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Table 1 Particle numbers in initial conditions

From: Computational modelling of the regulation of Insulin signalling by oxidative stress

Module

Species

Initial value (number of molecules)

Comments & References

Receptor binding

Ins

5 × 105, boundary

10-7 M

 

InR

9 × 104

BioNumbers [37]

 

Cytoplasm_InR

1 × 104

<< cell surface

 

PTP1B

1 × 105

assigned (PaxDb suggests PTPN1 5 × 105 in human, 5 × 104 in mouse) http://pax-db.org & [38, 39]

IRS

IRS1

1 × 105

[26] Appdx B

 

PI3K

1 × 104

[26] Appdx B

 

PP2A

5 × 105

[40]

Phosphatases

PTEN

1 × 105

PaxDb, human

 

GSH

100

assigned

 

NOX_inact

100

assigned

 

Cytoplasm_SOD2

4.17 × 104

scale 10-3 * PaxDb

 

Mt

50

assigned

 

extracellular_ROS

5 × 104, boundary

scale 10-3 * 10 μM

Akt

Akt

1 × 105

[41]

 

AS160

2 × 104

assigned

 

PKC

1 × 105

assigned same as Akt

 

PIP2

2 × 105

scale 10-3 *[26]; [42]

 

PIP3

1 × 103

scale 10-3 * [26]; [42]

 

cytoplasm_GLUT4

9.6 × 104

Total 1 × 105, assigned ((PaxDb suggests Slc2a4 5 × 104 in mouse)

 

cellsurface_GLUT4

4 × 103

 

JNK

JNK

16000

PaxDB (Mapk9)

 

IKK

2000

PaxDb (Ikbkb)

 

DUSP

1 × 105

assigned

FOXO

E2F1

300

assigned, to keep FOXO ~ 1000

 

cytoplasm_Foxo1_Pa0 Pd0_Pe0_pUb0 (Foxo with no PTMs)

1000

see [34]

  1. All other species are initially zero.
  2. Initial particle numbers in the model (all other species are initially zero).