Computational Analysis of GAT1 Mutations: Functional Consequences from Molecular Dynamics and Binding Free Energy Calculations

GABA transporter 1 (GAT1), encoded by the <i>SLC6A1</i> gene, is essential for maintaining inhibitory neurotransmission by mediating the reuptake of GABA from the synaptic cleft. Dysfunction of GAT1 has been linked to several neurological and neurodevelopmental disorders, including epilepsy and Alzheimer's disease. In this study, we performed a comprehensive computational investigation of reported GAT1 mutations to understand their structural and functional implications. Seven mutations (G63S, Y140C, Q291Δ, F294Δ, N310I, D451G, and G457H) were analyzed using homology modeling, structural validation tools, molecular dynamics (MD) simulation triplicates, and binding free energy calculations via the gmx_MMPBSA method. The wild-type consistently exhibited the most favorable interaction energy (-59.89 kcal/mol), the strongest binding free energy (ΔG = -28.29 kcal/mol), and the most stable hydrogen-bonding network. While all mutants displayed elevated RMSD and energy fluctuations relative to the wild-type, these changes predominantly reflected local conformational disturbances rather than global unfolding, indicating that the overall structural framework of GAT1 remains largely preserved. Among the mutants, G63S exerted the mildest effect on ligand stabilization, whereas Y140C, G457H, Q291Δ, and D451G produced substantial reductions in protein-ligand stability, weakened hydrogen bonding, and increased ligand mobility within the binding pocket. Free-energy analysis further highlighted the pronounced destabilizing influence of N310I, Q291Δ, and G457H on tiagabine binding. These findings provide mechanistic insights into how specific GAT1 mutations may alter transporter stability and function, offering a structural framework for future studies on GABAergic dysfunction and therapeutic development.