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Molecule Parameter List for RBS | 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. |
RBS acting as a Molecule in Kierzek_LacZ Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | RBS | Kierzek_LacZ
Accession No. : 29 | LacZ
Pathway No. : 141 | 0 | 0.99997 | No | | Ribosome binding site. Kierzek et al say: Based on Yarchuk et al 1992 J Mol Biol 226:581-596 we have assumed the following interdependence between translation and mRNA decay: (i) RNase E and ribosomes compete for the RBS (ii) if RNase E binds to the RBS faster than the ribosome, it degrades mRNA in the 5prime to 3prime direction and does not interfere with the movement of the ribosomes that have been already bound; and (iii) Every ribosome that successfully binds to the RBS completes translation of the protein. |
RBS 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 | | 1 | Ribosome_
binding | Kierzek_LacZ
Accession No. : 29 | LacZ
Pathway No. : 141 | 99.9927
(uM^-1 s^-1) | 2.25
(s^-1) | Kd(bf) = 0.0225(uM) | - | Substrate
RBS
Ribosome
Product
RibRBS
| | | Equations 5 and 6 from Kierzek et al. Association rate set to order of magnitude of diffusion-limited aggregation. Dissociation rate set to reproduce translation initiation frequency. | | 2 | 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. |
RBS 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 | 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. | | 2 | Clearance | Kierzek_LacZ
Accession No. : 29 | LacZ
Pathway No. : 141 | 0.5
(s^-1) | 0
(uM^-1 s^-1) | - | - | Substrate
RibRBS
Product
RBS
elRIB
| | | Equation 7 from Kierzek et al. Based on Draper , DE 1996 E coli and Salmonella 2nd Ed pp 902-908 ASM Press, Washington DC. This is the rate at which the RBS is cleared. |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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