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

Area of Science:

• Structural Biology
• Biochemistry
• Computational Biology

Background:

• Protein-protein interactions are crucial for cellular processes.
• Experimental determination of protein complex structures is challenging.
• Understanding these interactions is key to deciphering biological function.

Purpose of the Study:

• To determine the three-dimensional structure of the human uracil-DNA-glycosylase (hUNG) in complex with its inhibitor (UGI).
• To develop and validate a hybrid computational and experimental approach for protein complex structure determination.

Main Methods:

• Rigid-body computational docking of unbound protein structures.
• Hydrogen/deuterium exchange mass spectrometry (DXMS) to identify solvent-protected residues.
• Integration of DXMS data as constraints to filter docking models.

Main Results:

• DXMS revealed distinct folding patterns for unbound hUNG and UGI.
• DXMS identified specific regions of hUNG and UGI involved in the protein-protein interface.
• Filtering docking results with DXMS constraints successfully identified the correct hUNG-UGI complex structure.
• Incorporating DXMS data as potentials during docking was less effective than filtering.

Conclusions:

• The combined approach of computational docking and DXMS is effective for determining protein complex structures.
• DXMS-derived interface constraints are powerful filters for distinguishing correct models from computational docking.
• This method provides a flexible and accurate strategy for structural studies of protein interactions.