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Molecule Parameter List for CycE

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* 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	10	3	4	2	2

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 acting as a Molecule in Mammalian_cell_cycle Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
CycE	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	0	200	No

CycE acting as 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 / k20_lambdaE	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	100.002	5000	4	explicit E-S complex	Substrate Rb Product Rb_P
	For Km ~ 0, rate ~ kcat. rate = k20 * lambdaE = 10 * 5 7 Apr 2005. Actually need to put in substrate term too. Let Km = 10 >> sub. Then, rate ~ kcat * sub * prd /Km so kcat = Km * k20 * lambdaE = 10 * 10 * 5 = 500
2	CycE / k21_phiE	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	9.99968	2500	4	explicit E-S complex	Substrate PP1A Product PP1
	Rate is just K21 * phiE * [CycE]. K21 = 1, phiE = 25. So rate= 25 * [CycE] MM rate = kcat * E.S/(Km + S) Let Km << S, then we get rate = kcat * E So if Km = 0.01, kcat = 25 7 Apr 2005. Actually should include substrate term. So, Km = 10, kcat = Km * K21 * phiE = 250 18 Apr 2005. Speeded up 10x.
3	CycE / Ak6_etaE	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	10.0002	500	4	explicit E-S complex	Substrate CycA_Kip1 Product CycA degraded
	Rate = V6 [CycD_Kip1]. 6 Apr 2005. Rates were k1 = 500, k2 = 10, k3 = 1 in explicit E.S reaction form. Changed to MM as Km was too low. New values: Km = 10 kcat = Km * k6 * etaE = 500.*
4	CycE / k8_CycE	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	0.1	2	4	explicit E-S complex	Substrate CycE Product 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.
5	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.
6	CycE / k6_D_etaE	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	10.0002	500	4	explicit E-S complex	Substrate CycD_Kip1 Product CycD degraded
	Rate = V6 * [CycD_Kip1]. k3.k1/k2 = rate = k6 * etaE = 50. 6 Apr 2005. Old rates in explicit form were k1 = 500, k2 = 10, k3 = 1. Need to go back to MM form because the above explict rates give a very low Km, ie, lots of E.S complex. k6 = 100, etaE = 0.5, Let Km >> substrate, so Km = 10. Then kcat = Km * k6 * etaE = 500.
7	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.
8	CycE / k6_kip1_E	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	10.0002	500	4	explicit E-S complex	Substrate Kip1 Product degraded_kip
	Rate = V6 * [CycD_Kip1]. k3.k1/k2 = rate = k6 * etaE = 50. 6 Apr 2005. Old rates in explicit form were k1 = 500, k2 = 10, k3 = 1. Need to go back to MM form because the above explict rates give a very low Km, ie, lots of E.S complex. k6 = 100, etaE = 0.5, Let Km >> substrate, so Km = 10. Then kcat = Km * k6 * etaE = 500.
9	CycE / k20_lambdaE[1]	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	100.002	5000	4	explicit E-S complex	Substrate E2FAP.Rb Product E2FAP Rb_P
	For Km ~ 0, rate ~ kcat. rate = k20 * lambdaE = 10 * 5 7 Apr 2005. Actually need to put in substrate term too. Let Km = 10 >> sub. Then, rate ~ kcat * sub * prd /Km so kcat = Km * k20 * lambdaE = 10 * 10 * 5 = 500
10	CycE / k20_lambdaE[2]	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	100.002	5000	4	explicit E-S complex	Substrate E2FA.Rb Product E2FA Rb_P
	For Km ~ 0, rate ~ kcat. rate = k20 * lambdaE = 10 * 5 7 Apr 2005. Actually need to put in substrate term too. Let Km = 10 >> sub. Then, rate ~ kcat * sub * prd /Km so kcat = Km * k20 * lambdaE = 10 * 10 * 5 = 500

CycE 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 / k8_CycE	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	0.1	2	4	explicit E-S complex	Substrate CycE Product 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.
2	CycA / k8_CycA	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	0.1	2	4	explicit E-S complex	Substrate CycE Product degraded
3	CycB / k8_CycB	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	0.0999992	0.1	4	explicit E-S complex	Substrate CycE Product degraded

CycE acting as a Product of 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	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
3	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
4	E2FA / k7	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	1	1.2	4	explicit E-S complex	Substrate AminoAcids Product CycE
	Represented simply as [E2FA]k7, where k7 is 0.6 As AAs are at 1, we get rate = [AAs].[E2FA].kcat / (Km + [AAs]) So if we set Km = [AAs] = 1, then kcat = 1.2 gives our desired equation.*

CycE 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	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
2	k_prime_8	Mammalian_cell_ cycle Accession No. : 85	CycE_grp Pathway No. : 1078	0.1 (s^-1)	0 (s^-1)	-	-	Substrate CycE Product degraded
	k_prime_8 = 0.1

CycE acting as a Product in a reaction in Mammalian_cell_cycle Network

	Name	Accession Name	Pathway Name	Kf	Kb	Kd	tau	Reagents
1	k_prime7	Mammalian_cell_ cycle Accession No. : 85	CycE_grp Pathway No. : 1078	0 (s^-1)	0 (s^-1)	-	-	Substrate AminoAcids Product CycE
	This is set to zero in the paper, so this reaction isn't really doing anything.
2	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

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