Undergraduate · 30 min

Protein folding: hydrophobic collapse

Drive a model polypeptide from an open coil toward a compact fold by adding long-range contacts, and connect the picture to Anfinsen’s principle and modern structure prediction.

Goal

See how nonlocal contacts — mostly between hydrophobic residues — turn a floppy chain into a defined tertiary structure, and why $\Delta G$ of folding is small even though the search space is huge.

Apparatus and reagents

Virtual folding bench: a 48-residue model chain with hydrophobic beads highlighted and a slider that adds schematic long-range contacts; no chemicals needed.

Procedure

Start with zero contacts: drag the chain and note how open and irregular the coil is — this is the “denatured” ensemble.
Add 5–8 contacts and look at the red beads: they begin to pair up, sketching a hydrophobic core.
Push to 15–20 contacts: the structure looks knotted and compact, like a globular protein.
Count how many contacts join beads far apart in sequence versus neighbours: which ones stabilise a fold?
Imagine the same rule applied to a 300-residue protein: why does AlphaFold infer contacts from co-evolution rather than simulate folding?

What to observe

With few contacts the chain looks like spaghetti; with many, it collapses into a compact globule — the essence of hydrophobic collapse.
The dashed links mostly connect beads far apart along the chain — tertiary contacts, not local backbone bonds.
Even at maximum contacts, some red beads stay on the surface — real proteins are never perfectly hydrophobic inside.

Explanation

A folded protein buries hydrophobic side chains away from water, gaining favourable free energy; hydrogen bonds then lock secondary structure in the dehydrated core. The folded state wins only narrowly — $\Delta G_\mathrm{fold} \approx -20$ to $-65$ kJ/mol — because entropy fights collapse. Levinthal’s paradox (a chain cannot sample all conformations) is resolved by funnel-shaped energy landscapes, and AlphaFold sidesteps the search entirely by predicting inter-residue contacts learned from evolution.

History of the experiment

Anfinsen’s ribonuclease refolding (1961) proved sequence alone can specify the fold. Sixty years later AlphaFold2 (2020, Jumper, Hassabis et al.) solved the CASP14 challenge by predicting contacts from evolutionary couplings.

Chemists behind it

Christian B. Anfinsen David Baker Demis Hassabis John Jumper