| |
Name | Pathway Name /
Pathway No. | Accession
Type | Initial
Conc.
(uM) | Volume
(fL) | Buffered | Sum Total Of |
| 1 | Ca-ext | CaRegulation
Pathway No. 170 | 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. |
| 2 | CaMKII | CaMKII
Pathway No. 159 | 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 |
| 3 | CaMKII-CaM | CaMKII
Pathway No. 159 | 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 |
| 4 | CaMKII-thr286*-C
aM | CaMKII
Pathway No. 159 | Network | 0 | 1000 | No | - |
| | From Hanson and Schulman, the thr286 is responsible for autonomous activation of CaMKII. |
| 5 | CaMKII*** | CaMKII
Pathway No. 159 | 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. |
| 6 | CaMKII-thr286 | CaMKII
Pathway No. 159 | 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. |
| 7 | CaMK-thr306 | CaMKII
Pathway No. 159 | 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 |
| 8 | PP1-active | CaMKII
Pathway No. 159 | Network | 1.8 | 1000 | No | - |
| | Cohen et al Meth Enz 159 390-408 is main source of info concentration of enzyme = 1.8 uM |
| 9 | CaM | CaM
Pathway No. 160 | 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 |
| 10 | CaM-Ca4 | CaM
Pathway No. 160 | Network | 0 | 1000 | No | - |
| | The four-calcium-bound form of CaM. It is the active form for most reactions. |
| 11 | CaM-Ca3 | CaM
Pathway No. 160 | 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. |
| 12 | CaM-TR2-Ca2 | CaM
Pathway No. 160 | 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. |
| 13 | PKC-DAG-AA* | PKC
Pathway No. 161 | Network | 0 | 1000 | No | - |
| | Membrane translocated form of PKC-DAG-AA complex. |
| 14 | PKC-Ca-AA* | PKC
Pathway No. 161 | Network | 0 | 1000 | No | - |
| | Membrane bound and active complex of PKC, Ca and AA. |
| 15 | PKC-Ca-memb* | PKC
Pathway No. 161 | Network | 0 | 1000 | No | - |
| | This is the direct Ca-stimulated activity of PKC. |
| 16 | PKC-DAG-memb* | PKC
Pathway No. 161 | Network | 0 | 1000 | No | - |
| | Active, membrane attached form of Ca.DAG.PKC complex. |
| 17 | PKC-basal* | PKC
Pathway No. 161 | Network | 0.02 | 1000 | No | - |
| | This is the basal PKC activity which contributes about 2% to the maximum. |
| 18 | PKC-AA* | PKC
Pathway No. 161 | Network | 0 | 1000 | No | - |
| | This is the membrane-bound and active form of the PKC-AA complex. |
| 19 | PKC-Ca-DAG | PKC
Pathway No. 161 | Network | 0 | 1000 | No | - |
| | This is the active PKC form involving Ca and DAG. It has to translocate to the membrane. |
| 20 | PKC-DAG | PKC
Pathway No. 161 | Network | 0 | 1000 | No | - |
| | This is a DAG-bound intermediate used in synergistic activation of PKC by DAG and AA. |
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