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Model Parameters
See: Unit conversions and scratch work.
Vitamin A
| Var | Description | Turnover rate | Km | Citation |
| GGPP_synthase_endo | BTS1 GGPP synthase, endogenous to S.c. | 0.025 1/s | 0.0032 mM | [1] |
| phytoene_synth | Phytoene synthase (Capsicum annuum) | 0.0526 1/s | 0.003 mM | [2] |
| carotene_desat_1 | Carotene desaturase with substrate all-trans-zeta-carotene (Capsicum annuum) | 11.9665 1/s | 0.0084 mM | [3] |
| carotene_desat_2 | Carotene desaturase with substrate neurosporene (Capsicum annuum) | 0.9703 1/s | .009 mM | [4] |
| lycopene_cyc | Lycopene beta-cyclase (Erwinia uredova) | .00038623 1/s | .0018 mM | [5] |
Vitamin C
| Var | Description | Turnover rate | Km | Citation |
| GDP_D_mannose_epimerase | GDP-D-mannose-3",5"-epimerase (from Arabidopsis thaliana, native enzyme) | 0.041 1/s | 0.0045 mM | [6] |
| GDP_L_Gal_phosphorylase | GDP-L-Gal phosphorylase (from Arabidopsis thaliana) | 15 1/s | 0.01 mM | [7] |
| Gal_P_phosphatase | L-Gal-1-P phosphatase | 6 1/s | 0.107 mM | [8] |
| D_Ara_dehydrogenase | D-arabinose dehydrogenase (from Saccharomyces cerevisiae) | 125 1/s | 180 mM | [9], [10] |
| D_Ara_Lac_oxidase | D-arabinono-1,4-lactone oxidase (from Candida albicans) | 134 1/s | 53.7 mM | [11] |
Gene Expression
| Var | Description | Value | Units | Citation |
| RNAP falloff (E. coli) | 1 | 1/s | [12] | |
| Ribosome falloff (E. coli) | 0.01 | 1/s | [13] | |
| RNA degradation (E. coli) | 0.0058 | 1/s | [14] | |
| Mean haploid yeast volume (S. cerevisiae) | 37 | 1/μm3 | [15] | |
| Ribosome binding (E. coli) | 0.00016611 | 1/s | [16] |
[1]Lo, C.-H., Chang, Y.-H., Wright, J. D., Chen, S.-H., Kan, D., Lim, C., & Liang, P.-H. (2009). Combined experimental and theoretical study of long-range interactions modulating dimerization and activity of yeast geranylgeranyl diphosphate synthase. Journal of the American Chemical Society, 131(11), 4051-62. doi:10.1021/ja808699c
[2]Dogbo, O., Laferriére, A. , DʼHarlingue, A. , & Camara, B. (1988). Carotenoid biosynthesis: Isolation and characterization of a bifunctional enzyme catalyzing the synthesis of phytoene. PNAS 1988.
[3],[4]Breitenbach, J., & Sandmann, G. (2005). zeta-Carotene cis isomers as products and substrates in the plant poly-cis carotenoid biosynthetic pathway to lycopene. Planta, 220(5), 785-93. doi: 10.1007/s00425-004-1395-2.
[5]Schnurr, G., Misawa, N., & Sandmann, G. (1996). Expression, purification and properties of lycopene cyclase from Erwinia uredovora. The Biochemical journal.
[6]Wolucka, B., & Van Montagu, M. (2003). GDP-mannose 3',5'-epimerase forms GDP-L-gulose, a putative intermediate for the de novo biosynthesis of vitamin C in plants. The Journal of Biological Chemistry, 278(48), 47483, 90.
[7]Dowdle, J., Ishikawa, T., Gatzek, S., Rolinski, S., & Smirnoff, N. (2007). Two genes in Arabidopsis thaliana encoding GDP-L-galactose phosphorylase are required for ascorbate biosynthesis and seedling viability. The Plant journal : for cell and molecular biology, 52(4), 673-89.
[8]Torabinejad, J., Donahue, J. L., Gunesekera, B. N., Allen-Daniels, M. J., & Gillaspy, G. E. (2009). VTC4 is a bifunctional enzyme that affects myoinositol and ascorbate biosynthesis in plants. Plant physiology, 150(2), 951-61. doi:10.1104/pp.108.135129
[9]Amako, K., Fujita, K., Shimohata, T., Hasegawa, E., Kishimoto, R., & Goda, K. (2006). NAD+-specific D-arabinose dehydrogenase and its contribution to erythroascorbic acid production in Saccharomyces cerevisiae. Federation of European Biochemical Societies Letters, 580(27), 6428-34.
[10]Kim, S., Huh, W., Lee, B., & Kang, S. (1998). D-Arabinose dehydrogenase and its gene from Saccharomyces cerevisiae. Biochimica et Biophysica Acta, 1429, 29-39.
[11]Kim, S., Huh, W., Kim, J., Hwang, S., & Kang, S. (1996). D-arabinose dehydrogenase and biosynthesis of erythroascorbic acid in Candida albicans. Biochimica et Biophysica Acta, 1297(1), 1-8.
[12],[13],[14],[16]Ty Thompson. Rule-Based Modeling of BioBrick Parts. http://www.rulebase.org/books/184351-Rule-Based-Modeling-of-BioBrick-Parts.
[15]Tyson CB, Lord PG, Wheals AE. Dependency of size of Saccharomyces cerevisiae cells on growth rate. J Bacteriol. 1979 Apr138(1):92-8
