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Molecule Parameter List for CaM-TR2-Ca2 | The statistics table lists the distribution of a molecule acting either as a substrate, product, enzyme or as a molecule within the network.
The text color of a molecule is highlighted by  color. | | Statistics |
Accession and Pathway Details | |
| Accession Name | Accession No. | Accession Type | Pathway Link | AMPAR_CaMKII_
strong_coupling | 64 | Network |
Shared_Object_AMPAR_CaMKII_strong_coupling, CaMKII, CaM,
PP1, AMPAR_memb, PP2B,
PKA, AC, PP1_PSD,
AMPAR | | This is a model of tight coupling between the AMPAR trafficking bistability, and the CaMKII autophosphorylation bistability. In this model, the CaMKII activity is self sustaining only when AMPAR is turned on. Further, CaMKII turns on when AMPAR is turned on. |
CaM-TR2-Ca2 acting as a Molecule in AMPAR_CaMKII_strong_coupling Network
CaM-TR2-Ca2 acting as a Substrate in a reaction in AMPAR_CaMKII_strong_coupling Network
| Kd is calculated only for second order reactions, like nA+nB <->nC or nA<->nC+nD, where n is number and A,B,C,D are molecules, where as for first order reactions Keq is calculated.
Kd for higher order reaction are not consider. |
| Name | Accession Name | Pathway Name | Kf | Kb | Kd | tau | Reagents | CaM-TR2-Ca2-bind
-Ca | AMPAR_CaMKII_
strong_coupling
Accession No. : 64 | CaM
Pathway No. : 273 | 3.6
(uM^-1 s^-1) | 10
(s^-1) | Kd(bf) = 2.7778(uM) | - | Substrate
Ca
CaM-TR2-Ca2
Product
CaM-Ca3
| | K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get kb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10 |
CaM-TR2-Ca2 acting as a Product in a reaction in AMPAR_CaMKII_strong_coupling Network
| Kd is calculated only for second order reactions, like nA+nB <->nC or nA<->nC+nD, where n is number and A,B,C,D are molecules, where as for first order reactions Keq is calculated.
Kd for higher order reaction are not consider. |
| Name | Accession Name | Pathway Name | Kf | Kb | Kd | tau | Reagents | | CaM-TR2-bind-Ca | AMPAR_CaMKII_
strong_coupling
Accession No. : 64 | CaM
Pathway No. : 273 | 71.999
(uM^-2 s^-1) | 72
(s^-1) | Kd(af) = 1(uM) | - | Substrate
Ca
Ca
CaM
Product
CaM-TR2-Ca2
| | Lets use the fast rate consts here. Since the rates are so different, I am not sure whether the order is relevant. These correspond to the TR2C fragment. We use the Martin et al rates here, plus the Drabicowski binding consts. All are scaled by 3X to cell temp. kf = 2e-10 kb = 72 Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11. If kb=72, kf = 2e-10 (Exactly the same !).... |
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