Molecular Mechanisms of Topological Rearrangements in Integral Membrane Proteins

该项目研究了膜蛋白（即存在于细胞膜内的蛋白质）在蛋白质合成后获得相对于膜的正确方向的机制。膜蛋白对细胞功能至关重要，包括运输、信号传导和酶活性。为了正常工作，膜蛋白必须折叠成正确的拓扑结构，这要求蛋白质的所有结构元素获得相对于膜的特定方向。不能获得正确拓扑结构的膜蛋白在细胞中迅速降解。该项目使用分子模拟技术来解决膜蛋白拓扑结构如何建立的知识空白。这些知识将告知工程方法，以最大限度地提高正确的蛋白质生产。研究小组将包括本科生，包括来自代表性不足群体的学生，在跨学科的研究环境中培养下一代研究人员。基于该项目的学习模块将用于针对中学生的外展活动，以激励年轻学生从事研究事业。这个项目的结果也将被纳入研究生和高级本科课程。本项目将使用分子动力学模拟来研究一系列具有代表性的膜蛋白的实验表征拓扑重排。最近的实验结果表明，某些膜蛋白进行拓扑重排，亲水性蛋白元件直接穿过膜，即使这一过程应该面临很大的能量障碍。原子和粗粒度模拟，通过增强的采样技术加速，将执行表征亲水性蛋白质元件穿过膜的途径。这些模拟将阐明蛋白质、脂质和水的相互作用，促进生物学相关时间尺度上的拓扑重排。基于模拟的洞察力，序列突变将被测试为每个模型系统，以产生实验验证的预测。在本项目中开发和应用的模拟方法也将对研究与脂质翻转、膜蛋白构象变化或药物载体向细胞传递相关的类似双层易位过程具有价值。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

This project investigates the mechanisms by which membrane proteins (i.e., proteins that reside within the cell membrane) obtain correct orientations with respect to the membrane after protein synthesis. Membrane proteins are critical for cellular functions including transport, signaling, and enzymatic activity. To function properly, a membrane protein must fold into its correct topology, which requires all structural elements of the protein to obtain specific orientations with respect to the membrane. Membrane proteins that fail to obtain a correct topology are rapidly degraded in the cell. This project uses molecular simulation techniques to address gaps in the knowledge of how membrane protein topology is established. This knowledge will inform engineering approaches to maximize correct protein production. The research team will incorporate undergraduate students, including students from underrepresented groups, to train the next generation of researchers in an interdisciplinary research environment. Learning modules based on this project will be developed for outreach initiatives targeted at middle-school students to inspire young students to pursue research careers. Results from this project will also be incorporated into graduate and advanced undergraduate courses. This project will use molecular dynamics simulations to study experimentally characterized topological rearrangements in a series of representative membrane proteins. Recent experimental results have indicated that certain membrane proteins undergo topological rearrangements in which hydrophilic protein elements directly cross the membrane, even though this process should face a large energy barrier. Atomistic and coarse-grained simulations, accelerated by enhanced sampling techniques, will be performed to characterize the pathways by which hydrophilic protein elements cross the membrane. These simulations will elucidate the interplay of protein, lipid, and water interactions that facilitate topological rearrangements on biologically relevant timescales. Based on simulation insight, sequence mutations will be tested for each of the model systems to generate experimentally verifiable predictions. The simulation methods developed and applied in this project will also be of value for studying similar bilayer translocation processes relevant to lipid flip-flop, membrane protein conformational changes, or the delivery of drug carriers to cells.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.