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: 7723397
• 负责人: Wonpil Im
• 金额: $ 0.05万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-08-01 至 2009-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7723397
• 关键词: Binding; C-terminal; CDKN1A gene; Complex; Computer Retrieval of Information on Scientific Projects Database; Cytoplasm; Dimyristoylphosphatidylcholine; Funding; Grant; Helix (Snails); Homo; Image; Institution; Lipid Bilayers; Lipids; Membrane; Numbers; Research; Research Personnel; Resources; Shapes; Side; Source; Structure; Surface Tension; System; Temperature; Transmembrane Domain; United States National Institutes of Health; ear helix; molecular dynamics; oncoprotein p21; periplasm; pressure; restraint; simulation; size

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利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 MSCL是大电导的机械敏感通道，它形成一个均五聚体，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端的细胞质螺旋结构域。晶体结构(PDB ID：20AR)代表通道的关闭状态，显示漏斗状的孔，在周质一侧有一个大的开口，最窄的点靠近细胞质。假设由于膜张力引起的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抑制势应用于DMPC脂质双层中MSCL的TM螺旋来进行分子动力学模拟。不含C-末端螺旋的MSCL/DMPC复合体的初始结构(Gln110-Asn125)是利用CHARMM-GUIUS网站(http://www.charmm-gui.org).)中的膜生成器生成的将使用CT？P(恒定温度、表面张力和压力)动力学来允许系统尺寸在模拟期间沿XY轴变化。P21图像变换将被用来允许顶部和底部小叶中的脂质分子的数量在模拟期间变化。通过倾斜(1)TM1和TM2螺旋(10个约束)，(2)仅TM1螺旋(5个约束)，以及(3)仅TM2螺旋(5个约束)，将执行三种不同的模拟。TM1螺旋的倾斜角将逐渐变化，从35(PDB ID：20AR)到65×1，TM2的倾斜角从33(PDB ID：20AR)到63×1，一起或单独变化。我们将分析孔径、分子相互作用和压力分布随螺旋倾斜的变化，以从原子水平上探索MSCL可能的门控机制。