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Table 3 Elements, processes, and their parameters incorporated into the OT simulation model

From: Evolution of multiple phosphodiesterase isoforms in stickleback involved in cAMP signal transduction pathway

Elements/processes Element abbreviation/process # Type Parameter
Odorant -- Element Initial value = 10a
Olfactory receptor OR Element Initial value = 0 (default)
OR-odorant complex OR-odorant Element Initial value = 0 (default)
G protein olfactory type G(olf) Element Initial value = 0 (default)
Adenylate cyclase AC Element Initial value = 0 (default)
Cyclic adenylic acid cAMP Element Initial value = 0 (default)
Cyclic nucleotide gated channel CNG Element Initial value = 0 (default)
Calcium ion Ca2+ Element Initial value = 0 (default)
Chloride channel regulator CLCA Element Initial value = 0 (default)
Chloride ion Cl- Element Initial value = 0 (default)
Calmodulin CaM Element Initial value = 0 (default)
Phosphodiesterase 1C PDE1C Element Initial value = 0 (default)
Guanylate cyclase activator GCAP Element Initial value = 0 (default)
Guanylate cyclase pGC Element Initial value = 0 (default)
Guanosine 3',5'-cyclic phosphate cGMP Element Initial value = 0 (default)
Protein kinase, cGMP-dependent PKG Element Initial value = 0 (default)
Ca2+/CaM-dependent protein kinase CaMK2 Element Initial value = 0 (default)
cAMP-dependent protein kinase α PKA Element Initial value = 0 (default)
Phosducin Phd Element Initial value = 0 (default)
Translation 1 Process Rate = OR*0.05b
Degradation 2 Process Rate = OR*0.05b
Binding 3 Process Rate = Odorant*OR*0.7c
Dissociation 4 Process Rate = Odorant-OR*0.5c
Activation 5 Process Threshold = 2d
Activation 6, 8, 10, 14, 15
21, 22, 24, 25, 26
Process Threshold = 0 (default)
cAMP increase 7 Process Threshold = 0 (default)
Ion transport 9 Process Threshold = 0 (default)
Ion transport (depolarization) 11 Process Threshold = 0 (default)
Degradation 12 Process Rate = Cl- *0.8e
Degradation 13 Process Rate = 1.0 (default)f
Suppression 16, 27, 28 Process Threshold = 0 (default)
Activation 17 Process Threshold = 0 (default)g
cAMP decomposition 18 Process Threshold = 0g or 1g
Activation 19 Process Threshold = 0 (default)h
cAMP decomposition 20 Process Threshold = 0h or 1h
cGMP increase 23 Process Threshold = 0 (default)
  1. a Changing this value (5–20) did not affect the results of the simulation.
  2. b Processes 1 and 2 kept the OR at a constant concentration.
  3. c Processes 3 and 4 recovered the OR to its initial concentration after consumption of the odorants.
  4. d Determined a priori by test runs. If the threshold was 0, the simulation model did not work and resulted in computation error.
  5. e Process 12 recovered the polarization state of the olfactory receptor neutron model.
  6. f Process 13 was applied in the Ca2+-limited model.
  7. g Processes 17 and 18 were applied in the single PDE1C model.
  8. h Processes 19 and 20 were applied in the multiple PDE1C model.