Model CAB Glycogen Synthesis Model

Version 1

Model CAB — README

Overview. Model CAB captures the coupled GlgC → GlgA (+ GlgB primer assistance) system under 3‑PGA/Pi regulation. The model exposes GlgC supply, GlgA demand, and a primer effectiveness term from GlgB; it also provides a Pi response calibrated to 2 mM 3‑PGA and helper utilities for GlgA1/GlgA2.

Key parameters (assay context) • GlgA ceilings (Assay B): GlgA1 = 0.49 U·mg⁻¹; GlgA2 = 0.64 U·mg⁻¹. • GlgA Michaelis constants (Assay A; ADP‑Glc): GlgA1 Kₘ = 0.152 mM; GlgA2 Kₘ = 0.219 mM. • GlgC intrinsic activity: 8.9 U·mg⁻¹ (used as the cap for supply scaling). • GlgC activation by [GlgC] (titration): one‑site occupancy with Kd ≈ 60 nM (see Fig. 3A). • Substrate term for GlgC (G1P): near‑saturating at 1 mM; nominal Kₘ ≈ 0.3 mM. • Pi inhibition (with 2 mM 3‑PGA): IC₅₀ ≈ 0.87 mM, IC₉₀ ≈ 1.45 mM. (from Lee et al. 2025, Table 1) • GlgB/starch primer effect: demand_params_with_GlgB returns (Vmax_eff, Km_eff, f_B, f_starch) to fold into GlgA demand.

Core relationships (conceptual) • Effective GlgC supply vC′ = V_CMG · f_Pi,3PGA(Pi, [3‑PGA]) · f_act([GlgC]) · f_sub([Glc‑1P]). • GlgA demand vA = V_A,max,eff · S/(Kₘ + S) with V_A,max,eff and Kₘ modified by GlgB/starch. • In steady primer‑replete runs, the observed flux J is set by min{vC′, V_A,max,eff}. • PPi‑enabled reversal: v_r = f_Pi(Pi)·k_rev·S_excess·[PPi] with S_excess = max(S − τ·Kₘ, 0) and d[PPi]/dt = max(vC′ − vA, 0) − v_r − k_hyd·[PPi].

Quick start (Python) from model_cab import vC_MG_per_mgC, inh_Pi, demand_params_with_GlgB, _conv_C_to_A • Supply (U·mg⁻¹ referenced to GlgA): vC′ = vC_MG_per_mgC(Pi, threePGA, [GlgC]_nM, 1.0, iso) × _conv_C_to_A(iso) × k_iso • Demand (µM·min⁻¹): (Vmax_eff, Km_eff, fB, fS) = demand_params_with_GlgB(iso, B_nM, S_ug_per_mL) Version / provenance • This README summarizes the current CAB model used to generate the figures 6A,B and 7C. • Made by Kenric Lee and gallons of coffee, have fun modelling glycogen synthesis!