|
Enter a Search String | Special character and space not allowed in the query term.
Search string should be at least 2 characters long. |
Molecule Parameter List for Ribosome | 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. |
Ribosome acting as a Molecule in Kierzek_LacZ Network
Name | Accession Name | Pathway Name | Initial Conc. (uM) | Volume (fL) | Buffered | Ribosome | Kierzek_LacZ Accession No. : 29 | LacZ Pathway No. : 141 | 0.5834 | 0.99997 | Yes | Ribosome pool The language in the paper is a little ambiguous, but from simulation it turns out that they assume that the number of free ribosomes is held fixed at 350. In other words, buffered. |
Ribosome 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 | 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. |
Ribosome 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. |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR This Copyright is applied to ensure that the contents of this database remain freely available. Please see FAQ for details. |
|