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| '''This sandbox is in use until August 1, 2011 for UMass Chemistry 423. Others please do not edit this page. Thanks!''' | | '''This sandbox is in use for UMass Chemistry 423. Others please do not edit this page. Thanks!''' |
| Chem423 Team Projects: Understanding drug mechanisms
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| == Project Instructions == | | ==''' Spring 2016 Chem423 Team Projects'''== |
| | '''Understanding the chemical basis of disease and life processes''' |
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| | Follow instructions posted at [[Student Projects for UMass Chemistry 423 Spring 2016]]. |
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| '''1. Team & Structure selection, due 4/1/11: All projects & names must be posted on the list below, linking to sandbox pages displaying initial structure.''' | | ''Each team should together agree upon a topic and pdb code (check the list below to be sure your topic is not already taken), then log in to Proteopedia (see instructions in Moodle) and edit this section to list your topic and pdb code.'' |
| :Form teams of 4 people; include both chemistry and chemical engineering majors on each team. Start by finding a protein-drug or nucleic acid-drug complex with a known structure in the pdb that interests your team. Check the list below to see if another team has already chosen this complex. 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).
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| :Copy the message at the top of this page into your sandbox page to "reserve" your sandbox for this course.
| | '''2/8/16 Topics are all set and copied to [[Student Projects for UMass Chemistry 423 Spring 2016]] -- notify Prof Thompson of any changes by email.''' |
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| :Find the pdb id for your protein-drug complex in the Protein Data Bank. In your sandbox page click"edit this page" (top) and follow the directions to insert your rotating structure on your page. | | '''[[Sandbox Reserved 425|Team 1]]:''' Julie Boshar, |
| | Emily Boyle, |
| | Nicole Kirby, |
| | Cory Thomas, |
| | Connor Walsh -- fibroblast growth factor receptor/ Ponatinib (cancer)(4uxq) |
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| '''2. Project completion, due 4/22/11''' | | '''[[Sandbox Reserved 426|Team 2]]:''' Michael Beauregard, |
| ''Your proteopedia page should be organized into the following 5 required sections, with each team member responsible for one of these sections of the team project.''
| | Annie Burton, |
| | Jianlong Li, |
| | Daniel Marco, |
| | Nathaniel Park -- Drug intercalation complex of DNA (1xcs) |
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| a. Introduction
| | '''[[Sandbox Reserved 427|Team 3]]:''' Alex Debreceni, |
| :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 permission to use it. | | Robert Green, |
| b. Overall structure
| | Uday Prakhya, |
| :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? Below I illustrate 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.
| | Nicholas Rivelli, |
| c. Drug binding site
| | Elizabeth Swanson -- Vitamin D binding protein (1j7e) |
| :Describe features of the drug 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).
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| d. Additional features
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| :Describe and use green scenes to illustrate additional features of the protein. 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).
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| e. Credits -- at the end list who did which portion of the project:
| | '''[[Sandbox Reserved 428|Team 4]]:''' Roger Crocker, |
| :Introduction -- name of team member
| | Kate Daborowski, |
| :Overall structure -- name of team member
| | Patrick Murphy, |
| :Drug binding site -- name of team member
| | Benjamin Rizkin, |
| :Additional features -- name of team member
| | Aaron Thole -- Vitamin D receptor/vitamin D (1db1) |
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| '''3. In-class presentations, to be announced''' | | '''[[Sandbox Reserved 429|Team 5]]:''' Tyler Carpenter, |
| == Overall Structure ==
| | Samuel Pierce, |
| | Hyunjoon Choi, |
| | Anton El Khoury, |
| | Tiankai Zhang -- Penicillin binding protein/lactivicin (inhibitor) (2jch) |
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| {{STRUCTURE_1ema | PDB=1ema | SCENE= }}
| | '''[[Sandbox Reserved 430|Team 6]]:''' Cora Ricker, |
| 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]].
