Biochemistry 660, Molecular Graphics Module

My Molecule Presentation Instructions

In collaboration with student partner(s):

1. Pick 1-2 lab partners. The class will be divided into 13 groups of 2 students each to be decided on the first day of the 660 lab segment.

2. You and your partner(s) should go online to the pdb database and pick one (or more) crystal structure files (or an NMR structure set) that is of interest to you. It could perhaps be an enzyme related to your own research, a protease, an RNA (e.g. tRNA), a protein /nucleic acid complex, a set of amino acids, bases or whatever... just so long as there is a pdb file encoding it (or them).

3. Read the research papers associated with this (these) structures. Remember, pdb files have references listed at the top of each file just so you can learn the salient features of the molecule and why people consider it biologically interesting. You DO NOT need to go into great depth here, the idea is to gather some interesting information about mechanisms, active sites, substrates etc., so you will have some concepts to illustrate.

4. Using PyMol or any other molecular display programs available to you, create some nice images of your molecule(s) that illustrate key features of its molecular biology. For example, if you were working with HIV protease, you might be interested in highlighting the active site residues or the substrate binding pocket, among other features. On a tRNA, the anticodon loop or the bases that make contact with the synthetase might be of interest. In an NMR structure, the differences among the various structures might be of interest (where do they wiggle?) etc.. Get creative with several different views, using surfaces or electrostatic potential, or whatever, to highlight and illustrate any interesting points. You might wish to compare or contrast elements from related structures. (Where is the HIV protease different from the SIV protease, for example, and why might these differences be related to their activities?) Or perhaps you may wish to show how a substrate/inhibitor binds in an active site. Use your imagination! No holds barred!

5. Capture your images as PNG, JPEG (Macintosh) or GIF (PC) files, import them into Powerpoint, and create a short presentation (8-10 slides) telling a story about your molecule. Add text, builds, short movies (if you make them), or any other features of PowerPoint to your file that you think might be helpful and attractive.

6. During the MyMolecule lab session (date: see syllabus), you and your partner(s) should bring to lab, a (PC or Mac formatted) zip disc, CD or USB jump drive containing your "My Molecule" PPt slide presentation (see below for compatible formats). Be sure to include on this disc, any Quicktime, MPEG or AVI movies that are referenced by your file or they won't play when you want them. Each partner in the group should plan to participate in a 10 minute (total/group) oral presentation, with another 5 min for questions about graphic methods or topic content. Instructors will provide a Macintosh computer with zip/cd drive, hooked up to an XGA-level projector. These presentations will be graded (for all students in the group by all students in the class), on the basis of originality, clarity, and creative use of program tools to illustrate some salient aspect of protein/nucleic acid biochemistry. The idea here is to demonstrate that you can use the molecular graphics tools to develop illustrations or animations that are clear and informative to an audience.

7. All/both partners in each group must participate equally in the planning, execution and presentation phases of this project. Each will be assigned the same grade for the exercise according to feedback sheets filled out by your classmates and instructors (your audience) after each presentation.

8. We are not so much concerned with presentation content (which molecule you choose, or what you learned about it), but rather, how you choose to illustrate your points with the creative and clear use of graphics techniques. Have fun with this learning opportunity and your audience will have fun too!

Format for your presentation:

The instructor's Macintosh in the DMC or in the Biochem 175 lecture hall, is equipped with zip, cd and USB jump drive readers and can accept discs formatted for Macs or PCs. It also runs QuickTime and the latest version of PPt. However, to ensure that YOUR file made on your computer runs smoothly on this machine, it is a good idea to adhere to simple formatting caveats:

a. When creating your presentation in PPt, make sure in EDIT > PAGESETUP you have configured your file for OnScreenShow or it may have funny dimensions when you go to display it.

b. It is a good idea to keep the size of your PPt file under 10-20 Mb (you may need to trim your picture file resolution if they are too big). Be forwarned that files bigger than this, or even movies bigger than 2-3 Mb may have trouble playing on another machines. Be careful, because you don't want to spend your 10 min presentation, fixing your file. Test it ahead of time.

c. If you want to test a practice file or figures for preview, please be sure to bring a test disc the day BEFORE the last lab. You will not have access to the DMC lab outside of regular class hours.

d. If you use a PC to create your presentation, do NOT use keyboard shortcuts to insert symbols, Greek letters or bullets. Only fonts selected from the standard PPt font list, and which are also common to the DMC Macintosh will display without error. For safety, stick to simple fonts like: Arial, Times, Symbol, Courier, etc.

e. The Biochem Dept has set up 3 Macintosh stations programmed with all course-supported software. These will be available to you and you groups, outside of class hours. PyMol is available to you from links on our web site web.