Sandbox Reserved 439: Difference between revisions
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==Introduction== | ==Introduction== | ||
<font color='red'>Introduce 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 | <font color='red'>Introduce 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.</font> | ||
<scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>(Initial view)</scene> | <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>(Initial view)</scene> | ||
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==Overall Structure== | ==Overall Structure== | ||
<font color='red'>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.</font> | |||
<scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>(Initial view)</scene> | <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>(Initial view)</scene> | ||
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==Binding Interactions== | ==Binding Interactions== | ||
<font color='red'>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). 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.</font> | |||
<scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>(Initial view)</scene> | <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>(Initial view)</scene> | ||
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==Additional Features== | ==Additional Features== | ||
<font color='red'>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).</font> | |||
<scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>(Initial view)</scene> | <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>(Initial view)</scene> | ||
==Quiz Question | ==Quiz Question== | ||
<font color='red'>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.</font> | |||
<scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>(Initial view)</scene> | <scene name='User:Lynmarie_K_Thompson/Sandbox_1/Loadedfrompdb/4'>(Initial view)</scene> | ||
