Download Visually Demonstrating the Principles of Protein Folding

Visually Demonstrating the
Principles of Protein Folding
Bill McClung, Jeff Schwehm, Greg Wolffe
Teaching About Molecules
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Molecules are complicated 3D objects.
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We use 2D representations that are
difficult for students to visualize in 3D.
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3D visualization tools help convey the
story about these molecules.
Simple Ways To Think About Protein
Folding
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Primary Sequence
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Secondary Structure
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Tertiary Structure
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Quaternary Structure
FLWKDQI
Biochemical Properties Involved in
Protein or Peptide Folding
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Hydrophobicity
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Hydrophilicity
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Like Interacts with Like
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Secondary Structure Propensities of the
Amino Acids
Developing the Model
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Each amino acid has empirically
determined values of properties.
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Mathematical model uses amino acid
sequences and these values to predict
secondary structure.
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The model produces coordinates that
represent this secondary structure.
Generating the Visualization
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Model output is used to create an
interactive 3D ribbon diagram of the
molecule.
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Cross-platform Technology
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C/C++, Perl
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OpenGL
Instructor Usage
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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.
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