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Molecule Parameter List for neurogranin | 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. |
neurogranin acting as a Molecule in Ajay_Bhalla_2004_PKM_Tuning Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | neurogranin | Ajay_Bhalla_
2004_PKM_Tuning
Accession No. : 76 | CaM
Pathway No. : 323 | 10 | 1.5 | No | | Also known as RC3 and p17 and BICKS. Conc in brain >> 2 uM from Martzen and Slemmon J neurosci 64 92-100 1995 but others say less without any #s. Conc in dend spines is much higher than overall, so it could be anywhere from 2 uM to 50. We will estimate 10 uM as a starting point. Gerendasy et al JBC 269:35 22420-22426 1994 have a skeleton model (no numbers) indicating CaM-Ca(n) binding .... |
neurogranin acting as a Substrate for an Enzyme in Ajay_Bhalla_2004_PKM_Tuning Network
neurogranin acting as a Product of an Enzyme in Ajay_Bhalla_2004_PKM_Tuning Network
neurogranin acting as a Substrate 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 | neurogranin-bind
-CaM | Ajay_Bhalla_
2004_PKM_Tuning
Accession No. : 76 | CaM
Pathway No. : 323 | 0.3
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 3.3334(uM) | - | Substrate
CaM
neurogranin
Product
neurogranin-CaM
| | Surprisingly, no direct info on rates from neurogranin at this time. These rates are based on GAP-43 binding studies. As GAP-43 and neurogranin share near identity in the CaM/PKC binding regions, and also similarity in phosph and dephosph rates, I am borrowing GAP-43 kinetic info. See Alexander et al JBC 262:13 6108-6113 1987 |
neurogranin 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 | dephosph-neurogr
anin | Ajay_Bhalla_
2004_PKM_Tuning
Accession No. : 76 | CaM
Pathway No. : 323 | 0.005
(s^-1) | 0
(s^-1) | - | - | Substrate
neurogranin*
Product
neurogranin
| | This is put in to keep the basal levels of neurogranin* experimentally reasonable. From various papers, specially Ramakers et al JBC 270:23 1995 13892-13898, it looks like the basal level of phosph is between 20 and 40%. I est around 25 % The kf of 0.005 gives around this level at basal PKC activity levels of 0.1 uM active PKC. |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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