Difference between revisions of "Team:Aalto-Helsinki/Modeling micelle"
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<p>--picture of micelle somewhere near!--</p> | <p>--picture of micelle somewhere near!--</p> | ||
− | <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> | + | <p>Amphiphilic proteins are 10 nm long, 5 nm for both hydrophilic and hydrophobic parts. (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> |
<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> | <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>Calculations</h2> | <h2>Calculations</h2> | ||
− | <p>We can estimate how many amphiphilic proteins we can theoretically fit in one micelle by calculating how big solid angles they take with attached enzymes. The easiest way to estimate the solid angles is to think the amphiphilic proteins linked with enzymes as cones. | + | <p>We can estimate how many amphiphilic proteins we can theoretically fit in one micelle by calculating how big solid angles they take with attached enzymes. The easiest way to estimate the solid angles is to think the amphiphilic proteins linked with enzymes as cones. We can calculate the solid angle $\Omega$ for these by \[ \Omega = 2\pi \left( 1-\cos(\theta) \right), \] where $\theta$ is half of the apex angle. So for CAR we get \[ \Omega_{CAR} = 2\pi \left( 1-\cos\left( \arctan\left(\frac{3.5}{14.1}\right)\right) \right) \approx 0.185 \text{ rad} \] and for ADO \[ \Omega_{ADO} = 2\pi \left( 1-\cos\left( \arctan\left(\frac{2}{9.8}\right)\right) \right) \approx 0.127 \text{ rad}.\]</p> |
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+ | <p>--picture of this cone-like structure--</p> | ||
<h1>Discussion</h1> | <h1>Discussion</h1> |
Revision as of 10:54, 29 July 2015