Two Pleckstrin homology domains scaffold SNAP-47-containing SNARE complexes

Long-term potentiation depends on the controlled integration of AMPA receptors into the postsynaptic membrane of neurons, a process overseen by a SNARE complex consisting of SNAP-47, syntaxin-3, and synaptobrevin-2. Unlike other SNAP proteins, SNAP-47 showcases slower fusion kinetics and contains unexplained regions whose roles are not yet known.

Researchers have now employed biochemical techniques alongside artificial intelligence structure prediction tools and molecular dynamics simulations to explore the structure of SNAP-47-containing SNARE complexes.

AlphaFold3's predictions of the ternary SNAP-47-containing SNARE complex unveiled one known Pleckstrin homology domain (PH1) and one previously undiscovered PH domain (PH2). These domains were subsequently confirmed through experimental validation. Computational models using BioEmu and molecular dynamics simulations suggested that PH1 and PH2 establish a stable and energetically favorable interface.

When bound together, PH1 securely interacts with the SNARE coiled coil, while computational simulations indicating lysine acetylation, known to hinder SNAP-47 function, disrupt this PH1-SNARE interface.

The AMPAR insertion facilitated by SNAP-47-containing SNARE complexes is instigated by the calcium sensor synaptotagmin, and the researchers observed that PH1, PH2, and synaptotagmin-1 can concurrently interact with the plasma membrane, suggesting a conducive conformation for membrane fusion. Collectively, these findings offer fresh mechanistic insights into how PH domains regulate SNAP-47-mediated membrane fusion during synaptic plasticity.