User:Shai Biran/Practice Proteopedia tutorial shai4

From Proteopedia

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Contents 1 Adding Section Headings 2 Your Heading Here (maybe something like 'Structure') 3 Next 4 References

Adding Section Headings

1. In your assigned Sandbox page, now displaying your new text, click “edit this page”.
2. We want to make the word “GFP” bold. Select the word “GFP" and click on the button in the toolbar above the text-editing area with a big “B”.
3. The result should be three single quotation marks on either side of the word “GFP” like so: ’’’GFP’’’
4. Now make “1ema” into an interwiki link, so that it leads to the Proteopedia page for the PDB entry 1ema. Do this by selecting the text “1ema” and clicking on the button in the toolbar above the text-editing area with a big, #underlined, blue “Ab”.
5. The result should be two square inward-facing brackets on either side of the word “1ema”. It should look like this: 1ema
6. Save the page using the “Save page” button.

Your page should look like this: ↓↓↓↓↓↓↓↓↓↓↓↓

Your Heading Here (maybe something like 'Structure')

spinqualitylabelsall models Caption for this structure Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image This is a default text for your page Sandbox. 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 [1] or to the article describing Jmol [2] to the rescue. Introduction 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 , 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.[3] This is a sample scene created with SAT to by Group, and another to make 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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In the next page we will learn about Bold and Interwiki links

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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
3. ↑ 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