Cellular protein painting for structural and binding sites analysis via lysine reactivity profiling with o-phthalaldehyde

Abstract

The three-dimensional structure and the molecular interaction of proteins determine their roles in many cellular processes. Chemical protein painting with protein mass spectrometry can identify ligand binding sites, changes in protein structural conformations and protein-protein interactions. Nevertheless, most current protein painting techniques identified protein targets and binding sites of drugs in vitro using cell lysate or purified protein. Here, we screened 11 kinds of membrane-permeable lysine-reactive chemical probes for intracellular covalent labeling of endogenous proteins, which reveals ortho-phthalaldehyde (OPA) as the most reactive probe in intracellular environment. An MS workflow was developed and coupled with a new data analysis strategy termed RAPID (Reactive Amino acid Profiling by Inverse Detection) to enhance detection sensitivity. RAPID-OPA successfully identified structural change induced by allosteric drug TEPP-46 on its target protein PKM2, which was applied to profile conformation change of the proteome occurring in cells during thermal denaturation. Application of RAPID-OPA on cells treated with geldanamycin successfully revealed its binding sites on target proteins. Thus, RAPID-OPA for cellular protein painting permits the identification of ligand-binding sites and detection of protein structural changes occurring in cells.