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Molecule Parameter List for nucleotides

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

nucleotides 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	0	2

Accession and Pathway Details

Accession Name	Accession No.	Accession Type	Pathway Link
Kierzek_LacZ	29	Pathway	LacZ
An approximation to the Kierzek AM. et al. J Biol Chem. (2001) 276(11):8165-72 model of LacZ gene expression in E. coli. They use stochastic simulation and model cell growth. Despite these discrepancies, the continuous fixed size model is within a factor of 3 of their results. Parameter values are identical.

nucleotides acting as a Molecule in  Kierzek_LacZ Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
nucleotides	Kierzek_LacZ Accession No. : 29	LacZ Pathway No. : 141	0	0.99997	Yes

nucleotides acting as a Product in a reaction in  Kierzek_LacZ 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	RBS_degradation	Kierzek_LacZ Accession No. : 29	LacZ Pathway No. : 141	0.3 (s^-1)	0 (s^-1)	-	-	Substrate RBS Product nucleotides
	Equation 8 from Kierzek et al, set equal to transcription initiaton frequency. This is the decay rate of unprotected RBS.
2	mRNA_ degradation	Kierzek_LacZ Accession No. : 29	LacZ Pathway No. : 141	0.3 (s^-1)	0 (s^-1)	-	-	Substrate ElRNAP Product nucleotides
	Also equation 8 from Kierzek et al. Since RBS is assumed to be the rate-limiting part of the protein synthesis, we don't really need to worry about the fate of the ElRNAP. For balance we degrade it at the same rate as the RBS.