Abstract：
Proteins play an essential role in the vital biological processes governing cellular functions. Most proteins function as members of macromolecular machines, with the network of interacting proteins revealing the molecular mechanisms driving the formation of these complexes. Profiling the physiology-driven remodeling of these interactions within different contexts constitutes a crucial component to achieving a comprehensive systems-level understanding of interactome dynamics. Here, we apply co-fractionation mass spectrometry and computational modeling to quantify and profile the interactions of ∼2000 proteins in the bacterium Escherichia coli cultured under 10 distinct culture conditions. The resulting quantitative co-elution patterns revealed large-scale condition-dependent interaction remodeling among protein complexes involved in diverse biochemical pathways in response to the unique environmental challenges. The network-level analysis highlighted interactome-wide biophysical properties and structural patterns governing interaction remodeling. Our results provide evidence of the local and global plasticity of the E. coli interactome along with a rigorous generalizable framework to define protein interaction specificity. We provide an accompanying interactive web application to facilitate the exploration of these rewired networks.
摘要：
蛋白质在控制细胞功能的重要生物过程中起着至关重要的作用。大多数蛋白质是大分子机器的成员，相互作用的蛋白质网络揭示了驱动这些复合物形成的分子机制。在不同的环境中分析这些相互作用的生理学驱动的重塑构成了实现对相互作用体动力学的全面系统级理解的关键组成部分。这里,我们应用共分级分离质谱和计算模型来量化和分析细菌大肠杆菌中2000蛋白在10种不同的培养条件下培养的相互作用。所产生的定量共洗脱模式揭示了响应于独特的环境挑战，参与多种生化途径的蛋白质复合物之间的大规模条件依赖性相互作用重塑。网络级分析强调了相互作用的全基因组生物物理特性和控制相互作用重塑的结构模式。我们的结果提供了大肠杆菌相互作用组的局部和全局可塑性的证据，以及严格的可概括框架来定义蛋白质相互作用特异性。我们提供了随附的交互式Web应用程序，以促进对这些重新布线的网络的探索。
