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Molecule Parameter List for CycA

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

CycA 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	13	1	4	1	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.

CycA acting as a Molecule in  Mammalian_cell_cycle Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
CycA	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	0	200	No
rate = k4.Gamma_A * [CycA] * [Cdh1]/(J4 + [Cdh1]) J4 = 0.01 k4 = kcat = 40

CycA 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	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
2	CycA / k21_phiE_A	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	9.99968	2500	4	explicit E-S complex	Substrate PP1A Product PP1
	phiE is also used for the reaction catalyzed by A. So rates are identical to k21_phiE
3	CycA / Cdh1_CycA	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	0.01	12	4	explicit E-S complex	Substrate Cdh1 Product Cdh1_i
	J4 = Km = 0.01 k4 = 40. GammaA = 0.3 kcat = k4 * GammaA = 12
4	CycA / A_phosph_E2F	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	9.99992	10	4	explicit E-S complex	Substrate E2FA Product E2FAP
	Rate equn has form [CycA].[E2F].k23 k23 = 1 MM equn has form [CycA].[E2F].kcat/(Km + E2F) So, we set kcat = Km * k23 where Km >> E2F 25 Mar. Better: Use explicit enz form. rate = k3.k1/k2 if k3 << k2. Let k3 = 1, k2 = 10, so we get k1 = k23 * 10 = 10. 6 Apr. Problem with explicit form is that the enz-substrate complex may affect the levels of the CycA, B etc. Back to MM.
5	CycA / A_phosph_ E2FA.Rb	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	9.99992	10	4	explicit E-S complex	Substrate E2FA.Rb Product E2FAP.Rb
	Rate equn has form [CycA].[E2F].k23 k23 = 1 MM equn has form [CycA].[E2F].kcat/(Km + E2F) So, we set kcat = Km * k23 where Km >> E2F 25 March 2005 Use explicit form. rate = k23 = 1 = k3*k1/k2 where k3 << k2 So k3 = 1, k2 = 10, k1 = 10. 6 Apr 2005. Back to MM form because enz complex formation is depleting CycA, B etc.
6	CycA / Ak6_etaA	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	10.0002	500	4	explicit E-S complex	Substrate CycA_Kip1 Product CycA degraded
	See Ak6_etaE
7	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
8	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
9	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 = 100*0.5 = 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.
10	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
11	CycA / k6_kip1_A	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	10.0002	500	4	explicit E-S complex	Substrate Kip1 Product degraded_kip
	k3.k1/k2 = k6.etaA = 100*0.5 = 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.
12	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
13	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

CycA 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
Cdc20  / Cdc20_deg_CycA	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	10	200	4	explicit E-S complex	Substrate CycA Product degraded
Rate comes in as k30 = 20 Rate = [Cdc20]*[CycA] * k30. To put in MM form: Rate = [Cdc20]*[CycA] * kcat / (Km + [CycA]) where kcat = k30 * Km and Km >> [CycA]. Put Km = 1000, so kcat = 20000 25 March: use explicit enz form. Use rate = k3*k1/k2 = 20, which works if k2 >> k3. Then let k3 = 1, k2 = 10, k1 becomes 200 7 Apr 2005: Above won't work because of low Km consuming too much of the Cdc20 in the complex form. So use Km = 10, kcat = 200.

CycA 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  / 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.
2	CycA  / Ak6_etaA	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	10.0002	500	4	explicit E-S complex	Substrate CycA_Kip1 Product CycA degraded
	See Ak6_etaE
3	CycB  / Ak6_etaB	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	9.99992	1000	4	explicit E-S complex	Substrate CycA_Kip1 Product CycA degraded
	See Ak6_etaE
4	E2FA  / k29	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	1000.02	50	4	explicit E-S complex	Substrate Mass_dup Product CycA
	Represented as eps*k29*[E2FA]*[mass], where k29 is 0.05 Split into two steps, this one deals with the E2FA term. rate = Mass_dup * E2FA * kcat / (Km + Mass_dup) Note that Mass_dup will not change. Let Km >> Mass_dup and kcat = k29 * Km. then rate ~ Mass_dup * E2FA * k29 * Km / Km

CycA 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
k25	Mammalian_cell_ cycle Accession No. : 85	CycA_Grp Pathway No. : 1077	999.996 (uM^-1 s^-1)	10 (s^-1)	Kd(bf) = 0.01(uM)	-	Substrate CycA Kip1 Product CycA_Kip1

CycA acting as a Product 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
k_prime6	Mammalian_cell_ cycle Accession No. : 85	CycA_Grp Pathway No. : 1077	10 (s^-1)	0 (uM^-1 s^-1)	-	-	Substrate CycA_Kip1 Product CycA degraded