tactile teaching: exploring the molecular world with physical models of proteins and other molecular...
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Tactile Teaching:Exploring the Molecular World with Physical Models of Proteins
and Other Molecular Structures
by
Tim Herman and Margaret Franzen Milwaukee School of EngineeringCenter for BioMolecular Modeling
www.rpc.msoe.edu/cbm
K12 Science Partnership Lunch
American Society of Cell Biology46th Annual Meeting
The MSOE Center for BioMolecular Modeling
• We make physical models of molecular structures, using rapid prototyping technology.
• Science Education Outreach Mission
• Professional Development Program for High School Science Teachers
• Undergraduate Curriculum Development
www.rpc.msoe.edu/cbm
x,y,z coordinatesProtein Data Bank RP-RasMol
Z Corp 3D-Printer
Ply/Stl file
Protein Models….in 4 Easy StepsProtein Models….in 4 Easy Steps
Any image that can be created in the computer environment of RasMol,…
… can now be converted to a physical model by rapid prototyping.
A Protein Model Starts with its PDB File.
From the Protein Data Bank at www.pdb.org
X Y ZATOM 1 N SER 2 30.025 8.937 50.567 ATOM 2 CA SER 2 28.952 9.913 50.747 ATOM 3 C SER 2 27.609 9.398 50.264 ATOM 4 O SER 2 27.526 8.372 49.583 ATOM 5 CB SER 2 29.255 11.278 50.115 ATOM 6 OG SER 2 28.067 11.842 49.558 ATOM 7 N LYS 3 26.559 10.149 50.603 ATOM 8 CA LYS 3 25.219 9.795 50.206
1833 Total Atoms 239 amino acids
MOLECULAR CAD…MOLECULAR CAD…...its all about triangles.
A Heme GroupEach triangle,---
3 points and a vector
Physical Models are Thinking ToolsPhysical Models are Thinking Tools
• are (almost) universally effective in
capturing students’ interest
• allow you to “see” things that are
not obvious in computer-generated
images.
• stimulate questions.
• are synergistic with computer
visualization tools
www.rpc.msoe.edu/cbm
Physical Models
Powerful
Exploring the Models IExploring the Models I
Water Kits…
www.rpc.msoe.edu/cbm
Amino Acid Starter Kit
Because:
• Life happens in water.
• Proteins fold in water.
• How does a protein know what shape to fold up into?
• The basic laws of chemistry that drive protein folding.
Physical Models and Computer Visualization Physical Models and Computer Visualization --- are Synergistic--- are Synergistic
www.rpc.msoe.edu/cbm/resources
Example:
How stringently are the “Chemical Principles that Govern Protein Folding” applied to real proteins?
--- A Jmol Tutorial ---
www.rpc.msoe.edu/cbm/resources
Science Education Outreach Programs
• NIH SEPA Program
• Summer Course for High School Teachers
• Two Student Enrichment Programs
• SMART Teams
• Science Olympiad Protein Folding event
www.rpc.msoe.edu/cbm
• NSF-CCLI Curriculum Projects
• Proteins in Active Learning Modules
PALM Workshop – June 2007
The PALM ProjectThe PALM ProjectProteins in Active Learning ModulesProteins in Active Learning Modules
• An NSF-CCLI Project
Making the Molecular World “Real” through the use of:
1. Physical Models
2. Computer Visualization Tools (Jmol)
3. Illustrations
4. Flash Animations
5. Graphical Representations of Data
www.rpc.msoe.edu/cbm
Multiple Representations
of Molecular
Structures.
Molecular StoriesMolecular Stories
Compelling molecular stories begin with Physical Models…
www.rpc.msoe.edu/cbm
…and are elaborated with an artful combination of
Computer VisualizationsIllustrationsAnimations
Graphical Representations of Data
…and a good teacher!
Two Molecular StoriesTwo Molecular Stories
www.rpc.msoe.edu/cbm
Molecular Gymnastics Evolution in Action
The Influenza HA Protein Acetylcholinesterase
How the influenza virus hemagglutinin protein undergoes a dramatic conformational change
upon endocytosis, leading to fusion of the viral and cellular
membranes.
How an effort to control mosquito populations by spraying with an
insecticide inevitably leads to the emergence of resistant mosquitoes.
The MSOE Model Lending Library
• Physical Model Collections --- in suitcases
• Borrow for two weeks, “just like a book from
Inter-Library Loan”
• No Cost, --- except for return postage.
• In Two Formats:
• Classroom Sets
• Discussion Props / Lab Stations
www.rpc.msoe.edu/cbm/lib
• Introduction to Protein Structure
• Serine Protease Collection
• Ribosome Collection
• Membrane Transport Collection
• Zinc Finger Collection
• DNA Collection
• Acetylcholinesterase ~New~
• Immunology Collection ~New~
Discussion Props and Lab Stations
www.rpc.msoe.edu/cbm/lib
• Amino Acid Starter Kit©
• Water Kit© Collection
• NaCl Lattices
• Alpha Helix/Beta Sheet Collection ~New~
• BioInformatics Map of the β-Globin Gene©
• DNA Discovery Kit©
• Mini-Toober β-Globin Folding Kit©
• MHC Class I Collection ~New~
Classroom Sets
www.rpc.msoe.edu/cbm/lib
The PALM ProjectProteins in Active Learning Modules
A 3-Day Summer Workshop for Undergraduate Faculty
www.rpc.msoe.edu/cbm/courses
June 6-8, 2007
Milwaukee School of Engineering
Models / Jmols / Animations / Illustrations
Assessment Instruments
3D Molecular Designs3D Molecular Designs
• A Small Business, spun off of the CBM
• A Dual Mission:
• To develop and commercialize innovative instructional materials
•To create custom protein models for researchers.
www.3dmoleculardesigns.com
• R&D Program Supported by SBIR awards
• RP-RasMol design software; Water Kit; DNA Discovery Kit; Paper Bioinformatics Maps; Beta-Globin Toober Folding Kit etc.
Rapid Prototyping Technology
• An Additive Manufacturing Technology
• A Layer-by-Layer Approach
• Five Technologies
• Sterolithography
• Laminated Object Manufacturing
• Selective laser Sintering
• Fused Deposition Modeling
• Color Z Corporation 3D Printing
www.rpc.msoe.edu/cbm