RUI: Multiscale Models for ABC Transporter Molecular Dynamics

了解细胞表面生物分子的动力学，包括分子如何穿过细胞膜，对于基本了解生命过程至关重要。细胞膜通常作为屏障，选择性地限制进入细胞的物质。 该项目探索了转运蛋白或驻留在细胞膜上的大蛋白质主动跨细胞膜输出物质的机制。开发多尺度模拟来预测这些转运蛋白的分子行为。该项目为来自缅因州农村代表性不足群体的本科生和高中生提供科学方法、计算分析和分子科学方面的培训--这些方法对知识和社会的进一步进步至关重要。一个为期一周的夏季研讨会已经成立，介绍缅因州学生Unix编程和蛋白质建模。学生研究人员参与开展研究的各个方面，并接受统计热力学理论基础的高级培训。归国学生通过共同主持暑期工作坊、互动生物化学课程和分子可视化实验室获得教学经验。大肠杆菌ABC转运蛋白，MsbA，在其构象循环的不同状态，包括开放和封闭的面向内的构象和面向外的水解后构象。顺磁自旋标记测量随后证实了ATP依赖的交替访问的跨膜蛋白室的内部和细胞外双层小叶。该项目将这些现有的结构数据与伴随蛋白质构象循环的动态分子相互作用的功能图连接起来，并将ATP水解与底物易位结合起来。与分子和细胞生物科学部的跨尺度集成优先级相一致，从原子模拟开发了多尺度描述，以模拟驻留在其脂质双层环境中的大型分子机器的动力学。环状磷脂溶剂化的翻转酶的脂质底物易位的作用进行了具体探讨。该项目创建的力场脂质和蛋白质参数集不限于转运蛋白，并且对于膜蛋白系统，其扩散动力学和分子相互作用的模拟具有通用性。来自代表性不足群体的本科生和高中生被纳入计算科学的基础并接受培训。

Understanding the dynamics of biomolecules at the cell surface, including how molecules move across the cell membrane, is crucial to the basic understanding of life processes. The cell membrane normally acts as a barrier that selectively limits what enters the cell. This project explores the mechanisms by which transporters, or large proteins that reside in the cell membrane, actively export substances across the cell membrane. Multiscale simulations are developed to predict molecular behavior of these transporters. The project provides undergraduate and high school students from underrepresented groups in rural Maine with training in the scientific method, computational analysis, and molecular science--approaches vital to further advances in knowledge and society. A weeklong summer workshop has been established to introduce Maine students to Unix programming and protein modeling. Student researchers are involved in carrying out all aspects of the research and receive advanced training in the theoretical foundations of statistical thermodynamics. Returning students acquire teaching experience by co-facilitating summer workshops, interactive biochemistry classes, and molecular visualization labs.Experimental collaborators trapped the E. coli ABC transporter, MsbA, in distinct states of its conformational cycle, including open and closed inward-facing conformers and an outward-facing post-hydrolysis conformation. Paramagnetic spin label measurements subsequently confirmed the ATP-dependent alternating accessibility of the transmembrane protein chamber to the intra- and extracellular bilayer leaflets. This project connects these existing structural data with a functional picture of the dynamic molecular interactions that accompany protein conformational cycling and couple ATP hydrolysis to substrate translocation. Consistent with the Integrating Across Scales priority of the Division of Molecular and Cellular Biosciences, a multiscale description is developed from atomistic simulations to simulate the dynamics of a large molecular machine residing in its lipid bilayer environment. The role of annular phospholipid solvation on translocation of the flippase's lipid substrate is specifically explored. The force field lipid and protein parameter set created by the project is not limited to transporters and is of general utility for simulations of membrane protein systems, their diffusive dynamics, and molecular interactions. Undergraduate and high school students from underrepresented groups are incorporated and trained in the foundations of computational science.