Student Projects for UMass Chemistry 423 Spring 2016: Difference between revisions
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== Instructions == | == Instructions == | ||
===Deadlines=== | ===Deadlines=== | ||
:1. '''Optional Team or Teammate requests | :1. '''Optional Team or Teammate requests in Moodle by 1pm 2/1''' | ||
:2. '''Topic and pdb code due in Moodle Friday 2/5 1pm.''' Once you know your team assignment, select an available topic. Must be unique: first-come, first-served, so check the posted list in Moodle to be sure that your topic has not already been chosen. Follow the guidelines for topics (see Moodle). Choose from the list of suggested topics, OR choose another topic of interest and check (1) to be sure it is not on the "Topics to avoid" list, and (2) check with the instructor. You must check your topic (suggested or otherwise) to be sure there is not already a detailed Proteopedia page for the same complex or same pdb code. | You may request one teammate or a complete team of 5 people (including both chemistry and chemical engineering students). Teams of 5 people will be assigned and posted in Moodle, to include both chemistry and chemical engineering majors on most teams. | ||
:2. '''Topic and pdb code due in Moodle Friday 2/5 1pm.''' | |||
Once you know your team assignment, select an available topic. Must be unique: first-come, first-served, so check the posted list in Moodle to be sure that your topic has not already been chosen. Follow the guidelines for topics (see Moodle). Choose from the list of suggested topics, OR choose another topic of interest and check (1) to be sure it is not on the "Topics to avoid" list, and (2) check with the instructor. You must check your topic (suggested or otherwise) to be sure there is not already a detailed Proteopedia page for the same complex or same pdb code. | |||
Team/topic list will be posted in Moodle. Proteopedia 2016 Projects page will have links to each team’s sandbox page. | Team/topic list will be posted in Moodle. Proteopedia 2016 Projects page will have links to each team’s sandbox page. | ||
''' | :3. '''Start your team’s sandbox page by completing the "See Also" section by Monday 2/8. Are any human-authored Proteopedia pages too similar?''' | ||
Enter or edit your team's topic name and pdb code, and byline names. Complete the "See Also" section: add links to any related Proteopedia Topic Pages (not pages titled with the pdb code). Search for these, for example at http://proteopedia.org/wiki/index.php/Category:Topic_Page, Topic_pages, and Proteopedia:structure_Index. If you find another useful search strategy, post it under Help at Sandbox 423. If there is another page describing a complex with the same or a very similar molecule, you will need to choose a new topic. | Enter or edit your team's topic name and pdb code, and byline names. Complete the "See Also" section: add links to any related Proteopedia Topic Pages (not pages titled with the pdb code). Search for these, for example at http://proteopedia.org/wiki/index.php/Category:Topic_Page, Topic_pages, and Proteopedia:structure_Index. If you find another useful search strategy, post it under Help at Sandbox 423. If there is another page describing a complex with the same or a very similar molecule, you will need to choose a new topic. | ||
''' | :4. '''Sandbox page displaying initial structure and one green scene due by end of class workshop 2/12 -- bring your computers to class.''' | ||
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. | ||
''' | :5. '''Sandbox page with each section displaying an outline and at least one green scene due by beginning of class 2/24 -- bring your computers to class.''' | ||
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).''' | ||
===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.'' | |||
All sections will be within a single scrolling section (single JSmol window) -- I changed to this in March to speed up loading. 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 of (1) the protein complex, and (2) what is especially interesting about it. Include a clever caption for potential display at the Molecular Playground -- caption 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. | |||
f. 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. | |||
g. Credits -- list who did which portion of the project. If multiple people work on a section, use an asterisk to designate one person with primary responsibility. | |||
: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 | |||
h. 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== | ||
===Questions & Answers=== | ===Tips, Questions, & Answers=== | ||
Here are some from me and previous students. Post new ones at [[Sandbox423]]. | Here are some tips/questions/answers from me and previous students. Post new ones at [[Sandbox423]], where you can also find links to past projects. | ||
*For step-by-step instructions on creating example scenes, try [[Proteopedia:DIY:Scenes]]. | *For step-by-step instructions on creating example scenes, try [[Proteopedia:DIY:Scenes]]. | ||
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==Teams, Topics, and Links 2016== | ==Teams, Topics, and Links 2016== | ||
'''[[Sandbox Reserved 425|Team 1]]:''' Julie Boshar, | |||
Emily Boyle, | |||
Nicole Kirby, | |||
Cory Thomas, | |||
Connor Walsh -- fibroblast growth factor receptor/ Ponatinib (cancer)(4uxq) | |||
'''[[Sandbox Reserved 426|Team 2]]:''' Michael Beauregard, | |||
Annie Burton, | |||
Jianlong Li, | |||
Daniel Marco, | |||
Nathaniel Park -- Drug intercalation complex of DNA (1xcs) | |||
'''[[Sandbox Reserved 427|Team 3]]:''' Alex Debreceni, | |||
Robert Green, | |||
Uday Prakhya, | |||
Nicholas Rivelli, | |||
Elizabeth Swanson -- Vitamin D binding protein (1j7e) | |||
'''[[Sandbox Reserved 428|Team 4]]:''' Roger Crocker, | |||
Kate Daborowski, | |||
Patrick Murphy, | |||
Benjamin Rizkin, | |||
Aaron Thole -- Vitamin D receptor/vitamin D (1db1) | |||
'''[[Sandbox Reserved 429|Team 5]]:''' Tyler Carpenter, | |||
Samuel Pierce, | |||
Hyunjoon Choi, | |||
Anton El Khoury, | |||
Tiankai Zhang -- Penicillin binding protein/lactivicin (inhibitor) (2jch) | |||
'''[[Sandbox Reserved 430|Team 6]]:''' Cora Ricker, | |||
Lauren Timmins, | |||
Aidan Finnerty, | |||
Adam Murphy, | |||
Duy Nguyen -- Protein complex with blood clot inhibitor drug clopidogrel (Plavix) (4ntj) | |||
'''[[Sandbox Reserved 431|Team 7]]:''' Isabel Hand, | |||
Elizabeth Humble, | |||
Kati Johnson, | |||
Samantha Kriksceonaitis, | |||
Matthew Tiller -- Vitamin D activation by cytochrome P450, rickets (3c6g) | |||
'''[[Sandbox Reserved 432|Team 8]]:''' Laura Feeley, | |||
Katie Kwan, | |||
Daniel Peters, | |||
Ishtiaque Rafiyu, | |||
Luke Ruksnaitis -- Protein complex with cancer drug Alecensa-Alectinib (4uxl) | |||
'''[[Sandbox Reserved 433|Team 9]]:''' Soo Lim Park, | |||
Marissa Burgess, | |||
Benjamin Homyak -- Estrogen receptor beta/p-hydroxybenzene sulfonamide complexes (2yly) | |||
'''[[Sandbox Reserved 434|Team 10]]:''' Luke Schnitzler, | |||
Patrick Tonne, | |||
Owen O'Connor, | |||
Tyler Russell, | |||
Nicholas Sant -- Metabolic enzyme complex with substrate or inhibitor (4CYG) | |||
