Transcript Visually Demonstrating the Principles of Protein Folding

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 Technology

C/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.
