Table 3

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

Elements/processes

Element abbreviation/process #

Type

Parameter

Odorant

--

Element

Initial value = 10^a

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*0.05^b

Degradation

2

Process

Rate = OR*0.05^b

Binding

3

Process

Rate = Odorant*OR*0.7^c

Dissociation

4

Process

Rate = Odorant-OR*0.5^c

Activation

5

Process

Threshold = 2^d

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^- *0.8^e

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 = 0^g or 1^g

Activation

19

Process

Threshold = 0 (default)^h

cAMP decomposition

20

Process

Threshold = 0^h or 1^h

cGMP increase

23

Process

Threshold = 0 (default)

^a Changing this value (5–20) did not affect the results of the simulation.

^b Processes 1 and 2 kept the OR at a constant concentration.

^c Processes 3 and 4 recovered the OR to its initial concentration after consumption of the odorants.

^d Determined a priori by test runs. If the threshold was 0, the simulation model did not work and resulted in computation error.

^e Process 12 recovered the polarization state of the olfactory receptor neutron model.

^f Process 13 was applied in the Ca²⁺-limited model.

^g Processes 17 and 18 were applied in the single PDE1C model.

^h Processes 19 and 20 were applied in the multiple PDE1C model.

Sato et al. BMC Systems Biology 2009 3:23   doi:10.1186/1752-0509-3-23