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Team:TU Delft-Leiden/Modeling/EET/Deterministic
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Since localization is an important part of the assembly process, we will consider compounds in different areas of the cell as different species in our model. We will distinguish between the cytosol (abbreviated as cyt), the periplasm (peri), the inner membrane (mem1) and the outer membrane (mem2). | Since localization is an important part of the assembly process, we will consider compounds in different areas of the cell as different species in our model. We will distinguish between the cytosol (abbreviated as cyt), the periplasm (peri), the inner membrane (mem1) and the outer membrane (mem2). | ||
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An important part of the cytochromes that form part of the Mtr complex are heme molecules. Heme molecules enable the MtrA and MtrC proteins to accept and donate electrons. Heme is formed in the cytosol in a series of steps from the compound δ-aminolevunlinic acid (δ-ALA). After the heme is formed, it is transported to the periplasm. This process is catalyzed by the ccm cluster (ccmAH), which is located in the inner membrane [1]. These processes are described by reactions (1) and (2): | An important part of the cytochromes that form part of the Mtr complex are heme molecules. Heme molecules enable the MtrA and MtrC proteins to accept and donate electrons. Heme is formed in the cytosol in a series of steps from the compound δ-aminolevunlinic acid (δ-ALA). After the heme is formed, it is transported to the periplasm. This process is catalyzed by the ccm cluster (ccmAH), which is located in the inner membrane [1]. These processes are described by reactions (1) and (2): | ||
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Revision as of 23:51, 26 September 2014
Deterministic Model of the EET Module
One of the parts of our project is to enable cells to transport electrons to the extracellular environment, thus generating a current, as a response to a signal. To do this, the cell needs EET-complexes (Extracellular Electron Transport complexes). The EET complex consists of three proteins: MtrA, a cytochrome on the inside of the outer membrane, MtrB, a β-barrel protein located in the outer membrane, and MtrC, another cytochrome, located on the cell surface. This complex enables the cell to transport electrons from the cytoplasm of the cell to the extracellular environment [1].
The assembly of the trans-membrane EET complex depends on many factors other than transcriptional and translational control, as it requires a large amount of post-translational modifications. In this section, we will set up a simplified model of this assembly process, largely based on section 1.3 of the thesis of Jensen [1]. Our goal is to predict how many EET complexes are formed under different initial conditions.
In our modelling of the assembly of the EET complex, we will, in addition to the assembly mechanism, also focus on the apparent reduced cell viability. Jensen proposes two possible explanations for this: the formation of cytosolic aggregates, and reduced membrane integrity due to the high amount of trans-membrane protein complexes. We speculate that the specific carbon source (L-lactate) needed to enable extracellular electron transport might also reduce cell viability. For more information on this, please refer to Flux Balance Analysis.
Contents
Extensive Model
Since localization is an important part of the assembly process, we will consider compounds in different areas of the cell as different species in our model. We will distinguish between the cytosol (abbreviated as cyt), the periplasm (peri), the inner membrane (mem1) and the outer membrane (mem2).
An important part of the cytochromes that form part of the Mtr complex are heme molecules. Heme molecules enable the MtrA and MtrC proteins to accept and donate electrons. Heme is formed in the cytosol in a series of steps from the compound δ-aminolevunlinic acid (δ-ALA). After the heme is formed, it is transported to the periplasm. This process is catalyzed by the ccm cluster (ccmAH), which is located in the inner membrane [1]. These processes are described by reactions (1) and (2):
Simplified Model
