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Reaction List for pathway PP2B (Pathway Number 83) | | 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 reactions is not considered. |
| | Name | Kf | Kb | Kd | tau | Substrate | Product | | 1 |
Ca-bind-CaNAB | kf
(uM^-2 s^-1) | 1
(s^-1) | Kd(af) = 0.01(uM) | - | CaNAB
Ca
Ca
| 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. This doesn't really matter much because it will always be bound at physiological Ca. | | 2 |
Ca-bind-CaNAB-Ca
2 | kf
(uM^-2 s^-1) | 1
(s^-1) | Kd(af) = 0.527(uM) | - | Ca
Ca
CaNAB-Ca2
| 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 1994 Biochem 33:6859-6866, this specific parm on pg 6863, the Kact is 0.5 uM. Assume binding is fast, 1 sec. | | 3 |
CaM-Ca2-bind-CaN
AB | kf
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 4.1667(uM) | - | CaNAB-Ca4
CaM-TR2-Ca2
| CaMCa2-CANAB
| | | Based on Stemmer and Klee 1994 Biochem 33:6859-6866 This model is actually a simplification of the detail they report. In this model the Ca-binding affinity of CaM is not changed by binding to CaN. Rates here come from a detailed-balance argument. The reference rate is for CaMCa4 binding to CaNAB. This rate should be 1/2500 of that. | | 4 |
CaMCa3-bind-CaNA
B | kf
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 0.4468(uM) | - | CaM-Ca3
CaNAB-Ca4
| CaMCa3-CaNAB
| | | Rates derived from the CaMCa4 binding to CaNAB-Ca4 step. Due to detailed balance calculations taking the Ca affinity for CaM into account, this reaction should be 250 times slower. Close. | | 5 |
CaMCa4-bind-CaNA
B | kf
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 0.0017(uM) | - | CaM-Ca4
CaNAB-Ca4
| CaMCa4-CaNAB
| | | This step is the starting point for calculating all the CaM-binding steps to CaNAB-Ca4. The calculation goes like this: From Stemmer and Klee 1994 Biochem 33 6859-6866 we have rates for Ca binding to CaM.Ca4.CaN. From detailed balance (Kd must be 1 around a loop) we can set ratios of Kds for CaMCa3 binding to CaN, and CaM-Ca2 binding to CaN. Thus those rates can come once we know the Kd for the current reaction of CaMCa4 binding to CaN. We'll ignore the Ca binding steps to CaM.Ca4.CaN since the reactions around the remaining part of the loop will settle pretty fast to the same levels. Finally, we estimate the kf=0.001 here from a series of simulations matching the curves in Stemmer and Klee. |
Pathway Details Molecule List Enzyme List Reaction List
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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