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Molecule Parameter List for lac_mRNA

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_mRNA* 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	1	0	4	1	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_mRNA acting as a Molecule in Quorum_repressilator Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
lac_mRNA	Quorum_ repressilator Accession No. : 69	LacI_2nd_copy Pathway No. : 302	0	3	No
The m-RNA transcribed by the lac operator Elowitz, M. et al. (2000) Nature 403:335-338

lac_mRNA acting as an Enzyme in Quorum_repressilator Network

Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
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_mRNA 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_operator / Lac_basal_ transcription	Quorum_ repressilator Accession No. : 69	LacI_2nd_copy Pathway No. : 302	0.000555607	216	4	Classical Michaelis-Menten V = Etot.S.Kcat/Km+S	Substrate Nucleotides Product lac_mRNA
	Basal transcription of the Lac gene. Rates from Fig 2 Garcia and Elowitz et al.(2004) PNAS 101: 10955-60
2	Lac_operator_ 1st_bound / Lac_ transcription	Quorum_ repressilator Accession No. : 69	LacI_2nd_copy Pathway No. : 302	0.0005556	0.0005	4	Classical Michaelis-Menten V = Etot.S.Kcat/Km+S	Substrate Nucleotides Product lac_mRNA
	Transcription of the Lac gene with only one of its promoter sites activated. Rates from Box 1 Elowitz, M. et al. (2000) N Nature 403: 335-338
3	Lac_operator_ 2nd_bound / Lac_ transcription1	Quorum_ repressilator Accession No. : 69	LacI_2nd_copy Pathway No. : 302	0.0005556	0.0005	4	Classical Michaelis-Menten V = Etot.S.Kcat/Km+S	Substrate Nucleotides Product lac_mRNA
	Transcription of the Lac gene with both its promoter sites activated. Rates from Box 1 Elowitz, M. et al. (2000) Nature 403: 335-338
4	Lac_operator_ activator_bound / Lac_active_ transcription	Quorum_ repressilator Accession No. : 69	LacI_2nd_copy Pathway No. : 302	0.0005556	20	4	Classical Michaelis-Menten V = Etot.S.Kcat/Km+S	Substrate Nucleotides Product lac_mRNA
	Lac transcription from the activator bound Lac gene. kcat is taken from Garcia & Elowitz et al. (2004) PNAS 101: 10955-60

lac_mRNA 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
lac_mRNA_ degradation	Quorum_ repressilator Accession No. : 69	LacI_2nd_copy Pathway No. : 302	0.0058 (s^-1)	0 (s^-1)	-	-	Substrate lac_mRNA Product Degraded_lac_ mRNA
This reaction denotes the degradation of the lac m-RNA, the half life of which is two minutes. t1/2 = 0.693/k where k denotes kf Elowitz, M. et al. (2000) Nature 403:335-338

Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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