Student Projects for UMass Chemistry 423 Spring 2015
From Proteopedia
Contents |
Your Heading Here (maybe something like 'Structure')
1. Topics due Monday 2/9 11pm
- Teams of 4 people will be assigned, to include both chemistry and chemical engineering majors on most teams. You may request one teammate by emailing the TA by noon Feb 16.
- Once you know your team assignment, select an available topic (not already chosen by another team); see our course website for suggestions and guidelines to find a simple protein-ligand complex (eg protein-drug, nucleic acid-drug, or protein-DNA) with a known structure in the pdb that interests your team. If you want to choose a topic not on the list, be sure that it does not already have a detailed Proteopedia page and email Prof Thompson to get approval: send the pdb code for the complex and briefly explain the disease connection or why it is interesting. Add your topic to the team list at Sandbox423 by 2/24.
2. Sandbox page displaying initial structure, description, and one green scene due by end of class workshop 2/27
- Start your assigned sandbox page: Find the pdb id for your protein-ligand complex in the Protein Data Bank. 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 3/5
- 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 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.
4. Project near-final draft, due 1 week before presentation. Presentation dates will be assigned when topics are chosen. Prof Thompson will provide suggestions for improvements to your draft; you may also request feedback earlier.
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. 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.
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 a green scene suitable for the Molecular Playground: an attractive and informative illustration of the protein complex with an interesting short caption describing it.
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. Credits -- at the end list who did which portion of the project:
- Introduction -- name of team member
- Overall structure -- name of team member
- Drug binding site -- name of team member
- Additional features -- name of team member
f. 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!).
4. In-class presentations on assigned dates.
Function
Disease
Relevance
Structural highlights
This is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.
</StructureSection>
