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Molecule Parameter List for CaM-Ca4-PSD | 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. |
CaM-Ca4-PSD acting as a Molecule in AMPAR_traff_model1 Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | CaM-Ca4-PSD | AMPAR_traff_
model1
Accession No. : 60 | CaM
Pathway No. : 246 | 0 | 0.01 | No | | |
CaM-Ca4-PSD 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 | | 1 | CaMKII-bind-CaM-
PSD | AMPAR_traff_
model1
Accession No. : 60 | CaMKII
Pathway No. : 245 | 49.9998
(uM^-1 s^-1) | 0
(s^-1) | - | - | Substrate
CaM-Ca4-PSD
CaMKII-PSD
Product
CaMKII-CaM-PSD
| | 2 | CaMKII-thr286-bi
nd-CaM-PSD | AMPAR_traff_
model1
Accession No. : 60 | CaMKII
Pathway No. : 245 | 1000.02
(uM^-1 s^-1) | 0.1
(s^-1) | Kd(bf) = 0.0001(uM) | - | Substrate
CaM-Ca4-PSD
CaMKII-thr286-PS
D
Product
CaMKII-thr286-Ca
M-PSD
| | | Same values as for the main compartment Can the main compartment pool of Ca/CaM be used? | | 3 | equilib | AMPAR_traff_
model1
Accession No. : 60 | CaM
Pathway No. : 246 | 540
(s^-1) | 60
(s^-1) | Not applicable** | - | Substrate
CaM-Ca4-PSD
Product
CaM-Ca4
| | | Diffusional equilibrium between PSD- and cytosolic compartment. According to D. Bary in Cell Movements 2nd ed 2001 D for proteins is 5e-7 cm^2/s giving 10 ms for a translocation of 1 um. |
** 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
CaM-Ca4-PSD 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 | | 1 | CaMKII-diss-CaM | AMPAR_traff_
model1
Accession No. : 60 | CaMKII
Pathway No. : 245 | 5
(s^-1) | 0
(uM^-1 s^-1) | - | - | Substrate
CaMKII-CaM-PSD
Product
CaM-Ca4-PSD
CaMKII-PSD
| | 2 | CaM-Ca3-bind-Ca-
PSD | AMPAR_traff_
model1
Accession No. : 60 | CaM
Pathway No. : 246 | 0.465
(uM^-1 s^-1) | 10
(s^-1) | Kd(bf) = 21.5048(uM) | - | Substrate
Ca-PSD
CaM-Ca3-PSD
Product
CaM-Ca4-PSD
| | | Use K3 = 21.5 uM here from Stemmer and Klee table 3. kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10 |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
This Copyright is applied to ensure that the contents of this database remain freely available. Please see FAQ for details. |
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