Team:SydneyUni Australia/Modelling Model

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Revision as of 06:18, 28 October 2013

A Schematic of the Engineered Metabolic Pathway:

The above figure is a simplified schematic of the two metabolic pathways which are considered. The symbols in squares signify the intracellular concentrations of the associated metabolite (Greek letters) or enzyme (capital English letters). These symbols will be used throughout the analysis.

ODE Model

Shown below are the two systems of ODEs we used to model each pathway.

The non-monooxygenase pathway (with dhlA (A) and adh1b1*2 (B)).

The monooxygenase pathway (with p450 (C)).

Generally, each line represents how the metabolic intermediate changes over time; this is dictated by the relative rate at which the intermediate is formed vs. the rate at which it is used/removed.

The two above systems of ODEs were used to model two things:

1. The rate at which extracellular DCA is removed from solution (given the number of cells in solution) . This is considering the rate at which DCA crosses the plasma membrane (from solution to cytoplasm) of all cells in solution.

2. The rate at which the intracellular concentrations of the metabolic intermediates change over time within a single cell. This considers the relative activities of the enzymes of the metabolic pathway.

The symbols A, B, C, D & E represent the intracellular enzyme concentrations of 1,2-Dichloroethane Dechlorinase, Alcohol Dehydrogenase, Cytochrome p450, Chloroacetaldehyde Dehydrogenase and Haloacetate Dehydrogenase respectively. They have units of mM.

The symbols α_in, β, γ, δ and ε represent the intracellular concentrations of the metabolic intermediates DCA, 2-chloroethanol, chloroacetaldehyde, chloroacetate and glycolate respectively. They have units mM. α_out represents the extracellular concentration of DCA, i.e. the concentration of DCA in solution. It has units mM.

The symbol Ψ represents the concentration of cells in solution and has units cells/mL.

The function J(α_out,α_in) represents the rate which extracellular DCA moves across the plasma membrane and into the single cell (the flux rate). It is a function of the extra and intracellular concentrations of DCA and has a value of surface area per time m²s^-1. The value S represents the average surface area of the cellular membrane of E. coli. By multiplying S by J one achieves the total amount of DCA flowing into a single cell per unit time. The total amount of DCA flowing from solution is achieved by multiplying Ψ by S and J.

General Information regarding the Enzymes Involved in the Metabolic Pathway

Enzyme	Gene	Symbol	Constants	Substrate	Product	Ref
1,2-Dichloroethane Dechlorinase	dhlA	A	K_{M A} = 0.53 mM, k_{cat A} = 3.3 s^-1	DCA (α_in)	2-chloroethanol (β)	[1]
Alcohol Dehydrogenase	Adhlb 1/2*	B	K_{M B} = 0.94 mM, k_{cat B} = 0.0871 s^-1	2-chloroethanol (β)	chloroacetaldehyde (γ)	[2]
p450	p450	C	K_{M C} = 0.120 mM, k_{cat C} = 0.0113 s^-1	DCA (α_in)	chloroacetaldehyde (γ)	[3]
Chloroacetaldehyde Dehydrogenase	aldA	D	K_{M D} = 0.06mM, k_{cat D} = 0.60 s^-1	chloroacetaldehyde (γ)	chloroacetate (δ)	[4]
Haloacetate Dehydrogenase	dhlB	E	K_{M E} = 20 mM, k_{cat E} = 25.4 s^-1	chloroacetate (δ)	glycolate (ε)	[5]

A table that summarises the enzymes that compramise the engineered metabolic pathways. The constants presented were (painstakingly) obtained from the literature (referenced).

@@ Line 63: / Line 63: @@
 !Enzyme !! Gene !! Symbol !! Constants !! Substrate !! Product !! Ref
 |-
-|1,2-Dichloroethane Dechlorinase || dhlA || A || K<sub>M A</sub> = 0.53 mM, k<sub>cat A</sub> = 3.3 s<sup>-1</sup> || DCA || 2-chloroethanol || [1]
+|1,2-Dichloroethane Dechlorinase || dhlA || A || K<sub>M A</sub> = 0.53 mM, k<sub>cat A</sub> = 3.3 s<sup>-1</sup> || DCA (α<sub>in</sub>)|| 2-chloroethanol (β)|| [1]
 |-
-|Alcohol Dehydrogenase || Adhlb 1/2* || B || K<sub>M B</sub> = 0.94 mM, k<sub>cat B</sub> = 0.0871 s<sup>-1</sup>  || 2-chloroethanol || chloroacetaldehyde || [2]
+|Alcohol Dehydrogenase || Adhlb 1/2* || B || K<sub>M B</sub> = 0.94 mM, k<sub>cat B</sub> = 0.0871 s<sup>-1</sup>  || 2-chloroethanol (β) || chloroacetaldehyde (γ) || [2]
 |-
-|p450 || p450 || C || K<sub>M C</sub> = 0.120 mM, k<sub>cat C</sub> = 0.0113 s<sup>-1</sup>  || DCA || chloroacetaldehyde || [3]
+|p450 || p450 || C || K<sub>M C</sub> = 0.120 mM, k<sub>cat C</sub> = 0.0113 s<sup>-1</sup>  || DCA (α<sub>in</sub>)|| chloroacetaldehyde (γ) || [3]
 |-
-|Chloroacetaldehyde Dehydrogenase || aldA || D || K<sub>M D</sub> = 0.06mM, k<sub>cat D</sub> = 0.60 s<sup>-1</sup>  || chloroacetaldehyde || chloroacetate || [4]
+|Chloroacetaldehyde Dehydrogenase || aldA || D || K<sub>M D</sub> = 0.06mM, k<sub>cat D</sub> = 0.60 s<sup>-1</sup>  || chloroacetaldehyde (γ)|| chloroacetate (δ) || [4]
 |-
-|Haloacetate Dehydrogenase || dhlB || E || K<sub>M E</sub> = 20 mM, k<sub>cat E</sub> = 25.4 s<sup>-1</sup>  || chloroacetate || glycolate || [5]
+|Haloacetate Dehydrogenase || dhlB || E || K<sub>M E</sub> = 20 mM, k<sub>cat E</sub> = 25.4 s<sup>-1</sup>  || chloroacetate (δ) || glycolate (ε)|| [5]
 |}
 </center>
-A table that summarises the enzymes that we used in both of the engineered metabolic pathways. The constants presented were (painstakingly) obtained from the literature (referenced).
+A table that summarises the enzymes that compramise the engineered metabolic pathways. The constants presented were (painstakingly) obtained from the literature (referenced).