Team:Hong Kong HKUST/Model Alkane mfc

iGem HKUST 2018 Hielo by TEMPLATED

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 modelled chemical and we assume the general n-alkane followed 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) 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

Result

Discussion

From this ASS enzymatic model, we obtained specific pseudo rate constant with respect to alkane equals to

while we noticed that hexane reaction flux in Shewanella is

from the FBA model. The slower prediction in the FBA model might due to limited transport rate of large alkane molecule into the cell.

Assume in 1L batch reactor and general cell density for one unit of OD600 is 0.3gDW/L, the hexane uptake rate is estimated to be

by the following equation,

The ASS enzymatic reaction model predicts alkane conversion rate to reach

when 0.02uM initial alkane concentration is supplied under excess fumarate condition. This provides insight that micro-molar level of alkane is possible to generate current up to 2.189 A/gDW.

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

Parameter	Value	Source
Equivalent cell density to OD600	0.3gDW/L (E.coli)	Bionumbers

ASS enzymatic reaction model
Initial alkane concentration		Input
Initial fumarate concentration		Input
Total alkysuccinate synthase (ASS) enzyme concentration		[2]
Initial Alkylsuccinate concentration	0 mM	Input
	1.49	[2]
	5.88	[2]
	4.42	[2]
	2.06	[2]
	4.63	[2]
	1.49	[2]
	1.23	[2]
	1	[2]
	1.04	[2]
	2.16	[2]
	1.24	[2]
	5.45	[2]
	3.08	[2]
	6.94	[2]
	1.24	[2]
	1.25	[2]

References

[1] A. Herath, B. Wawrik, Y. Qin, J. Zhou and A. Callaghan, "Transcriptional response ofDesulfatibacillum 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.