| | Name | Accession Name | Pathway Name | Kf | Kb | Kd | tau | Reagents |
| 1 | CaM_dash_Ca3_
dash_bind_dash_
Ca | Differential syn
thesis of mRNA
Accession No. : 95 | kinetics
Pathway No. : 1115 | 0.465
(uM^-1 s^-1) | 10
(s^-1) | Kd(bf) = 21.5051(uM) | - | Substrate
Ca
CaM_dash_Ca3
Product
CaM_dash_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 |
| 2 | CaM_dash_bind_
dash_Ca | Differential syn
thesis of mRNA
Accession No. : 95 | kinetics
Pathway No. : 1115 | 8.4846
(uM^-1 s^-1) | 8.4853
(s^-1) | Kd(bf) = 1.0001(uM) | - | Substrate
Ca
CaM
Product
CaM_dash_Ca
|
| | 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 !) 19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into two steps, each binding 1 Ca. This improves numerical stability and is conceptually better too. Overall rates are the same, so each kf and kb is the square root of the earlier ones. So kf = 1.125e-4, kb = 8.4853 |
| 3 | CaM_dash_Ca2_
dash_bind_dash_
Ca | Differential syn
thesis of mRNA
Accession No. : 95 | kinetics
Pathway No. : 1115 | 3.6001
(uM^-1 s^-1) | 10
(s^-1) | Kd(bf) = 2.7777(uM) | - | Substrate
Ca
CaM_dash_Ca2
Product
CaM_dash_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 |
| 4 | CaM_dash_Ca_
dash_bind_dash_
Ca | Differential syn
thesis of mRNA
Accession No. : 95 | kinetics
Pathway No. : 1115 | 8.4846
(uM^-1 s^-1) | 8.4853
(s^-1) | Kd(bf) = 1.0001(uM) | - | Substrate
Ca
CaM_dash_Ca
Product
CaM_dash_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 !) 19 May 2006. Splitting the old CaM-TR2-bind-Ca reaction into two steps, each binding 1 Ca. This improves numerical stability and is conceptually better too. Overall rates are the same, so each kf and kb is the square root of the earlier ones. So kf = 1.125e-4, kb = 8.4853 |
| 5 | Ca_dash_bind_
dash_CaNAB_
dash_Ca2 | Differential syn
thesis of mRNA
Accession No. : 95 | kinetics
Pathway No. : 1115 | 3599.928
(uM^-2 s^-1) | 1
(s^-1) | Kd(af) = 0.0167(uM) | - | Substrate
Ca
Ca
CaNAB_dash_Ca2
Product
CaNAB_dash_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 |
| 6 | Ca_dash_bind_
dash_CaNAB | Differential syn
thesis of mRNA
Accession No. : 95 | kinetics
Pathway No. : 1115 | 10008360
(uM^-2 s^-1) | 1
(s^-1) | Kd(af) = 0.0003(uM) | - | Substrate
Ca
Ca
CaNAB
Product
CaNAB_dash_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 |
color.