Cross-linking mass spectrometry uncovers protein interactions and functional assemblies in synaptic vesicle membranes

Synaptic vesicles are storage organelles for neurotransmitters in the pre-synaptic cytosol. When an action potential arrives at the pre-synaptic terminal, they fuse with the pre-synaptic membrane and neurotransmitters are released. In this project, we set out to study the protein interactions formed in synaptic vesicle membranes. For this, we first assessed the proteome of five independent vesicle preparations. Using chemical cross-linking, we then tackled the interactions of the major protein components. To gain further insights, we combined this approach with a chemical labelling strategy. Specific protein interactions were then studied after (i) treating the vesicles with Botulinum neurotoxin B, (ii) binding the soluble SNARE complex, and (iii) fusion of the vesicles with empty liposomes. Our findings reveal stable interaction modules in synaptic vesicles.