Probing protein interactions with hydrogen/deuterium exchange and mass spectrometry—A review

Assessing the functional outcome of protein interactions in structural terms is a goal of structural biology, however most techniques have a limited capacity for making structure–function determinations with both high resolution and high throughput. Mass spectrometry can be applied as a reader of protein chemistries in order to fill this void, and enable methodologies whereby protein structure–function determinations may be made on a proteome-wide level. Protein hydrogen/deuterium exchange (H/DX) offers a chemical labeling strategy suitable for tracking changes in “dynamic topography” and thus represents a powerful means of monitoring protein structure–function relationships. This review presents the exchange method in the context of interaction analysis. Applications involving interface detection, quantitation of binding, and conformational responses to ligation are discussed, and commentary on recent analytical developments is provided.

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► Protein chemistry generates mass shifts useful for structure–function studies.
► H/DX supports a powerful mass shift method for protein interaction analysis.
► H/DX mass shifts are useful for determining binding data (Kd, off-rates).
► Improved H/DX–MS workflows can accommodate complex protein systems.