Antigen

Terminology

Antigens can be proteins, polysaccharides, lipids, nucleic acids or other biomolecules. This includes parts (coats, capsules, cell walls, flagella, fimbriae, and toxins) of bacteria, viruses, and other microorganisms. Non-microbial non-self antigens can include pollen, egg white, and proteins from transplanted tissues and organs or on the surface of transfused blood cells.

• Immunogen — an antigen that is capable of inducing an immune response, i.e., it is immunogenic. Antigen is often used interchangeably with this term, but this is not, strictly speaking, correct. All immunogens are antigens, but not all antigens are immunogens. The antigen within a vaccine is often referred to as an immunogen, even if, strictly speaking, its purified form cannot induce immune responses (requiring adjuvants to do so). For simplicity, many sources use the term "antigen" in place of "immunogen," but these terms should not be regarded as interchangeable.
• Allergen – A substance capable of causing an allergic reaction in sensitized individuals. The reaction may result after exposure via ingestion, inhalation, injection, or contact with skin.
• Tolerogen – A substance that invokes immune tolerance. This property is related to its molecular properties and circumstances such as route of administration.
• Superantigen – A class of antigens that cause non-specific activation of T-cells, resulting in polyclonal T-cell activation and massive cytokine release.
• Immunoglobulin-binding protein – Proteins such as protein A, protein G, and protein L that are capable of binding to antibodies at positions outside of the antigen-binding site (paratope). These are sometimes known as B cell superantigens.
• Epitope – The specific part of an antigen that is bound by an antibody (or T cell receptor), its antigenic determinant.
  Antigenic molecules, normally "large" biological polymers, usually present surface features that can act as points of interaction for specific antibodies. Any such feature constitutes an epitope. Most antigens have the potential to be bound by multiple antibodies, each of which is specific to one of the antigen's epitopes. Using the "lock and key" metaphor, the antigen can be seen as a string of keys (epitopes) each of which matches a different lock (antibody). Different antibody idiotypes, each have distinctly formed complementarity-determining regions. Antibodies may compete for binding when they recognize overlapping epitopes.
• Paratope — The specific part of the antibody that binds the antigen (in general, the complementarity-determining region, though sometimes framework regions may contribute).
• Agretope — The specific peptide sequence recognized by a major histocompatibility complex (MHC).
• Hapten — A small molecule that can only induce an immune response when attached to a larger carrier molecule, such as a protein. The hapten alone will not be recognized if not associated with a carrier.
• T-dependent antigen – Antigens that require the assistance of T cells to induce the formation of specific antibodies.
• T-independent antigen – Antigens that can induce the production of antibodies without the help of T cells.
  • T-independent type I antigen — Mitogens that induce nonspecific activation of B cells (at smaller doses, they initially appeared specific to particular B cells, suggesting erroneously that this was an antigen-specific process; subsequent investigation proved their nonspecific nature)
  • T-independent type II antigen — Antigens containing multiple repetitive motifs that allow them to crosslink B cell receptors and directly activate the B cells. Bacterial capsule polysaccharides are a common example.
• Immunodominant antigens – Antigens that dominate (over all others from a pathogen) in their ability to produce an immune response. T cell responses typically are directed against a relatively few immunodominant epitopes, although in some cases (e.g., infection with the malaria pathogen Plasmodium spp.) it is dispersed over a relatively large number of parasite antigens. These are contrasted with immunosubdominant (sometimes referred to just as "subdominant") antigens.

Antigen-presenting cells present antigens in the form of peptides on major histocompatibility complexes. All nucleated cells (i.e., all cells except for red blood cells) express MHC class I, which samples peptides from the cytosol, defaulting to presenting self-antigen (unless something foreign ends up in the cytosol or if the cell is capable of cross-presentation). Antigens originating from outside the cell make their way into the endomembrane system via processes like phagocytosis, endocytosis, or macropinocytosis and are loaded onto MHC class II molecules. In contrast to MHC class I, MHC class II is expressed on a limited subset of cells, the vast majority of which are immune cells (some epithelial cells at mucosal surfaces may also express MHC class II). Often, when people refer to antigen-presenting cells, they are actually referring to professional antigen-presenting cells. Professional antigen-presenting cells refer to B cells, dendritic cells, Langerhans cells, and macrophages, all of which express MHC class II and have the ability to activate naive T cells (other antigen-presenting cells cannot supply naive T cells with all the signals required for activation). The MHC locus is the most polymorphic region of the entire human genome, and it is responsible for the presentation of antigens to T cells. This extensive polymorphism provides population-level protection by increasing the likelihood that some individuals will mount effective immune responses against novel pathogens, thus helping to ensure species survival during epidemics. Cheetahs, for example, underwent a bottleneck event 10,000 years ago that greatly limited the diversity of their MHC locus and as a result, show increased susceptibility to infectious diseases, though this represents one of multiple factors affecting their conservation status.

