Sandbox423: Difference between revisions
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'''Team & Protein selection, due 3/30/11''' | '''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). | :Form teams of 4 people; include both chemistry and chemical engineering majors on each team. 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. | ||
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:Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load | :Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load | ||
and display another structure. | and display another structure. | ||
== Overall Structure == | |||
{{STRUCTURE_1ema | PDB=1ema | SCENE= }} | {{STRUCTURE_1ema | PDB=1ema | SCENE= }} | ||
The <scene name='Sandbox3/Secondary_structure/1'>overall structure</scene> of green fluorescent protein is an 11-stranded antiparallel beta barrel (yellow) surrounding a central helix (pink). The chromophore is part of the central helix. Information from [[1ema]]. | |||
'''Project completion, due 4/22/11''' | '''Project completion, due 4/22/11''' | ||
'' | ''Your proteopedia page should be organized into the following 4 required sections, with each team member responsible for one of these sections of the team project.'' | ||
1. Introduction | 1. Introduction | ||
: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. | :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 | 2. Overall structure | ||
: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? | :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? Above illustrates the start of an "overall structure" section on GFP. Additional description and green scenes could illustrate the polar/nonpolar distrubution of amino acids (is the inside of the barrel polar or nonpolar?), packing of amphipathic elements, etc. | ||
3. Drug binding site | 3. Drug binding site | ||
: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. | :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 | 4. Additional features | ||