Student Projects for UMass Chemistry 423 Spring 2016: Difference between revisions

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Each team member should read the primary reference for the pdb structure and create an outline for their section and at least one green scene. Teams will meet briefly during class to discuss the overall organization as needed to make it logical and avoid duplication. As individuals proceed to create their sections, they should watch the other sections and stay in contact as needed to create a coherent overall project.
Each team member should read the primary reference for the pdb structure and create an outline for their section and at least one green scene. Teams will meet briefly during class to discuss the overall organization as needed to make it logical and avoid duplication. As individuals proceed to create their sections, they should watch the other sections and stay in contact as needed to create a coherent overall project.
:6. '''Project completed (all sections) in Proteopedia by Sun 4/10. All team members also submit their text to Turn It In (see class Moodle page).'''
:6. '''Project completed (all sections) in Proteopedia by Sun 4/10. All team members also submit their text to Turn It In (see class Moodle page).'''
===Project Description===
''Your proteopedia page should be organized into the following required sections, with each team member responsible for one of sections a-e 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 (<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 (go into edit this page, to see how these references were done). 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!''
a. Introduction
:Introduce the protein function, how it is related to a disease, and what is important about the ligand in the complex. Make 1-2 green scenes suitable for the Molecular Playground: attractive and informative illustrations (1) the protein complex, and (2) what is especially interesting about it. Include clever captions for potential display at the Molecular Playground -- captions must be short, ideally < 10 words.
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.
c. Binding interactions
:Describe features of the drug or ligand or protein-protein binding site in words and make "green scenes" to illustrate your points. Show the interactions that stabilize binding of this molecule to the protein (ie H bonds).
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).
e. Quiz question
: Pose an interesting, quiz-worthy question that involves thinking and investigating the molecule with the green scenes that you provide here.
Submit the answer to your question in Moodle and do not share it with other students.
Best questions will be chosen for a Moodle quiz, so that students can explore your structure and green scenes to figure out the answer to your quiz question.
g. See also
:For the 2/8 deadline, all team members should look for related Proteopedia pages (e.g. same protein but with different ligands) and post links here.
h. Credits -- at the end list who did which portion of the project:
:Introduction -- name of team member
:Overall structure -- name of team member
:Binding interactions-- name of team member
:Additional features -- name of team member
:Quiz question -- name of team member
Teams with 6 members should have the additional person write an additional quiz question.
i. References
:This will include the published paper that describes your structure (the reference associated with your pdb code). Everyone should read this primary reference -- 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!). Additional sources must also be cited in this section.


==Help==
==Help==
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