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Molecule Parameter List for CaNAB_dash_Ca4 | 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. |
CaNAB_dash_Ca4 acting as a Molecule in mRNA synthesis Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | CaNAB_dash_Ca4 | mRNA synthesis
Accession No. : 94 | kinetics
Pathway No. : 1112 | 0 | 1000 | No | | |
CaNAB_dash_Ca4 acting as an Enzyme in mRNA synthesis Network
Enzyme Molecule /
Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | CaNAB_dash_Ca4 /
dephosph_
inhib1_noCaM
| mRNA synthesis
Accession No. : 94 | kinetics
Pathway No. : 1112 | 4.9708 | 0.034 | 4 | explicit E-S complex | Substrate
I1_star
Product
I1
| | The rates here are so slow I do not know if we should even bother with this enz reacn. These numbers are from Liu and Storm. Other refs suggest that the Km stays the same but the Vmax goes to 10% of the CaM stim levels. Prev: k1=2.2e-9, k2 = 0.0052, k3 = 0.0013 New : k1=5.7e-8, k2=.136, k3=.034 |
CaNAB_dash_Ca4 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. |
CaNAB_dash_Ca4 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 | Ca_dash_bind_
dash_CaNAB_
dash_Ca2 | mRNA synthesis
Accession No. : 94 | kinetics
Pathway No. : 1112 | 3599.928
(uM^-2 s^-1) | 1
(s^-1) | Kd(af) = 0.0167(uM) | - | Substrate
Ca
Ca
CaNAB_dash_Ca2
Product
CaNAB_dash_Ca4
| | This process is probably much more complicated and involves CaM. However, as I can't find detailed info I am bundling this into a single step. Based on Steemer and Klee pg 6863, the Kact is 0.5 uM. kf/kb = 1/(0.5 * 6e5)^2 = 1.11e-11 |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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