An extended chain of residues collapses into a compact 3D structure.
From the chapter: Chapter 17: Applications
Glossary: alphafold, protein folding, hydrophobic collapse
People: demis hassabis, john jumper, david baker
Transcript
A protein is a chain of amino acids that folds into a precise three-dimensional shape. The sequence determines the shape; the shape determines the function.
Here is the unfolded chain. Yellow circles are hydrophobic residues that avoid water. Blue circles are polar residues that prefer to face the surrounding solvent.
Inside a cell, the chain rapidly explores conformations driven by physical forces: hydrogen bonds, van der Waals contacts, and the hydrophobic effect.
Hydrophobic residues drift inward, hiding from water. Polar residues rotate outward to face the solvent. This is the hydrophobic collapse.
Within milliseconds the chain settles into its native fold, a single low-energy structure. This is what every protein in your body does, all the time.
Predicting that final shape from sequence was unsolved for fifty years. AlphaFold cracked it in 2020 using a neural network trained on the Protein Data Bank.