| |
Reaction
Name | Pathway Name /
Pathway No. | Kf | Kb | Kd | tau | Reagents |
| 1 | recycle** | AMPAR
Pathway No. 280 | 0.0008
(s^-1) | 0
(#^-1 s^-1) | Not applicable** | - | Substrate:
A831*_B831*
Products:
A831*_B831*
Anchor
|
| 2 | recycle_* | AMPAR
Pathway No. 280 | 0.0008
(s^-1) | 0
(#^-1 s^-1) | Not applicable** | - | Substrate:
A_B831*
Products:
A_B831*
Anchor
|
| 3 | recycle*_ | AMPAR
Pathway No. 280 | 0.0008
(s^-1) | 0
(#^-1 s^-1) | Not applicable** | - | Substrate:
A831*_B
Products:
A831*_B
Anchor
|
| 4 | recycle__ | AMPAR
Pathway No. 280 | 0.0008
(s^-1) | 0
(#^-1 s^-1) | Not applicable** | - | Substrate:
A_B
Products:
A_B
Anchor
|
| 5 | degrade** | AMPAR
Pathway No. 280 | 0
(s^-1) | 0
(s^-1) | - | - | Substrate:
A835*845*_
B835*845*
Products:
AMPAR_deg
|
| 6 | degrade_* | AMPAR
Pathway No. 280 | 0
(s^-1) | 0
(s^-1) | - | - | Substrate:
A845*_B831*845*
Products:
AMPAR_deg
|
| 7 | degrade*_ | AMPAR
Pathway No. 280 | 0
(s^-1) | 0
(s^-1) | - | - | Substrate:
A831*845*_B845*
Products:
AMPAR_deg
|
| 8 | degrade__ | AMPAR
Pathway No. 280 | 0
(s^-1) | 0
(s^-1) | - | - | Substrate:
A845*_B845*
Products:
AMPAR_deg
|
| 9 | exo_reg** | AMPAR
Pathway No. 280 | 0.0002
(#^-1 s^-1) | 0.008
(s^-1) | Not applicable** | - | Substrate:
A835*845*_
B835*845*
Anchor
Products:
A835*845*_
B835*845*
|
| 10 | exo_reg_* | AMPAR
Pathway No. 280 | 0.0002
(#^-1 s^-1) | 0.008
(s^-1) | Not applicable** | - | Substrate:
A845*_B831*845*
Anchor
Products:
A845*_B831*845*
|
| 11 | exo_reg*_ | AMPAR
Pathway No. 280 | 0.0002
(#^-1 s^-1) | 0.008
(s^-1) | Not applicable** | - | Substrate:
A831*845*_B845*
Anchor
Products:
A831*845*_B845*
|
| 12 | exo_reg__ | AMPAR
Pathway No. 280 | 0.0002
(#^-1 s^-1) | 0.008
(s^-1) | Not applicable** | - | Substrate:
A845*_B845*
Anchor
Products:
A845*_B845*
|
| Exo rates are scaled from earlier model versions to account for binding of anchor. We have about 200 molecules of anchor in the whole model. Here we select rates to give us a max of about 150 molecules of GluR at the synapse. | | 13 | 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. | | 14 | CaM-bind-AC1 | AC
Pathway No. 278 | 49.9997
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 0.02(uM) | - | Substrate:
CaM-Ca4
AC1
Products:
AC1-CaM
|
| Half-max at 20 nM CaM (Tang et al JBC 266:13 8595-8603 1991 kb/kf = 20 nM = 12000 #/cell so kf = kb/12000 = kb * 8.333e-5 | | 15 | dephosph-AC2 | AC
Pathway No. 278 | 0.1
(s^-1) | 0
(s^-1) | - | - | Substrate:
AC2*
Products:
AC2
|
| Random rate. | | 16 | dephosph-PDE | AC
Pathway No. 278 | 0.01
(s^-1) | 0
(s^-1) | - | - | Substrate:
cAMP-PDE*
Products:
cAMP-PDE
|
| The rates for this are poorly constrained. In adipocytes (probably a different PDE) the dephosphorylation is complete within 15 min, but there are no intermediate time points so it could be much faster. Identity of phosphatase etc is still unknown. | | 17 | CaM_bind_PDE1 | AC
Pathway No. 278 | 719.982
(uM^-1 s^-1) | 5
(s^-1) | Kd(bf) = 0.0069(uM) | - | Substrate:
PDE1
CaM-Ca4
Products:
CaM.PDE1
|
| For olf epi PDE1, affinity is 7 nM. Assume same for brain. Reaction should be pretty fast. Assume kb = 5/sec. Then kf = 5 / (0.007 * 6e5) = 1.2e-3 | | 18 | cAMP_diffusion | AC
Pathway No. 278 | 300
(s^-1) | 5.4
(s^-1) | Not applicable** | - | Substrate:
cAMP
Products:
cAMP_in_dend
|
| Represents diffusion, from a volume of 9e-20 to 5e-18. Assuming neck dimensions of 0.1 x 0.1 microns, this works out to a diffusion const of about 270 um^2/sec, which is pretty conservative. It is what cAMP does in frog cilia. | | 19 | cAMP-bind-site-B
1 | PKA
Pathway No. 277 | 54
(uM^-1 s^-1) | 33
(s^-1) | Kd(bf) = 0.6111(uM) | - | Substrate:
R2C2
cAMP
Products:
R2C2-cAMP
|
| Hasler et al FASEB J 6:2734-2741 1992 say Kd =1e-7M for type II, 5.6e-8 M for type I. Take mean which comes to 2e-13 #/cell Smith et al PNAS USA 78:3 1591-1595 1981 have better data. First kf/kb=2.1e7/M = 3.5e-5 (#/cell). Ogreid and Doskeland Febs Lett 129:2 287-292 1981 have figs suggesting time course of complete assoc is < 1 min. | | 20 | cAMP-bind-site-B
2 | PKA
Pathway No. 277 | 54
(uM^-1 s^-1) | 33
(s^-1) | Kd(bf) = 0.6111(uM) | - | Substrate:
R2C2-cAMP
cAMP
Products:
R2C2-cAMP2
|
| For now let us set this to the same Km (1e-7M) as site B. This gives kf/kb = .7e-7M * 1e6 / (6e5^2) : 1/(6e5^2) = 2e-13:2.77e-12 Smith et al have better values. They say that this is cooperative, so the consts are now kf/kb =8.3e-4 |
and 
color.
