Amino acids affect the tertiary structure of a protein primarily through interactions between their side chains (R groups). These interactions determine the protein's unique three-dimensional shape and stability. Key ways amino acids influence tertiary structure include:
- Hydrophobic interactions: Nonpolar, hydrophobic amino acid side chains cluster inside the protein away from water, while polar, hydrophilic side chains tend to be on the outside interacting with the aqueous environment. This drives the folding pattern of the protein
- Hydrogen bonds: Polar side chains can form hydrogen bonds with each other or with the backbone, stabilizing the folded structure
- Ionic bonds (salt bridges): Charged side chains of acidic and basic amino acids form ionic bonds, contributing to the protein’s shape
- Disulfide bonds: Covalent bonds form between sulfur-containing cysteine residues, creating strong "molecular safety pins" that lock parts of the protein together
- Other interactions: Coordinate bonds with metal ions and London dispersion forces (van der Waals forces) between nonpolar side chains also help stabilize the tertiary structure
In summary, the tertiary structure of a protein is shaped and stabilized by the chemical properties and interactions of amino acid side chains, including hydrophobic clustering, hydrogen bonding, ionic bonds, disulfide bridges, and other non-covalent forces
