2BB3 Assignment 2 2019 PDF

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BIOCHEMISTRY 2BB3 Assignment #2

Browse the literature (ie pubmed or go looking in the library in journals such as: Journal of Biological Chemistry, Science, Nature, Biochemistry, EMBO Journal, etc) for an ENZYME or better yet search for an ENZYME that is already of interest to you. Your challenge is to find the journal article that describes the structure of your protein of interest determined either by NMR, X-ray crystallography or Cryoelectron microscopy. Remember not all protein structures have yet been determined.

a) Describe the structure of the protein (from primary to quaternary). Illustrate the structure using pymol to generate a cartoon (ie ribbon) representation of the protein. Make sure you illustrate the protein structure well – you can give more than one image using different perspectives and you can show important regions, domains, residues etc. in various colours. (50 marks) b) You are asked to design a new drug (small compound) that would be a good inhibitor for your enzyme. (Hint: if possible find a structure of a protein that was determined with the substrate bound, then use the substrate as a starting point to design a high affinity, high specificity inhibitor). Draw your proposed compound, and describe the characteristics that it should have to make it an effective inhibitor. (30 marks) c) Run a docking simulation to see if your inhibitor binds well to the protein. Describe the results and what you think this might mean for future efforts at inhibitor design. You can find docking software and servers at www.click2drug.org. I would suggest using the molecular docking server at http://www.dockingserver.com/ or at https://mcule.com/apps/1-clickdocking/?utm_source=ccl%26utm_medium=maillist%26utm_campaign=1-clickdocking, but others programs/servers may also work well. (25 marks) d) Obtain the primary amino acid sequence of your protein and do a BLAST search to find out if it is similar to any other proteins. Do these proteins have similar function? Are the structures of these other proteins known? If so, compare them to your protein of interest – use pymol, be creative – enjoy! (25 marks) e) QUALITY of WRITTEN REPORT: Grammar, clarity, logic presentation of ideas, quality of images, etc. (20 marks)

Note: The original article from which you drew your information MUST be attached to the final report! Failure to do so will result in a penalty of 15 marks....