Science Olympiad Protein Modeling Challenge Exploring Protein Structure

Science Olympiad Protein Modeling Challenge: Exploring Protein Structure through Technology This program is sponsored by a grant from NIH-NCRR-SEPA and the HHMI Pre-College Science Education Program.

What do we do at the Center for Bio. Molecular Modeling? • Create accurate 3 D molecular models • Professional development programs • Science education outreach programs

The CBM offers concrete representations of “invisible” structures. Mental Image Textbook Illustration Computer Generated Image Physical Image

Protein Models…. in 4 Easy Steps Stl file x, y, z coordinates Protein Data Bank RP-Ras. Mol Z Corp Printer

The Science Olympiad Mission To promote and improve student interest in science and to improve the quality of K 12 science education throughout the nation.

Protein Modeling Event – Identify basic features of protein structure – Explore protein structure with a computer visualization program – Create physical models using the flexible modeling media, Mini. Toobers (or alternative materials)

Protein Modeling Event Pre-Build (40%) • pre-built model based on a PDB file On-Site Build (30%) • model built on-site during competition Exam (30%) • questions relating protein structure and function

Protein Data Bank

Protein Data Bank Molecule of the Month

Understanding Protein Biochemistry Resources can be found online at cbm. msoe. edu/stupro/so/index. html

Visualizing the Molecule Resources can be found online at cbm. msoe. edu/stupro/so/index. html

Marking the Toober • Once a computer visualization image has been determined, secondary structure location should be noted and then marked on the toober. • Positions of significant amino acids should be marked on the toober as well.

Folding the Toober Videos online demonstrate how to mark and fold the toober to mimic the image created using the visualization program Resources can be found online at cbm. msoe. edu/stupro/so/index. html

Zinc Finger Folding Activity • Zinc finger proteins bind DNA • A zinc finger domain contains a short alpha-helix, 2 beta-strands and conserved Cys, His amino acids that bind a molecule of zinc

Score your model! Using the rubric provided, score your neighbors’ model of a zinc finger. How well did they do?

What we look for when scoring the models • Positioning of the blue/red end caps correctly • Correct number of helices/sheets • Correct positioning of helices/sheets (topology) • Right-handed helices • Correct tertiary structure (relative position of helices/sheets to one another) • Model has correct shape (is it globular, saddle shaped, etc) • For prebuild – creative additions to help tell the story • For onsite build – provided amino acids are positioned correctly, on the toober, but also in 3 D space (pointing inward or outward)

Common Mistakes • Blue cap/red cap in wrong position • N-terminus, or the beginning of the protein, is the BLUE cap and C-terminus, or the end of the protein, is the RED cap • Missing secondary structures • Model has 3 helices, and it should have 4 (or vice versa) • Left-handed helices • Tertiary structure is incorrect • Protein should be globular and it is flat • Creative additions on the prebuild are inappropriate • Incorrect sidechains • Too much information (all of the sidechains) • Onsite amino acids are positioned incorrectly • In the wrong spot (position 49 rather than 59) • Amino acids are pointing in the wrong direction (should be pointing to the center of the protein and it is facing outward)

The exam • The exam is a combination of multiple choice and short answers questions. • Questions cover • Basic chemistry questions regarding atoms, bonds and reactions • Basic protein structure • Structure/function relationship questions • Specific protein questions (for 2010 – Influenza Hemagglutinin and Neuraminidase) • Application questions (what would happen if…) • Ties will be broken using specific (labeled)questions on the exam.

Protein Modeling Event Addresses National Science Content Standards • Science and Technology – Abilities of Technological Design – Understandings about Science and Technology • Life Science – The Cell • Science as Inquiry – Abilities Necessary to do Scientific Inquiry • Physical Science – Structure and Properties of Matter – Chemical Reactions

Protein Modeling Event Addresses National Science Content Standards • Science and Technology – Abilities of Technological Design – Understandings about Science and Technology • Life Science – The Cell • Science as Inquiry – Abilities Necessary to do Scientific Inquiry • Physical Science – Structure and Properties of Matter – Chemical Reactions

Protein Modeling Event Addresses National Science Content Standards • Science and Technology – Abilities of Technological Design – Understandings about Science and Technology • Life Science – The Cell • Science as Inquiry – Abilities Necessary to do Scientific Inquiry • Physical Science – Structure and Properties of Matter – Chemical Reactions

Protein Modeling Event Addresses National Science Content Standards • Science and Technology – Abilities of Technological Design – Understandings about Science and Technology • Life Science – The Cell • Science as Inquiry – Abilities Necessary to do Scientific Inquiry • Physical Science – Structure and Properties of Matter – Chemical Reactions

Protein Modeling Supports Science Olympiad Mission • Emphasis on teamwork

Protein Modeling Supports Science Olympiad Mission • Brings science to life, shows how science works, emphasizes problem solving aspects and understanding of concepts

Protein Modeling Supports Science Olympiad Mission • Promotes partnerships among community, businesses, industry, and education

Protein Modeling Supports Science Olympiad Mission • Promotes high level of achievement and demonstrates students can perform at levels approaching practicing scientists

The CBM works with you to offer this event within your state! • Provides curriculum training workshops and web based distribution of materials from the MSOE Center for Bio. Molecular Modeling web site (cbm. msoe. edu/stupro/so/index. html) • We can come to your state to provide a workshop

Model Lending Library

Professional Development Workshop Modeling the Molecular World Part I: Tactile Teaching with Physical Models A $200 workshop fee covers the cost of: • workshop materials, including hands-on models and instructional materials to take back to your classroom • 3 hours special graduate credit* • breakfast and snacks • dormitory housing for 1 week including room, bed linens, towels • lifetime membership in a community of innovative teachers making the molecular world come alive for their students * These graduate credits are intended for teacher certification purposes. They do not apply to other advanced degree programs. http: //cbm. msoe. edu/prof. Dev/mmw 1/index. html

SMART Teams: Students Modeling A Research Topic “SMART Teams become producers of visual artifacts, written in a tactile, 3 D language. ”