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Molecule Parameter List for CaMKII-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 | 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. |
CaMKII-CaM acting as a Molecule in AMPAR_traff_model1 Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | CaMKII-CaM | AMPAR_traff_
model1
Accession No. : 60 | CaMKII
Pathway No. : 245 | 0 | 0.09 | No | | |
CaMKII-CaM acting as a Summed Molecule in AMPAR_traff_model1 Network
CaMKII-CaM acting as a Substrate for an Enzyme in AMPAR_traff_model1 Network
CaMKII-CaM 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 | PP1-active /
Deph-thr286 | AMPAR_traff_
model1
Accession No. : 60 | PP1
Pathway No. : 247 | 5.09905 | 2.5 | 4 | explicit E-S complex | Substrate
CaMKII-thr286*-C
aM
Product
CaMKII-CaM
|
CaMKII-CaM 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 | | transloc_1 | AMPAR_traff_
model1
Accession No. : 60 | CaMKII
Pathway No. : 245 | 0
(#^-1 s^-1) | 0
(s^-1) | Not applicable** | - | Substrate
CaMKII-CaM
NMDAR
Product
CaMKII-CaM-PSD
| | Rates to match curve in fig2 from Shen and Meyer, Science 284:162-166(1999), calculated for 6:1 alpha:beta CaMKII heterodimers |
** This is a trasport reation between compartments of different volumes. Therefore Kd is not applicable. Please Note Kf, Kb units are in number of molecules instead of concentration
CaMKII-CaM 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 | | CaMKII-bind-CaM | AMPAR_traff_
model1
Accession No. : 60 | CaMKII
Pathway No. : 245 | 49.9997
(uM^-1 s^-1) | 5
(s^-1) | Kd(bf) = 0.1(uM) | - | Substrate
CaM-Ca4
CaMKII
Product
CaMKII-CaM
| | This is tricky. There is some cooperativity here arising from interactions between the subunits of the CAMKII holoenzyme. However, the stoichiometry is 1. Kb/Kf = 6e4 #/cell. Rate is fast (see Hanson et al Neuron 12 943-956 1994) so lets say kb = 10. This gives kf = 1.6667e-4 H&S AnnRev Biochem 92 give tau for dissoc as 0.2 sec at low Ca, 0.4 at high. Low Ca = 100 nM = physiol. |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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