CAREER: Dissecting the Molecular Mechanisms of Substrate Selection and Degradation by the 26S Proteasome

智力上的优点。 细胞内的蛋白质含量是不断变化的。根据细胞的需要，某些蛋白质被制造出来，而另一些蛋白质被去除或降解。蛋白质降解必须是高度特异性的，因此受到隔室蛋白酶的严格调控，隔室蛋白酶是一种大的桶形复合物，利用ATP水解产生的能量以机械方式解开蛋白质底物，然后将其转运到隔离的内室中进行降解。真核细胞中主要的ATP依赖性蛋白酶是26S蛋白酶体，其通过特异性降解参与例如细胞分裂、信号转导和程序性细胞死亡的调节蛋白来控制蛋白质周转和许多重要过程。大多数底物通过另一种小蛋白泛素的可逆附着而被标记为降解，泛素可以连续连接在一起形成多聚泛素链，作为蛋白酶体的靶向信号。本研究的目的是阐明泛素依赖的蛋白质降解的详细机制，通过使用新的方法的结构，定量生化和生物物理特性的26 S蛋白酶体。具体目标是：1）了解底物降解和先前泛素链去除之间的复杂耦合，2）获得蛋白酶体分子机器结构及其底物识别，解折叠和泛素去除机制的详细结构和功能见解，和3）使用前所未有的单分子测量来提供对底物识别和降解的机械化学的一瞥。阐明这些分子机制将有助于确定控制高度多样性蛋白质在体内降解的原理，从而进一步理解真核细胞中前体的各种调节功能。由于蛋白酶体在蛋白质周转和维持关键途径中的普遍功能，通过这项研究产生的结果和新工具将强烈影响其他细胞生物学研究和方法。更广泛的影响。 对底物加工的分子机制的详细了解将允许开发专用的蛋白酶体，用于暂时控制细胞中特定酶和其他蛋白质的消除，这对于生物工程和系统生物学中的应用是非常期望的，并且可以帮助药物前体或生物燃料的合成。拟议的研究将与教学和推广相结合，以加强科学，技术，工程和数学（STEM）领域的教育。由于其强烈的合作性质，研究项目为本科生，博士后和研究生在生物学，物理学和化学的交叉点提供了密集的跨学科培训。此外，为了在年轻时就开始科学教育和推广，将制定一项计划，包括高中生的夏季研究实习，为本科生，社区大学生和高中教师提供课程的实验室靴子营计划，以及在少数民族比例较高的地方公立特许学校组织科学展览会。

Intellectual merit. The protein content inside a cell is constantly changing. Depending on the cell's needs, certain proteins are made while others are removed or degraded. Protein degradation must be highly specific and is therefore tightly regulated by compartmental proteases, large barrel-shaped complexes that utilize the energy from ATP hydrolysis to mechanically unravel and then translocate protein substrates into a sequestered internal chamber for degradation. The major ATP-dependent protease in eukaryotic cells is the 26S proteasome, which controls protein turnover and numerous vital processes by specifically degrading regulatory proteins involved for instance in cell division, signal transduction, and programmed cell death. Most substrates are marked for degradation by the reversible attachment of another small protein, ubiquitin, which can be consecutively linked together to form poly-ubiquitin chains that act as a targeting signal to the proteasome. The goal of this research is to elucidate the detailed mechanisms of ubiquitin-dependent protein degradation by using novel approaches for the structural, quantitative biochemical, and biophysical characterization of the 26S proteasome. Specific aims are 1) to understand the intricate coupling between substrate degradation and the preceding removal of ubiquitin chains, 2) to gain detailed structural and functional insight into the architecture of the proteasome molecular machine and its mechanisms for substrate recognition, unfolding, and ubiquitin removal, and 3) to use unprecedented single-molecule measurements to provide a glimpse into the mechanochemistry of substrate recognition and degradation. It is expected that elucidating these molecular mechanisms will help to define the principles that control the degradation of highly diverse proteins in vivo, and thus further the understanding of the various regulatory functions of preoteasomes in eukaryotic cells. Due to the ubiquitous functions of the proteasome in protein turnover and maintenance of crucial pathways, the results and novel tools generated through this research will strongly impact other cell-biological studies and approaches. Broader impacts. A detailed knowledge of the molecular mechanisms for substrate processing will allow the development of dedicated proteasomes for the temporally controlled elimination of specific enzymes and other proteins in the cell, which is highly desired for applications in bioengineering and systems biology, and may aid the synthesis of drug precursors or biofuels. The proposed research will be integrated with teaching and outreach to strengthen education in the science, technology, engineering, and mathematics (STEM) fields. Due to their strongly collaborative nature, the research projects provide intense interdisciplinary training for undergraduates, postdocs, and graduate students at the intersection of biology, physics, and chemistry. Furthermore, in order to start science education and outreach already at a young age, a program will be developed that includes summer research internships for high school students, a Laboratory Boot Camp program with courses for undergraduates, community college students, and high school teachers, and the organization of science fairs at local public charter schools with high percentage of underrepresented minorities.