Difference between revisions of "Team:Aalto-Helsinki/Modeling micelle"

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<h1 style="text-align:center">Under construction</h1>
 
  
 
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<h2> Introduction </h2>
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<h1> Introduction </h1>
  
 
<p>--Picture of the pathway here, CAR, ADO and butyraldehyde highlighted to clarify what we are talking about.--</p>
 
<p>--Picture of the pathway here, CAR, ADO and butyraldehyde highlighted to clarify what we are talking about.--</p>
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<h2>Geometrical approach</h2>
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<h1>Geometrical approach</h1>
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<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. (--picture of micelle somewhere near!--)</p>
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<p>(Here where we got amphiphilic proteins sizes.) The <a>linker (here link for more info about this. Structure and such, does lab have that somewhere?)</a> 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 $\alpha$-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. </p>
  
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<p>Here geometry calculations. Perhaps as subcategories of where we got the values and why we can use those and then other category of the calculations.</p>
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<p>The mass of CAR is <a href = "http://www.uniprot.org/uniprot/B2HN69">127 797 DA</a> and the mass of ADO is <a href="http://www.rcsb.org/pdb/explore/explore.do?structureId=4KVS">27 569.15 Da</a>. Based on this information and <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3055910/">this paper</a> we can calculate that if the enzymes were spheres, their radiuses would be 3,5 nm for CAR and 2 nm for ADO. (do we need more info about these calculations here?)</p>
  
  
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<h2>Discussion and restrictions of our model</h2>
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<h1>Discussion</h1>
  
 
<p>Here text about how we didn't take into account any forces and how this model could be improved.</p>
 
<p>Here text about how we didn't take into account any forces and how this model could be improved.</p>

Revision as of 08:13, 29 July 2015

Introduction

--Picture of the pathway here, CAR, ADO and butyraldehyde highlighted to clarify what we are talking about.--

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.

--Basic picture of micelle to explain what is micelle here? Or is it essential since we explain it at the next part?--

We have made a model of effectiveness of having enzymes close together, 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, but could CAR and ADO be part of this kind of structure?

Geometrical approach

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. (--picture of micelle somewhere near!--)

(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 $\alpha$-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 peptide structure prediction software doesn't yield strong folding or helical structure.

The mass of CAR is 127 797 DA and the mass of ADO is 27 569.15 Da. Based on this information and this paper we can calculate that if the enzymes were spheres, their radiuses would be 3,5 nm for CAR and 2 nm for ADO. (do we need more info about these calculations here?)

Discussion

Here text about how we didn't take into account any forces and how this model could be improved.