Paratope in the context of "B cell"

An antibody (Ab), or immunoglobulin (Ig), is a large protein belonging to the immunoglobulin superfamily which is used by the immune system to identify and neutralize antigens such as bacteria and viruses, including those that cause disease. Each individual antibody recognizes one or more specific antigens, and antigens (a portmanteau of "antibody generator") of virtually any size and chemical composition can be recognized. Each of the branching chains comprising the "Y" of an antibody contains a paratope (the antigen-binding site) that specifically binds to one particular epitope (a specific part of an antigen bound by the paratope) on an antigen, allowing the two molecules to bind together with precision. Using this mechanism, antibodies can effectively "tag" the antigen (or a microbe or an infected cell bearing such an antigen) for attack by cells of the immune system, or can neutralize it directly (for example, by blocking a part of a virus that is essential for its ability to invade a host cell).

Antibodies may be borne on the surface of an immune cell, as in a B cell receptor, or they may exist freely by being secreted into the extracellular space. The term antibody generally refers to the free (secreted) form, while the term immunoglobulin can refer to either forms. Since they are, broadly speaking, the same protein, the terms are often treated as synonymous.

An epitope, also known as antigenic determinant, is the part of an antigen that is recognized by the immune system, specifically by antibodies, B cells, or T cells. The part of an antibody that binds to the epitope is called a paratope. Although epitopes are usually non-self proteins, sequences derived from the host that can be recognized (as in the case of autoimmune diseases) are also epitopes.

The epitopes of protein antigens are divided into two categories, conformational epitopes and linear epitopes, based on their structure and interaction with the paratope. Conformational and linear epitopes interact with the paratope based on the 3-D conformation adopted by the epitope, which is determined by the surface features of the involved epitope residues and the shape or tertiary structure of other segments of the antigen. A conformational epitope is formed by the 3-D conformation adopted by the interaction of discontiguous amino acid residues. In contrast, a linear epitope is formed by the 3-D conformation adopted by the interaction of contiguous amino acid residues. A linear epitope is not determined solely by the primary structure of the involved amino acids. Residues that flank such amino acid residues, as well as more distant amino acid residues of the antigen affect the ability of the primary structure residues to adopt the epitope's 3-D conformation. 90% of epitopes are conformational.