| |
Name | Accession
Type | Initial
Conc.
(uM) | Volume
(fL) | Buffered | Sum Total Of |
| 1 | Ca | Network | 0.08 | 0 | No | - |
| | This pool represents intracellular calcium. Resting levels are around 80 nM, but this is subject to all sorts of influxes and pumps. |
| 2 | Ca-ext | Network | 4000 | 0 | 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. |
| 3 | Ca-leak-from-ext
racell | Network | 0.0008 | 0 | 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. |
| 4 | Ca-sequester | Network | 6.3328 | 0 | 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 |
| 5 | Ca10-Cal | Network | 0 | 0 | No | - |
| | Calsequestrin with 10 Ca molecules bound |
| 6 | Ca15-Cal | Network | 0 | 0 | No | - |
| | Calsequestrin with 15 Ca molecules bound |
| 7 | Ca20-Cal | Network | 0 | 0 | No | - |
| | Calsequestrin with 20 Ca molecules bound |
| 8 | Ca25-Cal | Network | 0 | 0 | No | - |
| | Calsequestrin with 25 Ca molecules bound |
| 9 | Ca30-Calseq | Network | 0 | 0 | No | - |
| | Calsequestrin with 30 Ca molecules bound |
| 10 | Ca35-Calseq | Network | 0 | 0 | No | - |
| | Calsequestrin with 35 Ca molecules bound |
| 11 | Ca40-Cal | Network | 0 | 0 | No | - |
| | Calsequestrin with 40 Ca molecules bound |
| 12 | Ca5-Cal | Network | 0 | 0 | No | - |
| | Calsequestrin with 5 Ca molecules bound |
| 13 | CaEPump | Network | 0.01 | 0 | No | - |
| | The calcium electrogenic pump: Mc Burney and Neering, TINS 10(4), 1987, 163-169. We treat the pump as a simple Michaelis-Menten enzyme. Levels are constrained tightly by the need to generate Ca oscillations within the Othmer-Tang model. |
| 14 | Calseq | Network | 9.09 | 0 | No | - |
| | This is Calsequestrin or the calcium buffer in the ER. from Cala & Jones, JBC 258(19), 1983: 11932-36 Calseq is present as 4mg/g of membrane protein; membarne protein = 2% of cell mass = 0.02 * 1g/cc * (1e-9)cc =(2e-11) g Hence Calseq = 8e-14/550000 moles per (1.6e-13)l = 9.091uM As per Guidebook of the calcium-binding proteins by Celio; and Mitchell et al, JBC 263, 1988: 1376-81; 1 mol of Calsequestrin binds 40 mol of Ca. This is the stoichiometry we use. The affinity of Calsequestrin for Ca in our model is constrained by the levels of free Ca in the stores (Ca-sequester). We use a Kd such that Ca-sequester levels remain similar to levels in the CaRegulation model without Ca buffering. |
| 15 | capacitive_Ca_
entry* | Network | 0.01 | 0 | No | - |
| | This mechanism has taken a while to be more tightly confirmed as probably being the TRP channel. The channel is implemented to match experimental observations about capacitative Ca entry. Levels are unchanged from the CaReg model used to generate non-oscillatory Ca response in the IP3 metabolism network. |
| 16 | inact_cap_entry | Network | 0 | 0 | No | - |
| | represents the portion of the capacitative-Ca entry channel which is blocked when there is lots of Ca sequestered in the stores |
arrow indicates that ordering is done according to ascending or descending order.
and 
color.