| |
Reaction
Name | Pathway Name /
Pathway No. | Kf | Kb | Kd | tau | Reagents |
| 1 | Ca-bind-CaNAB | PP2B
Pathway No. 205 | 10008
(uM^-2 s^-1) | 1
(s^-1) | Kd(af) = 0.01(uM) | - | Substrate:
CaNAB
Ca
Ca
Products:
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 | | 2 | CaMK-thr286-bind
-CaM | CaMKII
Pathway No. 202 | 1000.2
(uM^-1 s^-1) | 0.1
(s^-1) | Kd(bf) = 0.0001(uM) | - | Substrate:
CaMKII-thr286
CaM-Ca4
Products:
CaMKII-thr286*-C
aM
|
| Affinity is up 1000X. Time to release is about 20 sec, so the kb is OK at 0.1 This makes Kf around 1.6666e-3 | | 3 | CaMCa4-bind-CaNA
B | PP2B
Pathway No. 205 | 600
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 0.0017(uM) | - | Substrate:
CaM-Ca4
CaNAB-Ca4
Products:
CaMCa4-CaNAB
|
| 4 | Inact-PP1 | PP1
Pathway No. 204 | 499.98
(uM^-1 s^-1) | 0.1
(s^-1) | Kd(bf) = 0.0002(uM) | - | Substrate:
I1*
PP1-active
Products:
PP1-I1*
|
| K inhib = 1nM from Cohen Ann Rev Bioch 1989, 4 nM from Foukes et al Assume 2 nM. kf /kb = 8.333e-4 | | 5 | CaM-TR2-bind-Ca | CaM
Pathway No. 203 | 72
(uM^-2 s^-1) | 72
(s^-1) | Kd(af) = 1(uM) | - | Substrate:
CaM
Ca
Ca
Products:
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 !).... | | 6 | CaMKII-bind-CaM | CaMKII
Pathway No. 202 | 49.9998
(uM^-1 s^-1) | 5
(s^-1) | Kd(bf) = 0.1(uM) | - | Substrate:
CaM-Ca4
CaMKII
Products:
CaMKII-CaM
|
| This is tricky. There is some cooperativity here arising from interactions between the subunits of the CAMKII holoenzyme. However, the stoichiometry is 1. Kb/Kf = 6e4 #/cell. Rate is fast (see Hanson et al Neuron 12 943-956 1994) so lets say kb = 10. This gives kf = 1.6667e-4 H&S AnnRev Biochem 92 give tau for dissoc as 0.2 sec at low Ca, 0.4 at high. Low Ca = 100 nM = physiol. | | 7 | CaM-TR2-Ca2-bind
-Ca | CaM
Pathway No. 203 | 3.6
(uM^-1 s^-1) | 10
(s^-1) | Kd(bf) = 2.7778(uM) | - | Substrate:
CaM-TR2-Ca2
Ca
Products:
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 | | 8 | Ca-bind-CaNAB-Ca
2 | PP2B
Pathway No. 205 | 3.6
(uM^-2 s^-1) | 1
(s^-1) | Kd(af) = 0.527(uM) | - | Substrate:
Ca
Ca
CaNAB-Ca2
Products:
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 | | 9 | CaMCa3-bind-CaNA
B | PP2B
Pathway No. 205 | 2.238
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 0.4468(uM) | - | Substrate:
CaM-Ca3
CaNAB-Ca4
Products:
CaMCa3-CaNAB
|
| 10 | dissoc-PP1-I1 | PP1
Pathway No. 204 | 1
(s^-1) | 0
(uM^-1 s^-1) | - | - | Substrate:
PP1-I1
Products:
PP1-active
I1
|
| Let us assume that the equil in this case is very far over to the right. This is probably safe. | | 11 | CaM-Ca3-bind-Ca | CaM
Pathway No. 203 | 0.465
(uM^-1 s^-1) | 10
(s^-1) | Kd(bf) = 21.5054(uM) | - | Substrate:
CaM-Ca3
Ca
Products:
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 | | 12 | neurogranin-bind
-CaM | CaM
Pathway No. 203 | 0.3
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 3.3333(uM) | - | Substrate:
neurogranin
CaM
Products:
neurogranin-CaM
|
| Surprisingly, no direct info on rates from neurogranin at this time. These rates are based on GAP-43 binding studies. As GAP-43 and neurogranin share near identity in the CaM/PKC binding regions, and also similarity in phosph and dephosph rates, I am borrowing GAP-43 kinetic info. See Alexander et al JBC 262:13 6108-6113 1987 | | 13 | CaM-Ca2-bind-CaN
AB | PP2B
Pathway No. 205 | 0.24
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 4.1667(uM) | - | Substrate:
CaNAB-Ca4
CaM-TR2-Ca2
Products:
CaMCa2-CANAB
|
| Disabled. See notes for PP2B7.g | | 14 | dephosph-neurogr
anin | CaM
Pathway No. 203 | 0.005
(s^-1) | 0
(s^-1) | - | - | Substrate:
neurogranin*
Products:
neurogranin
|
| This is put in to keep the basal levels of neurogranin* experimentally reasonable. From various papers, specially Ramakers et al JBC 270:23 1995 13892-13898, it looks like the basal level of phosph is between 20 and 40%. I est around 25 % The kf of 0.005 gives around this level at basal PKC activity levels of 0.1 uM active PKC. | | 15 | basal-activity | CaMKII
Pathway No. 202 | 0.003
(s^-1) | 0
(s^-1) | - | - | Substrate:
CaMKII
Products:
CaMKII-thr286
|
| This reaction represents one of the big unknowns in CaMK-II biochemistry: what maintains the basal level of phosphorylation on thr 286 ? See Hanson and Schulman Ann Rev Biochem 1992 61:559-601, specially pg 580, for review. I have not been able to find any compelling mechanism in the literature, but fortunately the level of basal activity is well documented. |
and 
color.
