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Molecule Parameter List for Rb

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 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	4	2	2	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 acting as a Molecule in  Mammalian_cell_cycle Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
Rb	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	10	200	No
Rbtot = 10, assigned to CoInit

Rb acting as a Summed Molecule in  Mammalian_cell_cycle Network

Accession Name	Pathway Name	Target	Input
Mammalian_cell_ cycle Accession No. : 85	Growth Pathway No. : 1069	Rb_dup	Rb

Rb 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	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	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
3	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
4	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

Rb 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	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 k19*PP1A. 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 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	k26	Mammalian_cell_ cycle Accession No. : 85	E2F Pathway No. : 1076	10 (uM^-1 s^-1)	200 (s^-1)	Kd(bf) = 20.0001(uM)	-	Substrate E2FA Rb Product E2FA.Rb
	k26 = 10, k26r =200 Unless k26 = 10000. There is a period in the paper but it may be a typo. The form of the equation is complex, but if k26 is large then there is more E2F:Rb, so that is the forward reaction here.
2	k26_P	Mammalian_cell_ cycle Accession No. : 85	E2F Pathway No. : 1076	10 (uM^-1 s^-1)	200 (s^-1)	Kd(bf) = 20.0001(uM)	-	Substrate E2FAP Rb Product E2FAP.Rb
	Same as k26, but acting on the phosph form.