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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.