYNAMICS ANALYSIS; CRYSTAL-STRUCTURE; PROTEIN; SIMULATION; PREDICTION; STABILITY;

D O I：

10.1246/bcsj.20210244

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

Lipid bilayers affect the structure and dynamics of membrane proteins significantly. In this study, to examine three AMBER-compatible force fields (GAFFlipid, Slipids, and Lipid14), we conducted molecular dynamics (MD) simulations of beta(2) adrenergic receptor (beta(2)AR) embedded in the palmitoyloleoyl-phosphatidyl-choline (POPC) bilayer. We found that the lipid force field affected protein structures (e.g., stability of the ionic lock) largely, even though they were distant from lipids. For example, while the R131-E268 salt bridge (ionic lock), which is involved in protein activation, opened frequently in GAFFlipid and Lipid14 systems, it mostly remained closed in the Slipids system. This difference should be attributed to the difference in the interaction energy between beta(2)AR and POPC bilayer; this energy was much smaller in the Slipids system than in the GAFFlipid and Lipid14 systems.

引用

页码：2569 / 2574

页数：6

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