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Molecule Parameter List for CycE_Kip1

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

*CycE_Kip1* 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	1	0	6	0	2	1

Accession and Pathway Details

Accession Name	Accession No.	Accession Type	Pathway Link
Mammalian_cell_ cycle	85	Network	Growth, CELLDIV, Rb_grp, IE_GRP, CycB_Grp, Cdc20_Grp, Cdh1_grp, E2F, CycA_Grp, CycE_grp, Early_Response_Genes, Delayed_Response_Genes, CycD_Grp
This is a fairly complete mass-action reimplementation of the Novak and Tyson mammalian cell cycle model. It is inexact on two counts. First, it replaces many rather abstracted equations with mass action and Michaelis-Menten forms of enzymes. Second, it does not handle the halving of cellular volume at the division point. Within these limitations, the model does most of what the original paper shows including oscillation of the relevant molecules.

CycE_Kip1 acting as a Molecule in Mammalian_cell_cycle Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
CycE_Kip1	Mammalian_cell_ cycle Accession No. : 85	CycE_grp Pathway No. : 1078	0	200	No

CycE_Kip1 acting as a Summed Molecule in Mammalian_cell_cycle Network

Accession Name	Pathway Name	Target	Input
Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	Tot_Kip1	CycE_Kip1 Kip1 CycA_Kip1 CycD_Kip1

CycE_Kip1 acting as a Substrate for an Enzyme in Mammalian_cell_cycle Network

	Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
1	CycE / k6_E_etaE	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	10.0002	500	4	explicit E-S complex	Substrate CycE_Kip1 Product CycE degraded
	k6 = 100, etaE = 0.5 Assume a large Km of 1000 so that the conc of the enzyme is negligible. Then rate is E.S.Vmax/Km. 6 April 2006 I had changed it over to an explict form earlier. Those values were k1 = 500, k2 = 10, k3 = 1. Cannot use as effective Km is very small so we would end up with lots of E.S complex. Change back to MM: Km = 10, kcat = Km * k6 * etaE = 500.
2	CycE / k8_CycE_Kip1	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	0.1	2	4	explicit E-S complex	Substrate CycE_Kip1 Product Kip1 degraded
	Autocatalysis step equation 5. Unfortunately cannot exactly represent the math of Equation 26. Note that we cannot merge this enzyme with k6_etaE because this is in the explicit form to get a little closer to the mathematical form.
3	CycA / k6_E_etaA	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	10.0002	500	4	explicit E-S complex	Substrate CycE_Kip1 Product CycE degraded
	See notes for k6_E_etaE. Explicit rates had been k1 = 500, k2 = 10, k3 = 1 but this gave a very low Km. So, back to MM: etaA = 0.5 so kcat = 500, Km = 10 as for k6_E_etaE
4	CycA / k8_CycA_Kip1	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	0.1	2	4	explicit E-S complex	Substrate CycE_Kip1 Product Kip1 degraded
5	CycB / k6_E_etaB	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	9.99992	1000	4	explicit E-S complex	Substrate CycE_Kip1 Product CycE degraded
	See notes for k6_E_etaE. Here etaB = 1 so kcat = 1000, Km as before is 10
6	CycB / k8_CycB_Kip1	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	0.0999992	0.1	4	explicit E-S complex	Substrate CycE_Kip1 Product Kip1 degraded
	k8 = 0.2, psiB = 0.05, so kcat = 0.1. J8 = 0.1

CycE_Kip1 acting as a Substrate in a reaction in Mammalian_cell_cycle 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	k_prime6	Mammalian_cell_ cycle Accession No. : 85	CycE_grp Pathway No. : 1078	10 (s^-1)	0 (uM^-1 s^-1)	-	-	Substrate CycE_Kip1 Product CycE degraded
2	k_prime_8_kip1	Mammalian_cell_ cycle Accession No. : 85	CycE_grp Pathway No. : 1078	0.1 (s^-1)	0 (uM^-1 s^-1)	-	-	Substrate CycE_Kip1 Product Kip1 degraded
	k_prime_8 = 0.1

CycE_Kip1 acting as a Product in a reaction in Mammalian_cell_cycle Network

Name	Accession Name	Pathway Name	Kf	Kb	Kd	tau	Reagents
k25	Mammalian_cell_ cycle Accession No. : 85	CycE_grp Pathway No. : 1078	999.996 (uM^-1 s^-1)	10 (s^-1)	Kd(bf) = 0.01(uM)	-	Substrate CycE Kip1 Product CycE_Kip1

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