| |
Reaction
Name | Pathway Name /
Pathway No. | Kf | Kb | Kd | tau | Reagents |
| 1 | CaTraspATPase | CaRegulation
Pathway No. 86 | 25
(s^-1) | 0
(#^-2 s^-1) | Not applicable** | - | Substrate:
CaTransp-2Ca
Products:
CaTransp
Ca-sequester
Ca-sequester
|
| kCa3 = 2 * Ca transporter rate since each step has 2 Ca++. = 0.5 uM/sec from Lauffenburger and Linderman 1993 Receptors pg 200. The amount of the activated transporter is about 0.01 uM = 6e3 #. from runs. So 0.01uM * kf * 2 = 0.5 uM/sec (no back reaction) so kf = 25, kb = 0 Alternatively, 6e3 * kf = 0.25 * 6e5, giving the same kf | | 2 | Ca-bind-to-Trans
p | CaRegulation
Pathway No. 86 | 3600
(uM^-2 s^-1) | 144
(s^-1) | Kd(bf) = 0.04(uM) | - | Substrate:
Ca_intracell
Ca_intracell
CaTransp
Products:
CaTransp-2Ca
|
| Rates from Lauffenberger and Linderman 1993 Receptors pg 200. Kd = KCa2 = 0.2 uM. | | 3 | IP3Rbind | CaRegulation
Pathway No. 86 | 0.05
(uM^-3 s^-1) | 1
(s^-1) | Kd(af) = 2.7144(uM) | - | Substrate:
IP3R
IP3
IP3
IP3
Products:
IP3R*
|
| Based on Lauffenburger and Linderman 1993 Receptors page 200. The binding of IP3 in this reaction has a Hill coeff of 3. The eqns of Mahama and Linderman (cited in the book as 1993 a) are equivalent to the binding all occurring in a single step, so that is how I am doing it in this version. Their Ki1 is 0.07 uM. Lots of other data sources: Ramos-Franco et al 1998 Biophys J 75:834-839 have Ca sensitivity curves. At 250 nM free Ca, the EC50 for type 1 is 58 nM and type 2 is 194 nM. Type 3 would be about 2 uM according to Newton et al 1994 JBC 268(46):28613-28619 For the purposes of this model we use a Kd of 2.7 uM which is high but may be OK at low calcium. The details of Ca interaction with the IP3R are not included in this model. | | 4 | inactivate_cap_
Ca | CaRegulation
Pathway No. 86 | 0
(#^-2 s^-1) | 1
(s^-1) | Not applicable** | - | Substrate:
Ca-sequester
Ca-sequester
capacitive_Ca_
entry*
Products:
inact_cap_entry
|
| The Kd is set to about 3 uM, so that at resting Ca the capacitive Ca entry is almost blocked. A 2nd order response makes the response steep. | | 5 | CaM-bind-AC1 | AC
Pathway No. 85 | 49.9998
(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 Assume a rapid CaM binding of 1/sec. | | 6 | dephosph-AC2 | AC
Pathway No. 85 | 0.1
(s^-1) | 0
(s^-1) | - | - | Substrate:
AC2*
Products:
AC2
|
| Rate constrained by balancing levels of phosphorylated form, especially given resting PKC levels. | | 7 | Gs-bind-AC2 | AC
Pathway No. 85 | 499.998
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 0.002(uM) | - | Substrate:
AC2
Gs-alpha
Products:
AC2-Gs
|
| Half-max at around 3nM = kb/kf from fig 5 in Feinstein et al PNAS USA 88 10173-10177 1991 kf = kb/1800 = 5.56e-4 kb Ofer Jacobowitz's thesis data indicates it is more like 2 nM. Jacobowitz, PhD Thesis, Mount Sinai School of Medicine. | | 8 | Gs-bind-AC1 | AC
Pathway No. 85 | 126
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 0.0079(uM) | - | Substrate:
Gs-alpha
AC1
Products:
AC1-Gs
|
| Half-max 8nM from Tang et al JBC266:13 8595-8603 kb/kf = 8 nM = 4800#/cell Also assume rapid binding of 1/sec. | | 9 | Gs-bind-AC2* | AC
Pathway No. 85 | 833.28
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 0.0012(uM) | - | Substrate:
Gs-alpha
AC2*
Products:
AC2*-Gs
|
