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Molecule Parameter List for CaM | 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. |
CaM acting as a Molecule in Ajay_Bhalla_2004_PKM_Tuning Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | CaM | Ajay_Bhalla_
2004_PKM_Tuning
Accession No. : 76 | CaM
Pathway No. : 323 | 20 | 1.5 | No | | There is a LOT of this in the cell: upto 1% of total protein mass. (Alberts et al) Say 25 uM. Meyer et al Science 256 1199-1202 1992 refer to studies saying it is comparable to CaMK levels. |
CaM acting as a Product of an Enzyme in Ajay_Bhalla_2004_PKM_Tuning Network
CaM 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 | | 1 | CaM-TR2-bind-Ca | Ajay_Bhalla_
2004_PKM_Tuning
Accession No. : 76 | CaM
Pathway No. : 323 | 72.0001
(uM^-2 s^-1) | 72
(s^-1) | Kd(af) = 1(uM) | - | Substrate
Ca
Ca
CaM
Product
CaM-TR2-Ca2
| | | Lets use the fast rate consts here. Since the rates are so different, I am not sure whether the order is relevant. These correspond to the TR2C fragment. We use the Martin et al rates here, plus the Drabicowski binding consts. All are scaled by 3X to cell temp. kf = 2e-10 kb = 72 Stemmer & Klee: K1=.9, K2=1.1. Assume 1.0uM for both. kb/kf=3.6e11. If kb=72, kf = 2e-10 (Exactly the same !).... | | 2 | 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 |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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