Protein Folding Lab

Protein Folding Simulation: From Sequence to Structure

This protein folding simulation illustrates how the amino acid sequence of a polypeptide — its primary structure — determines the final three-dimensional conformation through secondary structure formation (alpha helices and beta sheets), hydrophobic collapse, disulfide bonding, and chaperone assistance. Students can modify amino acid properties, observe how hydrophobic residues drive core packing, and explore what happens when misfolding occurs, as in diseases like Alzheimer's and Parkinson's associated with aggregated amyloid fibrils. It brings structural biochemistry to life as a free online educational tool.

What you can do in this simulation

• Observe secondary structure formation — alpha helices and beta sheets — driven by backbone hydrogen bonding
• Watch hydrophobic residues collapse into the core of the protein, away from aqueous solvent
• Model disulfide bond formation between cysteine residues and its effect on structural stability
• Introduce chaperone proteins (Hsp70 family) and see how they prevent premature aggregation
• Simulate a missense mutation and observe how a single amino acid change can disrupt folding or cause aggregation

Concepts covered

protein folding · secondary structure · hydrophobic effect · molecular chaperones · protein misfolding · structural biochemistry

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