| | Lauren Timmins, |
| | Aidan Finnerty, |
| | Adam Murphy, |
| | Duy Nguyen -- Protein complex with blood clot inhibitor drug clopidogrel (Plavix) (4ntj) |
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| | '''[[Sandbox Reserved 431|Team 7]]:''' Isabel Hand, |
| | Elizabeth Humble, |
| | Kati Johnson, |
| | Samantha Kriksceonaitis, |
| | Matthew Tiller -- Vitamin D activation by cytochrome P450, rickets (3c6g) |
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| == Project Teams, Topics, and Links ==
| | '''[[Sandbox Reserved 432|Team 8]]:''' Laura Feeley, |
| | Katie Kwan, |
| | Daniel Peters, |
| | Ishtiaque Rafiyu, |
| | Luke Ruksnaitis -- Protein complex with cancer drug Alecensa-Alectinib (4uxl) |
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| | '''[[Sandbox Reserved 433|Team 9]]:''' Soo Lim Park, |
| | Daniel Estabrook, |
| | Marissa Burgess, |
| | Miranda Goldman, |
| | Benjamin Homyak -- Estrogen receptor beta/p-hydroxybenzene sulfonamide complexes (2yly) |
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| sample entry: student1, student2, student3, student4 - HIV protease [[sandbox1]]
| | '''[[Sandbox Reserved 434|Team 10]]:''' Luke Schnitzler, |
| | Patrick Tonne, |
| | Owen O'Connor, |
| | Tyler Russell, |
| | Nicholas Sant -- Metabolic enzyme complex with substrate or inhibitor (4CYG) |
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| Nick DeGraan-Weber, Jackie Dorhout, Rachael Jayne, Mike Reardon - flu neuraminidase
| | == Examples == |
| | See |
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| ==Students looking for group members==
| | [[Student_Projects_for_UMass_Chemistry_423_Spring_2015#Teams, Topics, and Links 2015|2015 Team Projects]] |
| List yourself + your major, list partial groups looking for members, list your complex if you have chosen one. Contact others to form a group. Those not in Chemistry or Chemical Engineering count as either.
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| Jaclyn Somadelis, Chemical Engineering
| | [[Student_Projects_for_UMass_Chemistry_423_Spring_2012#Spring_2012_Chem423_Team_Projects|2012 Team Projects]] |
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| ==Help Editing==
| | [[Student_Projects_for_UMass_Chemistry_423_Spring_2011#Project Teams, Topics, Links, and Presentation Dates|2011 Team Projects]] |
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| Hint: Ctl-click or right-click on links below and select "Open Link in New Window"
| | ==Help== |
| | See [[Student Projects for UMass Chemistry 423 Spring 2016|Help]] |
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| [[Help:Editing]]
| | ==Questions & Answers== |
| :You can use the edit button on any page to find out how other users created effects that you see.
| | Here is a place to post new questions and answers for each other about how to do things in Proteopedia. Good tips will be added to the Help section for future classes (above link). |
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| [[http://meta.wikimedia.org/wiki/Cheatsheet Wikimedia cheat sheet]]
| | There is a recurring problem where sections below an edited section disappear (you can still see them in edit window). Don’t try to insert your scene into the command that loads the initial molecule (which may have caused the rest of the sections not to load). Write some text and then insert green scenes into text. -- Prof Thompson 2/17/16 |
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| [[http://en.wikipedia.org/wiki/How_to_edit General help with Wiki editing]], plus more [[http://en.wikipedia.org/wiki/Help:Wikitext_examples Wiki Text examples]]
| | Prof Thompson 3/3/16: To highlight part of your molecule and hide the rest |
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| Some of the above are for help editing Wikipedia pages, but the syntax is mostly the same. Proteopedia ADDS protein stuff to the WikiMedia markup language, which powers both WEB sites.
| | 1. always use "replace selection” to be sure you aren’t bringing along some other selection, and also use “hide selection” under representations. |
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| | 2. Turn on selection halos (under the structure “show selected with halos” - click the ON button). They make it much easier to keep track of what is selected, especially after multiple "invert selection" commands. |
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| | For example: |
| | selections: DNA, replace selection |
| | invert current selection (selects all but DNA) |
| | representations: hide selection (hides all but DNA) |
| | selections: invert selection (back to DNA) |
| | representations: backbone, set representation |