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Molecule Parameter List for 2_LuxR-AI

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

2_LuxR-AI 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	0	2	1

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

2_LuxR-AI acting as a Molecule in  Quorum_repressilator Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
2_LuxR-AI	Quorum_ repressilator Accession No. : 69	LuxI Pathway No. : 303	0	3	No
Dimer of Lux R - AI complex

2_LuxR-AI 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	Lac_operator_ activation_ reaction	Quorum_ repressilator Accession No. : 69	LacI_2nd_copy Pathway No. : 302	1000 (s^-1)	224 (s^-1)	Keq = 0.224(uM)	0.001sec	Substrate 2_LuxR-AI Product Lac_operator_ activator_bound
	It signifies the binding of the activator with the operator Kf = 1 /nM/sec Kb = 224 /sec Used first binding rates for repressor from Box 1 Elowitz, M. et al (2000) Nature 403:335-338
2	2_LuxR-AI_ degradation	Quorum_ repressilator Accession No. : 69	LuxI Pathway No. : 303	0.2 (s^-1)	0 (s^-1)	-	-	Substrate 2_LuxR-AI Product Degraded_2_ LuxR-AI
	Degradation of the dimer of the complex between Lux R and autoinducer. kf = 0.2, McMillen et al (2002) PNAS 99(2) 679-84

2_LuxR-AI acting as a Product 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
LuxR-AI_ complex_ dimerization	Quorum_ repressilator Accession No. : 69	LuxI Pathway No. : 303	1.8 (uM^-1 s^-1)	0.1 (s^-1)	Keq = 0.0556(uM)	-	Substrate LuxR-AI LuxR-AI Product 2_LuxR-AI
Dimerization of the complex between Lux R and the autoinducer protein Kf = 1.8e+18 /sec/M = 1.8 /sec/uM McMillen, M. et al. (2002) PNAS USA 99(2):679-684