The Autophagy Initiation Complexes

项目摘要 自噬是一种保守的机制，用于清除包涵体，受损的细胞器和所有其他细胞因子。 不需要的或有害的物质不能被蛋白酶体消化。在人类中，自噬具有重要的 在癌症、帕金森病、细胞内感染、神经变性和衰老中的作用。自噬包括 形成独特的杯状双膜，吞噬细胞，它膨胀，吞噬货物， 关闭以形成自噬体。细胞膜是如何被改造成吞噬细胞的杯状的， 是自噬的核心和棘手的问题我们将使用结构生物学，计算机模拟，和多- 彩色3D超分辨率成像的杯子，以解开由来已久的奥秘和塑造 圣杯了自噬启动由ULK 1/Atg 1蛋白激酶的激活和靶向驱动 复合物和III类磷脂酰肌醇激酶复合物I（PI 3 KC 3-C1）。项目的具体目标 是为了理解1）吞噬细胞的成核，和2）前自噬体结构的调节。目的 1开始的假设，独特的S形几何形状的支架蛋白Atg 17，发现 通过这个实验室，驱动细胞膜重塑成杯状。这一假说预测，在所有真核生物中， 新月形的S形或二聚体应该作为核心自噬起始机制的一部分而存在。我们将测试 使用X射线衍射、电子显微镜和透射电镜，假设ULK 1亚基FIP 200在哺乳动物自噬中具有这种作用 显微镜、理论建模和细胞成像，包括能够可视化的3D STORM显微镜 这些纳米级的杯子。我们将研究ATG 13、ATG 101和ULK 1是否以及如何在这方面合作。 过程，以及它们在空间和时间上是如何组织的。我们将研究PI 3 KC 3-C1的作用， 通过体外重建、电子显微镜和合成和合成的 蜂窝系统目标2将检查启动机制是如何定位到正确的位置并切换的 在细胞中正确的时间。我们将描述靶向ULK 1的分子和结构机制 ER出口网站，饥饿诱导的吞噬细胞成核发生。我们将确定 控制PI 3 KC 3-C1活性的调节电路。我们将检验VPS 15蛋白激酶 调节PI 3 KC 3-C1的组装和稳定性，随后调节VPS 34激酶活性， 变构和非催化方式。使用冷冻EM，质谱，生物化学和细胞成像，我们将 确定该回路是否以及如何用于ULK 1调节PI 3 KC 3-C1活性 通过蛋白质NRBF 2、Bcl-2和AMBRA 1的结合，抑制了细胞的磷酸化。我们亦会探讨 假设PI 3 KC 3可以通过BECN 1 BARA结构域在膜结合水平上调节， 使用PI 3 KC 3-C2-Rubicon复合物作为模型系统。

PROJECT SUMMARY Autophagy is a conserved mechanism for the clearance of inclusions, damaged organelles, and all other unneeded or harmful materials that cannot be digested by proteasomes. In humans, autophagy has major roles in cancer, Parkinson’s disease, intracellular infection, neurodegeneration, and aging. Autophagy involves the formation of a unique cup-shaped double membrane, the phagophore, which expands, engulfs cargo, and closes to form the autophagosome. How membranes are remodeled into the cup shape of the phagophore is a central and intractable question in autophagy. We will use structural biology, computer simulations, and multi- color 3D superresolution imaging of the cup to unravel the long-standing mystery of the origin and shaping of the cup. Autophagy initiation is driven by the activation and targeting of the ULK1/Atg1 protein kinase complex, and the class III phosphatidylinositol kinase complex I (PI3KC3-C1). The specific aims of the project are to understand 1) nucleation of the phagophore, and 2) regulation of the pre-autophagosomal structure. Aim 1 begins with the hypothesis that the unique S-shaped geometry of the scaffolding protein Atg17, discovered by this laboratory, drives remodeling of membrane into cups. This hypothesis predicts that in all eukaryotes, an S-shape or dimer of crescents should exist as part of the core autophagy initiation machinery. We will test the hypothesis that ULK1 subunit FIP200 has this role in mammalian autophagy using x-ray diffraction, electron microscopy, theoretical modeling, and cell imaging, including 3D STORM microscopy capable of visualizing these nanoscale cups in cells. We will work out whether and how ATG13, ATG101, and ULK1 cooperate in this process, and how they are organized structurally in space and time. We will examine the role of PI3KC3-C1 in cup formation through in vitro reconstitution, electron microscopy, and fluoresence imaging of synthetic and cellular systems. Aim 2 will examine how the initiation machinery is targeted to the right location and switched on at the correct time in cells. We will characterize the molecular and structural mechanisms for targeting ULK1 to ER exit sites, where starvation-induced phagophore nucleation occurs. We will determine the core regulatory circuitry that controls PI3KC3-C1 activity. We will test the hypothesis that the VPS15 protein kinase regulates the assembly and stability of PI3KC3-C1, and subsequently regulates VPS34 kinase activity in an allosteric and non-catalytic manner. Using cryo-EM, mass spectrometry, biochemistry, and cell imaging, we will determine whether and how this circuitry is used in the regulation of PI3KC3-C1 activity by ULK1 phosphorylation and by the binding of the proteins NRBF2, Bcl-2, and AMBRA1. We will also explore the hypothesis that PI3KC3 can be regulated at the level of membrane binding through the BECN1 BARA domain, using as a model system the PI3KC3-C2-Rubicon complex.