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JMS/Sandbox25

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(New page: ==Your Heading Here (maybe something like 'Structure')== <StructureSection load='Conevo_1.pdb' size='340' side='right' caption='Caption for this structure' scene=''> This is a default text...)
Current revision (20:58, 23 April 2015) (edit) (undo)
 
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==Your Heading Here (maybe something like 'Structure')==
==Your Heading Here (maybe something like 'Structure')==
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<StructureSection load='Conevo_1.pdb' size='340' side='right' caption='Caption for this structure' scene=''>
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<StructureSection load='Conevo_1.pdb' size='340' side='right' caption='Caption for this structure' scene='70/700369/Golden_comp_1/1'>
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This is a default text for your page '''JMS/Sandbox25'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.
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You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.
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== Function ==
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== Structural highlights ==
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== Disease ==
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key: w = whale; p = pig; s = seal; c = cat; m = muskrate; g = guniae pig.
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== Relevance ==
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<scene name='70/700369/Golden_comp_1/2'>all areas with possible change in net charge</scene> 8,12,31,53,57,82,84,87,113,116,121,122,132,140.
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== Structural highlights ==
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<scene name='70/700369/Golden_comp_1/3'>only times created a hydrophobic patch</scene> was w53p, c121s and g122m. in every other case removing a hydrophobic patch in each case!
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<scene name='70/700369/Golden_comp_1/4'>funny at 84</scene>, muskrat lost a hydrophic patch but becomes less charged.
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<scene name='70/700369/Golden_comp_1/6'>could have increased the charge AND the net charge at once ... but didn't!</scene> in blue. in red, is a conserved negatively charge aa - could been both or just increase in charge.
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This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.
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<scene name='70/700369/Golden_comp_1/7'>showing lost hydrophobic patch, increase in charge of muskrat 84 in purple, and the three increase in hydophobic patches in green</scene>
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p:w 12,53,87,113,116
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c:s 8,31,57,82,116,121
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g:m 12,82,84,113,122,132
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wm 12,113
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sm 82
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<scene name='70/700369/Golden_comp_1/9'>showing where each evolution step occurred by aquatic mammal.</scene>
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<scene name='70/700369/Globin/1'>dude!!</scene>a backbone of 3 myoglobin pairs, oxy and deoxy wt hemoglobin, and deoxy sickle cell, and the horse myoglobin dimer.
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showing 1mbn with the sites that have evolved. and hbB from sickle, with the e6v in halo. <scene name='70/700369/Globin/2'>funny no i6+ in aquatic mammals.</scene>
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w whale -> r c cat -> q s seal -> N g gunea pig -> o p pig m muskrat
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z oaa oxy y oab
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x doa deoxy w dob v doc u dod
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a-h ds{a-h} sickle cell
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t horse a s horse b
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<scene name='70/700369/Globin/5'>whale horse comparison</scene>
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<scene name='70/700369/Globin/6'>whale to horse comp. emphasizing halves of protein</scene>. next up is interface.
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note the v to i mutation in all three pairs! why?? also, horse is i..
</StructureSection>
</StructureSection>
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pymol sequence alignment
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[[Image:Comp_seq_1.png]]
== References ==
== References ==
<references/>
<references/>

Current revision

Your Heading Here (maybe something like 'Structure')

Caption for this structure

Drag the structure with the mouse to rotate

pymol sequence alignment Image:Comp_seq_1.png

References

  1. ↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
  2. ↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644

Proteopedia Page Contributors and Editors (what is this?)

Joseph M. Steinberger

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