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Molecule Parameter List for Ca_intracell | 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 |
Ca_intracell acting as a Molecule in Synaptic_Network Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | Ca_intracell | Synaptic_
Network
Accession No. : 16 | Shared_Object_
Synaptic_
Network
Pathway No. : 70 | 0.08 | 1000 | No | | This is the pool representing intracellular calcium. Resting levels are around 80 nM, but this is subject to all sorts of influxes and pumps. |
Ca_intracell acting as a Summed Molecule in Synaptic_Network Network
Ca_intracell 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 | CaEPump /
Ca-pump-out | Synaptic_
Network
Accession No. : 16 | CaRegulation
Pathway No. : 86 | 0.2 | 72 | 4 | explicit E-S complex | Substrate
Ca_intracell
Product
Ca-ext
| | From McBurney and Neering TINS 10(4) 164-169 1987. We are using the high-affinity pump here, Their numbers exceed M&L so I am reducing the rates by 10X. Need to check. k1 = 3e-3, k2 = 288, k3 = 72, n = 1000. This comes to a Km of 0.2 for Ca, and a Vmax of 72. |
Ca_intracell acting as a Substrate 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 | Ca-bind-to-Trans
p | Synaptic_
Network
Accession No. : 16 | CaRegulation
Pathway No. : 86 | 3600
(uM^-2 s^-1) | 144
(s^-1) | Kd(bf) = 0.04(uM) | - | Substrate
CaTransp
Ca_intracell
Ca_intracell
Product
CaTransp-2Ca
| | Rates from Lauffenberger and Linderman 1993 Receptors pg 200. Kd = KCa2 = 0.2 uM. |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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