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A linear or a sequential epitope is an epitope that is recognized by antibodies by its linear sequence of amino acids, or primary structure. In contrast, most antibodies recognize a conformational epitope that has a specific three-dimensional shape and its protein structure.
An antigen is any substance that the immune system can recognize as foreign. Since, antigens are usually proteins that are too large to bind as a whole to any receptor, only specific segments that form the antigen bind with a specific receptor. Such segments are called epitopes. Likewise, it is only paratope of the receptor that comes in contact with the epitope.
Proteins are composed of repeating nitrogen-containing subunits called amino acids. The linear sequence of amino acids that compose a protein is called its primary structure, which does not exist in nature. But, when a an antigen is broken down in a lysosome, it yields small peptides, which can be recognized through the amino acids that lie continuously in a line, and hence are called linear epitopes.[1]
While performing molecular assays involving use of antibodies such as in the Western blot, immunohistochemistry, and ELISA, one should carefully choose antibodies that recognize linear or conformational epitopes.[2]
For instance, if a protein sample is boiled, treated with beta-mercaptoethanol, and run in SDS-PAGE for the Western blot, the proteins are essentially denatured and therefore cannot assume its natural three-dimensional conformation. Therefore, antibodies that recognize linear epitope instead of conformational epitope are chosen for immunodetection. In contrast, in immunohistochemistry where protein structure is preserved, antibodies are preferred that recognize conformational epitope.
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