Structure, dynamics and causality in protein interaction networks

蛋白质相互作用网络的结构、动力学和因果关系

• 批准号: RGPIN-2015-05707
• 负责人: Michnick, Stephen
• 金额: $ 3.79万
• 依托单位: Université de Montréal
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2019
• 资助国家: 加拿大
• 起止时间: 2019-01-01 至 2020-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=690364
• 关键词: Structure; dynamics; causality; protein; interaction

Problem and Hypothesis: The importance of protein-protein interactions (PPIs) to biology is reflected in the enormous efforts to study them on a large scale, including our own efforts, which resulted in a first description of a PPI network in vivo (Tarassov, et al. Science, 2008). In the past funding period we have developed and validated a novel approach to study dynamics of biochemical networks and to determine protein functions, discovery of pathways and a novel mechanism of allostery. The method is based on measuring dynamics of homomeric protein complexes (HPC) on a large scale.***Objectives: Our specific aims are: Aim 1., to construct high-quality, mechanism-based sentinels of signal transduction and metabolic pathways based on HPC and analysis of underlying mechanisms of HPC dynamics. Aim 2. To use HPC analysis and mechanism-based HPC sentinels to predict signaling and metabolic network topology under specific nutrient limitation. Aim 3. To extend HPC dynamics to multiple perturbations and prediction of organization of biochemical networks in general. ***Methodologies: In addition to the DHFR PCA strain array described above, we will dissect the physical basis of changes in HPCs using mass spectroscopy, GFP fusions to the proteins to determine localization and abundance and a novel infrared fluorescent protein PCA to determine changes in subcellular localization of HPC and confocal microscopy. This will result in an array of HPCs with known underlying spatiotemporal changes in proteins complexes or abundance that we call HPC "sentinels" We will further apply a pipeline of analysis tools, largely based on existing strategies, to interpret HPC dynamics on specific signaling and metabolic pathways. ***This study will contribute to advancement of knowledge by: ***1- Providing a strategy to directly probe the dynamics of biochemical networks in vivo. ***2- Providing a complement to existing genetic and mass-spectroscopic strategies for determining gene function. ***3 - Revealing new principles and mechanisms of dynamic biochemical network organization. ***4 - Revealing novel functions of genes for which function is presently unknown.***5 - Contributing towards solving the mystery of the principles of formation and evolution of the cellular machinery, on which we have already made some progress. **

问题和假设：蛋白质 - 蛋白质相互作用（PPI）对生物学的重要性反映在巨大的大规模研究中，包括我们自己的努力，这导致了体内PPI网络的首次描述（Tarassov等人（Tarassov等人，Science，Science，2008年）。在过去的资金期间，我们已经开发了一种新的方法来研究生化网络的动力学，并确定蛋白质功能，发现途径和新颖的变构机制。该方法基于大规模测量同源蛋白复合物（HPC）的动力学。 AIM 2。使用HPC分析和基于机制的HPC哨兵来预测特定营养限制下的信号传导和代谢网络拓扑。目的3。将HPC动态扩展到多个扰动和整个生化网络组织的预测。 ***方法论：除了上述DHFR PCA菌株阵列外，我们还将使用质谱法，GFP融合到蛋白质的物理基础上，以确定定位和丰度，以及新型的红外荧光蛋白PCA，以确定HPC和共核显微镜亚细胞定位的变化。 这将导致一系列HPC在蛋白质络合物中具有已知的基本时空变化或我们称为HPC“ Sentinels”的大量时空变化，我们将进一步应用分析工具的管道，这在很大程度上基于现有策略，以在特定信号和代谢途径上解释HPC动态。 ***这项研究将通过：*** 1-提供一种策略来直接探测体内生化网络的动态。 *** 2-为确定基因功能的现有遗传和质谱策略提供补充。 *** 3-揭示动态生化网络组织的新原理和机制。 *** 4-揭示了目前未知功能的基因的新功能。*** 5-有助于解决形成原理和蜂窝机械进化原理的奥秘，我们已经取得了一些进步。 **