Protein Modeling

Protein Modeling is an academic event with a building portion to it. Competitors are expected to fold a pre-build model beforehand with "creative additions," fold an on-site model during the competition, and take a written test on the year's theme.

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Allowable Resources
2. EVENT PARAMETERS:

a. Pre-build models will be impounded one hour before the event begins.

b. Students may bring up to ten double-sided, 8.5”x11” pages of materials to the on-site competition.

Internet access will not be permitted during the competitions.

c. Students will need to bring a writing instrument.

d. Supervisors will provide all materials for on-site model construction.

e. Construction details are found at: http://cbm.msoe.edu/studProg/so/index.html

3. THE COMPETITION: This event has three parts: (1) a pre-build model (40% of total score), (2) an on-site

build model (30% of total score) and (3) an on-site exam (30% of total score).

a. Part I: The Pre-Build Model. Students will use a computer visualization program (Jmol) to design and

construct a model of a specific protein based on atomic coordinate data. For 2010, students will construct

a model of a specified portion of the hemagglutinin protein, based on the coordinate data found in the

5HMG.pdb file, which can be downloaded for free from the RCSB Protein Data Bank (www.pdb.org),

and is described in the April 2006 RCSB Molecule of the Month

(http://dx.doi.org/10.2210/rcsb_pdb/mom_2006_4) by David S. Goodsell. The pre-build models should

represent amino acids 1-160 of chain B of the PDB file 5HMG. Note that the same pre-build model

<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:18px;color:rgb(68,68,68);text-align:left;">should be brought to regional, state and national competitions, as the competition level increases, the

<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:18px;color:rgb(68,68,68);text-align:left;">scoring rubrics for the pre-build model will reflect higher expectations for model accuracy, detail and

<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:18px;color:rgb(68,68,68);text-align:left;">creativity.

<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:18px;color:rgb(68,68,68);text-align:left;">b. The pre-build model in its final form must be based on the alpha carbon backbone display of the model

<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:18px;color:rgb(68,68,68);text-align:left;">and must use a scale of 2 cm per amino acid. Students may use Mini-Toobers®1 to model their protein, or

<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:18px;color:rgb(68,68,68);text-align:left;">other comparable material2. Students will represent other important parts of the protein, such as amino

<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:18px;color:rgb(68,68,68);text-align:left;">acid sidechains, DNA or associated molecules, where applicable, with materials of their choosing. The

<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:18px;color:rgb(68,68,68);text-align:left;">additions to the model should focus on illustrating the significance of the structure to the function of the

<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:18px;color:rgb(68,68,68);text-align:left;">protein. A significant portion of the score will be derived from the creative additions to the model.

<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:18px;color:rgb(68,68,68);text-align:left;">Students must provide a 3”x5” note card explaining the creative additions to their model and what they

<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:18px;color:rgb(68,68,68);text-align:left;">represent. Students must deliver their pre-build model and 3”x5” card to judges at the competition site for

<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:18px;color:rgb(68,68,68);text-align:left;">impounding. The models will be impounded prior to the start of the on-site competition and will be

<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:18px;color:rgb(68,68,68);text-align:left;">available after scoring for public viewing. Models will be available for return to the students after the

<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:18px;color:rgb(68,68,68);text-align:left;">competition.

<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:18px;color:rgb(68,68,68);text-align:left;">c. Part II: The On-Site Model. During the on-site competition at Regional Competitions, students will

<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:18px;color:rgb(68,68,68);text-align:left;">design and build a physical model of a selected region of hemagglutinin (1HTM.pdb). During the on-site

<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:18px;color:rgb(68,68,68);text-align:left;">competition at the State and National Competitions, students will design and build a physical model of a

<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:18px;color:rgb(68,68,68);text-align:left;">selected region of the neuraminidase (2HU4.pdb), which is described in the May 2009 RCSB Molecule of

