| |
Name | Pathway Name /
Pathway No. | Accession
Type | Initial
Conc.
(uM) | Volume
(fL) | Buffered | Sum Total Of |
| 1 | Ca-ext | CaRegulation
Pathway No. 110 | 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 | ATP | IHP-system
Pathway No. 116 | Network | 2700.05 | 1000 | Yes | - |
| | Conc for mammalian brain from Huang et al, Biochem 37; 1998 |
| 3 | ADP | IHP-system
Pathway No. 116 | Network | 699.995 | 1000 | Yes | - |
| | Conc for mammaliam brain from Huang et al, Biochem 37; 1998 |
| 4 | inositol | 145_dephos
Pathway No. 114 | Network | 500 | 1000 | Yes | - |
| 5 | PIP2 | PLCbeta
Pathway No. 112 | Network | 150 | 1000 | Yes | - |
| | PIP2 conc: Willars et al; JBC 273 (9) 27.2.98; pp 5037-5046 |
| 6 | 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 |
| 7 | total-CaMKII | CaMKII
Pathway No. 106 | Network | 70 | 1000 | Yes | - |
| | This pool is purely here to provide a single, fixed number, which is the total amount of CaMKII. This is used by the autophosphorylation steps to scale down the rates so that the autophosphorylation reactions are independent of CaMKII levels. |
| 8 | IP5(13456) | IHP-system
Pathway No. 116 | Network | 53.9992 | 1000 | No | - |
| | Inositol(13456)pentakisphosphate Conc from Voglmaier et al, PNAS 93; 1996 |
| 9 | AA | PKC
Pathway No. 108 | 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. |
| 10 | IP6 | IHP-system
Pathway No. 116 | Network | 30.0005 | 1000 | No | - |
| | Inositol hexakisphosphate Conc from Voglmaier et al, PNAS 93; 1996 |
| 11 | IP1_pase | 145_dephos
Pathway No. 114 | Network | 25.64 | 1000 | No | - |
| | from Gee et al, Biochem J. 1988, 249, 883-889 Inositol monophosphate phosphatase; has two enzyme activities against Ins(4)P1 and Ins(1)P1 respectively |
| 12 | 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 |
| 13 | PP-IP4 | IHP-system
Pathway No. 116 | Network | 14.9999 | 1000 | No | - |
| | Diphosphoinositol tetrakisphosphate Conc from Saiardi et al, JBC 275; 2000 |
| 14 | IP_5pase1 | 145_dephos
Pathway No. 114 | Network | 12.346 | 1000 | No | - |
| | from Hansen et al, JBC 262(36); Dec 25 1987: 17319-26 InsP 5phosphatase1 has two 5-phosphatase activities: against Ins(145)P3 and Ins(1345)P4 respectively |
| 15 | 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. |
| 16 | Ca-sequester | CaRegulation
Pathway No. 110 | Network | 5.796 | 160 | No | - |
| | Sequestered Ca pool The vol is 0.16 * the vol of the cell as a whole. |
| 17 | IP_1pase | 145_dephos
Pathway No. 114 | Network | 5.0163 | 1000 | No | - |
| | from Inhorn and Majerus; JBC 262(33), 1987 pp 15946-15952 InsP-1-phosphatase has two enzyme activities against Ins(14)P2 and Ins(134)P3 respectively |
| 18 | IP5(12456) | MIPP
Pathway No. 105 | Network | 2.4 | 1000 | Yes | - |
| | Inositol(12456)pentakisphosphate Conc = 4% of total InsP5 |
| 19 | PP-IP5 | IHP-system
Pathway No. 116 | Network | 2 | 1000 | No | - |
| | Diphosphoinositol pentakisphosphate Conc from Huang et al, Biochem 37; 1998 |
| 20 | bisPP-IP4 | IHP-system
Pathway No. 116 | Network | 2 | 1000 | No | - |
| | Bis(diphospho)inositol tetrakisphosphate Conc from Huang et al, Biochem 37; 1998 |
and 
color.