Sandbox423
This sandbox is in use until August 1, 2011 for UMass Chemistry 423. Others please do not edit this page. Thanks!
L Thompson 3/16/11
Team & Protein selection, due 3/30/11
- Start by finding a protein-drug complex with a known structure that interests your team (see assignment sheet instructions). Check the list below to see if another team has already chosen this protein. If not, start a new sandbox page (just try sandbox## in the search box to find an unused number) and add a link for your team/protein to our class list below (use editing button above (Ab) or follow my model).
- Copy the message at the top of this page into your sandbox page to "reserve" this sandbox for this course.
- Find the pdb id for your protein-drug complex in the Protein Data Bank. I looked for the earliest GFP structure I could find in the protein data bank and found 1ema, then followed the directions below to pull up a rotating GFP on this page. You can use the edit button on any page to find out how other users created effects that you see.
- Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load
and display another structure.
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| 1ema, resolution 1.90Å () | |||||||||
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| Non-Standard Residues: | , | ||||||||
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| Resources: | FirstGlance, OCA, RCSB, PDBsum | ||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||
Project completion, due 4/22/11 Each of the 4 team members should complete one of the following 4 requirements for your team project.
1. Introduction -- name of team member
- Introduce the protein function and the disease treated by the drug. This must be written in your own words with citations to your sources.You cannot include a copyrighted figure unless you request information to use it.
2. Overall structure -- name of team member Describe the overall structure of your protein in words and make "green scenes" to illustrate your points. What elements of secondary structure are present (ie 5 alpha helices and 2 beta strands) and how are they organized? 3. Drug binding site -- name of team member Describe features of the drug binding site in words and make "green scenes" to illustrate your points. What interactions stabilize binding of this molecule to the protein. 4. Additional features Describe and use green scenes to illustrate additional features of the protein. What you do here depends on what information is available. If a structure of the protein-substrate complex is available, you could compare protein interactions with the substrate vs. with the drug. If the drug is a transition state inhibitor, explain and illustrate that (include figures describing the reaction).
Credits -- at the end list who did which portion of the project: 1. Introduction -- name of team member 2. Overall structure -- name of team member 3. Drug binding site -- name of team member 4. Additional features -- name of team member