| |
Name | Pathway Name /
Pathway No. | Accession
Type | Initial
Conc.
(uM) | Volume
(fL) | Buffered | Sum Total Of |
| 1 | 1345_3pase | 1345_dephos
Pathway No. 131 | Network | 0.1 | 1000 | No | - |
| | from Hoer et al, BiochemJ 270; 1990: 715-719 |
| 2 | AA | PKC
Pathway No. 123 | Network | 50 | 1000 | Yes | - |
| | Arachidonic Acid. This messenger diffuses through membranes as well as cytosolically, has been suggested as a possible retrograde messenger at synapses. |
| 3 | activeIP3R | Othmer-Tang-mode
l
Pathway No. 133Network | 0 | 1000 | No | - | |
| | This represents the active IP3 Receptor channel that conducts Ca across the ER membrane in the Othmer-Tang model. Its 0 uM initial concentration represents no active channels present under basal conditions. Its levels build up upon stimulation. |
| 4 | ADP | IHP-system
Pathway No. 130 | Network | 699.995 | 1000 | Yes | - |
| | Conc for mammaliam brain from Huang et al, Biochem 37; 1998 |
| 5 | ATP | IHP-system
Pathway No. 130 | Network | 2700.05 | 1000 | Yes | - |
| | Conc for mammalian brain from Huang et al, Biochem 37; 1998 |
| 6 | BetaGamma | Gq
Pathway No. 125 | Network | 0 | 1000 | No | - |
| | The betagamma subunits of Gq. This is an approximation to the possible combinations of betagamma subunits. Here they are all treated as a single pool. |
| 7 | bisPP-IP3 | IHP-system
Pathway No. 130 | Network | 0 | 1000 | Yes | - |
| | Bis(diphospho)inositol trisphosphate from Saiardi et al, JBC 275(32); 2000: 24686-92 |
| 8 | bisPP-IP4 | IHP-system
Pathway No. 130 | Network | 2 | 1000 | No | - |
| | Bis(diphospho)inositol tetrakisphosphate Conc from Huang et al, Biochem 37; 1998 |
| 9 | Blocked-rec-Gq | Gq
Pathway No. 125 | Network | 0 | 1000 | No | - |
| | This represents the blocked state of the receptor when bound to a competitive antagonist. Note that this is in the Gq bound form. Simulations had shown that with the available rates, the blocking was minimal if only the unbound receptor could bind the antagonist. |
| 10 | Ca | CaRegulation
Pathway No. 132 | Network | 0.08 | 1000 | No | - |
| | This pool represents intracellular calcium. Resting levels are around 80 nM, but this is subject to all sorts of influxes and pumps. |
| 11 | Ca-1pase-cmplx | 145_dephos
Pathway No. 128 | Network | 0 | 1000 | No | - |
| 12 | Ca-ext | CaRegulation
Pathway No. 132 | Network | 4000 | 100000 | Yes | - |
| | Extracell Ca conc = 4 mM Extracell vol assumed 100 X cell vol. It is anyway kept buffered for the purposes of the model, so the concentration won't change. |
| 13 | Ca-leak-from-ext
racell | CaRegulation
Pathway No. 132 | Network | 0.0008 | 1000 | No | - |
| | This represents the pool of Ca leak channels. The conc gradient is so large that this pool needs only small number of molecules. For an equilibrium at 0.1 uM we need flow of 36e3/sec. With a permeability of 0.01 and a conc gradient of 4mM->0.1 uM (4e4) we get flux = N * perm * g rad => N = 36e3 / (1e-2 * 4e3) = 900 if flux = 20e3, N =500, which is what we use. This works out to a concentration of 0.83 nM. |
| 14 | Ca-sequester | CaRegulation
Pathway No. 132 | Network | 6.3328 | 160 | No | - |
| | Sequestered Ca pool The vol is 0.16 * the vol of the cell as a whole. The Ca-sequester conc that we use is same as that used in our other models (see Bhalla and Iyengar, Science 283, 1999: 381-387 |
| 15 | Ca.IP3.IP3R | Othmer-Tang-mode
l
Pathway No. 133Network | 0 | 1000 | No | - | |
| | IP3-IP3Receptor complex with Ca bound at the activating site. |
| 16 | Ca10-Cal | CaRegulation
Pathway No. 132 | Network | 0 | 160 | No | - |
| | Calsequestrin with 10 Ca molecules bound |
| 17 | Ca15-Cal | CaRegulation
Pathway No. 132 | Network | 0 | 160 | No | - |
| | Calsequestrin with 15 Ca molecules bound |
| 18 | Ca2.IP3.IP3R | Othmer-Tang-mode
l
Pathway No. 133Network | 0 | 1000 | No | - | |
| | THe Ca-IP3-IP3Receptor complex with additional Ca bound to the inhibitory sites. This is the inactive state of the channel. |
| 19 | Ca20-Cal | CaRegulation
Pathway No. 132 | Network | 0 | 160 | No | - |
| | Calsequestrin with 20 Ca molecules bound |
| 20 | Ca25-Cal | CaRegulation
Pathway No. 132 | Network | 0 | 160 | No | - |
| | Calsequestrin with 25 Ca molecules bound |
arrow indicates that ordering is done according to ascending or descending order.
and 
color.