Protein Modeling

Protein Modeling was introduced as a trial in 2009 and as a National Event in 2010/2011.

Description
Students will explore protein structure and function by building 3D models of selected proteins based on computer models- one prior to competition, and one on site at the competition- and taking a test on both general protein-related concepts and information specific to the protein chosen for that year. For 2011, students will model proteins involved in reprogramming adult cells to become stem cells.

Scoring
As of 2009-10, 40% of the score was determined by the pre-build model, 30% by the on-site model, and 30% by the written test.

Pre-build Model
For the pre-build model, a section of a certain protein will be specified from the Protein Data Bank. Students will be provided beforehand with a Mini-Toober of the correct length, at a scale of 2 cm per amino acid residue, and red and blue plastic end-caps representing the carboxy and amino termini of the protein chain respectively. The model must be correctly folded, and the end-caps placed at the correct ends of the protein chain, but the model must also include "creative additions" that showcase the function of the selected protein. Students must decide for themselves which sidechains and/or ligands are important to the protein's function and should be displayed. These additions must be explained on a two-sided, 3x5 index card, along with a paragraph explanation of how they are relevant to the protein's function, and submitted with the model, typically at impound.

The pre-build model is scored based on:
 * Accuracy and correct placement of secondary structures (alpha helices and beta sheets)
 * Accuracy of tertiary structure (3D arrangement of secondary structures- e.g., two strands of a beta sheet being correctly placed next to each other, and a nearby helix being perpendicular to both)
 * Relevance and correct placement of sidechains or ligands you've chosen to display (and clarity/accuracy of the explanation on your card), as well as correct placement of end-caps
 * Relevance and creativity of "creative additions" (i.e., labeling the "fusion peptide" on hemagglutinin would get you points, but displaying every sidechain wouldn't, since that doesn't show any understanding of the protein's function)

On-Site Model
For the on-site model, a file will be specified from the Protein Data Bank, but the specific section of this protein that students are to build will not be stated until the competition. At the competition, students will be given a Mini-Toober of the correct length, at the same scale of 2 cm per amino acid residue, foam representations of important sidechains or associated ligands, and red and blue plastic end-caps representing the carboxy and amino termini of the protein chain respectively. The model must be correctly folded, the end-caps placed at the correct ends of the protein chain, and the given sidechains or ligands attached to the Mini-Toober at the correct locations and with the correct orientations.

The on-site model is scored based on:
 * Accuracy and correct placement of secondary structures (alpha helices and beta sheets)
 * Accuracy of tertiary structure (3D arrangement of secondary structures- e.g., two strands of a beta sheet being correctly placed next to each other, and a nearby helix being perpendicular to both)
 * Correct placement and orientation of given sidechains and ligands, as well as correct placement of end-caps

Written Test
The written test consists of multiple choice and short answer questions about both general protein topics (e.g., "What is the full name of the N-terminus of a protein chain?"), information specific to the selected protein (e.g., for the 2009-10 hemagglutinin, "Why are pigs important to the spread of influenza viruses?"), and information extremely specific to the PDB file (e.g., "What is the resolution in Angstroms of the PDB file 1HTM.pdb?"). Some of the short answer questions will be selected as tiebreaker questions, and will be designated as such. These still count normally toward your regular score on the test portion, but will be weighted more in the event of a tie.

These attributes are consistent across all levels of competition, because the Center for Biomolecular Modeling at MSOE provides all tests for the Protein Modeling event. However, the questions get more challenging (and there's more of them) at each successive level of competition.

Materials
As of 2009-10, ten two-sided 8.5x11 sheets of reference materials from any source, typed, handwritten, or graphics, were allowed, along with a scientific calculator and writing utensils (a Sharpie or other permanent marker is recommended for marking the Mini-Toober for the on-site model, as well as normal pens/pencils for taking the test).

Content
While this information may appear on the written test, it's also important to know for the construction of your models- particularly the pre-build model, on which you have to decide what's vital to show or not.

Structure Equals Function
This is the basic tenet of Protein Modeling. It's important to know what a protein's structure is like because its function is determined by its structure.

There are four different types of protein structure: primary, secondary, tertiary, and quaternary.

Primary Structure
Primary structure is the sequence of amino acid residues in a protein chain (they're called residues, by the way, because they're not individual amino acids anymore, having lost a hydrogen off their amino groups and a hydroxide ion off their carboxylic acid groups in the process of bonding through dehydration synthesis). There are 20 main varieties of amino acid, which differ only in their sidechain (sometimes called an "R group").

Each residue in a chain is given a number, starting at the amino terminus- that is, the end that has an amino group still present- with 1 and going up to the carboxy terminus- the end that has a carboxyl group still present.

Secondary Structure
Secondary structure is the first level of folding in a protein. Patterns called "motifs", such as alpha helices and beta sheets (by far the two most common), are caused by hydrogen bonding between nearby residues.

Alpha helices

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