Visually Demonstrating the Principles of Protein Folding

1
Visually Demonstrating the Principles of Protein
Folding

• Bill McClung, Jeff Schwehm, Greg Wolffe

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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.

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Simple Ways To Think About Protein Folding

• Primary Sequence
• Secondary Structure
• Tertiary Structure
• Quaternary Structure

FLWKDQI
4
Biochemical Properties Involved in Protein or
Peptide Folding

• Hydrophobicity
• Hydrophilicity
• Like Interacts with Like
• Secondary Structure Propensities of the Amino
  Acids

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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.

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Generating the Visualization

• Model output is used to create an interactive 3D
  ribbon diagram of the molecule.
• Cross-platform Technology
• C/C, Perl
• OpenGL

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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.

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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.