PNNL

Abstract

Current chemical cross-linking methods are commonly employed for mapping sites of interaction and three-dimensional structure in purified, known protein complexes. When applied in vivo in combination of co-immunoprecipitation methods, information on the sites of interaction between proteins are unattainable due to overwhelming sample complexity. We present results from a novel cross-linking strategy that allow simultaneous protein-protein interaction and surface topology measurement in vivo without any prior knowledge of the system. The strategy consists of: (i) cross-linking reaction: intact cell labeling with protein interaction reporters (PIRs); (ii) two-stage mass spectrometric analysis: stage 1 identification of PIR-labeled proteins and construction of a restricted database by 2D-LC/MS/MS; and stage 2 analysis of PIR-labeled peptides by multiplexed LC/FTICR-MS; (iii) data analysis: identification of cross-linked peptides and proteins of origin using accurate mass and other constraints. This strategy was applied to Shewanella oneidensis MR-1 bacterial cells and successfully identified a protein-protein interaction between SecA and a small outer membrane lipoprotein as well as their sites of interaction in vivo.