| Various references: Jacobowitz et al JBC 268(6):3829-3892 show that AC2 has a 2x rise in basal activation on phosphorylation, and a 2x rise in forskolin stimulated activation. Yoshimura and Cooper JBC 1993 268(7):4604-4607 say that type II is stimulated 9x over basal. Lustig et al 1993 JBC 268(19):13900-13905 syow a 2x activation by PDBu, and the Gs stimulated response is increased 2x-4x by PDBu. To match all these results with the binding of the unphosphorylated form we use a Kd of 1.2 nM here as compared with the Kd of 2 nM for the unphosphorylated reaction. | | 10 | dephosph-PDE | AC
Pathway No. 85 | 0.1
(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 is still unknown. | | 11 | CaM_bind_PDE1 | AC
Pathway No. 85 | 720
(uM^-1 s^-1) | 5
(s^-1) | Kd(bf) = 0.0069(uM) | - | Substrate:
PDE1
CaM-Ca4
Products:
CaM.PDE1
|
| Borisy et al J Neurosci 12(3):915-923 For olf epithelium PDE1, affinity is 7 nM CaM and about 2 uM Ca which is consistent with it binding Ca4.CaM at 7 nM. Assume same for brain. Reaction should be pretty fast. Assume kb = 5/sec. | | 12 | cAMP-bind-site-B
1 | PKA
Pathway No. 84 | 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. Smith et al PNAS USA 78:3 1591-1595 1981 say that Ka1 is 2.1e7/M which gives a Kd of 47 nM, Kan = 5e8/M or Kd of 2nM. I prefer numbers from Ogreid and Doskeland Febs Lett 129:2 287-292 1981. Their conditions are more physiological. They have figs suggesting time course of complete assoc is < 1 min. | | 13 | cAMP-bind-site-B
2 | PKA
Pathway No. 84 | 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 B1. This gives kf/kb = .7e-7M * 1e6 / (6e5^2) : 1/(6e5^2) = 2e-13:2.77e-12 | | 14 | cAMP-bind-site-A
1 | PKA
Pathway No. 84 | 75
(uM^-1 s^-1) | 110
(s^-1) | Kd(bf) = 1.4667(uM) | - | Substrate:
R2C2-cAMP2
cAMP
Products:
R2C2-cAMP3
|
| This site has a higher Kd for cAMP. See Ogreid and Doskeland 1982 FEBS Lett 150:1 161-166 | | 15 | cAMP-bind-site-A
2 | PKA
Pathway No. 84 | 75
(uM^-1 s^-1) | 32.5
(s^-1) | Kd(bf) = 0.4333(uM) | - | Substrate:
cAMP
R2C2-cAMP3
Products:
R2C2-cAMP4
|
| Cooperativity kicks in, now we have a low Kd for cAMP. | | 16 | Release-C1 | PKA
Pathway No. 84 | 60
(s^-1) | 18
(uM^-1 s^-1) | Kd(cb) = 0.3(uM) | - | Substrate:
R2C2-cAMP4
Products:
PKA-active
R2C-cAMP4
|
| The complex starts to dissociate and release the catalytic subunit C. This has to be fast, as the activation of PKA by cAMP is also fast. | | 17 | Release-C2 | PKA
Pathway No. 84 | 60
(s^-1) | 18
(uM^-1 s^-1) | Kd(cb) = 0.3(uM) | - | Substrate:
R2C-cAMP4
Products:
PKA-active
R2-cAMP4
|
| Second catalytic subunit is now released. | | 18 | inhib-PKA | PKA
Pathway No. 84 | 60
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 0.0167(uM) | - | Substrate:
PKA-active
PKA-inhibitor
Products:
inhibited-PKA
|
| See Doskeland and Ogreid Int J Biochem 13:1-19. Not clear what the rates are, but the reaction has to be fast and it has to have a pretty high affinity. The exact values are not critical under these conditions. | | 19 | Ca-bind-CaNAB-Ca
2 | PP2B
Pathway No. 83 | 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 1994 Biochem 33:6859-6866, this specific parm on pg 6863, the Kact is 0.5 uM. Assume binding is fast, 1 sec. | | 20 | Ca-bind-CaNAB | PP2B
Pathway No. 83 | 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. This doesn't really matter much because it will always be bound at physiological Ca. |
and 
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