Protein Modeling Event

Photo:Two students work on the challenge The Protein Modeling Event challenges students to create a 3-dimensional model of a protein using a Mini-Toober. A Mini-Toober is a foam-covered flexible wire that will hold its shape once folded. A protein is selected at the beginning of the Science Olympiad season. This protein will be tied to the Protein Data Bank’s Molecule of the Month Feature, written by David Goodsell. The data coordinates for the protein’s 3-dimensional shape can be downloaded for free from the Protein Data Bank. Students then visualize this protein using a computer visualization program (such as Jmol or RasMol; for more information please click here) to create an image of the protein. Once the students have designed an image of the protein on the computer screen, they then manipulate the Mini-Toober into the shape on the protein. Additional features are encouraged to be added to the simple backbone model representation of the protein. These additions could include important amino acid sidechains, molecules that the protein interacts with, ions that involved in the function of the protein, or other additional features that highlight the significance of the protein. The additional features that are included within the model should enhance the “molecular story” of the protein. This model should be able to help tell the structure/function relationship of this protein.

Event Details

Photo:A student shows off her work The Protein Modeling Event at the Regional and State Competitions is comprised of three parts:

The pre-build model (40% of total score)
The on-site model (30% of total score)
The on-site exam (30% of total score)

One protein will be selected each year as the focus of that year’s competitions. The pre-build will be of the entire protein and the on-site builds will be focused on specific domains or regions of the protein. The pre-build for both the regional and the state competitions is the same.

For 2009, the theme for the competitons will be Ribonucleases, which are described in the September 2008 RCSB PDB Molecule of the Month, written by David Goodsell. For the 2009 competitions, the pre-build model is to construct a model of the entire protein, ribonuclease A (based on 1RTA.pdb). For the on-site component at the Regional Competitions, one portion of ribonuclease A (1RTA.pdb) will be chosen to be modeled. For the on-site component at the State Competition, a selected region of the ribonuclease inhibitor (also described in the September 2008 RCSB PDB Molecule of the Month; based on 1DFJ.pdb) will be modeled.

The on-site exam will be a multiple choice/short answer written exam with questions about the relationship between protein structure and function, with an emphasis on the chosen protein for the year. During the on-site competition, students may use only the materials provided to answer the questions. Question content may not be limited to these materials.

Protein Modeling will be offered at the National Tournament in August, GA, May15-16, 2009. At the National Tournament, the Protein Modeling event will not have a pre-build component. The event will have two parts: the on-site build and the exam. The final score will be based on the on-site build (50%) and the exam (50%). For the National Tornament on-site build, a specific region of ribonuclease A (1RTA.pdb) will be selected to be modeled.