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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 | Synaptic_
Network | 16 | Network |
Shared_Object_Synaptic_Network, PKC, PLA2,
PLCbeta, Gq, MAPK,
Ras, EGFR, Sos,
PLC_g, CaMKII, CaM,
PP1, PP2B, PKA,
AC, CaRegulation | This model is an annotated version of the synaptic signaling network.
The primary reference is Bhalla US and Iyengar R. Science (1999) 283(5400):381-7 but several of the model pathways have been updated.
Bhalla US Biophys J. 2002 Aug;83(2):740-52
Bhalla US J Comput Neurosci. 2002 Jul-Aug;13(1):49-62 |
APC acting as a Molecule in Synaptic_Network Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | APC | Synaptic_
Network
Accession No. : 16 | PLA2
Pathway No. : 72 | 30 | 1000 | 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. For now it is treated as a buffered metabolite. |
APC acting as a Substrate for an Enzyme in Synaptic_Network Network
| | Enzyme Molecule /
Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | | 1 | PLA2-Ca* /
kenz | Synaptic_
Network
Accession No. : 16 | PLA2
Pathway No. : 72 | 20 | 5.4 | 4 | explicit E-S complex | Substrate
APC
Product
AA
| | | Based on Leslie and Channon 1990 BBA 1045:261, in relation to the other PLA2 inputs (not including MAPK). Ca alone is rather a weak input. | | 2 | PIP2-PLA2* /
kenz | Synaptic_
Network
Accession No. : 16 | PLA2
Pathway No. : 72 | 20 | 11.04 | 4 | explicit E-S complex | Substrate
APC
Product
AA
| | | Based on Leslie and Channon 1990 BBA 1045:261. | | 3 | PIP2-Ca-PLA2* /
kenz | Synaptic_
Network
Accession No. : 16 | PLA2
Pathway No. : 72 | 20 | 36 | 4 | explicit E-S complex | Substrate
APC
Product
AA
| | | Based on AA generation by different stimuli according to Leslie and Channon 1990 BBA 1045:261 | | 4 | DAG-Ca-PLA2* /
kenz | Synaptic_
Network
Accession No. : 16 | PLA2
Pathway No. : 72 | 20 | 60 | 4 | explicit E-S complex | Substrate
APC
Product
AA
| | | Based on Leslie and Channon 1990 BBA 1045:261. | | 5 | PLA2*-Ca /
kenz | Synaptic_
Network
Accession No. : 16 | PLA2
Pathway No. : 72 | 20 | 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, from Lin et al 1993 Cell 269-278 Nemenoff et al 1993 JBC 268:1960 Several forms contribute to the Ca-stimulated form, so this rate has to be a factor larger than their total contribution. I assign Vmax as the scale factor here because there is lots of APC substrate, so all the PLA2 complex enzymes are limited primarily by Vmax. |
APC acting as a Product in a reaction in Synaptic_Network 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 | Synaptic_
Network
Accession No. : 16 | PLA2
Pathway No. : 72 | 0.4
(s^-1) | 0
(s^-1) | - | - | Substrate
AA
Product
APC
| | Degradation pathway for AA. APC is a convenient buffered pool to dump it back into, though the actual metabolism is probably far more complex. For the purposes of the full model we use a rate of degradation of 0.4/sec to give a dynamic range of AA comparable to what is seen experimentally. Wijkander and Sundler 1991 Eur J Biochem 202:873 Leslie and Channon 1990 BBA 1045:261 |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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