| |
Name | Accession
Type | Initial
Conc.
(uM) | Volume
(fL) | Buffered | Sum Total Of |
| 1 | Ca-ext | Network | 4000 | 0 | Yes | - |
| | Extracell Ca conc = 4 mM Extracell vol assumed 100 X cell vol It is kept buffered anyway for the puroposes of the model, so the concentration won't change. |
| 2 | Ca-leak-from-ext
racell | Network | 0.0008 | 0 | No | - |
| | This represents the pool of Ca leak channels. The concentration gradient is so large that this pool only needs a 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 concentration gradient of 4mM->0.1 uM (4e4) we get flux = N * perm * grad => 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. |
| 3 | Ca-leak-to-cytop
lasm | Network | 0.024 | 0 | Yes | - |
| | This pool represents the channels which leak Ca into the cytoplasm. It is a probably a composite of various channels depending on cell type. Membrane potential will obviously affect the leak amount, but that is not considered. The amounts and total flux are constrained by the need to balance the Ca flux and keep basal Ca levels around 80 nM. |
| 4 | Ca-sequester | Network | 6.3328 | 0 | No | - |
| | This is the sequestered Calcium pool. The vol is 0.16 * the vol of the cell as a whole. This pool should really equilibrate with a highly buffered pool of Calcium, but that is not present in this version of the model. |
| 5 | CaEPump | Network | 0.005 | 0 | No | - |
| | The calcium electrogenic pump. See McBurney and Neering 1987 TINS 10(4):164-169 We treat the pump as a simple Michaelis-Menten enzyme. Levels are constrained tightly by the need to keep resting Ca levels at about 80 nM. |
| 6 | 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. In this model the channel is implemented to match experimental observations about capacitive Ca entry. Levels are set by two constraints: the resting Ca levels, and the height of the response to IP3. |
| 7 | CaTransp | Network | 0.24 | 0 | No | - |
| | The calcium transporter levels are constrained by the resting levels of Ca in the cell. The rate of Ca sequestration depends on the amount of this pool. |
| 8 | CaTransp-2Ca | Network | 0 | 0 | No | - |
| | This is equivalent to the enzyme-substrate complex. 2 Ca are bound to the transporter. The ATP is ignored. |
| 9 | inact_cap_entry | Network | 0 | 0 | No | - |
| | This represents the portion of the capacitive-Ca entry channel which is blocked when there is lots of Ca sequestered in the stores. |
| 10 | IP3R | Network | 0.0166 | 0 | No | - |
| | The number of the IP3Rs in the cell is present only implicitly in the model, and is lumped in with the total permeability of the IP3R pool. The latter term is constrained by the height of the Ca transient. |
| 11 | IP3R* | Network | 0 | 0 | No | - |
| | This is the ligand-bound form of the IP3 receptor. |
arrow indicates that ordering is done according to ascending or descending order.
and 
color.