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Team:University of Ottawa/Modeling/Parameters
From 2008.igem.org
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| - | Weiss, R. and M.-T. Chen (2005). "Artificial cell-cell communication in yeast Saccharomyces cerevisiae using signaling elements from Arabidopsis thaliana." Nature Biotechnology 23(12): 1551-1555. | + | # Weiss, R. and M.-T. Chen (2005). "Artificial cell-cell communication in yeast Saccharomyces cerevisiae using signaling elements from Arabidopsis thaliana." Nature Biotechnology 23(12): 1551-1555. |
| - | Hillen, W. and C. Berens (1994). "Mechanisms underlying expression of Tn10 encoded tetracycline resistance." Annu. Rev. Microbiol. 48: 345-369. | + | # Hillen, W. and C. Berens (1994). "Mechanisms underlying expression of Tn10 encoded tetracycline resistance." Annu. Rev. Microbiol. 48: 345-369. |
Kleinschmidt, C., K. Tovar, et al. (1987). "Dynamics of repressor-operator recognition:Tn10 encoded tetracycline resistance control." Biochemistry 27: 1094-1104. | Kleinschmidt, C., K. Tovar, et al. (1987). "Dynamics of repressor-operator recognition:Tn10 encoded tetracycline resistance control." Biochemistry 27: 1094-1104. | ||
| + | # Schmulling T, Werner T, Riefler M, Krupkova E, Bartrina y Manns I (2003) Structure and function of cytokinin oxidase/dehydrogenase genes of maize, rice, Arabidopsis and other species. J Plant Res 116:241-252 | ||
| + | |||
| + | # Laskey, J.G., P. Patterson, et al. (2003). "Rate enhancement of cytokinin oxidase/dehydrogenase using 2,6-dichloroindophenol as an electron acceptor." Plant Growth Regulation 40: 189–196. | ||
| + | |||
| + | # Frebortova, J., M.W. Fraaije, et al. (2004). "Catalytic reaction of cytokinin dehydrogenase: preference for quinones as electron acceptors." Biochem. J. 380: 121–130. | ||
| + | |||
| + | |||
| + | |||
Blake, W., G. Balazsi, et al. (2006). "Phenotypic consequences of promoter-mediated transcriptional noise." Molecular Cell 24: 853-865. | Blake, W., G. Balazsi, et al. (2006). "Phenotypic consequences of promoter-mediated transcriptional noise." Molecular Cell 24: 853-865. | ||
Revision as of 00:42, 29 October 2008
Values in µM, min, and mL unless specified.
| Parameter | Value | Source |
| Population and culture | ||
| kn | 3.85e-3 | [1] observed division rate |
| Nmax | 1e8 | [1] |
| V | 1e-11 | [1] |
| kdil | varied | [1] |
| IP binding to receptor | ||
| kassoc | 5e-3 | [1] |
| kdissoc | 4.55e-3 | [1] |
| Synthesis of CRE1, YPD1, SKN7 species | ||
| ks1 | 6.16e-5 | [1] |
| ks2 | 6.00e-4 | [1] |
| ks3 | 2.46e-4 | [1] |
| kdimer | 20 | [1] |
| Phosphorylation/ | ||
| kp1 | 0.1 | [1] |
| kp2 | 1243 | [1] |
| kp3 | 56 | [1] |
| kp-3 | 4.8 | [1] |
| kdp1 | 5.33e-2 | [1] |
| kdp3 | 2.89e-3 | [1] |
| kdp3 | 4.80e-3 | [1] |
| Decay constants | ||
| kd1 | 5.33e-2 | [1] |
| kd2 | 2.89e-3 | [1] |
| kd3 | 4.80e-3 | [1] |
| kdip | 5e-4 | [1] |
| kdgfp | 5.77e-3 | [1] |
| kdtet | 3.85e-3 | Cell division rate (assumed stable) |
| kdckx | <=3.85e-3 | Cell division rate, or lower if diffusion is significant. |
| Basal expression | ||
| kbgfp, kbtet, kbckx | 6e-6 | adapted from [1] |
| ktdim | 1e3 | arbitrary |
| Induced expression | ||
| kgfp | 6e-3 | adapted from [1] |
| ktet | varied | - |
| kckx | varied | - |
| Kg, Kt, Kc | varied | - |
| αg, αt αc | varied | - |
| Ki | 5e-6 | Kass = 2e11 M-1 [2, 3] |
| β | varied | - |
| kipt4 | varied | - |
| IPT4 enzyme kinetics | - | |
| ksip | Varied | - |
| CKX enzyme kinetics | ||
| Km | 40 µM | [ ] |
| kcat | 0.5-1000 s-1 | [ ], [ ] |
References
- Weiss, R. and M.-T. Chen (2005). "Artificial cell-cell communication in yeast Saccharomyces cerevisiae using signaling elements from Arabidopsis thaliana." Nature Biotechnology 23(12): 1551-1555.
- Hillen, W. and C. Berens (1994). "Mechanisms underlying expression of Tn10 encoded tetracycline resistance." Annu. Rev. Microbiol. 48: 345-369.
Kleinschmidt, C., K. Tovar, et al. (1987). "Dynamics of repressor-operator recognition:Tn10 encoded tetracycline resistance control." Biochemistry 27: 1094-1104.
- Schmulling T, Werner T, Riefler M, Krupkova E, Bartrina y Manns I (2003) Structure and function of cytokinin oxidase/dehydrogenase genes of maize, rice, Arabidopsis and other species. J Plant Res 116:241-252
- Laskey, J.G., P. Patterson, et al. (2003). "Rate enhancement of cytokinin oxidase/dehydrogenase using 2,6-dichloroindophenol as an electron acceptor." Plant Growth Regulation 40: 189–196.
- Frebortova, J., M.W. Fraaije, et al. (2004). "Catalytic reaction of cytokinin dehydrogenase: preference for quinones as electron acceptors." Biochem. J. 380: 121–130.
Blake, W., G. Balazsi, et al. (2006). "Phenotypic consequences of promoter-mediated transcriptional noise." Molecular Cell 24: 853-865.
