Allele-specific conformational rescue of KIF1A T99M by genetic suppressors in a <i>C. elegans</i> model of KIF1A-associated neurological disorder

KIF1A-associated neurological disorder (KAND) arises from mutations in the microtubule motor KIF1A, disrupting synaptic vesicle transport. Here, we investigate the pathogenic T99M substitution in the P-loop of KIF1A, which induces steric hindrance, impairing ATP/ADP coordination and motor activity. Using CRISPR-engineered Caenorhabditis elegans expressing the homologous UNC-104(T95M) mutation, we conducted forward genetic screens and identified recurrent intragenic suppressors (T95V and T95I; T95V/I) that restored animal motility and synaptic vesicle distribution. Molecular dynamics simulations revealed that replacing the methionine residue with valine or isoleucine residues alleviated steric clashes in the nucleotide-binding pocket and stabilized Mg2+-ATP coordination. Biochemical assays showed that T95V/I partially recovered microtubule gliding velocity and processivity, demonstrating that even modest motor reactivation mitigates neuronal dysfunction. Inspired by prior success showing that treatment with the plant flavonol fisetin rescues the effects of the KIF1A R11Q variant, we propose allele-specific conformational stabilization as a therapeutic strategy for KAND. Our findings highlight the structural plasticity of motor domains and provide a framework for precision therapies targeting pathogenic variants through genetic suppressors.