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Molecule Parameter List for ElRNAP | 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 |
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. |
ElRNAP acting as a Molecule in Kierzek_LacZ Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | ElRNAP | Kierzek_LacZ
Accession No. : 29 | LacZ
Pathway No. : 141 | 0 | 0.99997 | No | | Polymerase elongating a given mRNA molecule. Kierzek et al assume that the RNA polymerase completes synthesis of the mRNA molecule with a rate sufficient to allow for a ribosome movement rate of 15 amino acids/sec. They do not explicitly model the elongation of mRNA. |
ElRNAP 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 | 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. |
ElRNAP 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 | | RNASynthesis | Kierzek_LacZ
Accession No. : 29 | LacZ
Pathway No. : 141 | 1
(s^-1) | 0
(uM^-3 s^-1) | - | - | Substrate
TrRNAP
Product
ElRNAP
P
RBS
RNAP
| | Equation 4 from Kierzek et al. They say: To clear the promoter region, active RNA polymerase must move 30 to 60 nucleotides (ref Record et al 1996 E coli and Salmonella 2nd ed pp 792-821 ASM Press, Washington DC) Since rate of polymerase movement is about 40 nucleotides/sec, this step takes about 1 sec. The length of the mRNA chain that is synthesized during this time corresponds roughly to the length of the leader region containing the ribosome binding site (RBS). Therefore the synthesis of the RBS and promotor clearance occur at approximately the same rate of 1 per sec. .... Therefore we modeled these two processes by the single first order reaction with a rate constant of 1 per sec. |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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