423 Project Template
From Proteopedia
Asp Receptor Ligand-binding domain (1wat)[1]
by [list all teammate names here] Student Projects for UMass Chemistry 423 Spring 2016
This is an example page. Edit appropriately for your project. Upon completion of each task, delete instructions in red. See Sandbox Reserved 439 for original instructions 1. Add a citation to the primary reference at the end of the title above: you should all read this paper! Go to the pdb and search for your pdb code. Go down to the abstract and click "Search on Pubmed".
In pubmed, copy the PMID code you see right below the abstract, and paste it to replace xxx after PMID in your title (first edited line above). ** I can't figure out why the title citation gets repeated (refs 1 and 2) when it is cited in the text... We'll just live with it.** 2. Each section should start with an "initial view" green scene. These can be the same for all sections or can be set by the section author. Section text should provide an interesting description (suitable for non-experts), and illustrate your points about the complex with multiple green scenes. Section text should not exceed the length of the structure window (<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 this example (go into edit this page, to see how title reference was done). Make it interesting and accessible to a non-scientist! Show clearly some chemical details to illustrate the chemistry of life processes!
IntroductionIntroduce the protein function, how it is related to a disease or fundamental process, and what is important about the ligand in the complex. Make a few green scenes suitable for the Molecular Playground: attractive and informative illustrations of (1) the protein complex, and (2) what is especially interesting about it. Think of a clever caption for potential display at the Molecular Playground -- caption must be short, ideally < 10 words. Edit the StructureSectionLoad command (4th edited line from the top) to insert your caption. The ligand binding domain of the aspartate receptor is a dimer of two 4-helix bundles that is shown here with the bound.[2] Overall StructureDescribe 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. In this the N and C termini are at the bottom of the structure; this is where the connections to the transmembrane helices have been truncated. Binding InteractionsDescribe 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). The binding interactions of interest are those with the small molecule inhibitor or drug discussed in the paper. There are typically additional "ligands", which could be salts and other component of the buffer -- not interesting, do not discuss these. When the protein is colored according to , residues at the ligand site are the most conserved.
Interactions that stabilize ligand binding[3] include hydrogen bonding from Tyr149 and Gln152 backbone carbonyls and Thr154 sidechain OH to the and hydrogen bonding from the sidechain nitrogens of Arg64, Arg69, and Arg73 to the two . Additional FeaturesDescribe 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).
Quiz QuestionPose 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.
See AlsoCreditsIntroduction - name of team member Overall Structure - name of team member Binding Interactions - name of team member Additional Features - name of team member Quiz Question 1 - name of team member References
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