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Molecule Parameter List for CaNAB_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. |
CaNAB_dash_Ca2 acting as a Molecule in mRNA synthesis Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | CaNAB_dash_Ca2 | mRNA synthesis
Accession No. : 94 | kinetics
Pathway No. : 1112 | 0 | 1000 | No | | |
CaNAB_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 | 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 |
CaNAB_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 | Ca_dash_bind_
dash_CaNAB | mRNA synthesis
Accession No. : 94 | kinetics
Pathway No. : 1112 | 10008360
(uM^-2 s^-1) | 1
(s^-1) | Kd(af) = 0.0003(uM) | - | Substrate
Ca
Ca
CaNAB
Product
CaNAB_dash_Ca2
| | going on the experience with CaM, we put the fast (high affinity) sites first. We only know (Stemmer and Klee) that the affinity is < 70 nM. Assuming 10 nM at first, we get kf = 2.78e-8, kb = 1. Try 20 nM. kf = 7e-9, kb = 1 |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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