Robust and comprehensive Protein-Protein Interaction analysis with the Evosep One

Introduction and Talk by Nicolai Bache, Head of applications, Evosep

An atlas of protein-protein interactions across mouse tissues

Cellular processes arise from the dynamic organization of proteins in networks of physical interactions. Mapping the complete network of biologically relevant protein-protein interactions, the interactome, has therefore been a central objective of high-throughput biology. However, the dynamics of protein interactions across physiological contexts remain poorly understood.

Here, we develop a quantitative proteomic approach combining protein correlation profiling with stable isotope labelling of mammals (PCP-SILAM) to map the interactomes of seven mouse tissues. The resulting maps provide the first proteome-scale survey of interactome dynamics across mammalian tissues, revealing over 125,000 unique interactions at a quality comparable to the highest-quality human screens. We identify systematic suppression of cross-talk between the evolutionarily ancient housekeeping interactome and younger, tissue-specific modules. Rewiring of protein interactions across tissues is widespread, and rewired proteins are tightly regulated by multiple cellular mechanisms and implicated in disease.

Our study opens up new avenues to uncover regulatory mechanisms that shape in vivo interactome responses to physiological and pathophysiological stimuli in mammalian systems.

Presenter: Leonard Foster (Assistant Prof. at University of British Columbia)

IN-Cell Protein Footprinting Coupled with Mass Spectrometry for Structural Biology Across the Proteome

In recent years, protein footprinting coupled with mass spectrometry has been used to identify protein-protein interaction sites and regions of conformational change through modification of solvent accessible sites in proteins.

The footprinting method, fast photochemical oxidation of proteins (FPOP), utilizes hydroxyl radicals for protein modification. To date, FPOP has been used in vitro on relatively pure protein systems. We have further extended the FPOP method for in vivo analysis of proteins both in cells and in C. elegans, an animal model for human disease. We have optimized experimental conditions so that the method can modify thousands of proteins for structural biology across the proteome.

Presenter: Lisa Jones (Associate Professor at University of Maryland, Baltimore (UMB))