Antibody

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 those that exist on bacteria and virus cells, including those that cause disease. Each individual antibody recognizes one or more specific antigens, and antigens of virtually a

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 those that exist on bacteria and virus cells, including those that cause disease. Each individual antibody recognizes one or more specific antigens,[1][2] and antigens (a portmanteau of "antibody generator") of virtually any size and chemical composition can be recognized.[3] 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.[4]

To allow the immune system to recognize millions of different antigens, the antigen-binding paratopes at each tip of the antibody come in an equally wide variety. The rest of an antibody's structure is much less variable; in humans, antibodies occur in five classes or isotypes: IgA, IgD, IgE, IgG, and IgM. Human IgG and IgA antibodies are also divided into discrete subclasses (IgG1, IgG2, IgG3, and IgG4; IgA1 and IgA2). The class refers to the functions triggered by the antibody (also known as effector functions), in addition to some other structural features. Antibodies from different classes also differ in where they are released in the body and at what stage of an immune response. Between species, while classes and subclasses of antibodies may be shared (at least in name), their function and distribution throughout the body may be different, which complicates the use of animal models in studying antibodies. For example, mouse IgG1 is closer to human IgG2 than to human IgG1 in terms of its function.

The term humoral immunity is often treated as synonymous with the antibody response, describing the function of the immune system that exists in the body's humors (fluids) in the form of soluble proteins, as distinct from cell-mediated immunity, which generally describes the responses of T cells (especially killer T cells). In general, antibodies are considered part of the adaptive immune system, though this classification can become complicated. For example, natural IgM,[5] which are made by B-1 cells that have properties more similar to innate immune cells than adaptive, refers to IgM antibodies made independently of an immune response that demonstrate polyreactivity—i.e. they recognize multiple distinct (unrelated) antigens. These can work with the complement system in the earliest phases of an immune response to help facilitate clearance of the offending antigen and delivery of the resulting immune complexes to the lymph nodes or spleen for initiation of an immune response. Hence in this capacity, the functions of antibodies are more akin to that of innate immunity than adaptive. Nonetheless, in general, antibodies are regarded as part of the adaptive immune system because they demonstrate exceptional specificity (with some exceptions), are produced through genetic rearrangements (rather than being encoded directly in the germline), and are a manifestation of immunological memory.

Sources of antibodies

Antibodies arise from antibody-secreting cells, a term that encompasses plasmablasts and plasma cells. B cells themselves are not able to secrete antibody and can only present immunoglobulins on their surface because they do not express the critical transcription factor BLIMP-1, which establishes the antibody-secreting cell transcriptional program (including altering alternative splicing and polyadenylation to generate the secreted form of the immunoglobulin heavy chain rather than the membrane-bound one; secretion of antibody is not protease-dependent).[6]

In the course of an immune response, B cells can progressively differentiate into antibody-secreting cells or into memory B cells.[7] Plasmablasts and plasma cells differ mainly in the degree to which they secrete antibodies, their lifespan, metabolic adaptations, and surface markers.[8] Plasmablasts are rapidly proliferating, short-lived cells produced in the early phases of the immune response (classically described as arising from extrafollicular reactions rather than from a germinal center) which have the potential to differentiate further into plasma cells.[9] Occasionally plasmablasts are mis-described as short-lived plasma cells; formally this is incorrect because plasma cells do not divide (they are terminally differentiated), and rely on survival niches comprising specific cell types and cytokines to persist.[10] It is commonly said that plasma cells do not express surface immunoglobulin (whereas plasmablasts do), but this depends on the class of antibody that the plasma cell generates (IgG-secreting plasma cells do not, but IgM, IgA, and IgE plasma cells do).[11][12] Plasma cells will secrete huge quantities of antibody regardless of whether or not antigen is present, ensuring that antibody levels to the antigen in question do not fall to zero, provided the plasma cell stays alive. The rate of antibody secretion, however, can be regulated, for example, by the presence of adjuvant molecules that stimulate the immune response such as toll-like receptor ligands.[13] Long-lived plasma cells can live for potentially the entire lifetime of the organism.[14] Classically, the survival niches that house long-lived plasma cells reside in the bone marrow,[15] though it cannot be assumed that any given plasma cell in the bone marrow will be long-lived. However, other work indicates that survival niches can readily be established within the mucosal tissues, though the classes of antibodies involved show a different hierarchy from those in the bone marrow.[16][17]

B cells can also differentiate into memory B cells which can persist for decades, similarly to long-lived plasma cells. These cells can be rapidly recalled in a secondary immune response, undergoing class switching, affinity maturation, and differentiating into antibody-secreting cells.

