| | Enzyme Molecule /
Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents |
| 1 | CaEPump /
Ca-pump-out | Osc_Ca_
IP3metabolism
Accession No. : 24 | CaRegulation
Pathway No. : 132 | 0.0899977 | 200 | 4 | explicit E-S complex | Substrate
Ca
Product
Ca-ext
|
| | Both affinity and Vmax of the Ca-pump are higher than those used in the model that generates non-oscillatory Ca dynamics. Km has been decreased from 0.2 to 0.09 uM and Vmax increased from 72 to 200. The parameters are constrained by the need to generate Ca oscillations by the Othmer-Tang model. |
| 2 | ER_pump /
ER_pump | Osc_Ca_
IP3metabolism
Accession No. : 24 | Othmer-Tang-mode
l
Pathway No. : 133 | 0.150007 | 10 | 4 | explicit E-S complex | Substrate
Ca
Product
Ca-sequester
|
| | Othmer and Tang use a Km of 0.5 uM, but this does not generate proper Ca oscillations in our model. So we have decreased Km to 0.15 uM. This is closer to the 0.1 uM value used by Keizer and De Young in Tang et al, Biophys J 70, 1996 |
| | Name | Accession Name | Pathway Name | Kf | Kb | Kd | tau | Reagents |
| 1 | CaM-TR2-bind-Ca | Osc_Ca_
IP3metabolism
Accession No. : 24 | CaM
Pathway No. : 122 | 72
(uM^-2 s^-1) | 72
(s^-1) | Kd(af) = 1(uM) | - | Substrate
Ca
Ca
CaM
Product
CaM-TR2-Ca2
|
| | We use the Martin et al 1985 Eur J Biochem 151(3):543-550 rates here, plus the Drabikowski and Brzeska 1982 JBC 257(19):11584-11590 binding consts. All are scaled by 3X to cell temperature. kf = 2e-10 kb = 72 Stemmer & Klee 1994 Biochem 33:6859-6866 have values of : K1=.9, K2=1.1. Assume 1.0uM for both |
| 2 | CaM-TR2-Ca2-bind
-Ca | Osc_Ca_
IP3metabolism
Accession No. : 24 | CaM
Pathway No. : 122 | 3.6
(uM^-1 s^-1) | 10
(s^-1) | Kd(bf) = 2.7778(uM) | - | Substrate
Ca
CaM-TR2-Ca2
Product
CaM-Ca3
|
| | Stemmer and Klee 1994 Biochem 33:6859-6866 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 |
| 3 | CaM-Ca3-bind-Ca | Osc_Ca_
IP3metabolism
Accession No. : 24 | CaM
Pathway No. : 122 | 0.465
(uM^-1 s^-1) | 10
(s^-1) | Kd(bf) = 21.5054(uM) | - | Substrate
Ca
CaM-Ca3
Product
CaM-Ca4
|
| | Use K3 = 21.5 uM here from Stemmer and Klee table 3. Stemmer and Klee 1994 Biochem 33:6859-6866 kb/kf =21.5 * 6e5 so kf = 7.75e-7, kb = 10 |
| 4 | PKC-act-by-Ca | Osc_Ca_
IP3metabolism
Accession No. : 24 | PKC
Pathway No. : 123 | 0.6
(uM^-1 s^-1) | 0.5
(s^-1) | Kd(bf) = 0.8333(uM) | - | Substrate
Ca
PKC-cytosolic
Product
PKC-Ca
|
| | This Kd is a straightforward result from the Schaechter and Benowitz 1993 J Neurosci 13(10):4361 curves. The time-course is based on the known rapid activation of PKC and also the fact that Ca association with proteins is typically quite fast. My guess is that this tau of 2 sec is quite conservative and the actualy rate may be much faster. The parameter is quite insensitive for most stimuli. |
| 5 | Act-PLC-Ca | Osc_Ca_
IP3metabolism
Accession No. : 24 | PLCbeta
Pathway No. : 126 | 3
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 0.3333(uM) | - | Substrate
Ca
PLC
Product
PLC-Ca
|
| | Affinity for Ca = 1uM without AlF, 0.1 with: from Smrcka et al science 251 pp 804-807 1991 so [Ca].kf = kb so kb/kf = 1 * 6e5 = 1/1.66e-6 Assigned affinity to a Kd of 0.333 to maintain balance. |
| 6 | PLC-Gq-bind-Ca | Osc_Ca_
IP3metabolism
Accession No. : 24 | PLCbeta
Pathway No. : 126 | 30
(uM^-1 s^-1) | 1
(s^-1) | Kd(bf) = 0.0333(uM) | - | Substrate
Ca
PLC-Gq
Product
PLC-Ca-Gq
|
| | this step has a high affinity for Ca, from Smrcka et al. 0.1uM so kf /kb = 1/6e4 = 1.666e-5:1. See the Act-PLC-by-Gq reaction. Raised kf to 5e-5 based on match to conc-eff curves from Smrcka et al. |
| 7 | Ca-inhib-1pase | Osc_Ca_
IP3metabolism
Accession No. : 24 | 145_dephos
Pathway No. : 128 | 1
(uM^-1 s^-1) | 6
(s^-1) | Kd(bf) = 5.9999(uM) | - | Substrate
Ca
IP_1pase
Product
Ca-1pase-cmplx
|
| | Ki from Inhorn & Majerus, BiochemJ 262(33); 1987: 15946-52 |
| 8 | bind_inact_Ca | Osc_Ca_
IP3metabolism
Accession No. : 24 | Othmer-Tang-mode
l
Pathway No. : 133 | 1.8001
(uM^-1 s^-1) | 0.21
(s^-1) | Kd(bf) = 0.1167(uM) | - | Substrate
Ca
Ca.IP3.IP3R
Product
Ca2.IP3.IP3R
|
| | from the O-T model in Tang et al, Biophys J 70, 1996 |
| 9 | bind_act_Ca | Osc_Ca_
IP3metabolism
Accession No. : 24 | Othmer-Tang-mode
l
Pathway No. : 133 | 15
(uM^-1 s^-1) | 1.65
(s^-1) | Kd(bf) = 0.11(uM) | - | Substrate
Ca
IP3.IP3R
Product
Ca.IP3.IP3R
|
| | from the O-T model in Tang et al, Biophys J 70, 1996 |
color.