The Structures of Proteins

The chemistry of amino acid side chains determines how a protein folds and its three-dimensional shape. Hydrogen bonds form alpha-helixes and beta-pleated sheets in a protein’s secondary structure.


These are stabilized by interactions of nearby amino acids in the polypeptide backbone. These interactions also form ionic and disulfide bridges.

Primary Structure

The primary structure of proteins is the exact sequence of amino acids that make up the polypeptide chain. This is encoded in DNA and determines the shape and function of the protein. A change in the sequence will completely alter the protein’s function.

After the sequence is translated from mRNA into a linear polypeptide chain, it must fold to form its characteristic three dimensional shape. This folding is facilitated by the fact that peptide bonds can be formed between non-polar amino acid groups. This gives rise to a variety of stable patterns of folding known as alpha helixes and beta pleated sheets.

A few atoms in the chains are also able to form hydrogen bonds with each other. These give the chain an additional level of stability. In the case of the alpha helix, this gives it its helix-like appearance. Beta sheets are more flat. These are often found between alpha helices, with a -helix containing two anti-parallel beta strands joined by a -turn (which has a distinct 3.6 residue per turn repeat).

In some cases, the chains of amino acids will form shapes other than helixes and sheets. One example is the fibrous, or globular, protein structure. These are soluble in water and include such proteins as silk, hair, wool, and insulin. These structures are formed when the polypeptide chains run parallel and are held together by hydrogen and disulfide bonds.

Secondary Structure

Proteins are shaped by their secondary structures, which are local arrangements of amino acid side chains. The polypeptide chain can flex in two ways – either by looping outward (forming an alpha helix) or folding in on itself to form a beta pleated sheet. The shape of the protein is stabilized by hydrogen bonds between the amide groups on adjacent amino acid residues, and by other forces such as electrostatic interactions, disulphide bridges and van der Waals forces.

The most commonly observed forms of protein secondary structure are the alpha helix and the beta-pleated sheet. The amino acid side chains in an a-helix can be arranged in a variety of ways but are generally held within the helix by hydrogen bonding with the carbonyl groups of the backbone atoms. These bonds are stabilised by the fact that successive amino acids in a protein have different dihedral angles around the carbonyl group and so tend to adopt specific positions in the so-called Ramachandran plot.

Beta-pleated sheets are a more complex type of protein secondary structure. These are long strands of a protein in which adjacent polypeptide chains fold together, with each turn of the sheet forming two or more hydrogen bonds between the carbonyl groups on opposite sides of the sheet. These are also stabilised by the -NH group of each amino acid and the -CO group of the backbone. Other secondary structure is less well defined, forming random coils or turns and loops of varying lengths. These can be unstructured regions of the protein, or can have a functional role.

Tertiary Structure

The tertiary structure of proteins is a result of interactions between amino acid side chains that are located far away from one another in the polypeptide chain. These interactions are more complex than those involved in primary and secondary structures. Some of these interactions include ionic bonds formed between amino acids that have oppositely charged side chains; disulfide bridges (the only other covalent bond, besides the peptide bond, that holds protein subunits together); and hydrophobic interactions where non-polar amino acids cluster.

Hydrophobic interactions are particularly important in forming the tertiary structure of proteins. When a protein folds into its tertiary structure, the amino acids with hydrophobic side chains are usually found on the inside of the protein, whereas those with hydrophilic side chains are typically on the surface of the protein. This allows the polar amino acids to interact with water molecules and form hydrogen bonds, which help stabilize the protein’s shape.

The tertiary structure of proteins may also be stabilized by other interactions, such as sulphur bridges formed by the thiol groups of cysteine amino acids. These sulphur bridges are not part of the primary or secondary structure, but because they contribute to the stability of the protein’s tertiary structure, they are often included in discussions about proteins’ structure.

Quaternary Structure

The quaternary structure of proteins refers to the arrangement of protein molecules in a multi-subunit complex. It is the final level of protein folding and is crucial to protein function and activity. It is stabilized by the interaction of tertiary structures with each other via non-covalent bonds and can be influenced by other molecules, such as ligands and cofactors. The quaternary structure of a protein determines its overall shape. For example, in the case of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAH7PS), the quaternary structure favors the dimeric form of the enzyme over the tetramer because of the presence of “patches” on the interfaces formed by the subunits. The quaternary structure can be disrupted by substitutions of the amino acids that make up the protein.

In general, tertiary structure is stabilized by the formation of hydrogen bonding interactions between atoms in the backbone of the polypeptide chain (the part that is not occupied by R groups). These interactions are usually weak and include van der Waals interactions, electrostatic forces of attraction, salt bridges, disulfide bridges, and hydration interactions.

Many proteins are actually assemblies of several polypeptide chains referred to as protein sub-units or protein fragments. These sub-units have primary, secondary and tertiary structures that are specifically arranged to give the protein its final specific shape. The quaternary structure is stabilized by the same types of interactions, although to a lesser degree than in the case of single molecule proteins.