Difference between revisions of "Team:Aalto-Helsinki/Modeling micelle"
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<p>The product of second to last enzyme of our pathway, butyraldehyde, is toxic to the cell. Because of that and about 15 naturally occurring butyraldehyde-eating enzymes in the cell it is essential for the propane production that Butyraldehyde goes swiftly to the enzyme we want it to go, ADO. As the solution to this our team wanted to put CAR and ADO close together in a micelle so that butyraldehyde would go with more probability to ADO than to any other enzyme. </p> | <p>The product of second to last enzyme of our pathway, butyraldehyde, is toxic to the cell. Because of that and about 15 naturally occurring butyraldehyde-eating enzymes in the cell it is essential for the propane production that Butyraldehyde goes swiftly to the enzyme we want it to go, ADO. As the solution to this our team wanted to put CAR and ADO close together in a micelle so that butyraldehyde would go with more probability to ADO than to any other enzyme. </p> | ||
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<p>We have made a <a href="https://2015.igem.org/Team:Aalto-Helsinki/Modeling_synergy">model of effectiveness of having enzymes close together</a>, but our team also wanted to know if the micelle structure was possible at the first place. We know (references as links for this statement!) that it is possible to form the micelle without any proteins at the end and with green fluorecent protein (Gfp), but could CAR and ADO be part of this kind of structure? </p> | <p>We have made a <a href="https://2015.igem.org/Team:Aalto-Helsinki/Modeling_synergy">model of effectiveness of having enzymes close together</a>, but our team also wanted to know if the micelle structure was possible at the first place. We know (references as links for this statement!) that it is possible to form the micelle without any proteins at the end and with green fluorecent protein (Gfp), but could CAR and ADO be part of this kind of structure? </p> | ||
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<h2 id="micellestructure">Micelle structure</h2> | <h2 id="micellestructure">Micelle structure</h2> | ||
+ | <figure style="float:right;margin-left:20px;"> | ||
+ | <img src="https://static.igem.org/mediawiki/2015/d/da/Aalto-Helsinki_Micelle_structure.png" style="width:200px;"/> | ||
+ | <figcaption>2d simplification of micelle</figcaption> | ||
+ | </figure> | ||
<p>The micelle is formed by amphiphilic proteins that have both hydrophilic and hydrophobic parts. At the end of hydrophilic part there is short protein, a linker that attaches CAR or ADO to the amphiphilic part.</p> | <p>The micelle is formed by amphiphilic proteins that have both hydrophilic and hydrophobic parts. At the end of hydrophilic part there is short protein, a linker that attaches CAR or ADO to the amphiphilic part.</p> | ||
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<p>Amphiphilic proteins are 10 nm long, 5 nm for both hydrophilic and hydrophobic parts. (Here where we got amphiphilic proteins sizes.) The linker (here link for more info about this. Structure and such, does lab have that somewhere?) consists of eight amino acids, for which the maximum lengths are 3,8Å. From this we can calculate that at most the length of one linker is 2,8 nm. If the linker would form α-helical structure, then the length for one peptide would be about 1,5 Å so the one linker would be 1,2 nm long. (we need some source for the Å-lengths) However, we can estimate that the linkers are straight, since when running the structure in <a href="http://mobyle.rpbs.univ-paris-diderot.fr">peptide structure prediction software</a> doesn't yield strong folding or helical structure. CAR uses two of these linkers and ADO one. </p> | <p>Amphiphilic proteins are 10 nm long, 5 nm for both hydrophilic and hydrophobic parts. (Here where we got amphiphilic proteins sizes.) The linker (here link for more info about this. Structure and such, does lab have that somewhere?) consists of eight amino acids, for which the maximum lengths are 3,8Å. From this we can calculate that at most the length of one linker is 2,8 nm. If the linker would form α-helical structure, then the length for one peptide would be about 1,5 Å so the one linker would be 1,2 nm long. (we need some source for the Å-lengths) However, we can estimate that the linkers are straight, since when running the structure in <a href="http://mobyle.rpbs.univ-paris-diderot.fr">peptide structure prediction software</a> doesn't yield strong folding or helical structure. CAR uses two of these linkers and ADO one. </p> |
Revision as of 07:52, 4 August 2015