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Table 3 Dynamic variables and constants of basal cyclic nucleotide signaling.

From: Time-resolved in silico modeling of fine-tuned cAMP signaling in platelets: feedback loops, titrated phosphorylations and pharmacological modulation

Model parameter

Values

Foundations/assumptions

Reference

Dynamic variables

   

x1: c(cAMP)

4 μM

Basal levels

[14]

x2:c(cGMP)

0.4 μM

Basal levels

[14]

x3:c(PDE2) active

0.05 mg/l

Model-based simulation

This study

  

Experimentally: 63.46 mg/l

 

x4:c(PDE3) active

2.3 mg/l

Model-based simulation

This study

  

Experimentally: 225 mg/l

 

x5:c(PDE5) active

1 mg/l

Model-based simulation

This study

  

Experimentally: 1359 mg/l

 

x6:c(PDE2) inactive

(63.46 -x3) mg/l

  

x7:c(PDE3) inactive

(225 - x4) mg/l

  

x8:c(PDE5) inactive

(1359 - x5) mg/l

  

x9:c(AMP)

μM; simulated

  

x10:c(GMP)

μM; simulated

  

Constants

   

k1: Vmax PDE2

120 μmol/min/mg

cAMP turnover

[2, 16]

k2:Km PDE2

50 μM

cAMP turnover

[2, 16]

k3:Vmax PDE3

3 μmol/min/mg

cAMP turnover

[2, 16]

k4:Km PDE3

0.2 μM

cAMP turnover

[2, 16]

k5:Vmax PDE2

120 μmol/min/mg

cGMP turnover

[2, 16]

k6:Km PDE2

35 μM

cGMP turnover

[2, 16]

k7:Vmax PDE3

0.3 μmol/min/mg

cGMP turnover

[2, 16]

k8:Km PDE3

0.02 μM

cGMP turnover

[2, 16]

k9:Vmax PDE5

5 μmol/min/mg

cGMP turnover

[2, 16]

k10:Km PDE5

5 μM

cGMP turnover

[2, 16]

k11:kcAMP

8 μmol/min

Basal influx of cAMP

[17–19]

k12:kcGMP

1 μmol/min

Basal influx of cGMP

[64, 65]

k13:Deactivation PDE2

  

This study

k14:Activation PDE2

k13-k18: = 0

 

This study

k15:Deactivation PDE3

for simulation of

 

This study

k16:Activation PDE3

basal levels

 

This study

k17:Deactivation PDE5

(resting conditions)

 

This study

k18:Activation PDE5

  

This study

k19:hPDE2

2

Hill coefficient

[15, 16]

  1. Description of the model parameters and constants of the formalized the system of ODEs modeling the basal cyclic nucleotide signaling (see Appendix).