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| Default ordering is done according to Pathway Number. Table headers can be used for changing the default ordering. arrow indicates that ordering is done according to ascending or descending order. The entries are grouped according to Pathway Number and are alternately color coded using and color. |
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Name | Pathway Name / Pathway No. | Accession Type | Initial Conc. (uM) | Volume (fL) | Buffered | Sum Total Of | 1 | ATP | AC
Pathway No. 278 | Network | 2000 | 0.09 | Yes | - | | ATP is present in all cells between 2 and 10 mM. See Lehninger | 2 | temp-PIP2 | Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. 271Network | 2.5 | 0.09 | Yes | - | | | This isn't explicitly present in the M&L model, but is obviously needed. I assume its conc is fixed at 1uM for now, which is a bit high. PLA2 is stim 7x by PIP2 @ 0.5 uM (Leslie and Channon BBA 1045:261(1990) Leslie and Channon say PIP2 is present at 0.1 - 0.2mol% range in membs, which comes to 50 nM. Ref is Majerus et al Cell 37 pp 701-703 1984 Lets use a lower level of 30 nM, same ref.... | 3 | AMPAR_deg | AMPAR
Pathway No. 280 | Network | 0 | 0.09 | Yes | - | 4 | basal_CaMKII_ cyt | Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. 271Network | 2 | 0.09 | Yes | - | 5 | PKC-control | Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. 271Network | 0.1 | 0.09 | Yes | - | 6 | Ca_control_cyt | Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. 271Network | 0.08 | 0.09 | Yes | - | 7 | Ca_control_PSD | Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. 271Network | 0.08 | 0.01 | Yes | - | 8 | basal_CaMKII_ PSD_control | Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. 271Network | 2 | 0.01 | Yes | - | 9 | AMPAR_bulk | Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. 271Network | 0.0093 | 5 | Yes | - | 10 | CaM-Ca4 | Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. 271Network | 0 | 0.09 | No | - | 11 | PP1-active | Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. 271Network | 1.8 | 0.09 | No | - | | | Cohen et al Meth Enz 159 390-408 is main source of info conc = 1.8 uM | 12 | cAMP | Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. 271Network | 0 | 0.09 | No | - | | | The conc of this has been a problem. Schaecter and Benowitz use 50 uM, but Shinomura et al have < 5. So I have altered the cAMP-dependent rates in the PKA model to reflect this. | 13 | Ca | Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. 271Network | 0.08 | 0.09 | No | - | 14 | PKA-active | Shared_Object_ AMPAR_CaMKII_ strong_coupling Pathway No. 271Network | 0 | 0.09 | No | - | 15 | CaMKII | CaMKII
Pathway No. 272 | Network | 20 | 0.09 | 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. | 16 | CaMKII-CaM | CaMKII
Pathway No. 272 | Network | 0 | 0.09 | No | - | 17 | CaMKII-thr286*-C aM | CaMKII
Pathway No. 272 | Network | 0 | 0.09 | No | - | | From Hanson and Schulman, the thr286 is responsible for autonomous activation of CaMKII. | 18 | CaMKII*** | CaMKII
Pathway No. 272 | Network | 0 | 0.09 | 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. | 19 | CaMKII-thr286 | CaMKII
Pathway No. 272 | Network | 0 | 0.09 | No | - | | I am not sure if we need to endow this one with a lot of enzs. It is likely to be a short-lived intermediate, since it will be phosphorylated further as soon as the CAM falls off. | 20 | CaMK-thr305 | CaMKII
Pathway No. 272 | Network | 0 | 0.09 | 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 | | | | | | | | | |
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