Student Projects for UMass Chemistry 423 Spring 2016: Difference between revisions
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a. Introduction | 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 clever captions for potential display at the Molecular Playground -- captions must be short, ideally < 10 words. | :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 clever captions for potential display at the Molecular Playground -- captions must be short, ideally < 10 words. | ||
b. Overall structure | 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. | :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 | 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). | :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 | 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). | :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 | e. Quiz question | ||
: Pose an interesting, quiz-worthy question that involves thinking and investigating the molecule with the green scenes that you provide here. | : 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. | ||
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 | f. See also | ||
