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Structures of Protein

BioCodeKb - Bioinformatics Knowledgebase

Structures of Protein

Proteins are macromolecules and have four different levels of structure including primary, secondary, tertiary and quaternary.

Primary Structure

The primary structure is the sequence of amino acids that make up a polypeptide chain. It describes the unique order in which amino acids are linked together to form a protein. 

Proteins are constructed from a set of 20 amino acids. The three-dimensional shape of a protein is determined by its primary structure. The order of amino acids establishes a protein's structure and specific function. The distinct instructions for the order of amino acids are designated by the genes in a cell.

Secondary Structure

Secondary Structure is the coiling or folding of a polypeptide chain that gives the protein its 3-D shape. There are two types of secondary structures observed in proteins. One type is the alpha (α) helix structure. The second type is the beta (β) pleated sheet.

In an helix, the carbonyl (C=O) of one amino acid is hydrogen bonded to the amino H (N-H) of an amino acid that is four down the chain. This pattern of bonding pulls the polypeptide chain into a helical structure that resembles a curled ribbon, with each turn of the helix containing 3.6 amino acids. The R groups of the amino acids stick outward from the helix, where they are free to interact.

In a β pleated sheet, two or more segments of a polypeptide chain line up next to each other, forming a sheet-like structure held together by hydrogen bonds. The hydrogen bonds form between carbonyl and amino groups of backbone, while the R groups extend above and below the plane of the sheet. The strands of a β pleated sheet may be parallel, pointing in the same direction, or antiparallel, pointing in opposite directions.

Tertiary Structure

Tertiary Structure is the comprehensive 3-D structure of the polypeptide chain of a protein. There are many types of bonds and forces that hold a protein in its tertiary structure.

  • Hydrophobic interactions

  • Hydrogen bonding

  • ionic bonding

  • covalent bonding

Quaternary Structure

Quaternary Structure refers to the structure of a protein macromolecule formed by interactions between multiple polypeptide chains. Each polypeptide chain is known as a subunit. Proteins with quaternary structure may consist of more than one of the same type of protein subunit. They may also be composed of different subunits. Hemoglobin is an example of a protein with quaternary structure.

Structural domain

A structural domain is an element of the protein's overall structure that is self-stabilizing and often folds independently of the rest of the protein chain. Domains often are named and singled out because they figure prominently in the biological function of the protein they belong to.

Structural and sequence motif

The structural and sequence motifs are short segments of protein three-dimensional structure or amino acid sequence that were found in a large number of different proteins.

Supersecondary structure

The supersecondary structure is a specific combination of secondary structure elements, such as β-α-β units or a helix-turn-helix motif. Some of them may be also known as structural motifs.

Protein fold

A protein fold means the general protein architecture, like a helix bundle, β-barrel, Rossmann fold or different "folds" provided in the Structural Classification of Proteins database.


A superdomain consists of two or more nominally unrelated structural domains that are inherited as a single unit and occur in different proteins. An example is provided by the protein tyrosine phosphatase domain and C2 domain pair in PTEN, several tensin proteins, auxilin and proteins in plants and fungi.

Each protein has its own unique shape. If the temperature or pH of a protein's environment is changed, or if it is exposed to chemicals, these interactions may be disrupted, causing the protein to lose its three-dimensional structure and turn back into an unstructured string of amino acids.


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