Mathematical modelling of mutant glycoprotein fate in the ER

BackgroundThe endoplasmic reticulum (ER) coordinates glycoprotein quality control through competing pathways: ER quality control (ERQC) and ER-associated degradation (ERAD). The fate of a glycoprotein is tied to its N-glycan(s) structure, which serves as a "molecular barcode" for quality control. In particular, modulation of ERQC/ERAD can increase leakage of responsive (i.e., non-inactive) glycoprotein mutants that remain misfolded yet retain biological activity once outside the ER. Rescue of secretion of such mutants is a promising therapeutic strategy for the therapy of congenital rare disease due to a missense mutation in a secreted glycoprotein gene, but the relative merits of UGGT vs. EDEM inhibition to release a mutant from the ER remain to be explored. MethodsAn ordinary differential equation (ODE) framework ("ER Glycoprotein Outcome", ERGO) evaluates time-dependent ER concentrations of 13 N-glycospecies of a single mutant glycoprotein (G1M9, G1M8B, G1M8C, G1M7BC, M9, M8A, M8B, M8C, M7AB, M7AC, M7BC, M6, M5) within the ER lumen, under a set of chosen hypotheses. All reactions follow mass-action kinetics with ER enzymes/lectins kinetic constants and concentrations as fixed parameters. The ODE system is solved in Python with adaptive Runge-Kutta integration. Simulations initialise from a single glycoform (M9, 1 {micro}M) and track glycoform distributions over [~]28 h. Starting glycoform concentrations and overall time can be customised. Given the lack of comprehensive kinetic data in the literature, parameter values reflect educated guesses, rather than measured constants. ResultsFour simulation scenarios explore the dynamics of ERQC vs ERAD: (A) baseline scenario with all enzymes active; (B) UGGT inhibition, which abolishes re-glucosylation, disrupts CNX/CRT cycles, and accelerates substrate flux toward ERAD-prone glycoforms; (C) inhibition of all ER mannosidases, preventing trimming-dependent ERAD commitment and prolonging ER retention of early glycoforms; (D) combined UGGT and ER mannosidases inhibition, mimicking experimental rescue of misfolded substrates by blockade of both glucosylation-driven ER retention and trimming-driven degradation signals. We further quantify the rate of CNX/CRT engagement ( carousel rides) by combining analytical estimates with Monte Carlo-style simulations of individual mutant glycoprotein fates.