2016 Protein Modeling Overview

This year's Theme: Proteins Involved in the Biosynthesis and Subsequent Signaling of the Neurotransmitters Dopamine and Serotonin.

Inspiration for the theme: Sepiapterin Reductase and the Beery Twins. Learn more.

This year's event is a formal collaboration between:

The regional, state and national events were sponsored by:

Part 1: Pre-Build Model

Every team must submit a pre-build model of a specific portion of Sepiapterin Reductase. The pre-build model is worth 40% of a team's final score for the event.

Alexis and Noah Beery, inspiration for the 2016 Protein Modeling competition.
Before the event:
  1. Build a model of part of the Sepiapterin Reductase molecule found in PDB entry 1sep.pdb, adding details that represent important parts of the structure.
  2. Additions to the model should highlight the significance of structure to function of the protein. (Do not highlight all amino acids in the protein).
Details:
  • The pre-build model will be created using a purchased "pre-build" Mini-Toober kit from 3D Molecular Designs, or with found materials of the participant's choosing such as KwikTwist tie-down ropes.
  • The same pre-build model will be used at each level of the competition (invitational, regional, state and national). Participants will take their pre-build model home after each event. Participants are allowed to make improvements or enhancements to your model as the team progresses through the various levels of competition.
  • The pre-build model must be impounded prior to the beginning of the event, usually the morning of the event.
  • The pre-build model should be submitted with written description (500 words or less, single spaced, 10 point font) of the model's colors and creative additions. Note that the format of this description has changed from prior years.
Resources
  • Participant Resources
    • This Year's Theme (tabs)
      • ⇒ "The Beery Twins' Story"- information about the function of Sepiapterin Reductase, and genetics of the Beery family.
      • ⇒ "Proteins, DNA and Genomes" - information on protein structure, flow of genetic information, genomes and personalized medicine.
      • ⇒ "This Year's Proteins" - Details about modeling targets for all levels of competition and information about their functions.
    • Building your model
      • Provides instructions for building the protein model using:
        • The visualization environment and how to manipulated it
        • Videos showing how to fold a mini-toober model
        • Deciding which residues of the model are important for its function and/or structural stability
    • The Pre-build Visualization Environment
      • Provides an JSmol environment to display the Sepiapterin Reductase protein based on the PDB file 1sep.pdb. The pre-build modeling target is limited to amino acids 93-261 of chain A of the protein.
    • Pre-build model details at This Year's Theme ⇒ This Year's Proteins (tab) ⇒ Pre-build model section
    • Annotated primary citation describing the structure of Sepiapterin Reductase
  • Additional model building resources from the RCSB PDB
  • Molecule of the Month on Tetrahydrobiopterin Biosynthesis
  • Skills required to learn about a molecular structural view of biology and medicine
Part 2: On-Site Model

Every team will create an on-site model of a specific protein structure on the day of the event. The on-site model is worth 30% of a team's final score for the event.

Model of a synapse highlighting modeling targets for various levels of the 2016 Protein Modeling competition.

For the various levels of competition, build selected regions of the specified protein.

  1. Invitational: G-Protein 1gia.pdb
  2. Regional: DOPA Decarboxylase 1js3.pdb
  3. State: Dopamine Transporter 4m48.pdb
  4. National: Dopamine Receptor 3pbl.pdb
Details
  • Each level of the competition (invitational, regional, state and national) will have its own specific protein structure for the on-site model.
  • Participants will be assigned the specific regions of the protein that they need to model at the event.
  • Participants will not be allowed to take their on-site models home after each event
  • The Mini-Toober and any additional materials for the on-site model will be provided to each team at the time of the competition.
  • Participants will only have the competition time period to complete your model.
Resources
Part 3: On-Site Exam

Each team will complete an on-site exam during the competition. The on-site written exam is worth 30% of a team's final score for the event.

Participants taking the on-site exam and building a protein model during the competition.
Details

Exams may cover topics related to the structure, function, importance and history of the protein(s) being discussed. Questions may also be asked from the relevant rcsb.org Molecule of the Month articles, or basic concepts of protein structure and biochemistry.

Resources
  • Carefully reviewing all sections of the "Participant Resources" on the MSOE CBM website is the best way to prepare for the on-site exam.
  • Participants will only have the competition time period to complete their on-site exam.