Protein Modeling Challenge
for High School Students
Center for Science and Mathematics Education
Date of Competition:
December 8, 2010, 8:30am to 1:00pm
September 30, 2010
1. Description: Epidermal Growth factor, its structure, function and role in lung cancer are the central themes for the competition this year. The students will build a model of the kinase domain of Epidermal Growth Factor (EGFR) at their schools. On December 8 at Stony Brook University, the students will build another model of a portion of EGFR or a related protein and answer questions about protein chemistry, biology and lung cancer. You can read more about this receptor in the June 2010 RCSB Molecule of the Month written by David S. Goodsell (www.pdb.org). This competition is designed for students who have completed or are taking regents level chemistry and biology. All teams must be accompanied by a teacher who has taken one of the training sessions. There will be a limit of 36 teams in the competition. Team size is unlimited, but each team can only send three students to the competition on December 8. All team members will receive a certificate of participation. Your school can register one team on a first-come first-served basis; if space permits we will accept multiple teams from a school.
2. Competition: This event has three parts: a pre-built model (Part I), an on-site build model (Part II) and an on-site exam (Part III). Students may not bring any materials or computers of any kind into the on-site competition on December 8.3. Scoring: 40% of the event score will be based on the pre-build protein model (Part I), 30% on the on-site build (Part II) and 30% on the written exam (Part III). The pre-build protein model (Part I) will be scored based on the accuracy and scale of the alpha-helix and beta-sheet secondary structures, other elaborations and enhancements on the protein backbone such as side chains, DNA or associated molecules. The focus of the model should be on creatively telling the story of the molecule’s significance, structure and function. The on-site build protein model (Part II) will be scored based on accuracy of folding the Mini-Toober model and positioning specific amino acid side chains and/or accessory molecules. The exam (Part III) will be scored for accuracy. Ties will be broken using questions on the written exam selected by the event supervisor before the start of the competition.
a. Part I: The Pre-Build Model. Registered teams will receive a kit containing a Mini-Toober for building a model at a scale of 2cm/amino acid. Students will represent other important parts of the protein, such as amino acid side chains, DNA or associated molecules, where applicable, with materials of their choosing. The additions to the Mini-Toober® model should focus on illustrating the significance of the structure to the function of the protein. The models will be evaluated for accuracy. Students must provide a 3x5 note card explaining the creative additions to their model and what they represent. Models must arrive at Stony Brook University by December 1 for judging. The models will be returned.
b. Part II: The On-Site Model. During the on-site competition, students will build a model of a region of EGFR or a related protein. Students will use a computer provided at the competition with the Jmol application, a text editor, PDB file, structure summary page and Molecule of the Month files on it to guide their model construction. Students may only use one of the computers provided at the competition with the above-mentioned files on it to guide their model construction. Any model handed to the judges after the end of the competition time (50 minutes) will not be accepted for scoring.
c. Part III: The On-Site Written Exam. During this section of the competition, students will complete a multiple choice/short answer written exam with questions about the relationship between protein structure and function, with an emphasis on EGFR. During the on-site competition, students may use only the materials provided to answer the questions. Question content will not be limited to these materials. Any test papers handed to the judges after the end of the competition time (50 minutes) will not be accepted for scoring.
There are several resources available to help you to prepare for this event and we encourage you to explore these resources.
•MSOE Center for BioMolecular Modeling Science Olympiad website. You can download a powerpoint that goes through the parameters of the event, the RasMol program and written workshop materials to help you prepare for this event: http://www.rpc.msoe.edu/cbm/scienceolympiad/
•MSOE Model Lending Library http://www.rpc.msoe.edu/cbm/lib/. You may borrow molecular models that allow you to explore the basics of protein structure. We recommend the IP collection: Introduction to Protein Structure.
Mini-Toobers® are products of 3D Molecular Designs, Wauwatosa, WI, www.3dmoleculardesigns.com
For questions, please contact:
Joan Kiely at firstname.lastname@example.org
December 6th: Registration for Protein Modeling Comptetion
January 29: Registration for North America Computational Linguistics Olympiad
November 22: Geology Open Night: "Exotic chemistry at extreme conditions: from new materials to models of planetary interiors" (Dr. Artem Oganov)
December 6: Astronomy Open Night: "The Hunt for Dark Matter" (Dr. Rouven Essig)
January 30: North American Computational Linguistics Olympiad (NACLO) Round One
February 28: Protein Modeling Challenge