Combining H/D Exchange Mass Spectrometry and Computational Docking To Derive the Structure of Protein–Protein Complexes

Protein–protein interactions are essential for biological function, but structures of protein–protein complexes are difficult to obtain experimentally. To derive the protein complex of the DNA-repair enzyme human uracil-DNA-glycosylase (hUNG) with its protein inhibitor (UGI), we combined rigid-body computational docking with hydrogen/deuterium exchange mass spectrometry (DXMS). Computational docking of the unbound protein structures provides a list of possible three-dimensional models of the complex; DXMS identifies solvent-protected protein residues. DXMS showed that unbound hUNG is compactly folded, but unbound UGI is loosely packed. An increased level of solvent protection of hUNG in the complex was localized to four regions on the same face. The decrease in the number of incorporated deuterons was quantitatively interpreted as the minimum number of main-chain hUNG amides buried in the protein–protein interface. The level of deuteration of complexed UGI decreased throughout the protein chain, indicatin...