<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:18px;color:rgb(68,68,68);text-align:left;">the Month written by David S. Goodsell. (http://dx.doi.org/10.2210/rcsb_pdb/mom_2009_5)

<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:18px;color:rgb(68,68,68);text-align:left;">d. Students will utilize a computer provided with the Jmol application at the competition. Students must

<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:18px;color:rgb(68,68,68);text-align:left;">utilize only one of the identical computers provided at the competition with the above-mentioned files on

<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:18px;color:rgb(68,68,68);text-align:left;">it to guide their model construction. All construction materials for the model (Mini-Toobers®1, foam

<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:18px;color:rgb(68,68,68);text-align:left;">amino acid sidechains, crosslinkers and plastic red and blue end caps) will be provided. Any model not

<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:18px;color:rgb(68,68,68);text-align:left;">handed to the judges by the end of the competition time (50 minutes) will not be accepted for scoring.

<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:18px;color:rgb(68,68,68);text-align:left;">e. Part III: The On-Site Written Exam. During the 50-minute competition, students will answer a

<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:18px;color:rgb(68,68,68);text-align:left;">multiple choice/short answer written exam with questions about the relationship between protein structure

<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:18px;color:rgb(68,68,68);text-align:left;">and function, with an emphasis on swine flu and the role of hemagglutinin and neuraminidase. During the

<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:18px;color:rgb(68,68,68);text-align:left;">on-site competition, students may use only the materials brought with them (the 10 pages) to answer the

<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:18px;color:rgb(68,68,68);text-align:left;">New York

<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:18px;color:rgb(68,68,68);text-align:left;">State

<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:18px;color:rgb(68,68,68);text-align:left;">Trial Event

<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:18px;color:rgb(68,68,68);text-align:left;">questions. Any exams not handed to the judges by the end of the competition time will not be accepted for

<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:18px;color:rgb(68,68,68);text-align:left;">scoring. Illegible answers will not receive credit.

Helpful Hints
<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:18px;color:rgb(68,68,68);text-align:left;">Tips:


 * Get the prebuild model done as soon as you get materials and make it pretty and have lots of extras
 * It would have helped a lot to show how the protein attaches to the cell surface
 * On-site model is very important since it practically determines your score since the prebuild model and test can be aced
 * Basically memorize how to build every section of the protein
 * Learn to use jmol at an expert level before even thinking about building anything
 * Use the legit materials. They might be expensive, but they are worth it for their attractiveness and ease of use
 * These materials should be received from States/Nationals people very early, so if you don't get it, please bug Dempsey until you do.
 * Note that the test seems to be a lot of chemistry/biochem/microbiology inherently in the event description, but that there was a lot on diseases at the 2010 national test.

Current Topic
<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:18px;color:rgb(68,68,68);text-align:left;">PROTEIN MODELING CHALLENGE

<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:18px;color:rgb(68,68,68);text-align:left;">1. DESCRIPTION: Students will use computer visualization and online resources to guide them in

<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:18px;color:rgb(68,68,68);text-align:left;">constructing physical models of proteins involved in swine flu (H1N1), with a focus on two proteins used in

<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:18px;color:rgb(68,68,68);text-align:left;">the naming of the flu viruses: Hemagglutinin (H) and Neuraminidase (N).

More Links
<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:19px;color:rgb(68,68,68);text-align:left;">External Resources:

<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:19px;color:rgb(68,68,68);text-align:left;">http://cbm.msoe.edu/modGallery/hemagglutinin/HAviewer.swf http://cbm.msoe.edu/stupro/so/index.html http://cosmiclog.msnbc.msn.com/_news/2010/08/04/4814345-gamers-solve-protein-puzzles - About "foldit" which is a game about protein folding which can be downloaded here: http://fold.it/portal/

<p style="margin-top:0px;margin-bottom:0px;font-family:SegoeUI,LucidaGrande,Arial;line-height:19px;color:rgb(68,68,68);text-align:left;">http://cbm.msoe.edu/stupro/so/2011EventResources.html