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Molecule Parameter List for CycD

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

*CycD* 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	3	0	4	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.

CycD acting as a Molecule in Mammalian_cell_cycle Network

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

CycD 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	CycD / k20_lambdaD	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	100	3300	4	explicit E-S complex	Substrate Rb Product Rb_P
	With a low Km, rate ~ kcat. Here we have rate = k20 * lambda_d = 10 * 3.3 = 33. 7 Apr 2005. Actually should have the substrate term in here. Use the form Km >> substrate, so rate = kcat * sub * enz / Km so kcat = Km * k20 * lambda_d = 10 * 10 * 3.3 = 330
2	CycD / k20_lambdaD[1]	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	100	3300	4	explicit E-S complex	Substrate E2FAP.Rb Product E2FAP Rb_P
	With a low Km, rate ~ kcat. Here we have rate = k20 * lambda_d = 10 * 3.3 = 33. 7 Apr 2005. Actually should have the substrate term in here. Use the form Km >> substrate, so rate = kcat * sub * enz / Km so kcat = Km * k20 * lambda_d = 10 * 10 * 3.3 = 330 The idea here is that these reactions phosphorylate the Rb protein attached to E2FAP, so that Rb_P is released and E2FAP is left.
3	CycD / k20_lambdaD[2]	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	100	3300	4	explicit E-S complex	Substrate E2FA.Rb Product E2FA Rb_P
	With a low Km, rate ~ kcat. Here we have rate = k20 * lambda_d = 10 * 3.3 = 33. 7 Apr 2005. Actually should have the substrate term in here. Use the form Km >> substrate, so rate = kcat * sub * enz / Km so kcat = Km * k20 * lambda_d = 10 * 10 * 3.3 = 330 The idea here is that these reactions phosphorylate the Rb protein attached to E2FA, so that Rb_P is released and E2FA is left.

CycD 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_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.
2	CycA / k6_D_etaA	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	10.0002	500	4	explicit E-S complex	Substrate CycD_Kip1 Product CycD degraded
	k3.k1/k2 = k6.etaA = 1000.5 = 50 Also k3 << k2. Assume ratio is 10. Let k3 be reasonable, say 1. Then k2 = 10, k1 = 500. 6 April 2005: The above rates are bad because they give a very low Km and too much E.S. complex. So, back to MM: Km >> substrate, so Km = 10. Then kcat = Km k6 * etaA = 10 * 100 * 0.5 = 500.
3	CycB / k6_D_etaB	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	9.99992	1000	4	explicit E-S complex	Substrate CycD_Kip1 Product CycD degraded
	6 Apr 2005. Earlier used explicit E.S complex form with k1 = 1000, k2 = 10, k3 = 1. This gave low Km and lots of E.S. complex. So shift to MM form: k6 = 100, etaB = 1. Let Km = 10 >> substrate. Then kcat = Km * k6 * etaB = 1000
4	DRG / k9	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	1.00002	5	4	explicit E-S complex	Substrate AminoAcids Product CycD
	Represented simply as [DRG]k9, where k9 is 2.5. As AAs are at 1, we get rate = [AAs].[DRG].kcat / (Km + [AAs]) So if we set Km = [AAs] = 1, then kcat = 5 gives our desired equation.*

CycD 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	k10	Mammalian_cell_ cycle Accession No. : 85	CycD_Grp Pathway No. : 1081	5 (s^-1)	0 (s^-1)	-	-	Substrate CycD Product degraded
2	k24	Mammalian_cell_ cycle Accession No. : 85	CycD_Grp Pathway No. : 1081	999.996 (uM^-1 s^-1)	10 (s^-1)	Kd(bf) = 0.01(uM)	-	Substrate CycD Kip1 Product CycD_Kip1
	k24 = 1000 k24r = 10

CycD acting as a Product in a reaction in Mammalian_cell_cycle Network

Name	Accession Name	Pathway Name	Kf	Kb	Kd	tau	Reagents
k_prime6	Mammalian_cell_ cycle Accession No. : 85	CycD_Grp Pathway No. : 1081	10 (s^-1)	0 (uM^-1 s^-1)	-	-	Substrate CycD_Kip1 Product CycD degraded

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