Transcript Protein Modeling Challenge Science Olympiad Trial Event

Protein Modeling Challenge
Science Olympiad Trial Event
Shannon Colton, Ph.D., Event Supervisor
Gary Graper, Event Technical Advisor
Protein Modeling Challenge
• To compete successfully in the Protein
Modeling Challenge, you will:
– Identify basic features of protein structure
– Explore protein structure with the
computer visualization program Jmol
– Create physical models using the flexible
modeling media, Mini-Toobers
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Web-Based Resources
•
This PowerPoint presentation will serve as an interactive resource for
your team to gain the knowledge they need to be successful in the
Protein Modeling Challenge
•
You will find links distributed throughout this presentation, indicated
by the blue underlined text
•
Follow these links to the appropriate sources
•
Good luck and have fun!
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Protein Structure
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Proteins are macromolecules
•
Amino acids are the basic building blocks of proteins
Sidechain (R-Group)
Alpha-Carbon
Carboxyl
Group
Nitrogen
Amino Group
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Protein Structure Resources
• The following links will serve as tools to help you learn the
basic information needed to be successful in this challenge.
Please follow these links:
– Basic Introduction to Protein Structure and Modeling
(www; this link will bring you to a webpage that has multiple
pdfs pertaining to protein structure at the bottom of the
page)
– Collection of models and activities: Introduction To Protein
Structure (ITOPS)
(www)
– MSOE Model Lending Library
(www)
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Amino Acids Have Unique
Chemical Characteristics
•
Each amino acid has the same “backbone” structure, but has
different chemical groups (R groups or sidechains) attached
•
Construct an amino acid and a dipeptide with a molymod kit (ITOPS)
(pdf)
NH2-CH-COOH
R
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Proteins Have Secondary Structure
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A linear chain of amino acids is the
protein “primary” structure
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A chain of amino acids will
spontaneously form stable “secondary
structures”, ie: beta-sheet or alphahelix
•
Alpha Helix
Construct an alpha-helix and betasheet activity (ITOPS, Introduction To
Protein Structure)
(pdf)
Beta-sheet
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Proteins Fold Into a
Tertiary Structure
•
Proteins spontaneously fold into a specific three dimensional “tertiary” structure
that governs a protein’s function
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Proteins Fold Into a
Tertiary Structure
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Protein folding is due to the behavior of different chemical groups
on amino acids in an aqueous environment
•
Explore amino acid sidechain chemistry and protein folding with
the Amino Acid Starter Kit Activity (ITOPS, Introduction To Protein
Structure)
(pdf)
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Defining Protein Structure
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The 3-dimensional structure of proteins is often determined by x-ray diffraction or
NMR analysis
•
Each atom in a protein is assigned a specific set of X, Y, Z coordinates in 3D space
to create a PDB data file
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Protein Data Bank
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PDB file lists the X, Y, Z coordinates for each atom in a protein
•
Protein Data Bank website is the location to download PDB files
(www)
•
PDB Molecule of the Month features the structure and function
of a different protein each month
(www)
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Molecule of the Month (MOM)
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A monthly PDB feature written by David Goodsell
–
Features a specific molecule
–
Describes protein function
–
Relates structure with function
Ribonucleases
September 2008
Molecule of the Month
(www)
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Jmol
•
•
Jmol is a computer visualization software that displays data from
a PDB file as a “3D” image of the molecule on the computer
screen
Jmol is Java-based and will work on most computers
•
We will use this website on the day of competitions.
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RasMol versus Jmol
•
•
•
Many of you may be familiar with RasMol. RasMol is a great program and may be
continued to be used by Science Olympiad Teams. However, since there have not
been updates to RasMol to allow for it to operate easily on Macs, Jmol will be the
computer visualization program to be used in the future.
The commands that you have used in RasMol are almost the same in Jmol.
You may practice using Jmol by using the this website.
