Regulation of Neurexin 1β Tertiary Structure and Ligand Binding through Alternative Splicing

Neurexins and neuroligins play an essential role in synapse function, and their alterations are linked to autistic spectrum disorder. Interactions between neurexins and neuroligins regulate inhibitory and excitatory synaptogenesis in vitro through a "splice-insert signaling code." In particular, neurexin 1β carrying an alternative splice insert at site SS#4 interacts with neuroligin 2 (found predominantly at inhibitory synapses) but much less so with other neuroligins (those carrying an insert at site B and prevalent at excitatory synapses). The structure of neurexin 1β+SS#4 reveals dramatic rearrangements to the "hypervariable surface," the binding site for neuroligins. The splice insert protrudes as a long helix into space, triggers conversion of loop β10-β11 into a helix rearranging the binding site for neuroligins, and rearranges the Ca²⁺-binding site required for ligand binding, increasing its affinity. Our structures reveal the mechanism by which neurexin 1β isoforms acquire neuroligin splice isoform selectivity.