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Molecule Parameter List for Rb_P

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

*Rb_P* 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	2	12	0	0

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.

Rb_P acting as a Molecule in Mammalian_cell_cycle Network

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

Rb_P 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	PP1 / k19_prime	Mammalian_cell_ cycle Accession No. : 85	Rb_grp Pathway No. : 1071	99.9992	0.1	4	explicit E-S complex	Substrate Rb_P Product Rb
	k19_prime is actually zero, but I do not want NaNs (numerical errors due to divide-by-zero) so I set kcat to a very small value. 7 Apr 2005. Same reasoning, now set Km to 10.
2	PP1A / k19	Mammalian_cell_ cycle Accession No. : 85	Rb_grp Pathway No. : 1071	100	2000	4	explicit E-S complex	Substrate Rb_P Product Rb
	This is part of Eqn 20. k19 = 20. It is meant to represent a dephosph step of Rb_p. rate is k19PP1A. rate in MM form is kcat PP1A * Rb_P / (Km + Rb_P) Assume Km << Rb_P. To do so, Km = 0.01 Then kcat = k19. 7 Apr 2005. Actually should include substrate term. Take Km = 10 >> sub. Then kcat = Km * k19 = 200 18 April. Actually substrate levels are near 10. So need to scale up. Km = 100, kcat = Km * k19 = 2000

Rb_P 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	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.
4	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
5	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
6	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
7	CycA / k20_lambdaA	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	100	3000	4	explicit E-S complex	Substrate Rb Product Rb_P
	Km ~ 0, so rate ~ kcat. Here rate = k20 lambdaA = 10 * 3 7 Apr 2005: Fix it: rate should have substrate term in it. Set Km = 10 >> substrate. Then, kcat = Km * k20 * lambdaA = 10 * 10 * 3 = 300*
8	CycA / k20_lambdaA[1]	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	100	3000	4	explicit E-S complex	Substrate E2FAP.Rb Product E2FAP Rb_P
	Km ~ 0, so rate ~ kcat. Here rate = k20 lambdaA = 10 * 3 7 Apr 2005: Fix it: rate should have substrate term in it. Set Km = 10 >> substrate. Then, kcat = Km * k20 * lambdaA = 10 * 10 * 3 = 300*
9	CycA / k20_lambdaA[2]	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	100	3000	4	explicit E-S complex	Substrate E2FA.Rb Product E2FA Rb_P
	Km ~ 0, so rate ~ kcat. Here rate = k20 lambdaA = 10 * 3 7 Apr 2005: Fix it: rate should have substrate term in it. Set Km = 10 >> substrate. Then, kcat = Km * k20 * lambdaA = 10 * 10 * 3 = 300*
10	CycB / k20_lambdaB	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	100.002	5000	4	explicit E-S complex	Substrate Rb Product Rb_P
	With Km ~ 0, rate ~ kcat. Here rate = k20 lambdaB = 10 * 5 7 Apr 2005. Changed to include substrate term. Use Km = 10 >> sub, so kcat = Km * k20 * lambdaB = 10 * 10 * 5 = 500*
11	CycB / k20_lambdaB[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
	With Km ~ 0, rate ~ kcat. Here rate = k20 lambdaB = 10 * 5 7 Apr 2005. Changed to include substrate term. Use Km = 10 >> sub, so kcat = Km * k20 * lambdaB = 10 * 10 * 5 = 500*
12	CycB / k20_lambdaB[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
	With Km ~ 0, rate ~ kcat. Here rate = k20 lambdaB = 10 * 5 7 Apr 2005. Changed to include substrate term. Use Km = 10 >> sub, so kcat = Km * k20 * lambdaB = 10 * 10 * 5 = 500*

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