Visually Demonstrating the Principles of Protein Folding

Bill McClung, Jeff Schwehm, Greg Wolffe

Teaching About Molecules

Molecules are complicated 3D objects.

We use 2D representations that are

difficult for students to visualize in 3D.

3D visualization tools help convey the

story about these molecules.

Simple Ways To Think About Protein Folding

Primary Sequence

Secondary Structure

Tertiary Structure

Quaternary Structure

FLWKDQI

Biochemical Properties Involved in Protein or Peptide Folding

Hydrophobicity

Hydrophilicity

Like Interacts with Like

Secondary Structure Propensities of the

Amino Acids

Developing the Model

Each amino acid has empirically determined values of properties.

Mathematical model uses amino acid sequences and these values to predict secondary structure.

The model produces coordinates that represent this secondary structure.

Generating the Visualization

Model output is used to create an

interactive 3D ribbon diagram of the

molecule.

Cross-platform TechnologyC/C++, Perl

OpenGL

Instructor Usage

Not to accurately predict protein folding. To demonstrate the principles of secondary

structure formation. Used as a bridge to “real, industrial strength”

tools. (PDB tools) Targeted for high school students and lower

level undergraduates. Courses: Biology, Chemistry, Biochemistry

and General Science.

Student Usage

Can select and/or modify amino acid sequences to develop an intuition of the resulting 3D structure.

Can change the weighting of properties such as hydrophobicity or propensities to develop a deeper understanding of the effect of these properties on folding behavior.