CAREER: Research and education on protein folding as an energy source at the bacterial outer membrane

所有革兰氏阴性菌周围都有两层不同的膜。这些膜含有大量的膜蛋白。在内膜中，大多数蛋白质采用螺旋形式，称为α -螺旋折叠，而在外膜中，它们几乎都通过并排排列的蛋白质链形成片状结构，称为β -薄片折叠。外膜含有具有大而开放的孔隙的蛋白质，这使得它无法包含储存在小分子（如ATP）或离子梯度形式中的化学能。因此，对于复杂的过程，如蛋白质插入膜或通过膜分泌蛋白质，需要替代能源。这个项目的目标是确定蛋白质折叠本身作为能量来源的可行性。该项目旨在改变高中生物教学中的常见范式，在这种范式中，细胞和系统通常被视为静态和高度定向的。通过模拟数据的分子可视化，蛋白质的动态性质变得很明显。针对特定主题的多个模块，如膜的组装和通过膜结合通道的扩散，将在北乔治亚地区的高中教室中开发和实施。这些模块强调为观察到的行为构建解释模型，这是未来科学标准的关键要素。它们的实现将通过可视化程序VMD的简化接口的开发得到帮助。评估模块的影响将首先在三个教室进行，然后通过网络传播到更广泛的受众。研究生和本科生将高度参与整个过程，给予他们不仅仅是研究的训练。人们提出了多种理论模型来解释蛋白质折叠形成β片是如何提供能量的。在本提案中，将进行计算研究，以确定这些结构形成的能量方面，通过蛋白质折叠(1)在隔离中，(2)在插入外膜结合蛋白中，(3)在分泌跨膜的自转运蛋白域。这些过程能量方面的定量测定将用于评价和改进现有模式。对两个特定系统的研究将用于阐明BamA如何插入外膜蛋白以及自转运蛋白如何分泌毒力蛋白域，两者都通过自身折叠获得能量。具体目标是：(1)表征自由能景观和β -片结构的稳定性；(2)确定BamA如何催化膜外蛋白的插入和折叠；(3)解析自转运蛋白折叠事件的分子序列；(4)将生物系统动力学融入高中教学。主要的方法是分子动力学（MD）模拟。所有模拟结果将与实验紧密结合，包括回顾性和前瞻性。

All Gram-negative bacteria possess two distinct membranes surrounding them. These membranes contain numerous membrane proteins. In the inner membrane, most proteins adopt a helical form termed alpha-helical fold, whereas in the outer membrane they almost all form sheet-like structures by side-by-side alignment of protein strands, which is termed beta-sheet fold. The outer membrane contains proteins with large, open pores, rendering it unable to contain chemical energy stored in small molecules such as ATP or in the form of an ion gradient. Therefore, an alternative source of energy is required for complex processes such as insertion of proteins to membrane or secretion of proteins through the membrane. It is the goal of this project to determine the feasibility of protein folding itself as the source of energy. This project seeks to change a common paradigm in high school biology instruction, in which cells and the systems contained within are often seen as static and highly directed. Through molecular visualization of simulation data, the dynamic nature of proteins becomes readily apparent. Multiple modules on specific topics, such as the assembly of membranes and diffusion through membrane-bound channels, will be developed and implemented in high school classrooms in the North Georgia area. These modules emphasize the construction of explanatory models for the observed behavior, a key element of future science standards. Their implementation will be aided by the development of a simplified interface for the visualization program VMD. Assessment of the modules' impact will first be conducted in three classrooms before expanding to a wider audience through web distribution. Graduate and undergraduate students will be highly involved in the entire process, giving them training beyond just research. Multiple theoretical models have been proposed to explain how the folding of proteins to form beta-sheet can provide energy. In this proposal, computational investigations will be performed to determine, the energetic aspects of the formation of these structures through protein folding (1) in isolation, (2) in the insertion of outer-membrane-bound proteins and (3) in the secretion of auto transporter domains across the membrane. Quantitative determination of the energetic aspects of these processes will be used to evaluate and refine existing models. Investigations into two specific systems will be used to elucidate how outer-membrane proteins are inserted by BamA and how virulence protein domains are secreted by autotransporters, both being energized by their own folding. The specific objectives are to (1) characterize the free-energy landscape and stability of beta-sheet structures; (2) determine how BamA catalyzes the insertion and folding of outer-membrane proteins; (3) resolve the molecular sequence of events in autotransporter folding; and (4) integrate dynamics of biological systems into high school instruction. The primary method to be used is molecular dynamics (MD) simulation. All simulation results will be closely coupled to experiments, both retrospectively and prospectively.