Single Molecule Studies to Dissect Allosteric Communication Networks in Protein Kinase A

信号蛋白是生物信号传递的核心组成部分，使细胞能够在细胞外环境和细胞内部进行通信。从定义生物系统如何检测和转导信号，到为生物技术应用重新设计蛋白质功能，再到确定变构抑制剂的新结合位点，了解信号蛋白的运作方式具有重要而广泛的意义。camp依赖性蛋白激酶A （PKA）是所有真核细胞中的主要信号蛋白，包含大多数信号蛋白复合物中的结构和功能元件，包括模块化结构域组织、配体结合协同性、通过柔性连接体结构域传递信号以及配体诱导的构象变化。该蛋白将被用作模型系统，定量定义生物信号如何从一个结构域转导到另一个结构域，以调节和激活蛋白质功能。该项目将为本科生和研究生提供生物学、物理学和计算建模领域的研究机会。本项目将采用单分子生物物理技术结合分子动力学模拟来研究PKA不同结构元件之间的通讯机制。该项目的目标是确定在不同的生物状态（载脂蛋白、活性和非活性状态）下这种通讯机制是如何建立的，以及cAMP结合是如何激活蛋白质的。预计这些研究开发的工具和方法将广泛应用于推进对各种相关和不相关的具有模块化结构的激酶的了解，例如参与血管舒张和血小板活化的cgmp依赖性蛋白激酶，或参与细胞迁移、分化和凋亡的蛋白激酶C。最后，这个项目的跨学科性质将为来自不同背景的研究生和本科生提供独特的研究机会。

Signaling proteins are  the core building blocks in the transmission of biological signals, allowing cells to communicate between the extracellular environment and the cellular interior.  Understanding how signaling proteins operate has important and broad implications, from defining how biological systems detect and transduce signals, to reengineering protein function for biotechnological applications, to identifying new binding sites for allosteric inhibitors. The cAMP-dependent Protein Kinase A (PKA) is a major signaling protein in all eukaryotic cells that incorporates structural and functional elements seen in most signaling protein complexes, including a modular domain organization, ligand binding cooperativity, signaling through flexible linker domains, and ligand-induced conformational changes. This protein will be used as a model system to quantitatively define how biological signals are transduced from one domain to another to regulate and activate protein function. This project will provide research opportunities to undergraduate and graduate students at the interface of biology, physics and computational  modeling.This project will use single-molecule biophysical techniques in combination with molecular dynamic simulations to investigate the mechanism of communication between different structural elements of PKA. The goal of this project is to determine how such communication mechanisms are established in different biological states (apo, active and  inactive  states), and how cAMP binding activates the protein. It is expected that the tools and methods developed from these studies will have widespread applications to advance knowledge in a variety of related and unrelated kinases that display modular architectures, such as cGMP-dependent protein kinase involved in vasodilation and  platelet activation, or  protein kinase C involved in cell migration, differentiation, and apoptosis. Lastly, the interdisciplinary nature of this project will provide unique research opportunities to graduate and undergraduate students from different backgrounds.