| |
Name | Accession Name /
Accession No. | Pathway Name /
Pathway No. | Accession
Type | Initial
Conc.
(uM) | Volume
(fL) | Buffered | Sum Total Of |
| 1 | Total_CaMKII | CaMKII
Accession No. 33 | CaMKII
Pathway No. 174 | Network | 127.325 | 0.1309 | No | - |
| | This is not directly in the Holmes model. It is a trick used in GENESIS/Kinetikit to scale activity down for intramolecular reactions. Here it is used to scale the autophosph reactions such that only neighboring subunits will phosphorylate each other. This is done by scaling down the actual conc (in the enzyme parent, Tot-active-CaMKII) by the total conc such that instead of a conc, we the fraction of nearby subunits that will be active. Note that this conc of 10000 CaMKII subunits is 10 times the true conc, since only 1/10 of the molecules are neighboring molecules. |
| 2 | CaMKII | fig3_CaMKII
Accession No. 2 | CaMKII
Pathway No. 13 | Network | 70 | 1000 | No | - |
| 3 | total-CaMKII | fig3_CaMKII
Accession No. 2 | CaMKII
Pathway No. 13 | Network | 70 | 1000 | Yes | - |
| 4 | CaMKII | fig4_synapse
Accession No. 3 | CaMKII
Pathway No. 26 | Network | 70 | 1000 | No | - |
| 5 | total-CaMKII | fig4_synapse
Accession No. 3 | CaMKII
Pathway No. 26 | Network | 70 | 1000 | Yes | - |
| 6 | CaMKII | Synaptic_
Network
Accession No. 16 | CaMKII
Pathway No. 80 | 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 | Synaptic_
Network
Accession No. 16 | CaMKII
Pathway No. 80 | 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 | CaMKII | NonOsc_Ca_
IP3metabolism
Accession No. 23 | 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 |
| 9 | total-CaMKII | NonOsc_Ca_
IP3metabolism
Accession No. 23 | 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. |
| 10 | CaMKII | Osc_Ca_
IP3metabolism
Accession No. 24 | CaMKII
Pathway No. 121 | 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 |
| 11 | total-CaMKII | Osc_Ca_
IP3metabolism
Accession No. 24 | CaMKII
Pathway No. 121 | 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. |
| 12 | CaMKII | NonOsc_Ca_
IP3metabolism
Accession No. 31 | CaMKII
Pathway No. 145 | 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 |
| 13 | total-CaMKII | NonOsc_Ca_
IP3metabolism
Accession No. 31 | CaMKII
Pathway No. 145 | 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. |
| 14 | CaMKII | Osc_Ca_
IP3metabolism
Accession No. 32 | 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 |
| 15 | total-CaMKII | Osc_Ca_
IP3metabolism
Accession No. 32 | CaMKII
Pathway No. 159 | 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. |
| 16 | CaMKII | CaMKII_2003
Accession No. 49 | CaMKII
Pathway No. 202 | Network | 70 | 1000 | No | - |
| | Huge conc 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. |
| 17 | CaMKII | MAPK_network_
2003
Accession No. 50 | CaMKII
Pathway No. 216 | Network | 70 | 1000 | No | - |
| | Huge conc 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. |
| 18 | CaMKII | Ajay_Bhalla_
2004_PKM_Tuning
Accession No. 76 | CaMKII
Pathway No. 322 | Network | 70 | 1.5 | No | - |
| | Huge conc 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. |
| 19 | CaMKII | Ajay_Bhalla_
2004_PKM_MKP3_
Tuning
Accession No. 77 | CaMKII
Pathway No. 339 | Network | 70 | 1.5 | No | - |
| | Huge conc 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. |
| 20 | CaMKII | Ajay_Bhalla_
2004_Feedback_
Tuning
Accession No. 78 | CaMKII
Pathway No. 357 | Network | 70 | 1.5 | No | - |
| | Huge conc 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. |
and 
color.