Systematic identification of structure-specific protein-protein interactions.

Area of Science:

• Proteomics
• Structural Biology
• Biochemistry

Background:

• Protein physical interactions (PPIs) are crucial for cell function and disease.
• Current methods struggle to identify structure-specific PPIs and interaction interfaces proteome-wide.
• Understanding these specific interactions is key to deciphering disease mechanisms.

Purpose of the Study:

• To develop and validate a method for screening structure-specific protein-protein interactions (PPIs) proteome-wide.
• To identify conformation-specific interactors of alpha-synuclein, a key protein in Parkinson's disease.
• To demonstrate the method's applicability to other proteins, including Rab GTPases.

Main Methods:

• Limited proteolysis-mass spectrometry (LiP-MS) was employed to probe protease susceptibility changes.
• The method was validated using known antibody-target and membrane protein interactions.
• LiP-MS was applied to alpha-synuclein and Rab GTPases in different conformational states.

Main Results:

• LiP-MS successfully detected well-characterized PPIs and pinpointed interaction interfaces.
• Conformation-specific interactors for alpha-synuclein monomers and fibrils were identified.
• Differential interactors were detected for GDP- and GTP-bound Rab GTPases, highlighting the method's sensitivity.

Conclusions:

• LiP-MS is a powerful approach for identifying structure-specific interactomes.
• This method can uncover novel insights into protein interactions in various functional states.
• The technique has broad applicability for studying protein interactomes in health and disease.