CD4 T cells (in general, helper T cells) are able to recognize MHC class II molecules using CD4, and their T-cell receptor recognizes the specific peptide-MHC complex sequence. In contrast, CD8 T cells (in general, killer T cells) are able to recognize MHC class I molecules through the α₃ domain of MHC class I (it does not recognize β2 microglobulin). T cell receptors are, in general, highly specific to particular peptide-MHC complexes. Some peptide sequences can only be presented by a specific type of MHC protein because they require specific amino acid sequences within the binding groove to associate with them. These are known as MHC-restricted peptides. If an individual does not express the relevant MHC protein needed for a given MHC-restricted peptide, they will not be able to present that antigen to T cells. This can be an important consideration in the design of vaccines, as a robust immune response should be generated in every vaccinee, which will not be possible if it has too many MHC-restricted peptide sequences and the vaccinee does not express the correct MHC polymorphism for effective presentation to T cells. Because the T cell receptor cannot recognize anything not presented on an MHC, conventional (see next paragraph) T cells are not capable of responding to non-peptide antigens (lipids, carbohydrates, etc), except in the case of post-translational modifications to peptides that end up being presented. This is important because polysaccharide vaccines elicit antibody responses without T cell help, and as a result, those antibody responses tend to be weak and short-lived (and young children have a particularly difficult time generating these antibodies for developmental reasons, which is a major issue because the polysaccharides in question are present on the surfaces of pathogenic bacteria). However, attaching the polysaccharide to a carrier protein (especially an immunogenic one, such as tetanus toxoid) enables B cells that recognize the polysaccharide to get help from T cells that recognize the carrier protein's peptides. These are known as conjugate vaccines or glycoconjugates. Moreover, the processing of an antigen by an antigen-presenting cell causes loss of the tertiary structure of the protein, meaning that T cells recognize linear epitopes only (the amino acids recognized have to be next to each other in the primary structure).

There are also subsets of T cells known as unconventional T cells that may recognize non-peptide antigens, or peptides. Many of these subsets show predominantly innate, rather than adaptive, functions. For example, γδ T cells express a T-cell receptor comprising γ and δ chains instead of the α and β chains that conventional T cell receptors use, and they are able to recognize antigen without the need for presenting it on MHC proteins (though some have shown the ability to recognize MHC-presented antigens), instead having a mode of recognition that resembles that of antibodies, or recognizing phosphoantigens (antigens that are phosphorylated) through butyrophilin. Mucosa-associated invariant T cells (MAIT) cells recognize ligands presented by the MHC-related protein MR1, which presents metabolites of riboflavin, pyridoxine, and folates. NKT cells recognize glycolipid antigens presented on CD1d, most prominently α-galactosylceramide.

In contrast to T cell receptors, antibodies can recognize any type of molecule at virtually any size and can recognize either linear or conformational epitopes (the amino acids that comprise an epitope do not need to be next to each other in the primary structure but do need to be near one another when the protein is folded). At the molecular level, an antigen can be characterized by its ability to bind to an antibody's paratopes. Different antibodies have the potential to discriminate among specific epitopes present on the antigen surface.

Antigenic specificity

Antigenic specificity is the ability of the host cells to recognize an antigen specifically as a unique molecular entity and distinguish it from another with exquisite precision. Antigen specificity is due primarily to the side-chain conformations of the antigen. It is measurable and need not be linear or of a rate-limited step or equation. Both T cells and B cells are cellular components of adaptive immunity.