A pathogenic mutation in α-SNAP impairs membrane lipid binding by concealing a critical hydrophobic loop.

The soluble N-ethylmaleimide-sensitive factor attachment protein alpha (α-SNAP) is essential for vesicle trafficking, coordinating trans-SNARE zippering and cis-SNARE disassembly. α-SNAP also regulates autophagy, apoptosis, calcium signaling, and AMPK activity. The hyh missense mutation M105I produces a distinctive neurodevelopmental phenotype, yet its pathogenic mechanism remains unclear. Because many α-SNAP functions rely on lipid binding, we examined whether M105I alters this property. In silico modeling revealed structural rearrangements that conceal the N-terminal hydrophobic loop, and molecular dynamics simulations predicted reduced binding free energy and weakened protein-lipid interactions. These predictions were validated in vitro and in hyh mouse brains, showing diminished membrane association, particularly at the plasma membrane. Liposome flotation assays with plasma-membrane-derived lipids confirmed that M105I directly impairs lipid binding and that membrane composition influences this interaction. Thus, defective lipid engagement emerges as a central determinant of α-SNAP dysfunction and likely contributes to the pathogenesis of hyh phenotype.