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Molecule Parameter List for Ca-sequester

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-sequester* 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	0	1	9	0

Accession and Pathway Details

Accession Name	Accession No.	Accession Type	Pathway Link
Osc_Ca_ IP3metabolism	32	Network	MIPP, CaMKII, CaM, PKC, IP3-3K, Gq, PLCbeta, 134_dephos, 145_dephos, IP4-system, IHP-system, 1345_dephos, CaRegulation, Othmer-Tang-model
This network models an oscillatory calcium response to GPCR mediated PLCbeta activation, alongwith detailed InsP3 metabolism in the neuron. It is similar to the Osc_Ca_IP3metab model (accession 24) except that some enzymes in the InsP3 metabolism network have been modified to have reversible kinetics rather than Michaelis-Menten kinetics. The 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-sequester acting as a Molecule in Osc_Ca_IP3metabolism Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
Ca-sequester	Osc_Ca_ IP3metabolism Accession No. : 32	CaRegulation Pathway No. : 170	6.3328	160	No
Sequestered Ca pool The vol is 0.16 the vol of the cell as a whole. The Ca-sequester conc that we use is same as that used in our other models (see Bhalla and Iyengar, Science 283, 1999: 381-387*

Ca-sequester acting as a Product of an Enzyme in Osc_Ca_IP3metabolism Network

Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
ER_pump / ER_pump	Osc_Ca_ IP3metabolism Accession No. : 32	Othmer-Tang-mode l Pathway No. : 171	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

Ca-sequester acting as a Substrate in a reaction in Osc_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	inactivate_cap_ Ca	Osc_Ca_ IP3metabolism Accession No. : 32	CaRegulation Pathway No. : 170	0 (#^-2 s^-1)	10 (s^-1)	Not applicable**	-	Substrate Ca-sequester Ca-sequester capacitive_Ca_ entry* Product inact_cap_entry
	For non-oscillatory Ca dynamics Kd was set at 3 uM. This did not allow for Ca oscillations characteristic of the Othmer-Tang model. The rates here are constrained solely by the need to generate Othmer-Tang type Ca oscillations.
2	Ca5-bind-Cal	Osc_Ca_ IP3metabolism Accession No. : 32	CaRegulation Pathway No. : 170	0.0005 (uM^-5 s^-1)	1 (s^-1)	-	-	Substrate Ca-sequester Ca-sequester Ca-sequester Ca-sequester Ca-sequester Calseq Product Ca5-Cal
	There are actually 5 Ca-sequester substrates for this reaction, along with one Calseq. Due to system limitations only four are entered.
3	Ca10-bind-Cal	Osc_Ca_ IP3metabolism Accession No. : 32	CaRegulation Pathway No. : 170	0.0005 (uM^-5 s^-1)	1 (s^-1)	-	-	Substrate Ca-sequester Ca-sequester Ca-sequester Ca-sequester Ca-sequester Ca5-Cal Product Ca10-Cal
	There are actually 5 Ca-sequester substrates for this reaction, along with Ca5-Cal. Due to system limitations only four are entered.
4	Ca15-bind-Cal	Osc_Ca_ IP3metabolism Accession No. : 32	CaRegulation Pathway No. : 170	0.0005 (uM^-5 s^-1)	1 (s^-1)	-	-	Substrate Ca-sequester Ca-sequester Ca-sequester Ca-sequester Ca-sequester Ca10-Cal Product Ca15-Cal
	There are actually 5 Ca-sequester substrates for this reaction, along with Ca10-Cal. Due to system limitations only four are entered.
5	Ca20-bind-Cal	Osc_Ca_ IP3metabolism Accession No. : 32	CaRegulation Pathway No. : 170	0.0005 (uM^-5 s^-1)	1 (s^-1)	-	-	Substrate Ca-sequester Ca-sequester Ca-sequester Ca-sequester Ca-sequester Ca15-Cal Product Ca20-Cal
	There are actually 5 Ca-sequester substrates for this reaction, along with Ca15-Cal. Due to system limitations only four are entered.
6	Ca25-bind-Cal	Osc_Ca_ IP3metabolism Accession No. : 32	CaRegulation Pathway No. : 170	0.0005 (uM^-5 s^-1)	1 (s^-1)	-	-	Substrate Ca-sequester Ca-sequester Ca-sequester Ca-sequester Ca-sequester Ca20-Cal Product Ca25-Cal
	There are actually 5 Ca-sequester substrates for this reaction, along with Ca20-Cal. Due to system limitations only four are entered.
7	Ca35-bind-Cal	Osc_Ca_ IP3metabolism Accession No. : 32	CaRegulation Pathway No. : 170	0.0005 (uM^-5 s^-1)	1 (s^-1)	-	-	Substrate Ca-sequester Ca-sequester Ca-sequester Ca-sequester Ca-sequester Ca30-Calseq Product Ca35-Calseq
	There are actually 5 Ca-sequester substrates for this reaction, along with Ca30-Cal. Due to system limitations only four are entered.
8	Ca40-bind-Cal	Osc_Ca_ IP3metabolism Accession No. : 32	CaRegulation Pathway No. : 170	0.0005 (uM^-5 s^-1)	1 (s^-1)	-	-	Substrate Ca-sequester Ca-sequester Ca-sequester Ca-sequester Ca-sequester Ca35-Calseq Product Ca40-Cal
	There are actually 5 Ca-sequester substrates for this reaction, along with Ca35-Cal. Due to system limitations only four are entered.
9	Ca30-bind-Cal	Osc_Ca_ IP3metabolism Accession No. : 32	CaRegulation Pathway No. : 170	0.0005 (uM^-5 s^-1)	1 (s^-1)	-	-	Substrate Ca-sequester Ca-sequester Ca-sequester Ca-sequester Ca-sequester Ca25-Cal Product Ca30-Calseq
	There are actually 5 Ca-sequester substrates for this reaction, along with Ca25-Cal. Due to system limitations only four are entered.

Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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