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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 | AMPAR_traff_
model1 | 60 | Network |
Shared_Object_AMPAR_traff_model1, CaMKII, CaM,
PP1, PP2B, PP1_PSD,
PKA, AC, AMPAR,
AMPAR_memb | | This is the basic model of AMPAR trafficking bistability. It is based on Hayer and Bhalla, PLoS Comput. Biol. 2005. It includes the degradation and turnover of AMPARs. The CaMKII portion of the model is not bistable. |
neurogranin acting as a Molecule in AMPAR_traff_model1 Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | neurogranin | AMPAR_traff_
model1
Accession No. : 60 | CaM
Pathway No. : 246 | 10 | 0.09 | 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 AMPAR_traff_model1 Network
neurogranin acting as a Product of an Enzyme in AMPAR_traff_model1 Network
Enzyme Molecule /
Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | CaM_Ca_n-CaNAB /
dephosph_
neurogranin
| AMPAR_traff_
model1
Accession No. : 60 | PP2B
Pathway No. : 248 | 10.012 | 0.67 | 3.98507 | explicit E-S complex | Substrate
neurogranin*
Product
neurogranin
| | From Seki et al ABB 316(2):673-679 |
neurogranin acting as a Substrate in a reaction in AMPAR_traff_model1 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 | AMPAR_traff_
model1
Accession No. : 60 | CaM
Pathway No. : 246 | 0.3
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 3.3333(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 AMPAR_traff_model1 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 | AMPAR_traff_
model1
Accession No. : 60 | CaM
Pathway No. : 246 | 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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