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Molecule Parameter List for CaM_dash_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 | | mRNA synthesis | 94 | Network |
kinetics, compartment_1, compartment_2 | | The model consists of three major pathways: Calcium-calmodulin dependent protein kinase IV (CaMKIV), Mitogen-activated protein kinase (MAPK) and Protein Phosphatase 1 (PP1). Each of these converged on CREB activation. We also modeled further interactions with Transducer of regulated CREB activity 1 (TORC1) and the protein kinase A (PKA) pathway. |
CaM_dash_Ca2 acting as a Molecule in mRNA synthesis Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | CaM_dash_Ca2 | mRNA synthesis
Accession No. : 94 | kinetics
Pathway No. : 1112 | 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_Ca2 acting as a Substrate in a reaction in mRNA synthesis 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 | | 1 | CaM_dash_Ca2_
dash_bind_dash_
Ca | mRNA synthesis
Accession No. : 94 | kinetics
Pathway No. : 1112 | 3.6001
(uM^-1 s^-1) | 10
(s^-1) | Kd(bf) = 2.7777(uM) | - | Substrate
Ca
CaM_dash_Ca2
Product
CaM_dash_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 | | 2 | CaM_dash_Ca2_
dash_bind_dash_
CaNAB | mRNA synthesis
Accession No. : 94 | kinetics
Pathway No. : 1112 | 0.24
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 4.1667(uM) | - | Substrate
CaM_dash_Ca2
CaNAB_dash_Ca4
Product
CaMCa2_dash_
CANAB
| | | Disabled. See notes for PP2B7.g |
CaM_dash_Ca2 acting as a Product in a reaction in mRNA synthesis 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 | mRNA synthesis
Accession No. : 94 | kinetics
Pathway No. : 1112 | 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 |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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