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]
Significance
While performing molecular assays involving use of antibodies such as in Western blot, immunohistochemistry, ELISA, and others, care is taken into choosing 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 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 in which protein structure is preserved, antibodies that recognize conformational epitope is preferred.
