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Molecule Parameter List for Lac-1

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

Lac-1 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	0	2	5	0

Accession and Pathway Details

Accession Name	Accession No.	Accession Type	Pathway Link
Quorum_ repressilator	69	Network	Shared_Object_Quorum_repressilator,  TetR,  LacI,   Lambda-cl,  LacI_2nd_copy,  LuxI
This model represents a single cell with the repressilator circuit, which is part of a population of similar cells. The repressilator circuit is a network of three proteins, i.e. LacI, TetR, Lambda-cI. The single repressilator model is at accession number 68 in the DOQCS database. In the current model, the LacI is coupled with LuxI which forms an Autoinducer(AI) protein, which couples to LuxR which activates LacI. The AI protein difffuses across the cell membrane so that the population of cells can interact. The lifetime ratio is the ratio between the mRNA and protein lifetimes. This ratio in different cells is chosen from a random gaussian distribution of mean 1 and standard deviation 0.05. The lifetime ratio of this example cell is 0.9837

Lac-1 acting as a Molecule in  Quorum_repressilator Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
Lac-1	Quorum_ repressilator Accession No. : 69	LacI Pathway No. : 300	0	3	No
Lac translated from lac m-RNA Derived from Figure 1(c) stochastic version Elowitz, M. et al. (2000) Nature 403:335-338

Lac-1 acting as a Product of an Enzyme in  Quorum_repressilator Network

	Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
1	lac_mRNA1  / lac_translation	Quorum_ repressilator Accession No. : 69	LacI Pathway No. : 300	0.000555595	0.167	4	Classical Michaelis-Menten V = Etot.S.Kcat/Km+S	Substrate Amino_Acids Product Lac-1
	Translation of the lac mRNA. Rates from Box 1 Elowitz, M. et al (2000) Nature 403: 335-338
2	lac_mRNA  / lac_translation	Quorum_ repressilator Accession No. : 69	LacI_2nd_copy Pathway No. : 302	0.000555595	0.167	4	Classical Michaelis-Menten V = Etot.S.Kcat/Km+S	Substrate Amino_Acids Product Lac-1
	Translation of the lac mRNA. Rates from Box 1 Elowitz, M. et al (2000) Nature 403: 335-338

Lac-1 acting as a Substrate in a reaction in  Quorum_repressilator 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	TetR_operator_ inhibition_ reaction	Quorum_ repressilator Accession No. : 69	TetR Pathway No. : 299	1000.01 (uM^-1 s^-1)	224 (s^-1)	Kd(bf) = 0.224(uM)	-	Substrate Lac-1 TetR_operator Product TetR_operator_ 1st_bound
	It signifies the first binding of the repressor with the operator Kf = 1 /nM/sec Kb = 224 /sec Box 1 Elowitz, M. et al. (2000) Nature 403:335-338
2	TetR_operator_ inhibition_ reaction[1]	Quorum_ repressilator Accession No. : 69	TetR Pathway No. : 299	1000.01 (uM^-1 s^-1)	9 (s^-1)	Kd(bf) = 0.009(uM)	-	Substrate Lac-1 TetR_operator_ 1st_bound Product TetR_operator_ 2nd_bound
	It signifies the second binding of the repressor with the operator Kf = 1 /nM/sec Kb = 9 /sec Box 1 Elowitz, M. et al. (2000) Nature 403:335-338
3	Lac_degradation	Quorum_ repressilator Accession No. : 69	LacI Pathway No. : 300	0.0057 (s^-1)	0 (s^-1)	-	-	Substrate Lac-1 Product Degraded_lac
	This reaction denotes the degradation of Lac, Kf is chosen from a random gaussian distribution. Ref: Fig 2 Garcia & Elowitz et al (2004) PNAS 101(30) 10955-60
4	LuxI_operator_ inhibitor_ reaction[1]	Quorum_ repressilator Accession No. : 69	LuxI Pathway No. : 303	1000.01 (uM^-1 s^-1)	9 (s^-1)	Kd(bf) = 0.009(uM)	-	Substrate Lac-1 LuxI_operator_ 1st_bound Product LuxI_operator_ 2nd_bound
	This signifies the second binding of the repressor with the operator Kf = 1 /nM/sec Kb = 9 /sec Garcia-Ojalvo, J. et al. (2004) PNAS USA 101(30):10955-10960 As described for components of the Repressilator in Box 1 Elowitz, M. et al. (2000) Nature 403:335-338
5	LuxI_operator_ inhibitor_ reaction	Quorum_ repressilator Accession No. : 69	LuxI Pathway No. : 303	1000.01 (uM^-1 s^-1)	224 (s^-1)	Kd(bf) = 0.224(uM)	-	Substrate Lac-1 LuxI_operator Product LuxI_operator_ 1st_bound
	This signifies the second binding of the repressor with the operator Kf = 1 /nM/sec Kb = 224 /sec Garcia-Ojalvo, J. et al. (2004) PNAS USA 101(30):10955-10960 As described for components of the Repressilator in Box 1 Elowitz, M. et al. (2000) Nature 403:335-338