Computational Genomics of Signal Transduction

描述（由申请人提供）：所有细胞都使用信号传导途径来检测环境刺激并产生适当的行为反应。这些途径是人类疾病的关键组成部分，允许病原体检测和入侵人类宿主，当功能不正常时，导致癌症和其他疾病。在原核生物和真核生物中，信号转导途径涉及多种蛋白质-蛋白质相互作用，其通过蛋白质的共价修饰（例如磷酸化）或相互作用介导的蛋白质构象变化来促进信息传递。了解信号转导通路中的蛋白质-蛋白质相互作用将有利于影响人类健康的广泛领域。 细菌的趋化系统代表了当今生物学中研究得最好的信号转导。该途径允许细菌通过细胞膜中的化学感受器检测外部刺激，并通过组氨酸蛋白激酶磷酸化反应调节蛋白来控制细胞的游泳行为。趋化性途径已经研究了很多年，提供了丰富的结构、生化和遗传信息。然而，关于该系统的许多重要问题仍然没有答案：信号复合物如何组装，例如：信号如何终止，以及受体的共价修饰如何有助于适应。我们的长期目标是了解活细胞如何在分子水平上检测，传输和适应各种信号。在这个建议中，我们将应用计算基因组学和生物物理学方法来理解细菌趋化性信号转导途径的三个关键步骤：激发，信号终止和适应。新的方法将被用来研究蛋白质-蛋白质相互作用在每个领域。这将涉及创建一个自然分类的趋化性蛋白质的基础上系统发育分析，鉴定进化相关的亚组内的保守残基，协方差分析的共同发展的残基，和分子对接模拟测试模型的蛋白质-蛋白质相互作用。在目标1中，这些方法将被应用到化学感受器（MCP），支架蛋白（CheW）和组氨酸激酶（CheA）之间的相互作用参与的兴奋途径。目的2将集中在反应调节剂（CheY）和磷酸酶参与终止兴奋性信号之间的相互作用。目的3将探讨相互作用的适应途径，涉及共价修饰的化学感受器与甲基转移酶，甲酯酶，脱酰胺酶的活动至关重要。 这项工作将产生细菌趋化性途径中蛋白质-蛋白质相互作用的可测试模型，这将推动我们的合作者和其他实验室进行进一步的实验和系统生物学研究。通过这些研究了解到的原理将提供有关信号转导的重要信息，并有助于设计针对控制人类病原体毒力的信号通路的新疗法。 公共卫生相关性：信号转导是对所有生物体至关重要的普遍生物学过程，并且是针对包括癌症和传染病在内的各种疾病的新药设计的目标。我们将详细研究细菌中的信号转导途径，以了解在许多生物体中管理类似过程的普遍原则。所获得的结果可用于鉴定针对病原菌的新治疗剂的靶点。

DESCRIPTION (provided by applicant): Signal transduction pathways are used by all cells to detect environmental stimuli and generate appropriate behavioral responses. These pathways are critical components of human disease, allowing pathogens to detect and invade the human host and when not functioning properly, leading to cancer and other diseases. In both prokaryotic and eukaryotic organisms, signal transduction pathways involve multiple protein-protein interactions that facilitate information transfer by covalent modification of proteins (e.g. phosphorylation) or interaction-mediated conformational changes in the proteins. Understanding protein-protein interactions within signal transduction pathways will benefit a wide range of fields impinging on human health. The chemotaxis system of bacteria represents the best studied signal transduction in biology today. This pathway allows bacteria to detect external stimuli via chemoreceptors in the cell membrane and control the cell's swimming behavior through phosphorylation of a response regulator protein by a histidine protein kinase. The chemotaxis pathway has been studied for many years, providing a wealth of structural, biochemical, and genetic information. However, many important questions about the system remain unanswered: how the signaling complex is assembled, for example: how signals are terminated, and how covalent modification of receptors contributes to adaptation. Our long term goal is to understand how living cells detect, transmit, and adapt to various signals on a molecular level. In this proposal we will apply computational genomic and biophysical approaches to understanding three key steps of the bacterial chemotaxis signal transduction pathway: excitation, signal termination, and adaptation. Novel methodology will be utilized to study protein- protein interactions in each of these areas. This will involve creating a natural classification of chemotaxis proteins based on phylogenetic analysis, identification of conserved residues within evolutionarily related subgroups, co-variance analysis of co-evolving residues, and molecular docking simulations to test models of protein-protein interactions. In Aim 1, these methods will be applied to the interactions between the chemoreceptors (MCPs), the scaffolding protein (CheW), and the histidine kinase (CheA) involved in the excitation pathway. Aim 2 will concentrate on interactions between the response regulator (CheY) and phosphatases involved in termination of the excitatory signal. Aim 3 will investigate interactions critical to the adaptation pathway involving covalent modification of the chemoreceptor by enzymes with methytransferase, methylesterase, or deamidase activities. This work will produce testable models of protein-protein interactions within the bacterial chemotaxis pathway that will drive further experimental and systems biology research by our collaborators and other laboratories. The principles learned through these studies will provide important information about signal transduction and aid the design of new therapeutics targeting the signaling pathways that control virulence in human pathogens. PUBLIC HEALTH RELEVANCE: Signal transduction is a universal biological process vital to all organisms and is a target for the design of new drugs against a variety of conditions including cancer and infectious diseases. We will study in detail a signal transduction pathway in bacteria in order to gain understanding of universal principles that govern similar processes in many organisms. The results obtained may be used to identify targets for new therapeutic agents against pathogenic bacteria.