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Macromolecular Structure..... About the Molecular Tutorial Assignment

This assignment involves the construction of a web page to illustrate aspects of the structure-function relationships for a particular molecule**. In creating a tutorial to teach your colleagues about the structural intricacies of a particular molecule, you will learn a lot (the goal of this assignment), not only about the molecule you have chosen, but also about general principles of macromolecular structure. Your tutorial must include at least one reference from the primary research literature describing the crystal or NMR structure of the molecule at high resolution (< 3 angstroms). Good source journals for papers describing macromolecular structure are Nature, Science, Nature Structural Biology, Structure, Cell, Protein Science.

The Protein Data Base (PDB) contains an extensive collection of molecules for which structural data is available. The downloadable *.pdb files are text files containing the atomic coordinates of particular molecules.
You may search this database a number of ways (see The WWW links section of The Online Macromolecular Museum).

To produce a desired tutorial, you must learn two new skills:

1) How to build HTML (HyperText Markup Language) web pages (with an editor), to produce a "framed" web page

2) How to use RasMol/Chime scripting to manipulate the molecule in ways to illustrate points in your tutorial

In order to receive high marks, your tutorials must be well written and scripted in a manner that promotes easy visualization of the structural features you are discussing. Your tutorials will be based on the published work of structural biologists, so you should pay attention to the major points of the papers that are the basis for your project. NEVER quote directly from the papers you are referencing. ALWAYS use you own words to make your points. Spend time crafting your explanations so they are clear, succinct, specific, and formal. You are writing for a professional audience. See some of the tutorials co-authored by students at The Online Macromolecular Museum to get a good idea of what good tutorials look like. Avoid useless words such as basically (e.g.: "Basically, the function of the beta subunit is to clamp polymerase onto the DNA" should read "The function of the beta subunit is to clamp polymerase onto the DNA").

** Possible molecules for this semester are:

• MutL - DNA excision repair protein
• ribosome structure
• nucleosome structure
• SH2-SH3 domain (cell signaling)
• K+ channel (membrane permeability)
• porin trimer (membrane permeability)
• Aquaporin channel (membrane permeability)
• actin or tubulin or intermediate filaments (cytoskeletal proteins)
• cell adhesion molecules (CAMs)
• proteosome (protein degradation machine)
• cytochrome oxidase (electron transport)
• hedgehog, armadillo, wingless proteins (cell signaling)

The important due dates to keep in mind are:

Feb 19. (pick molecule)

Feb. 26 (one page description of molecule)

March 5 (oral presentation - chalk talk)

April 4 (first draft)

April 25 (second draft)

May 2 (practice oral presentation)

May 9 (final oral presentation)

May 16 (final project due)