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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

Ca participated as	Molecule	Sum total of	Enzyme	Substrate of an enzyme	Product of an enzyme	Substrate in Reaction	Product in Reaction
No. of occurrences	1	0	0	1	0	8	0

Accession and Pathway Details

Accession Name	Accession No.	Accession Type	Pathway Link
NonOsc_Ca_ IP3metabolism	23	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. The calcium response is non-oscillatory. 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. : 23	CaRegulation Pathway No. : 110	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. : 23	CaRegulation Pathway No. : 110	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. : 23	CaM Pathway No. : 107	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. : 23	CaM Pathway No. : 107	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. : 23	CaM Pathway No. : 107	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. : 23	PKC Pathway No. : 108	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. : 23	CaRegulation Pathway No. : 110	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. : 23	PLCbeta Pathway No. : 112	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. : 23	PLCbeta Pathway No. : 112	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. : 23	145_dephos Pathway No. : 114	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