Tactile Teaching: Exploring the Molecular World with Physical Models of Proteins and Other Molecular Structures by Tim Herman and Margaret Franzen Milwaukee.

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