Skip to main content

Table 1 Concentrations of external metabolites, enzymes, transporters and inhibitors

From: Kinetic modeling and exploratory numerical simulation of chloroplastic starch degradation

Species Symbol Sub-cellular Location Concentration (μM)
External Metabolites    
H+ H+_CY Cytosol 0.1
Starch(Gn) Starch_CS Chloroplast Stroma 0.6*
Starch glucosyl unit GlcStarch_CS Chloroplast Stroma 1000
ATP pool ATPtot_CY Cytosol 10000
ADP pool ADPtot_CY Cytosol 10000
Phosphate pool Pitot_CY Cytosol 10000
Glucose-1-phosphate pool Glc1Ptot_CY Cytosol 10000
Glucose-6-phosphate pool Glc6Ptot_CY Cytosol 10000
Enzymes    
β-amylase β-amylase_CS Chloroplast Stroma 3.8 × 10-2
Isoamylase (debranching enzyme) ec_3_2_1_68_CS Chloroplast Stroma 1.475 × 10-1
DPE1 enzyme ec_ 2_4_1_25_CS Chloroplast Stroma 2
DPE2 enzyme ec_ 2_4_1_25_CY Cytosol 2
Cytosolic glucan phosphorylase (CGP) ec_2_4_1_1_CY Cytosol 2
Hexokinase ec_2_7_1_1_CY Cytosol 10
Transporters    
Maltose (MEX) tc_2_A_84_1_2_CIMS Chloroplast Intermembrane
Space
2
Plastidic Glucose (pGlcT) tc_2_A_1_1_17_CIMS Chloroplast Intermembrane
Space
20
Inhibitors    
Reduced Glutathione GSH_CY Cytosol 1000
Glucose-1,6-bisphosphate pool Glc16BPtot_CY Cytosol 10000
2,3-bis-phosphoglycerate pool 23BPGtot_CY Cytosol 10000
  1. The pH of the cytosol is assumed to remain at 7, so that the cytosolic proton concentration is always kept at 0.1 μM. The three species-reduced glutathione, glucose-1,6-bisphosphate and 2,3-bisphosphoglycerate act only as hexokinase inhibitors and are treated as parameters. We have used the mass concentration of the β-amylase (7.83 × 10-3 gm L-1) and isoamylase (1.18 × 10-2 gm L-1) enzymes mentioned in the caption of Figure 1 in Ref. [29]. For potato β-amylase, the molecular weight is 206 kD, so that we are effectively using a β-amylase concentration of 3.8 × 10-2 μM. Potato isoamylase peptides have a molecular weight of about 80 kDa, so that the effective isoamylase concentration that we are using is effectively 1.475 × 10-1 μM.
  2. *The molecular weight of starch in our model is assumed to be equal to that of Starch B (2.7 × 105) in Ref. [1]. Assuming that starch has a molecular formula of the form H(C6H10O5)n(OH), we calculate a value of 1667 for n, which interprets as one molecule starch contains 1667 glucosyl units. Thus 1000 μM of starch glucosyl units is equivalent to 0.6 μM of starch. Hence the concentration of starch is determined by the concentration of starch glucosyl units.