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Molecule Parameter List for I1 | 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. |
I1 acting as a Molecule in mRNA synthesis Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | I1 | mRNA synthesis
Accession No. : 94 | kinetics
Pathway No. : 1112 | 1.8 | 1000 | No | | I1 is a 'mixed' inhibitor, but at high enz concs it looks like a non-compet inhibitor (Foulkes et al Eur J Biochem 132 309-313 9183). We treat it as non-compet, so it just turns the enz off without interacting with the binding site. Cohen et al ann rev bioch refer to results where conc is 1.5 to 1.8 uM. In order to get complete inhib of PP1, which is at 1.8 uM, we need >= 1.8 uM. |
I1 acting as a Substrate for an Enzyme in mRNA synthesis Network
Enzyme Molecule /
Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | PKA_dash_active /
PKA_dash_
phosph_dash_I1
| mRNA synthesis
Accession No. : 94 | kinetics
Pathway No. : 1112 | 7.5 | 9 | 4 | explicit E-S complex | Substrate
I1
Product
I1_star
| | #s from Bramson et al CRC crit rev Biochem 15:2 93-124. They have a huge list of peptide substrates and I have chosen high-ish rates. These consts give too much PKA activity, so lower Vmax 1/3. Now, k1 = 3e-5, k2 = 36, k3 = 9 (still pretty fast). Also lower Km 1/3 so k1 = 1e-5 Cohen et al FEBS Lett 76:182-86 1977 say rate =30% PKA act on phosphokinase beta. |
I1 acting as a Product of an Enzyme in mRNA synthesis Network
| | Enzyme Molecule /
Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | | 1 | PP2A /
PP2A_dash_
dephosph_dash_
I1
| mRNA synthesis
Accession No. : 94 | kinetics
Pathway No. : 1112 | 7.8283 | 6 | 4.16666666667 | explicit E-S complex | Substrate
I1_star
Product
I1
| | | PP2A does most of the dephosph of I1 at basal Ca levels. See the review by Cohen in Ann Rev Biochem 1989. For now, lets halve Km. k1 was 3.3e-6, now 6.6e-6 | | 2 | CaM(Ca)n_dash_
CaNAB /
dephosph_inhib1 | mRNA synthesis
Accession No. : 94 | kinetics
Pathway No. : 1112 | 4.9708 | 0.34 | 4 | explicit E-S complex | Substrate
I1_star
Product
I1
| | | | | 3 | 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 |
I1 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 | dissoc_dash_
PP1_dash_I1 | mRNA synthesis
Accession No. : 94 | kinetics
Pathway No. : 1112 | 1
(s^-1) | 0
(uM^-1 s^-1) | - | - | Substrate
PP1_dash_I1
Product
I1
PP1_dash_
active_c
| | Let us assume that the equil in this case is very far over to the right. This is probably safe. |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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