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Exploring Protein
Structure with Jmol
•
Jmol allows you to identify elements of protein structure
– Helix (magenta)
– Sheet (yellow)
– N-terminus (or first amino acid in the protein
(blue)
– C-terminus (or the last amino acid in the protein)
(red)
– Amino acid sidechains (CPK)
– Alpha-carbon backbone model format
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Jmol Resources
• Use the following resources as tools in learning Jmol:
– Jmol free download
(www)
– Alternatively, use the same website that will be used on the
day of the competition (www)
– Assistance on downloading and installing Jmol on your
computer (pdf)
– Reference Card of Jmol commands, condensed
(www)
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Jmol Exercises
• Explore the structure of a zinc finger domain and beta-globin proteins and
practice RasMol
– Zinc Finger Exercise (www)
Answers (www)
– Beta Globin Exercise (www)
Answers (www)
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Mini-Toober Models
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Mini-Toobers are a flexible modeling media
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Developed by 3D Molecular Designs (3DMD) with a Small Business Initiative
Research grant (SBIR) from the National Science Foundation (NSF)
(www)
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Create Physical
Mini-Toober Models
•
•
Identify protein structural features using Jmol
(ie: helix, sheet)
Identify important amino acid sidechains that
play a significant role in the function of the
protein
– This can be accomplished by exploring the story
of the protein
– David Goodsell’s Molecule of the Month is a great
place to start
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Mini-Toober Models (cont.)
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Mark location of structures on Mini-Toober using a marker or pen
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Fold Mini-Toober into a 3D model representing protein based on the image you
created using Jmol
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Example Protein:
Zinc Finger Protein
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Zinc finger proteins bind DNA
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A zinc finger domain contains a short alpha-helix, 2 beta-strands and conserved
Cys, His amino acids that bind a molecule of zinc
•
For more information about the zinc finger protein, you can read David Goodsell’s
Molecule of the Month (www)
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Zinc Finger Folding Exercise
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Zinc Finger Folding Activity is available from MSOE Lending Library
– This activity will allow you to fold a toober into a zinc finger to
practice modeling proteins (www)
•
Challenge: Download the 1ZAA pdb file, create an image in Jmol,
identify key structural features, and fold a Mini-Toober model
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Protein Modeling Challenge
Science Olympiad Trial Event
• 2009 Event Rules
(www)
• Protein Modeling Event
– Pre-build model (40% of total score)
– On-site build (30% of total score)
– Written exam (30% of total score)
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Protein Modeling 2008
Prebuild
•
•
The 2008 Protein Modeling Event focused on the calcium-binding
protein – Calmodulin, described in the August 2003 Molecule of
the Month (www)
Teams constructed a model of the entire calmodulin protein for the
prebuild
Prebuild Rubric (pdf) – 40% of the final score
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Protein Modeling 2008
Onsite Builds
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For onsite competitions, selected regions of the calmodulin were
modeled
Regional Onsite Build Rubric (pdf) – 30% of the regional final score
State Onsite Build Rubric (pdf) – 30% of the state final score
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Protein Modeling 2008
Exam
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Teams also completed an exam based on protein structure and
specifically on the function of calmodulin
2008 State Exam (pdf) – 40% of final score
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National Science Content
Standards
•
•
•
•
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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
Detailed Alignment
(www)
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PDB Newsletter Features Protein
Modeling
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PDB Newsletter, No. 26, Summer 2005
(www)
PDB Newsletter, No. 33, Spring 2006
(www)
PDB Newsletter, No. 36, Winter 2008
(www)
PDB Newsletter, No. 38, Summer 2008
(www)
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Protein Modeling Supports Science
Olympiad Mission
• Emphasis on teamwork
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Protein Modeling Supports Science
Olympiad Mission
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Provides curriculum training workshops and web based distribution of materials
from the MSOE Center for BioMolecular Modeling web site
(www)
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Protein Modeling Supports
Science Olympiad Mission
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Brings science to life, shows how science works, emphasizes problem solving
aspects and understanding of concepts
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Protein Modeling Supports Science
Olympiad Mission
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Promotes partnerships among community, businesses, industry, and education
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Protein Modeling Supports
Science Olympiad Mission
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Promotes high level of achievement and demonstrates students can perform at
levels approaching practicing scientists
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CBM Programs
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Teacher Professional Development (www)
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–
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Genes, Schemes, Molecular Machines
Modeling the Molecular World
Molecular Stories of Research-Based Health Care
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SMART Teams (Students Modeling A Research Topic)
(www)
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MSOE Model Lending Library
(www)
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Science Olympiad Protein Modeling Challenge
(www)
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Additional Information
•
For more information, or to ask questions, please contact:
Shannon Colton, Ph.D., [email protected] or 414-277-2824
http://cbm.msoe.edu
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