Glucagon-like peptide-1 receptor (GLP-1R) agonists show substantial inter-individual variability in efficacy, but the structural basis by which common GLP-1R variants alter receptor behavior remains unclear. We examined the GLP-1R R131Q variant using all-atom molecular dynamics simulations across four conditions (wild type [WT] and R131Q in ligand-free and GLP-1-bound states; 8-11 replicas per condition; 600 ns each) together with isogenic human induced pluripotent stem cell (iPSC)-derived pancreatic models. In ligand-free simulations, principal component analysis identified a variant-enriched subensemble associated with coordinated deviations spanning TM1 and the ECL3-side region. Residue-131-centered analysis showed weakening of WT-like local anchoring and a variant-specific increase in Q131-R376 close occupancy from near zero in WT to 0.101. In bound simulations, the ligand-free-specific Q131-R376 signature was lost. Instead, the variant weakened the residue-131-E128 local anchor and redistributed receptor-peptide interface and deep-pocket contact states, consistent with upper-receptor repacking. MM/GBSA analysis showed weaker estimated overall GLP-1 binding energetics in R131Q together with redistribution of energetic contributions within the bound receptor-peptide interface. In iPSC-derived pancreatic β-like cells and exendin-4-stimulated endocrine progenitors, R131Q was associated with increased β-cell maturity markers and enhanced mitochondrial, antioxidant, and stress-response readouts, including increased IDH2/MDH1 expression and enhanced mitochondrial staining. Together, these findings support a state-dependent model in which R131Q rewires local and distal GLP-1R conformational ensembles, with associated mitochondrial and stress-response phenotypes in human pancreatic models.
