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Molecule Parameter List for CaM_dash_Ca | 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 | | CaMKIV_submodel | 93 | Network |
kinetics, compartment_1 | | Calcium-calmodulin dependent protein kinase IV (CaMKIV) pathway is one of the sub-model in signaling cascade regulating mRNA synthesis |
CaM_dash_Ca acting as a Molecule in CaMKIV_submodel Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | CaM_dash_Ca | CaMKIV_submodel
Accession No. : 93 | kinetics
Pathway No. : 1110 | 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. |
CaM_dash_Ca acting as a Substrate in a reaction in CaMKIV_submodel 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_dash_Ca_
dash_bind_dash_
Ca | CaMKIV_submodel
Accession No. : 93 | kinetics
Pathway No. : 1110 | 8.4846
(uM^-1 s^-1) | 8.4853
(s^-1) | Kd(bf) = 1.0001(uM) | - | Substrate
Ca
CaM_dash_Ca
Product
CaM_dash_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 !) 19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into two steps, each binding 1 Ca. This improves numerical stability and is conceptually better too. Overall rates are the same, so each kf and kb is the square root of the earlier ones. So kf = 1.125e-4, kb = 8.4853 |
CaM_dash_Ca acting as a Product in a reaction in CaMKIV_submodel 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_dash_bind_
dash_Ca | CaMKIV_submodel
Accession No. : 93 | kinetics
Pathway No. : 1110 | 8.4846
(uM^-1 s^-1) | 8.4853
(s^-1) | Kd(bf) = 1.0001(uM) | - | Substrate
Ca
CaM
Product
CaM_dash_Ca
| | 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 !) 19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into two steps, each binding 1 Ca. This improves numerical stability and is conceptually better too. Overall rates are the same, so each kf and kb is the square root of the earlier ones. So kf = 1.125e-4, kb = 8.4853 |
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