User:Shai Biran/Practice Proteopedia tutorial shai2
From Proteopedia
< User:Shai Biran(Difference between revisions)
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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. | ||
| - | Green fluorescent protein ( | + | Green fluorescent protein (GFP), originally isolated from the jellyfish Aequorea victoria (PDB entry 1ema), fluorsceses green (509nm) when exposed to blue light (395nm and 475nm). It is one of the most important proteins used in biological research because it can be used to tag otherwise invisible gene products of interest and thus observe their existence, location and movement. |
| - | + | Exploring the Structure | |
| - | GFP is a beta barrel protein with 11 beta sheets. It is a 26.9kDa protein made up of 238 amino acids. The | + | GFP is a beta barrel protein with 11 beta sheets. It is a 26.9kDa protein made up of 238 amino acids. The chromophore, responsible for the fluorescent properties of the protein, is buried inside the beta barrel as part of the central alpha helix passing through the barrel. The chromophore forms via spontaneous cyclization and oxidation of three residues in the central alpha helix: -Thr65 (or Ser65)-Tyr66-Gly67. This cyclization and oxidation creates the chromophore's five-membered ring via a new bond between the threonine and the glycine residues.<ref>PMID:8703075</ref> |
| - | + | ||
== Function == | == Function == | ||
Current revision
Contents |
From the GFP example page -
- Select the two paragraphs of text, and copy them (ctrl-v). Start from “Green Fluorescent Protein... ” and include the heading “Exploring the Structure” as well as both paragraphs.
- Go back to the browser window with your assigned Sandbox page (the one you cleared earlier), and click “edit this page”.
- Insert a blank line just after the automatic text on that page that ends with ‘…to the rescue’
- After the blank line, paste the text that you copied in step (3). Save using the “Save page” button.
Your page should look like this: ↓↓↓↓↓↓↓↓↓↓↓↓
Your Heading Here (maybe something like 'Structure')
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Next
In the next page we will learn to add Section Headings
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
- ↑ Ormo M, Cubitt AB, Kallio K, Gross LA, Tsien RY, Remington SJ. Crystal structure of the Aequorea victoria green fluorescent protein. Science. 1996 Sep 6;273(5280):1392-5. PMID:8703075
