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).