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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_
model0 | 59 | Network |
Shared_Object_AMPAR_traff_model0, CaMKII, CaM,
PP1, PP2B, PP1_PSD,
PKA, AC, AMPAR,
AMPAR_memb | | This is model 0 from Hayer and Bhalla, PLoS Comput Biol 2005. It has a bistable model of AMPAR traffick, plus a
non-bistable model of CaMKII. This differs from the reference model (model 1) in that model0 lacks degradation and turno
ver reactions for AMPAR. |
CaM-Ca4-PSD acting as a Molecule in AMPAR_traff_model0 Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | CaM-Ca4-PSD | AMPAR_traff_
model0
Accession No. : 59 | CaM
Pathway No. : 236 | 0 | 0.01 | No | | |
CaM-Ca4-PSD acting as a Substrate in a reaction in AMPAR_traff_model0 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_
model0
Accession No. : 59 | CaMKII
Pathway No. : 235 | 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_
model0
Accession No. : 59 | CaMKII
Pathway No. : 235 | 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_
model0
Accession No. : 59 | CaM
Pathway No. : 236 | 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_model0 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_
model0
Accession No. : 59 | CaMKII
Pathway No. : 235 | 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_
model0
Accession No. : 59 | CaM
Pathway No. : 236 | 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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