| |
Name | Pathway Name /
Pathway No. | Accession
Type | Initial
Conc.
(uM) | Volume
(fL) | Buffered | Sum Total Of |
| 21 | Ca40-Cal | CaRegulation
Pathway No. 110 | Network | 0 | 160 | No | - |
| | Calsequestrin with 40 Ca molecules bound |
| 22 | Ca5-Cal | CaRegulation
Pathway No. 110 | Network | 0 | 160 | No | - |
| | Calsequestrin with 5 Ca molecules bound |
| 23 | CaEPump | CaRegulation
Pathway No. 110 | Network | 0.005 | 1000 | No | - |
| | The calcium electrogenic pump: Mc Burney and Neering, TINS 10(4), 1987, 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 80 nM. |
| 24 | Calseq | CaRegulation
Pathway No. 110 | Network | 9.09 | 160 | 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; membrane protein = 2% of cell mass = 0.02 * 1g/cc * (1e-9)cc = (2e-11) g Hence Calseq = 8e-14/55000 moles per (1.6e-13)l = 9.091uM As per Guidebook to 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. |
| 25 | CaM | CaM
Pathway No. 107 | Network | 20 | 1000 | No | - |
| | LOT of this present in the cell: upto 1% of total protein mass. (Alberts et al, Mol Biol of the Cell, Garland Publishers) says 25 uM. Meyer et al, Science 256; 1992: 1199-1202 refer to studies saying it is comparable to CaMK levels. (Kakiuchi et al, J Biochem 92; 1982; 1041-48) say conc in cerebral cortex & cerebellum homogenates: 20-30uM Lower conc in other tissues: lung, adrenal gland, liver, kidney, spleen = 6,5,5,3,2 uM respectively |
| 26 | CaM-Ca3 | CaM
Pathway No. 107 | Network | 0 | 1000 | No | - |
| | The TR1 end now begins to bind Ca. This form has 2 Ca's on the TR2 end, and one on the TR1. |
| 27 | CaM-Ca4 | CaM
Pathway No. 107 | Network | 0 | 1000 | No | - |
| | The four-calcium-bound form of CaM. It is the active form for most reactions. |
| 28 | CaM-TR2-Ca2 | CaM
Pathway No. 107 | Network | 0 | 1000 | No | - |
| | This is the intermediate where the TR2 end (the high-affinity end) has bound the Ca but the TR1 end has not. |
| 29 | CaMK-thr306 | CaMKII
Pathway No. 106 | Network | 0 | 1000 | No | - |
| | This forms due to basal autophosphorylation, but I think it has to be considered as a pathway even if some CaM is floating around. In either case it will tend to block further binding of CaM, and will not display any enzyme activity. See Hanson and Schulman JBC 267:24 pp17216-17224 1992 |
| 30 | CaMKII | CaMKII
Pathway No. 106 | Network | 70 | 1000 | No | - |
| | Huge concentration of CaMKII. In PSD it is 20-40% of protein, so we assume it is around 2.5% of protein in spine as a whole. This level is so high it is unlikely to matter much if we are off a bit. This comes to about 70 uM. Seen the review: Hanson and Schulman 1992 Ann. Rev. Biuochem 60:559-601 |
| 31 | CaMKII*** | CaMKII
Pathway No. 106 | Network | 0 | 1000 | No | - |
| | From Hanson and Schulman, the CaMKII does a lot of autophosphorylation just after the CaM is released. This prevents further CaM binding and renders the enzyme quite independent of Ca. |
| 32 | CaMKII-CaM | CaMKII
Pathway No. 106 | Network | 0 | 1000 | No | - |
| | This is the regular, CaM-activated form of CaMKII. See the review Hanson and Schulman 1992 Ann. Rev. Biochem 60:559-601 |
| 33 | CaMKII-thr286 | CaMKII
Pathway No. 106 | Network | 0 | 1000 | No | - |
| | The threonine-286 phosphorylated form of CaMKII. It is likely to be a short-lived intermediate, since it will be phosphorylated further as soon as the CAM falls off. |
| 34 | CaMKII-thr286*-C
aM | CaMKII
Pathway No. 106 | Network | 0 | 1000 | No | - |
| | From Hanson and Schulman, the thr286 is responsible for autonomous activation of CaMKII. |
| 35 | capacitive_Ca_
entry* | CaRegulation
Pathway No. 110 | Network | 0.01 | 1000 | 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 capacitative Ca entry. Levels are set by two constraints: the resting Ca levels, and the height of the response to IP3. |
| 36 | CaTransp | CaRegulation
Pathway No. 110 | Network | 0.24 | 1000 | 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. |
| 37 | CaTransp-2Ca | CaRegulation
Pathway No. 110 | Network | 0 | 1000 | No | - |
| | equivalent to the enzyme-substrate complex. 2 Ca are bound to the transporter. ATP is ignored. |
| 38 | DAG | PLCbeta
Pathway No. 112 | Network | 0 | 1000 | No | - |
| | Basal levels of Diacylglycerol in model are 5.06 uM. DAG is pretty nasty to estimate. Data sources are many and varied and sometimes difficult to reconcile. Welsh and Cabot 1987 JCB 35:231-245: DAG degradation Bocckino et al JBC 260(26):14201-14207: hepatocytes stim with vasopressin: 190 uM. Bocckino et al 1987 JBC 262(31):15309-15315: DAG rises from 70 to 200 ng/mg wet weight, approx 150 to 450 uM. Prescott and Majerus 1983 JBC 258:764-769: Platelets: 6 uM. Also see Rittenhouse-Simmons 1979 J Clin Invest 63. Sano et al JBC 258(3):2010-2013: Report a nearly 10 fold rise. Habenicht et al 1981 JBC 256(23)12329-12335: 3T3 cells with PDGF stim: 27 uM Cornell and Vance 1987 BBA 919:23-36: 10x rise from 10 to 100 uM |
| 39 | DIPP1 | IHP-system
Pathway No. 116 | Network | 0.1267 | 1000 | No | - |
| | Diphosphoinositol-Polyphosphate Phosphohydrolase from Safrany et al, EMBO J 17(22); 1998: 6599-607 |
| 40 | G*GDP | Gq
Pathway No. 111 | Network | 0 | 1000 | No | - |
| | This should correctly be called GDP.G_alpha. The name is preserved for backward compatibility reasons. |
arrow indicates that ordering is done according to ascending or descending order.
and 
color.