2.3.3—Interactions holding protein shape

A polypeptide’s tertiary structure is its overall three-dimensional shape. Interactions between R groups help hold that shape, and interactions between separate polypeptide chains can contribute when a protein has quaternary structure.

• Hydrophobic interactions: non-polar R groups tend to cluster away from water, helping form the protein’s interior.
• Hydrogen bonds: polar groups can form many relatively weak attractions that help stabilise particular folds.
• Ionic bonds: oppositely charged R groups attract and can support the folded arrangement.
• Disulfide bonds: two cysteine R groups can form a strong covalent bridge that stabilises the chain.
• Quaternary assembly: the same kinds of interactions can help hold multiple folded subunits together in a functional protein.

The exact R-group sequence determines which interactions are possible and where they occur. The resulting shape creates specific surfaces, pockets or binding sites, so changing the fold can change the protein’s function even when the peptide sequence itself has not been cut apart.

These are not all the same kind of link or the same strength: disulfide bonds are covalent, while hydrophobic interactions and many hydrogen-bond/ionic attractions are non-covalent. Do not list an interaction without identifying the relevant R groups, and do not treat a protein’s shape as independent of its sequence.