Tertiary folding can result from one or more of several types of bonding:

• Hydrogen bonding between backbone and side-chain groups not involved in alpha-helix or beta-sheet structure.

• Ionic bonding between positively and negatively charged amino acid side chains.

• Hydrophobic bonding, in which hydrophobic side chains associate together to remove themselves from water.

• Covalent bonding of two -SH groups to form an -S-S linkage called a disulfide bridge. These covalent bonds give the folded protein additional strength.

Alkaline phosphatase is an example of a protein with many levels of structure. This enzyme hydrolyzes (releases) phosphate groups from a variety of organic molecules. It consists of two polypeptide chains and, when folded, contains substantial regions of beta sheet and alpha helix, as well as less compactly folded regions of random coil, shown in the ribbon model above.

Other proteins fold differently. Some proteins, such as silk, contain only beta sheet; others, such as myoglobin, contain only alpha helix.

Alpha-helical regions are represented by light-blue (or turquoise) coiled ribbons, and beta-sheet regions are represented by dark-blue flat ribbons with arrowheads indicating the direction of the backbone chain. Regions of random coil (no regular structure) are displayed as thinner strands.