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Antibody-protein interactions: benchmark datasets and prediction tools evaluation
{{DEFAULTSORT:Conformational Epitope Molecular biology
In immunology
Immunology is a branch of biology and medicine that covers the study of Immune system, immune systems in all Organism, organisms.
Immunology charts, measures, and contextualizes the Physiology, physiological functioning of the immune system in ...
, a conformational epitope is a sequence of sub-units (usually amino acids
Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although over 500 amino acids exist in nature, by far the most important are the Proteinogenic amino acid, 22 α-amino acids incorporated into p ...
) composing an antigen
In immunology, an antigen (Ag) is a molecule, moiety, foreign particulate matter, or an allergen, such as pollen, that can bind to a specific antibody or T-cell receptor. The presence of antigens in the body may trigger an immune response.
...
that come in direct contact with a receptor
Receptor may refer to:
* Sensory receptor, in physiology, any neurite structure that, on receiving environmental stimuli, produces an informative nerve impulse
*Receptor (biochemistry), in biochemistry, a protein molecule that receives and respond ...
of the immune system
The immune system is a network of biological systems that protects an organism from diseases. It detects and responds to a wide variety of pathogens, from viruses to bacteria, as well as Tumor immunology, cancer cells, Parasitic worm, parasitic ...
.
An ''antigen'' is any substance that the immune system can recognize as foreign. Antigens are usually protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...
s that are too large to bind as a whole to any receptor so only specific segments, that form the antigen, bind with a specific receptor. Such segments are called ''epitope
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 e ...
s''. Likewise, it is only the paratope
In immunology, a paratope, also known as an antigen-binding site, is the part of an antibody which recognizes and binds to an antigen. It is a small region at the tip of the antibody's antigen-binding fragment and contains parts of the antibody' ...
of the receptor that comes in contact with the epitope.
Proteins are composed of repeating nitrogen
Nitrogen is a chemical element; it has Symbol (chemistry), symbol N and atomic number 7. Nitrogen is a Nonmetal (chemistry), nonmetal and the lightest member of pnictogen, group 15 of the periodic table, often called the Pnictogen, pnictogens. ...
-containing subunits called amino acid
Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although over 500 amino acids exist in nature, by far the most important are the 22 α-amino acids incorporated into proteins. Only these 22 a ...
s that in nature do not exist as straight chains but as folded whorls with complex loops. The latter is known as the tertiary structure
Protein tertiary structure is the three-dimensional shape of a protein. The tertiary structure will have a single polypeptide chain "backbone" with one or more protein secondary structures, the protein domains. Amino acid side chains and the ...
of a protein. So, whenever a receptor interacts with an undigested antigen, the surface amino acids that come in contact may not be continuous with each other if the protein is unwound. Such discontinuous amino acids that come together in three-dimensional conformation and interact with the receptor's paratope are called conformational epitopes. In contrast, if the antigen is digested, small segments called peptide
Peptides are short chains of amino acids linked by peptide bonds. A polypeptide is a longer, continuous, unbranched peptide chain. Polypeptides that have a molecular mass of 10,000 Da or more are called proteins. Chains of fewer than twenty am ...
s are formed, which bind with major histocompatibility complex
The major histocompatibility complex (MHC) is a large Locus (genetics), locus on vertebrate DNA containing a set of closely linked polymorphic genes that code for Cell (biology), cell surface proteins essential for the adaptive immune system. The ...
molecules, and then later with T cell receptor
The T-cell receptor (TCR) is a protein complex, located on the surface of T cells (also called T lymphocytes). They are responsible for recognizing fragments of antigen as peptides bound to major histocompatibility complex (MHC) molecules. ...
s through amino acids that are continuous in a line. These are known as linear epitope
In immunology, a linear epitope (also sequential epitope) is an epitope—a binding site on an antigen—that is recognized by antibodies by its linear sequence of amino acids (i.e. primary structure). In contrast, most antibodies recognize a co ...
s.
See also
*Antigen
In immunology, an antigen (Ag) is a molecule, moiety, foreign particulate matter, or an allergen, such as pollen, that can bind to a specific antibody or T-cell receptor. The presence of antigens in the body may trigger an immune response.
...
* Linear epitope
In immunology, a linear epitope (also sequential epitope) is an epitope—a binding site on an antigen—that is recognized by antibodies by its linear sequence of amino acids (i.e. primary structure). In contrast, most antibodies recognize a co ...
* Epitope mapping
In immunology, epitope mapping is the process of experimentally identifying the binding site, or ''epitope'', of an antibody on its target antigen (usually, on a protein). Identification and characterization of antibody binding sites aid in the d ...
, finding (on an antigen protein) the epitope(s) for a specific antibodyReferences
External links
Antibody-protein interactions: benchmark datasets and prediction tools evaluation
{{DEFAULTSORT:Conformational Epitope Molecular biology