JMS/Sandbox/SMART HLA
From Proteopedia
(Difference between revisions)
(New page: ==Your Heading Here (maybe something like 'Structure')== <StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''> This is a default text for you...) |
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==Your Heading Here (maybe something like 'Structure')== | ==Your Heading Here (maybe something like 'Structure')== | ||
| - | <StructureSection load=' | + | <StructureSection load='1mbn' size='340' side='right' caption='Caption for this structure' scene=''> |
This is a default text for your page '''JMS/Sandbox/SMART HLA'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs. | This is a default text for your page '''JMS/Sandbox/SMART HLA'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs. | ||
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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== Structural highlights == | == Structural highlights == | ||
| - | + | <scene name='70/705122/Myoglobin_pairs/1'>aligned sperm whale w, pig p, grey seal s, and cat c. | |
| - | + | w and p are a group, and s and c, are a group.</scene> | |
| + | <br/><br/><scene name='70/705122/Myoglobin_pairs/2'>general disk like structure of myoglobin, with heme ligand.</scene> | ||
| + | <br/><br/><scene name='70/705122/Myoglobin_pairs/3'>hydrophobic residues (gly, ala,val,leu,ile,pro,phe,met,trp), that are on surface</scene> | ||
| + | <br/><br/><scene name='70/705122/Hydrophobic_core/1'>hydrophic residues only in the core</scene> | ||
| + | <br/><br/><scene name='70/705122/Myoglobin_pairs/4'>hydrophic residues only in the core</scene> | ||
| + | <br/><br/><scene name='70/705122/Myoglobin_pairs/5'>general statement that w and p differ in several amino acids</scene> | ||
| + | <br/><br/><scene name='70/705122/Sickle_hemoglobin_chain_close/1'>hemoglobin as classic case of hydrophobic patch based aggregation</scene> | ||
| + | <br/><br/><scene name='70/705122/Sickle_hemoglobin_chain_close/2'>zoomed out. hemoglobin as classic case of hydrophobic patch based aggregation</scene> | ||
| + | <br/><br/><scene name='70/705122/Myoglobin_pairs/6'>divergent charged aa leading to delta 4</scene> | ||
| + | <br/><br/><scene name='70/705122/Myoglobin_pairs/7'>stick/wireframe. divergent charged aa leading to delta 4</scene> | ||
| + | <br/><br/><scene name='70/705122/Myoglobin_pairs/8'>mutations not in site of heme, so not o-binding. rather, net charge change leading to solubility increase.</scene> | ||
| + | <br/><br/><scene name='70/705122/Myoglobin_pairs/9'>no negative to hydrophobic mutations for pig to whale, which would have increased net charge at the expense of creating hydrophobic patches.</scene> | ||
| + | <br/><br/><scene name='70/705122/Myoglobin_pairs/10'>with halos. no negative to hydrophobic mutations for pig to whale, which would have increased net charge at the expense of creating hydrophobic patches.</scene> | ||
| + | <br/><br/><scene name='70/705122/Sickle_hemoglobin_chain_close/2'>zoomed out. hemoglobin as classic case of hydrophobic patch based aggregation</scene> | ||
| + | <br/><br/><scene name='70/705122/Myoglobin_pairs/11'>mutations overwhelming occur on the surface.</scene> | ||
</StructureSection> | </StructureSection> | ||
| + | |||
| + | all switches: 1,4,12,15,27,28,35,51,53,66,74,87,101,123,126,128,132,140,142,151 | ||
| + | <br/><br/> | ||
| + | charge switches: 12,53,87,113,116 | ||
| + | |||
== References == | == References == | ||
<references/> | <references/> | ||
Current revision
Your Heading Here (maybe something like 'Structure')
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all switches: 1,4,12,15,27,28,35,51,53,66,74,87,101,123,126,128,132,140,142,151
charge switches: 12,53,87,113,116
References
- ↑ 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
- ↑ 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
