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Visually Demonstrating the Principles of Protein Folding

Explore the principles of protein folding through a 3D visualization tool. Understand primary to quaternary structures, biochemical properties, and model development using cross-platform technology.

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Visually Demonstrating the Principles of Protein Folding

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  1. Visually Demonstrating the Principles of Protein Folding Bill McClung, Jeff Schwehm, Greg Wolffe

  2. 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.

  3. 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

  5. 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.

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

  7. 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.

  8. 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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