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Molecule Parameter List for Ca | The statistics table lists the distribution of a molecule acting either as a substrate, product, enzyme or as a molecule within the network.
The text color of a molecule is highlighted by  color. | | Statistics |
Accession and Pathway Details | |
| Accession Name | Accession No. | Accession Type | Pathway Link | NonOsc_Ca_
IP3metabolism | 31 | Network |
MIPP, CaMKII, CaM,
PKC, IP3-3K, CaRegulation,
Gq, PLCbeta, 134_dephos,
145_dephos, IP4-system, IHP-system,
1345_dephos | | This network models detailed metabolism of Ins(145)P3, integrated with GPCR mediated PLCbeta activation and Ca release by the InsP3 receptor in the neuron. It is similar to the NonOsc_Ca_IP3metab model (accession 23) except that some enzymes have been modified to have reversible kinetics rather than Michaelis-Menten kinetics. These modified enzymes belong to the groups: IP4-system, IP3-3K, 145_dephos and 134_dephos. Mishra J, Bhalla US. Biophys J. 2002 Sep;83(3):1298-316. |
Ca acting as a Molecule in NonOsc_Ca_IP3metabolism Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | Ca | NonOsc_Ca_
IP3metabolism
Accession No. : 31 | CaRegulation
Pathway No. : 149 | 0.08 | 1000 | No | | This pool represents intracellular calcium. Resting levels are around 80 nM, but this is subject to all sorts of influxes and pumps. |
Ca acting as a Substrate for an Enzyme in NonOsc_Ca_IP3metabolism Network
Enzyme Molecule /
Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | CaEPump /
Ca-pump-out | NonOsc_Ca_
IP3metabolism
Accession No. : 31 | CaRegulation
Pathway No. : 149 | 0.2 | 72 | 4 | explicit E-S complex | Substrate
Ca
Product
Ca-ext
| | From McBurney and Neering, TINS 10(4), 1987, 164-169 1987. We are using the high-affinity pump here. Their numbers exceed M&L so I am reducing the rates by 10X. Need to check. k1 = 3e-3, k2 = 288, k3 = 72, n = 1000. This comes to a Km of 0.2 for Ca, and a Vmax of 72. |
Ca acting as a Substrate in a reaction in NonOsc_Ca_IP3metabolism Network
| Kd is calculated only for second order reactions, like nA+nB <->nC or nA<->nC+nD, where n is number and A,B,C,D are molecules, where as for first order reactions Keq is calculated.
Kd for higher order reaction are not consider. |
| | Name | Accession Name | Pathway Name | Kf | Kb | Kd | tau | Reagents | | 1 | CaM-TR2-bind-Ca | NonOsc_Ca_
IP3metabolism
Accession No. : 31 | CaM
Pathway No. : 146 | 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 | NonOsc_Ca_
IP3metabolism
Accession No. : 31 | CaM
Pathway No. : 146 | 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 | NonOsc_Ca_
IP3metabolism
Accession No. : 31 | CaM
Pathway No. : 146 | 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 | NonOsc_Ca_
IP3metabolism
Accession No. : 31 | PKC
Pathway No. : 147 | 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 | Ca-bind-to-Trans
p | NonOsc_Ca_
IP3metabolism
Accession No. : 31 | CaRegulation
Pathway No. : 149 | 3600
(uM^-2 s^-1) | 144
(s^-1) | Kd(af) = 0.2(uM) | - | Substrate
Ca
Ca
CaTransp
Product
CaTransp-2Ca
| | | Rates from Lauffenburger abd Linderman 1993 Receptors pg 200. Kd = KCa2 = 0.2 uM | | 6 | Act-PLC-Ca | NonOsc_Ca_
IP3metabolism
Accession No. : 31 | PLCbeta
Pathway No. : 151 | 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. | | 7 | PLC-Gq-bind-Ca | NonOsc_Ca_
IP3metabolism
Accession No. : 31 | PLCbeta
Pathway No. : 151 | 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. | | 8 | Ca-inhib-1pase | NonOsc_Ca_
IP3metabolism
Accession No. : 31 | 145_dephos
Pathway No. : 153 | 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 |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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