| |
Reaction
Name | Pathway Name /
Pathway No. | Kf | Kb | Kd | tau | Reagents |
| 1 | CaMKII-bind-CaM-
PSD | Shared_Object_
AMPAR_CaMKII_
strong_coupling
Pathway No. 271 | 49.9998
(uM^-1 s^-1) | 0
(s^-1) | - | - | Substrate:
CaMKII-PSD
CaM-Ca4-PSD
Products:
CaMKII-CaM-PSD
|
| 2 | transloc_1 | Shared_Object_
AMPAR_CaMKII_
strong_coupling
Pathway No. 271 | 0
(#^-1 s^-1) | 0
(s^-1) | Not applicable** | - | Substrate:
CaMKII-CaM
NMDAR
Products:
CaMKII-CaM-PSD
|
| Rates to match curve in fig2 from Shen and Meyer, Science 284:162-166(1999), calculated for 6:1 alpha:beta CaMKII heterodimers | | 3 | transloc_2 | Shared_Object_
AMPAR_CaMKII_
strong_coupling
Pathway No. 271 | 0
(#^-1 s^-1) | 0
(s^-1) | Not applicable** | - | Substrate:
CaMKII-thr286*-C
aM
NMDAR
Products:
CaMKII-thr286-Ca
M-PSD
|
| Same as for transloc_1 | | 4 | back_1 | Shared_Object_
AMPAR_CaMKII_
strong_coupling
Pathway No. 271 | 0.3
(s^-1) | 0
(#^-1 s^-1) | Not applicable** | - | Substrate:
CaMKII-PSD
Products:
CaMKII
NMDAR
|
| Rates set by the translocation experiments of Shen and Meyer, Science 1999. | | 5 | back_2 | Shared_Object_
AMPAR_CaMKII_
strong_coupling
Pathway No. 271 | 0.3
(s^-1) | 0
(#^-1 s^-1) | Not applicable** | - | Substrate:
CaMKII-thr305-PS
D
Products:
CaMK-thr305
NMDAR
|
| Same as for back_1 | | 6 | CaMKII-thr286-bi
nd-CaM-PSD | Shared_Object_
AMPAR_CaMKII_
strong_coupling
Pathway No. 271 | 1000.02
(uM^-1 s^-1) | 0.1
(s^-1) | Kd(bf) = 0.0001(uM) | - | Substrate:
CaMKII-thr286-PS
D
CaM-Ca4-PSD
Products:
CaMKII-thr286-Ca
M-PSD
|
| Same values as for the main compartment Can the main compartment pool of Ca/CaM be used? | | 7 | Ca_stoch_cyt | Shared_Object_
AMPAR_CaMKII_
strong_coupling
Pathway No. 271 | 100
(s^-1) | 100
(s^-1) | Keq = 1(uM) | 0.005sec | Substrate:
Ca_control_cyt
Products:
Ca
|
| 8 | equilib | Shared_Object_
AMPAR_CaMKII_
strong_coupling
Pathway No. 271 | 540
(s^-1) | 60
(s^-1) | Not applicable** | - | Substrate:
CaM-Ca4-PSD
Products:
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. | | 9 | Inact-PP1 | Shared_Object_
AMPAR_CaMKII_
strong_coupling
Pathway No. 271 | 499.98
(uM^-1 s^-1) | 0.1
(s^-1) | Kd(bf) = 0.0002(uM) | - | Substrate:
I1*
PP1-active_PSD
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 | | 10 | CaM-Ca3-bind-Ca | Shared_Object_
AMPAR_CaMKII_
strong_coupling
Pathway No. 271 | 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 | | 11 | endo_const | Shared_Object_
AMPAR_CaMKII_
strong_coupling
Pathway No. 271 | 0.0004
(s^-1) | 0.0014
(s^-1) | Not applicable** | - | Substrate:
GluR23_M
Products:
GluR23_I
|
| 12 | CaMKII-diss-CaM | Shared_Object_
AMPAR_CaMKII_
strong_coupling
Pathway No. 271 | 5
(s^-1) | 0
(uM^-1 s^-1) | - | - | Substrate:
CaMKII-CaM-PSD
Products:
CaM-Ca4-PSD
CaMKII-PSD
|
| 13 | PKC-stoch-input | Shared_Object_
AMPAR_CaMKII_
strong_coupling
Pathway No. 271 | 2.5
(s^-1) | 2.5
(s^-1) | Keq = 1(uM) | 0.2sec | Substrate:
PKC-control
Products:
PKC-active
|
| 14 | Ca_stoch_PSD | Shared_Object_
AMPAR_CaMKII_
strong_coupling
Pathway No. 271 | 100
(s^-1) | 100
(s^-1) | Keq = 1(uM) | 0.005sec | Substrate:
Ca_control_PSD
Products:
Ca-PSD
|
| 15 | Stoch_Basal_
CaMKII_PSD | Shared_Object_
AMPAR_CaMKII_
strong_coupling
Pathway No. 271 | 1
(s^-1) | 1
(s^-1) | Keq = 1(uM) | 0.5sec | Substrate:
basal_CaMKII_
PSD_control
Products:
basal_CaMKII_
PSD
|
| 16 | turnover | Shared_Object_
AMPAR_CaMKII_
strong_coupling
Pathway No. 271 | 0.018
(s^-1) | 1
(s^-1) | Not applicable** | - | Substrate:
AMPAR_bulk
Products:
A_B
|
| Represents both synthesis and degradation of the receptor. The rate is set to be rather fast for now. The forward rate also includes scaling terms because the AMPAR_bulk is in the dendritic volume of 5e-18. This means that we need to lower Kf to account for the difference in volumes. Effectively Kf is 1/sec, but the scaled version becomes 9e-20/5e-18 = 0.018 | | 17 | Ca-bind-CaNAB-Ca
2 | PP2B
Pathway No. 276 | 3.6001
(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 | | 18 | Ca-bind-CaNAB | PP2B
Pathway No. 276 | 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 | | 19 | CaMCa4-bind-CaNA
B | PP2B
Pathway No. 276 | 599.994
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 0.0017(uM) | - | Substrate:
CaM-Ca4
CaNAB-Ca4
Products:
CaM_Ca_n-CaNAB
|
| 20 | dissoc-PP1-I1 | PP1_PSD
Pathway No. 279 | 1
(s^-1) | 0
(uM^-1 s^-1) | - | - | Substrate:
PP1-I1
Products:
I1
PP1-active_PSD
|
| Let us assume that the equil in this case is very far over to the right. This is probably safe. |
and 
color.
