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.

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。所列机构为 研究中心，而研究中心不一定是研究者所在的机构。 MscL是大电导的机械敏感性通道，形成同源五聚体孔，其中每个亚基包含参与通道门控的两个跨膜（TM）结构域（TM 1和TM 2）和C-末端胞质螺旋结构域。晶体结构（PDB ID：20 AR）代表通道的闭合状态，显示在周质侧上具有大开口的漏斗形孔和靠近细胞质的最西点。假设TM螺旋倾斜，由于膜张力驱动MscL门控，我们将进行分子动力学模拟，通过应用最近开发的螺旋倾斜约束潜力的TM螺旋的MscL在DMPC脂质双层。使用CHARMM-GUI网站（http：//www.example.com）中的Membrane Builder生成不含C-末端螺旋（Gln 110-Asn 125）的MscL/DMPC复合物的初始结构。www.charmm-gui.org 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着XY轴在模拟期间变化。P21图像变换将用于允许顶部和底部瓣叶中的脂质分子数量在模拟期间变化。将通过倾斜（1）TM 1和TM 2螺旋（10个约束）、（2）仅TM 1螺旋（5个约束）和（3）仅TM 2螺旋（5个约束）进行三种不同的模拟。TM 1螺旋的倾斜角将从35（PDB ID：20 AR）逐渐变化到65（1），TM 2的倾斜角从33（PDB ID：20 AR）逐渐变化到63（1），一起或单独变化。我们将分析的变化的孔径，分子间的相互作用，和压力分布作为一个功能的螺旋倾斜，探索可能的门控机制的MscL在原子水平上。