Difference between revisions of "Team:Hong Kong HKUST/Model Alkane mfc"

ASS enzymatic reaction model
Formation of alkylsuccinate is the first step of alkane metabolism. The enzyme involved was reported as alkylsuccinate synthase[1].

The overall enzymatic reaction:

The mechanism of this enzymatic reaction includes three main steps, H-abstraction, fumarate addition and thiyl radical regeneration [2]. This model used n-butane as the modeled chemical and we assumed the general n-alkane will follow similar reaction mechanism. Each reaction was treated as a sub-mechanism consisting of 3 steps, reactant complex (RC) formation, transition state (TS) crossing and product separation. The following are the rate constants involved in the sub-mechanism

The H-abstraction step (1) are modelled as,

The fumarate addition step (2) are modelled as,

The thiyl radical regeneration step (3) are modelled as,

Assume

(1)   The system is in a closed homogeneous batch reactor with infinite capacity

(2)   The reaction proceeds until final alkane concentration is negligible

(3)   Each step of the mechanism follows the Law of mass action

The reaction rates of each component are modelled as a system of ODE

Assume pseudo-steady state for the enzyme and intermediates, such that

Figure 3. Alkane degradation rate catalyzed by alkylsuccinate synthase

(Please refer to this document for the list of parameters used.)

References:

ASS Enzymatic Alkane Degradation

1. A. Herath, B. Wawrik, Y. Qin, J. Zhou and A. Callaghan, "Transcriptional response of Desulfatibacillum alkenivoransAK-01 to growth on alkanes: insights from RT-qPCR and microarray analyses", FEMS Microbiology Ecology, vol. 92, no. 5, p. fiw062, 2016.
2. V. Bharadwaj, S. Vyas, S. Villano, C. Maupin and A. Dean, "Unravelling the impact of hydrocarbon structure on the fumarate addition mechanism – a gas-phase ab initio study", Physical Chemistry Chemical Physics, vol. 17, no. 6, pp. 4054-4066, 2015.

FBA

1. Orth, J.D., Thiele, I. and Palsson, B.(2010). What is Flux Balance Analysis? Nature Biotechnology, [1112-9778], Volume:28, Issue:3, Page:245, doi:10.1038/nbt.1614 Available at https://www.nature.com/articles/nbt.1614
2. 2012.igem.org. (2015). Team: NTU-Singapore/Modeling. [online] Available at: https://2015.igem.org/Team:NTU-Singapore/Modeling
3. L. Mao and W. Verwoerd, "Theoretical exploration of optimal metabolic flux distributions for extracellular electron transfer by Shewanella oneidensisMR-1", Biotechnology for Biofuels, vol. 7, no. 1, 2014.
4. G. Newton, S. Mori, R. Nakamura, K. Hashimoto and K. Watanabe, "Analyses of Current-Generating Mechanisms of Shewanella loihica PV-4 and Shewanella oneidensis MR-1 in Microbial Fuel Cells", Applied and Environmental Microbiology, vol. 75, no. 24, pp. 7674-7681, 2009.
5. L. Berthe-Corti and W. Ebenhöh, "A mathematical model of cell growth and alkane degradation in Wadden Sea sediment suspensions", Biosystems, vol. 49, no. 3, pp. 161-189, 1999.
6. B. Virdis, S. Freguia, R. Rozendal, K. Rabaey, Z. Yuan and J. Keller, "Microbial Fuel Cells", Treatise on Water Science, pp. 641-665, 2011.
7. M. Pandurangachar, B. Kumara Swamy, B. Chandrashekar, Ongera Gilbert, Sathish Reddy and B. Sherigara, "Electrochemical Investigations of Potassium Ferricyanide and Dopamine by 1-butyl-4-methylpyridinium tetrafluoro borate Modified Carbon Paste Electrode: A Cyclic Voltammetric Study",International Journal of Electrochemical Science, vol. 5, no. 8, pp. 1187-1202, 2010.
8. U. Schröder, "Anodic electron transfer mechanisms in microbial fuel cells and their energy efficiency", Phys. Chem. Chem. Phys., vol. 9, no. 21, pp. 2619-2629, 2007.