Coarse-Grained Molecular Dynamics of Protein-lipid Interaction between CD3ε and PIP2 in Lipid Raft Nanodomains
10.13865/j.cnki.cjbmb.2021.04.1671
- Author:
Ang-Ran FAN
1
;
Ke YANG
1
;
Xu WANG
1
;
Qian HUA
1
;
Rui-Juan DONG
1
;
Peng WEI
1
;
Yi-Fan SHI
2
;
Wei-Hang CHEN
3
Author Information
1. Scientific Research Center, School of Traditional Chinese Medicine, Beijing University of Chinese Medicine
2. Department of Education, Dongzhimen Hospital, Beijing University of Chinese Medicine
3. Department of Acupuncture-Moxibustion, School of Acupuncture-Moxibustion and Tuina, Beijing University of Chinese Medicine
- Publication Type:Journal Article
- Keywords:
coarse-grained;
lipid raft;
molecular dynamics simulation;
phosphatidylinositol diphosphate (PIP2);
protein-lipid interaction
- From:
Chinese Journal of Biochemistry and Molecular Biology
2021;37(5):627-635
- CountryChina
- Language:Chinese
-
Abstract:
Lipid raft nanodomains of plasma membrane are rich in saturated lipids‚ cholesterol‚ sphingolipids‚ functioning as multimolecular platforms to recruit signaling and trafficking proteins involved in an array of physiological processes‚ which are critical for regulating signal transduction in cell. The staggering complexity of cell membranes and the transient formation of nanodomains greatly hinder research on lipid rafts by traditional experimental means. Molecular dynamics simulations have provided important insight into the organizational principles of cell membranes recently. Simulated membrane systems are under a transition from simple membrane models to multicomponent systems‚ culminating in realistic models of various cell types. Coarse-grained models have been extensively adopted as a powerful tool to explore membrane organization and interactions between lipids and proteins‚ providing efficient computational speed and enabling complex systems. In this work‚ coarse-grained molecular dynamics simulations with MARTINI force field were performed to build a raft-forming membrane with mixed lipids‚ including negatively charged lipid PIP2. Mixed lipids in this model were spontaneously partitioned into binary-phase membrane during 5 μs simulations by low temperature (295 K) treatment‚ forming lipid ordered (Lo) and liquid-disordered (Ld) nanodomains. Results of membrane thickness‚ lipid distribution‚ membrane fluidity‚ order parameters of the acyl tails‚ radial distribution functions were consistent with simulation and experimental data. Addition of small amounts of PIP2 did not affect the raft formation‚ and it showed remarkable affinity to lipid raft nanodomains. Simulations of the signaling transmembrane protein CD3ε in our raft-forming membranes were further performed to study the protein-lipid interaction as well. Results showed that the cytoplasmic tail of CD3ε was recruited to the Lo/ Ld boundary due to PIP2 binding‚ and this binding was regulated by Ca
