Computational Genomics of Signal Transduction

描述（由申请人提供）：所有细胞都使用信号转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，使病原体能够发现并侵入人类宿主，如果功能不正常，就会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，通过蛋白质的共价修饰（如磷酸化）或相互作用介导的蛋白质构象变化促进信息传递。了解信号转导途径中的蛋白质-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。这种途径允许细菌通过细胞膜上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动行为。趋化途径已被研究多年，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未得到解答：例如，信号复合物如何组装，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方法来理解细菌趋化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这些领域。这将涉及基于系统发育分析创建趋化蛋白的自然分类，识别进化相关亚群中的保守残基，共同进化残基的协方差分析，以及测试蛋白质-蛋白质相互作用模型的分子对接模拟。在Aim 1中，这些方法将应用于化学感受器（MCPs）、支架蛋白（CheW）和组氨酸激酶（CheA）之间的相互作用。目的2将集中于反应调节因子（CheY）和参与兴奋性信号终止的磷酸酶之间的相互作用。目的3将研究对适应途径至关重要的相互作用，包括甲基转移酶、甲基酯酶或脱酰胺酶活性对化学受体的共价修饰。这项工作将产生细菌趋化途径中蛋白质-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一步的实验和系统生物学研究。通过这些研究学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性的信号通路的新疗法。

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.