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Model Building Quick Hints

Please note: this will be updated for 2010 soon NEW! This video demonstrates how to build a toober model -- great practice for the prebuild and onsite builds at the Olympiad.

Not sure what a PDB file is? This great video illustrates the connection between the PDB file and the 3D model.

firstglance.jmol.org is a good tool for exploring protein structure.

FOR MAKING THE MODEL TO BRING TO IMPOUND

Using the PDB file (which you can read in a text editor or MSWord) and Jmol, you should be able to find which amino acid marks the start and which marks the end of each element. Then you can note where these amino acids are on your toober.

  • Be careful with the end caps --
    • Blue End Cap indicates the N-terminal end (ends with an amino acid with a free amine group (-NH2)). This is where your model begins.
    • Red End Cap indicates the C-terminal end (ends with a free carboxyl group (-COOH)). This is where your model ends.
  • The toober represents the backbone of the protein; you'll want to show the beta sheets and alpha helices.
    • It helps to have something to wrap the toober around to make the helices -- try taping 3 pencils together to get the right width.
    • Which direction should the helices go in?
    • Beta sheets can be difficult to show--you can make little "bumps" in the toober. It's also a good idea to mark it somehow, and to explain that marking in your abstract.
  • The scale used should be 2 cm = 1 amino acid
  • Out of the amino acids, which ones are involved in the function of the protein? What is the protein's "story"?
  • Which sections of the structure are on the same plane? Rotate the molecule in the viewer, and try to match your model with what you see on screen.
  • The Mini-Toober should be used to build the alpha carbon backbone. You are encouraged to represent other important parts of the protein with materials of your choosing to illustrate the significance of the structure to the function.
  • Review the resources available from this website
  • Be sure to bring your model to impound!!

FOR THE WRITTEN ABSTRACT

You should bring a brief abstract that describes your model. If you have marked any structural or functional details in your model, please describe it in your abstract.

FOR THE ONSITE BUILD

You'll be expected to locate and correctly place key amino acids on your model.

USING JMOL

Jmol is an open-source Java viewer for chemical structures in 3D. You can use Jmol from the Display Options section of PDB entry 5hmg's Structure Explorer page or access it through firstglance.jmol.org.

The RCSB PDB website offers Help with Jmol commands and A Flash movie describing how to use Jmol.

Advanced help is available from jmol.sourceforge.net/docs/JmolUserGuide.

Another tutorial is available from Wiley's Interactive Concepts in Biochemistry.