MOLECULAR DYNAMICS STUDIES OF GATING MECHANISM OF MSCL AS A FUNCTION OF HELIX T

MSCL门控机制作为螺旋T函数的分子动力学研究

• 批准号: 7956256
• 负责人: Wonpil Im
• 金额: $ 0.08万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-08-01 至 2010-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7956256
• 关键词: Binding; Biomedical Research; C-terminal; Complex; Computer Retrieval of Information on Scientific Projects Database; Cytoplasm; Funding; Grant; High Performance Computing; Homo; Image; Institution; Lipid Bilayers; Lipids; Membrane; Research; Research Personnel; Resources; Shapes; Side; Source; Structure; Surface Tension; System; Temperature; Transmembrane Domain; United States National Institutes of Health; molecular dynamics; periplasm; pressure; restraint; simulation; web site

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. MscL, the mechanosensitive channel of large conductance, forms a homo-pentameric pore in which each subunit contains two transmembrane (TM) domains (TM1 and TM2) involved in the channel gating, and a C-terminal cytoplasmic helical domain. The crystal structure (PDB ID:2OAR) represents a closed state of the channel, showing a funnel shaped pore with a large opening on the periplasmic side and the narrowest point near the cytoplasm. Assuming that TM helix tilting due to membrane tension drives MscL gating, we will perform molecular dynamics simulations by applying the recently developed helix tilt restraint potential to the TM helices of MscL in a DMPC lipid bilayer. An initial structure of the MscL/DMPC complex without C-terminal helix (Gln110-Asn125) was generated using Membrane Builder in the CHARMM-GUI website (http://www.charmm-gui.org). CT?P (constant temperature, surface tension, and pressure) dynamics will be used to allow the system size along the XY axes to vary during the simulation. The P21 image transformation will be used to allow the number of lipid molecules in the top and bottom leaflets to vary during the simulations. Three different simulations will be performed by tilting (1) both TM1 and TM2 helices (10 restraints), (2) only TM1 helices (5 restraints), and (3) only TM2 helices (5 restraints). The tilt angles of TM1 helices will be gradually varied from 35 (PDB ID:2OAR) to 65 by 1 and those of TM2 from 33 (PDB ID:2OAR) to 63 by 1, together or separately. We will analyze the change of the pore size, molecular interactions, and pressure profile as a function of helix tilt to explore the possible gating mechanisms of MscL at the atomic level.

该子项目是利用该技术的众多研究子项目之一 资源由 NIH/NCRR 资助的中心拨款提供。子项目和 研究者 (PI) 可能已从 NIH 的另一个来源获得主要资金， 因此可以在其他 CRISP 条目中表示。列出的机构是 对于中心来说，它不一定是研究者的机构。 MscL 是大电导的机械敏感通道，形成同源五聚体孔，其中每个亚基包含两个参与通道门控的跨膜 (TM) 结构域（TM1 和 TM2），以及一个 C 端细胞质螺旋结构域。晶体结构（PDB ID：2OAR）代表通道的闭合状态，呈现漏斗状孔，周质侧开口较大，最窄点靠近细胞质。假设膜张力导致的 TM 螺旋倾斜驱动 MscL 门控，我们将通过将最近开发的螺旋倾斜约束势应用于 DMPC 脂质双层中 MscL 的 TM 螺旋来进行分子动力学模拟。使用 CHARMM-GUI 网站 (http://www.charmm-gui.org) 中的 Membrane Builder 生成无 C 端螺旋 (Gln110-Asn125) 的 MscL/DMPC 复合物的初始结构。 CT?P（恒定温度、表面张力和压力）动力学将用于允许系统尺寸沿 XY 轴在模拟过程中发生变化。 P21 图像转换将用于允许顶部和底部小叶中的脂质分子数量在模拟过程中发生变化。将通过倾斜 (1) TM1 和 TM2 螺旋（10 个约束）、(2) 仅 TM1 螺旋（5 个约束）和 (3) 仅 TM2 螺旋（5 个约束）来执行三种不同的模拟。 TM1 螺旋的倾斜角将从 35 (PDB ID:2OAR) 逐渐变化到 65°，变化 1，TM2 的倾斜角从 33 (PDB ID:2OAR) 逐渐变化到 63，变化 1，一起或单独变化。我们将分析孔径、分子相互作用和压力分布随螺旋倾斜度的变化，以探索原子水平上 MscL 可能的门控机制。