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Molecule Parameter List for APC | 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 | Ajay_Bhalla_
2004_PKM_Tuning | 76 | Network |
PKC, Shared_Object_Ajay_Bhalla_2004_PKM_tuning, PLA2,
PLCbeta, Gq, MAPK,
Ras, EGFR, Sos,
PLC_g, CaMKII, CaM,
PP1, PP2B, PKA,
AC, PKM | | This model is taken from the Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80. This is the reference feedforward model from Figure 8a. |
APC acting as a Molecule in Ajay_Bhalla_2004_PKM_Tuning Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | APC | Ajay_Bhalla_
2004_PKM_Tuning
Accession No. : 76 | PLA2
Pathway No. : 314 | 30 | 1.5 | Yes | | arachodonylphosphatidylcholine is the favoured substrate from Wijkander and Sundler, JBC 202 pp 873-880, 1991. Their assay used 30 uM substrate, which is what the kinetics in this model are based on. For the later model we should locate a more realistic value for APC. |
APC acting as a Substrate for an Enzyme in Ajay_Bhalla_2004_PKM_Tuning Network
| | Enzyme Molecule /
Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | | 1 | PLA2-Ca* /
kenz | Ajay_Bhalla_
2004_PKM_Tuning
Accession No. : 76 | PLA2
Pathway No. : 314 | 20 | 5.4 | 4 | explicit E-S complex | Substrate
APC
Product
AA
| | | 10 x raise oct22 12 x oct 24, set k2 = 4 * k3 | | 2 | PIP2-PLA2* /
kenz | Ajay_Bhalla_
2004_PKM_Tuning
Accession No. : 76 | PLA2
Pathway No. : 314 | 19.9998 | 11.04 | 4 | explicit E-S complex | Substrate
APC
Product
AA
| | | 10 X raise oct 22 12 X further raise oct 24 to allow for correct conc of enzyme | | 3 | PIP2-Ca-PLA2* /
kenz | Ajay_Bhalla_
2004_PKM_Tuning
Accession No. : 76 | PLA2
Pathway No. : 314 | 20 | 36 | 4 | explicit E-S complex | Substrate
APC
Product
AA
| | | 10 x raise oct 22 12 x and rescale for k2 = 4 * k3 convention oct 24 Increase further to get the match to expt, which was spoilt due to large accumulation of PLA2 in the enzyme complexed forms. Lets raise k3, leaving the others at k1 = 1.5e-5 and k2 = 144 since they are large already. | | 4 | DAG-Ca-PLA2* /
kenz | Ajay_Bhalla_
2004_PKM_Tuning
Accession No. : 76 | PLA2
Pathway No. : 314 | 19.9996 | 60 | 4 | explicit E-S complex | Substrate
APC
Product
AA
| | | 10 X raise oct 22 12 X raise oct 24 + conversion to k2 =4 * k3 | | 5 | PLA2*-Ca /
kenz | Ajay_Bhalla_
2004_PKM_Tuning
Accession No. : 76 | PLA2
Pathway No. : 314 | 20.0002 | 120 | 4 | explicit E-S complex | Substrate
APC
Product
AA
| | | This form should be 3 to 6 times as fast as the Ca-only form. I have scaled by 4x which seems to give a 5x rise. 10x raise Oct 22 12 x oct 24, changed k2 = 4 * k3 |
APC acting as a Product in a reaction in Ajay_Bhalla_2004_PKM_Tuning 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 | | Degrade-AA | Ajay_Bhalla_
2004_PKM_Tuning
Accession No. : 76 | PLA2
Pathway No. : 314 | 0.4
(s^-1) | 0
(s^-1) | - | - | Substrate
AA
Product
APC
| | I need to check if the AA degradation pathway really leads back to APC. Anyway, it is a convenient buffered pool to dump it back into. For the purposes of the full model we use a rate of degradation of 0.2/sec Raised decay to 0.4 : see PLA35.g notes for Feb17 |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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