跨膜蛋白CD3ε与磷脂酰肌醇二磷酸在脂筏域体系中蛋白质-脂质相互作用的粗粒化模拟研究  

Coarse-Grained Molecular Dynamics of Protein-lipid Interaction between CD3ε and PIP2 in Lipid Raft Nanodomains

作　　者：范盎然 杨珂 王旭 施逸凡 陈伟航 华茜 董瑞娟 魏鹏 FAN Ang-Ran;YANG Ke;WANG Xu;SHI Yi-Fan;CHEN Wei-Hang;HUA Qian;DONG Rui-Juan;WEI Peng(Scientific Research Center,School of Traditional Chinese Medicine,Beijing University of Chinese Medicine,Beijing 100029,China;Department of Education,Dongzhimen Hospital,Beijing University of Chinese Medicine,Beijing 100700,China;Department of Acupuncture-Moxibustion,School of Acupuncture-Moxibustion and Tuina,Beijing University of Chinese Medicine,Beijing 100029,China)

机构地区：[1]北京中医药大学中医学院科研中心,北京100029 [2]北京中医药大学第一临床医学院教育处,北京100700 [3]北京中医药大学针灸推拿学院针灸基础系,北京100029

出　　处：《中国生物化学与分子生物学报》2021年第5期627-635,共9页Chinese Journal of Biochemistry and Molecular Biology

基　　金：国家自然科学基金项目(No.31800652);北京中医药大学青年科学家培育计划资助。

摘　　要：细胞膜局部区域可形成富含饱和脂质、胆固醇、鞘脂的脂筏域作为其信号转导调控平台。传统实验手段在研究脂筏及其功能时受到系统复杂度高及区域结构瞬时性强等制约。近年来,分子动力学模拟技术为细胞膜的组织原则提供了重要的理论支撑,从简单的单一组分模型到多组分系统转变,最终形成了越来越多的细胞膜仿真模型。其中,粗粒化模拟由于其简化模型,可大副拓展模拟体系的复杂程度与模拟时间,在细胞膜以及蛋白质-脂质相互作用相关研究中得到了广泛应用。本文采用MARTINI粗粒化力场模拟,构建了一种含有阴离子脂质磷脂酰肌醇二磷酸(phosphatidylinositol diphosphate, PIP2)的混合膜体系。模拟结果表明,该体系在适当温度及饱和度条件下,能自发分层形成脂筏域;膜厚度、膜组分分布、膜组分流动性等多种参数均表明,脂筏结构形成且符合其结构特征;少量PIP2添加不影响分层特性且PIP2对脂筏具有显著亲和性。此外,利用该模型以跨膜信号蛋白CD3ε为例研究了脂筏域体系中蛋白质-脂质相互作用。结果表明,PIP2-CD3ε胞内区相互作用可能是脂筏招募CD3ε的驱动力,且该过程可受钙离子调控。本工作体现了粗粒化模拟在仿真膜相关研究中的巨大优势及良好应用前景。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 Ca2+. These findings provided insights into lipid raft str

关 键 词：脂筏 分子动力学模拟 粗粒化 磷脂酰肌醇二磷酸 蛋白质-脂质相互作用 

分 类 号：Q6-3[生物学—生物物理学] Q51