3. Mapping biological interfaces by HDMS
Hydrogens in amides constituting a protein backbone undergo continuous exchange with hydrogens in a solvent. The exchange rate of each amide hydrogen varies significantly, depending on solvent accessibility (Figure 1). By incubating a protein complex in a solvent containing excess deuterium oxide (D2O), the exchange rate can be quantitatively measured by a mass increase of the complex, a basic principle of hydrogen-deuterium exchange coupled to mass spectrometry (HDMS). Regional mass changes measurable by proteolytic fragments of the complex followed by high-quality MS can be translated into residue- or peptide-level solvent accessibilities which are useful to infer overall protein conformation and, in particular, potential interfacial areas where the exchange rate differs in a bound state relative to an unbound state.
In comparison to CLMS, HDMS is more applicable to any size of a protein complex and involves relatively simple data interpretation. On the other hand, HDMS does not freeze the complex but monitors the time course of changes which might not be significant for unstructured or transient interfaces where H-D exchange is too fast to detect. For more details about the work-flow of HDMS and data processing which are beyond the scope of this review, interested readers are referred to several reviews elsewhere (Anderson et al., 2018; Masson et al., 2019; Zhang et al., 2012).