Sandbox423: Difference between revisions
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'''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 | 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). | :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. | :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. | :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. | and display another structure. | ||
{{STRUCTURE_1ema | PDB=1ema | SCENE= }} | {{STRUCTURE_1ema | PDB=1ema | SCENE= }} | ||
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 | |||