Legends of Figures
Figure 1. Structural information obtainable from CLMS and HDMS. In CLMS, a crosslinking reagent makes a covalent, site-specific bridge between binding proteins. The crosslinked complex is subjected to mass spectrometry to provide contact residues or inter-residue distance. In HDMS, the hydrogen (H)-deuterium (D) exchange rate in amides of binding proteins varies depending on solvent accessibility. Relative to residues or areas in non-interfaces, those in binding interfaces generally exhibit lower D/H exchange, a mass change identifiable by mass spectrometry.
Figure 2. Crosslinking techniques employed in CLMS to unveil biological interfaces. (A) Photo-reactive unnatural amino acid (UAA) site-specifically incorporated into a predetermined position is irradiated by UV when proteins are interacting. The formation of a crosslink observed by gel electrophoresis or mass spectrometry indicates the UAA-incorporated site is within a potential binding interface. (B) A photo-activatable or chemical crosslinker with defined geometry and bifunctional, residue-specific reactivity forms a crosslink between interacting proteins. Mass analyses provides an abundance of inter-residue distance constraints surrounding interfacial regions.
Figure 3. Major protein complexes and their native interfaces investigated by HDMS. (A) Antibody-antigen complex. (B) Self-associated protein oligomers. (C) Membrane proteins associated with cell membranes.
Figure 4. Computer-aided, integrative structural modeling to provide near-physiological landscape of binding interfaces of proteins complexes with high resolution and fidelity. Design of PPI modulators based on biological interfaces thus obtained would allow new drug discovery with higher potency and efficacy.