Team:Oxford/what are microcompartments
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<h1>Introduction: what are microcompartments?</h1> | <h1>Introduction: what are microcompartments?</h1> | ||
- | In order to produce an efficient bioremediation system, we had to think outside the box and not only improve the expression and function proteins we were working with, but optimise the bacteria themselves for degradation of toxic compounds. We found that microcompartments, which are explained on this page, are ideally suited for our purposes. | + | In order to produce an efficient bioremediation system, we had to think outside the box and not only improve the expression and function proteins we were working with, but optimise the bacteria themselves for the degradation of toxic compounds. We found that microcompartments, which are explained on this page, are ideally suited for our purposes. |
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Microcompartments are proteinaceous capsules that have only recently been discovered to exist in a wide range of bacteria. They contain enzymes required for a particular metabolic process. The carboxysome is a particularly well-studied example of a specialised microcompartment, and is shown here as a schematic diagram (S. Frank et al, 2013). | Microcompartments are proteinaceous capsules that have only recently been discovered to exist in a wide range of bacteria. They contain enzymes required for a particular metabolic process. The carboxysome is a particularly well-studied example of a specialised microcompartment, and is shown here as a schematic diagram (S. Frank et al, 2013). | ||
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- | The Pdu microcompartment that we are using in our project is composed of several proteins encoded in an operon consisting of the genes pduA, -B, -T, -U, -N, -J, -K. These are expressed in various stoichiometries to form different polyhedral shapes with a diameter of | + | The Pdu microcompartment that we are using in our project is composed of several proteins encoded in an operon consisting of the genes pduA, -B, -T, -U, -N, -J, -K. These are expressed in various stoichiometries to form different polyhedral shapes with a diameter of 200-250 nm. The faces of the polyhedron are formed by the hexagonal shell proteins PduA, PduB, and PduJ, while PduN is thought to form the vertices (Joshua B. Parsons et al, 2010). |
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We are expressing the pdu-ABTUNJK codon in E. coli in the pUNI vector, shown below, which we received from the University of Dundee iGEM team. | We are expressing the pdu-ABTUNJK codon in E. coli in the pUNI vector, shown below, which we received from the University of Dundee iGEM team. | ||
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- | The pdu microcompartments which we are introducing into our bacteria are very similar in shape and structure to carboxysomes | + | The pdu-encoded microcompartments which we are introducing into our bacteria are very similar in shape and structure to carboxysomes, so we used their structure as a starting point for predicting the microcompartment structure. Thus, our initial carboxysome-based structure was a perfect icosahedron with diameter 120nm as established from literature. Following this, we further developed the model by noting that many of the images taken of pdu microcompartments suggest slight and random deviations from an icosahedron. |
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Taking this into consideration, we have developed a simulation which generates pdu microcompartment structures by starting with a regular icosahedron and randomly distorting the location of each co-ordinate by up to 5% of total edge length. | Taking this into consideration, we have developed a simulation which generates pdu microcompartment structures by starting with a regular icosahedron and randomly distorting the location of each co-ordinate by up to 5% of total edge length. | ||
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- | The aim of this model was to predict a theoretical maximum number of enzyme molecules that can be packed into a single microcompartment. To get a first estimate, without taking into consideration whether this volume of protein would interrupt the biological processes in the cell, we approached | + | The aim of this model was to predict a theoretical maximum number of enzyme molecules that can be packed into a single microcompartment. To get a first estimate, without taking into consideration whether this volume of protein would interrupt the biological processes in the cell, we approached the problem volumetrically. |
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- | Due to the complexity of the enzyme movements and their interactions, | + | Due to the complexity of the enzyme movements and their interactions, we simplified their structures by approximating them as ellipsoids with axes lengths calculated through modelling the monomers and predicting the structures of the FdhA tetramer and DcmA hexamer respectively. |
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<img src="https://static.igem.org/mediawiki/2014/1/12/Oxford_Leroy_pic1.png" style="float:left;position:relative; width:100%;" /> | <img src="https://static.igem.org/mediawiki/2014/1/12/Oxford_Leroy_pic1.png" style="float:left;position:relative; width:100%;" /> | ||
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- | Once treated as ellipsoids, the problem was then reduced to the classical ‘sand packing’ problem. Because the dimensions of these proteins was substantially smaller than the icosahedron (by approximately a factor of 20 in every dimension), | + | Once treated as ellipsoids, the problem was then reduced to the classical ‘sand packing’ problem. Because the dimensions of these proteins was substantially smaller than the icosahedron (by approximately a factor of 20 in every dimension), we assumed that the geometry of the container i.e. the microcompartment, was not significant. |
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Another assumption made in these calculations was that the enzymes could be treated as homogenous. They are of very similar dimensions, varying by no more than 20-30% on any axis, and also have very similar sphericities- the key variable in determining the packing efficiency of the molecules. Sphericity is defined as: | Another assumption made in these calculations was that the enzymes could be treated as homogenous. They are of very similar dimensions, varying by no more than 20-30% on any axis, and also have very similar sphericities- the key variable in determining the packing efficiency of the molecules. Sphericity is defined as: | ||
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<h1>Results</h1> | <h1>Results</h1> | ||
- | Because enzyme-enzyme interactions are very difficult to predict, and it is difficult to assign an analogous friction factor to their movements, | + | Because enzyme-enzyme interactions are very difficult to predict, and it is difficult to assign an analogous friction factor to their movements, we took the average of the predicted porosities across a range of different friction factors and alternative methods to give a predicted porosity of 37.3%. |
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Combining this information with the relative expression rates of the two enzymes, we predict that: | Combining this information with the relative expression rates of the two enzymes, we predict that: |
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