Student Projects for UMass Chemistry 423 Spring 2015: Difference between revisions

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'''2. Sandbox page displaying initial structure and one green scene due by end of class workshop 2/27'''
'''2. Sandbox page displaying initial structure and one green scene due by end of class workshop 2/27'''
:In your assigned sandbox page click"edit this page" (top) and follow the directions to insert your rotating structure on your page. Describe and illustrate with a green scene the secondary structure of your protein.
:In your assigned sandbox page click "edit this page" (top) and follow the directions to insert your rotating structure on your page. Describe and illustrate with a green scene the secondary structure of your protein.


'''3. Sandbox page with each section displaying an outline and at one least green scene due by beginning of class 3/11'''
'''3. Sandbox page with each section displaying an outline and at one least green scene due by beginning of class 3/11'''
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'''4. Project completed (all sections) by Fri 4/3.
'''4. Project completed (all sections) by Fri 4/3.


''Your proteopedia page should be organized into the following required sections, with each team member responsible for one of sections a-d of the team project.''
''Your proteopedia page should be organized into the following required sections, with each team member responsible for one of sections a-f of the team project.''
Each section should have its own JMol window. Provide an interesting description (suitable for non-experts), and illustrate your points about the complex with multiple green scenes. Be concise: the written description should not extend beyond the jmol window. Do not include any copyrighted figures. All sections must be written in your own words with citations to your sources, following the reference format in the example below. You may include links to other interesting information or scenes but you must create your own scenes for display on your page.  
Each section should have its own JMol window. Provide an interesting description (suitable for non-experts), and illustrate your points about the complex with multiple green scenes. Be concise (<300 words)! Do not include any copyrighted figures! All sections must be written in your own words with citations to your sources, following the reference format in the example below. You may include links to other interesting information or scenes but you must create your own scenes for display on your page.  


''Make it interesting and accessible to a non-scientist!  Show clearly some chemical details to illustrate the chemistry of life processes!''
''Make it interesting and accessible to a non-scientist!  Show clearly some chemical details to illustrate the chemistry of life processes!''
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a. Introduction
a. Introduction
:Introduce the protein function, how it is related to a disease, and what is important about the ligand in the complex. Make a green scene suitable for the Molecular Playground: an attractive and informative illustration of the protein complex with an interesting short caption describing it.  
:Introduce the protein function, how it is related to a disease, and what is important about the ligand in the complex. Make a green scene suitable for the Molecular Playground: an attractive and informative illustration of the protein complex. Include a clever -- this caption must be short, ideally < 10 words, potentially for display at the Molecular Playground.
b. Overall structure
b. 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? 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.
: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? 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.
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d. Additional features
d. Additional features
:Describe and use green scenes to illustrate additional features of the macromolecule. 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 (eg include a reaction scheme with structures of the substrate, transition state and product -- but don't borrow a published scheme).
:Describe and use green scenes to illustrate additional features of the macromolecule. 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 (eg include a reaction scheme with structures of the substrate, transition state and product -- but don't borrow a published scheme).
e. Quiz question 1
: Pose an interesting, quiz-worthy question that involves thinking and investigating the molecule with the green scenes that you provide here.
f. Quiz question 2
: Pose an interesting, quiz-worthy question that involves thinking and investigating the molecule with the green scenes that you provide here.


e. Credits -- at the end list who did which portion of the project:
g. Credits -- at the end list who did which portion of the project:
:Introduction -- name of team member
:Introduction -- name of team member
:Overall structure -- name of team member
:Overall structure -- name of team member
:Drug binding site -- name of team member
:Drug binding site -- name of team member
:Additional features -- name of team member
:Additional features -- name of team member
 
: Quiz question 1
f. References
: Quiz question 1
Teams with 7 members can have 2 people work on the Drug binding site or Additional features section.
h. References
:This will include the published paper that describes your structure (the reference associated with your pdb code). You will get much of your information about specific interactions to look for and highlight in the structure from this reference (which is much easier than trying to find these on your own with no guidance!).
:This will include the published paper that describes your structure (the reference associated with your pdb code). You will get much of your information about specific interactions to look for and highlight in the structure from this reference (which is much easier than trying to find these on your own with no guidance!).
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