A novel method for large-scale confirmation of protein structures and surface accessible modification sites

Abstract

Protein function is modulated via different levels including their structure and chemical modifications, but method for monitoring of protein structures and their modifications on a large scale is far from mature. In this study, we present a shot-gun proteomic method, which combine ultrafiltration with limited tryptic proteolysis (FLiP) to enrich the surface accessible peptides and modification sites on protein structures. FLiP enable high throughput confirmation of the structural information of 1939 proteins. Based on this, we identified 120 types of modifications located on the surface accessible regions of proteins, including some rare modification types like phosphorylation of asparagine and acetylation of threonine. Our data provides a comprehensive picture of the spatial distribution of multiple modification types on protein structures. Collectively, our work provides a promising tool for large-scale confirmation of protein structures and unbiased discovery of multiple proteins surface assessable post-translational modifications, which may also benefits the study of rare modification types.

Keywords: Limited tryptic digestion; Mass spectrometry; Post-translational modification; Protein structure; Proteomics.