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Molecule Parameter List for Protein

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

Protein 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	1	1

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.

Protein acting as a Molecule in  Kierzek_LacZ Network

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

Protein acting as a Substrate 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
Prot_ degradation	Kierzek_LacZ Accession No. : 29	LacZ Pathway No. : 141	0.0001 (s^-1)	0 (s^-1)	-	-	Substrate Protein Product AAs
Equation 10 from Kierzek et al. Assume a half-life of 3 hours for beta-galactosidase in E coli, from Berquist and Truman 1978 Mol. Cell. Genet. 164, 105-108.

Protein 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
Prot_elongation	Kierzek_LacZ Accession No. : 29	LacZ Pathway No. : 141	0.015 (s^-1)	0 (uM^-1 s^-1)	-	-	Substrate elRIB Product Protein Ribosome
Equation 9 from Kierzek et al. They say that this step should be RibRBS-> Protein, but based on text and the logic of the synthesis, it should really be ElRIB, the Ribosome elongating protein chain, that should give rise to the protein. The calculation is: ribosome moves at 15 AAs /sec. The protein is 1024 AAs long. So protein is formed at 0.015/sec.