Cross-Linking Mass Spectrometry to Capture Protein Network Dynamics of Cell Membranome

Abstract

Interactions among proteins are fundamental in driving functions and activities that regulate cell biology, mechanotransduction, and cell-to-cell communication/recognition. Recently, cross-linking mass spectrometry (XL-MS) has emerged as a powerful tool for interaction discovery and characterization, driving the enlightenment of novel binding partners otherwise undetected. Covalent linkages of two amino acid residues of proteins (or within complexes) in close proximity can be identified by MS, thus providing structural insights such as distance restraints or unraveling interaction dynamics.The XL-MS workflow described here is applied to map the plasma membrane protein (PMP) networks since they play important roles in the modulation of diverse molecular processes, including transport, signal transduction, endocytosis, and secretion. The strategy includes cross-linking of PMP-enriched fractions, label-free nanoLC-MS/MS, and bioinformatics data analysis. "Membranome" interconnections constitute around 30% of the mammalian proteome and 60% of all drug targets. Exploring such networks under different biological conditions is a promising and unbiased approach to depicting regulatory pathways that govern cell behavior.

Keywords: Cross-linking mass spectrometry; Interactomics; Membranomics; Protein dynamics; Protein-protein interactions; Regulatory networks; Structural proteomics; XL-MS.