|
Enter a Search String | | Special character and space not allowed in the query term.
Search string should be at least 2 characters long. |
Molecule Parameter List for Ca | 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_CaMKII_
weak_coupling | 65 | Network |
Shared_Object_AMPAR_CaMKII_weak_coupling, CaMKII, CaM,
PP1, PP2B, PP1_PSD,
AMPAR, PKA, AC,
AMPAR_memb, PP1_CaMKII_PSD, CaMKII_PSD | | This is a model of weak coupling between the AMPAR traffikcing bistability, and the CaMKII autophosphorylation bistability. In this model, there are three stable states: Both off, AMPAR on, or both on. The fourth possible state: CaMKII on but AMPAR off, is not truly stable, since over the course of hours the AMPAR also turns on. |
Ca acting as a Molecule in AMPAR_CaMKII_weak_coupling Network
Ca acting as a Substrate in a reaction in AMPAR_CaMKII_weak_coupling 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 | AMPAR_CaMKII_
weak_coupling
Accession No. : 65 | CaM
Pathway No. : 283 | 71.999
(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 | CaM-TR2-Ca2-bind
-Ca | AMPAR_CaMKII_
weak_coupling
Accession No. : 65 | CaM
Pathway No. : 283 | 3.6
(uM^-1 s^-1) | 10
(s^-1) | Kd(bf) = 2.7778(uM) | - | Substrate
Ca
CaM-TR2-Ca2
Product
CaM-Ca3
| | | K3 = 21.5, K4 = 2.8. Assuming that the K4 step happens first, we get kb/kf = 2.8 uM = 1.68e6 so kf =6e-6 assuming kb = 10 | | 3 | Ca-bind-CaNAB-Ca
2 | AMPAR_CaMKII_
weak_coupling
Accession No. : 65 | PP2B
Pathway No. : 285 | 3.6001
(uM^-2 s^-1) | 1
(s^-1) | Kd(af) = 0.527(uM) | - | Substrate
Ca
Ca
CaNAB-Ca2
Product
CaNAB-Ca4
| | | This process is probably much more complicated and involves CaM. However, as I can't find detailed info I am bundling this into a single step. Based on Steemer and Klee pg 6863, the Kact is 0.5 uM. kf/kb = 1/(0.5 * 6e5)^2 = 1.11e-11 | | 4 | Ca-bind-CaNAB | AMPAR_CaMKII_
weak_coupling
Accession No. : 65 | PP2B
Pathway No. : 285 | 10008
(uM^-2 s^-1) | 1
(s^-1) | Kd(af) = 0.01(uM) | - | Substrate
Ca
Ca
CaNAB
Product
CaNAB-Ca2
| | | going on the experience with CaM, we put the fast (high affinity) sites first. We only know (Stemmer and Klee) that the affinity is < 70 nM. Assuming 10 nM at first, we get kf = 2.78e-8, kb = 1. Try 20 nM. kf = 7e-9, kb = 1 | | 5 | CaM-Ca3-bind-Ca | AMPAR_CaMKII_
weak_coupling
Accession No. : 65 | Shared_Object_
AMPAR_CaMKII_
weak_coupling
Pathway No. : 281 | 0.465
(uM^-1 s^-1) | 10
(s^-1) | Kd(bf) = 21.5054(uM) | - | Substrate
Ca
CaM-Ca3
Product
CaM-Ca4
| | | Use K3 = 21.5 uM here from Stemmer and Klee table 3. kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10 |
Ca acting as a Product in a reaction in AMPAR_CaMKII_weak_coupling 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. |
| 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. |
|
