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Protein Folding: The Sequence Builds the Shape

Slide a chain of hydrophobic and polar beads from stretched to folded, watch the hydrophobic core bury itself into the low-energy native fold, and compare it against an exposed misfold.

Prologue · 1/5

One connected string of beads

A protein is a chain of amino-acid beads strung in a single line. In this experience we reduce their nature to two kinds — hydrophobic (H, warm colours), which dislikes water, and hydrophilic (P, cool colours), which is on good terms with it. A freshly made chain is stretched out like this, with the hydrophobic beads exposed to water — an uncomfortable state. First, take a look at the order of the sequence.

Trace, along the stretched chain, in what order the warm (H) and cool (P) beads are arranged.

Degree of folding 0% — extended ↔ fully folded

E=H-H contacts − exposure penalty=6.0

Folding StateNative · fold 0%

Energy6.0

Core buried17%

Compactness0%