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.