Structure

Antibodies are heavy (~150 kDa) proteins of about 10 nm in size,[18] arranged in three globular regions that roughly form a Y shape.

In humans and most other mammals, an antibody unit consists of four polypeptide chains; two identical heavy chains and two identical light chains connected by disulfide bonds.[19] Each chain is a series of domains: somewhat similar sequences of about 110 amino acids each. These domains are usually represented in simplified schematics as rectangles. Light chains consist of one variable domain VL and one constant domain CL, while heavy chains contain one variable domain VH and three to four constant domains CH1, CH2, ...[20]

Structurally an antibody is also partitioned into two antigen-binding fragments (Fab), containing one VL, VH, CL, and CH1 domain each, as well as the crystallisable fragment (Fc), forming the trunk of the Y shape.[21] In between them is a hinge region of the heavy chains, whose flexibility allows antibodies to bind to pairs of epitopes at various distances, to form complexes (dimers, trimers, etc.), and to bind effector molecules more easily.[22]

In an electrophoresis test of blood proteins, antibodies mostly migrate to the last, gamma globulin fraction. Conversely, most gamma-globulins are antibodies, which is why the two terms were historically used as synonyms, as were the symbols Ig and γ. This variant terminology fell out of use due to the correspondence being inexact and due to confusion with γ (gamma) heavy chains which characterize the IgG class of antibodies.[23][24]

Antigen-binding site

The variable domains can also be referred to as the FV region. It is the subregion of Fab that binds to an antigen. More specifically, each variable domain contains three hypervariable regions – the amino acids seen there vary the most from antibody to antibody. When the protein folds, these regions give rise to three loops of β-strands, localized near one another on the surface of the antibody. These loops are referred to as the complementarity-determining regions (CDRs), since their shape complements that of an antigen. Three CDRs from each of the heavy and light chains together form an antibody-binding site whose shape can be anything from a pocket to which a smaller antigen binds, to a larger surface, to a protrusion that sticks out into a groove in an antigen. Typically though, only a few residues contribute to most of the binding energy.[1]

The existence of two identical antibody-binding sites allows antibody molecules to bind strongly to multivalent antigen (repeating sites such as polysaccharides in bacterial cell walls, or other sites at some distance apart), as well as to form antibody complexes and larger antigen-antibody complexes.[1]

The structures of CDRs have been clustered and classified by Chothia et al.[25] and more recently by North et al.[26] and Nikoloudis et al.[27] However, describing an antibody's binding site using only one single static structure limits the understanding and characterization of the antibody's function and properties. To improve antibody structure prediction and to take the strongly correlated CDR loop and interface movements into account, antibody paratopes should be described as interconverting states in solution with varying probabilities.[28]

In the framework of the immune network theory, CDRs are also called idiotypes. According to immune network theory, the adaptive immune system is regulated by interactions between idiotypes.[29]

Fc region

The Fc region (the trunk of the Y shape) is composed of constant domains from the heavy chains. Its role is in modulating immune cell activity: it is where effector molecules bind to, triggering various effects after the antibody Fab region binds to an antigen.[1][22] Effector cells (such as macrophages or natural killer cells) bind via their Fc receptors (FcR) to the Fc region of an antibody, while the complement system is activated by binding the C1q protein complex (also via the Fc region). IgG or IgM can bind to C1q, but IgA cannot, therefore IgA does not activate the classical complement pathway.[30]

Another role of the Fc region is to selectively distribute different antibody classes across the body. In particular, the neonatal Fc receptor (FcRn) binds to the Fc region of IgG antibodies to transport it across the placenta, from the mother to the fetus. In addition to this, binding to FcRn endows IgG with an exceptionally long half-life relative to other plasma proteins of 3-4 weeks. IgG3 in most cases (depending on allotype) has mutations at the FcRn binding site which lower affinity for FcRn, which are thought to have evolved to limit the highly inflammatory effects of this subclass.[31]

Antibodies are glycoproteins,[32] that is, they have carbohydrates (glycans) added to conserved amino acid residues.[32][33] These conserved glycosylation sites occur in the Fc region and influence interactions with effector molecules.[32][34]

Protein structure

The N-terminus of each chain is situated at the tip. Each immunoglobulin domain has a similar structure, characteristic of all the members of the immunoglobulin superfamily: it is composed of between 7 (for constant domains) and 9 (for variable domains) β-strands, forming two beta sheets in a Greek key motif. The sheets create a "sandwich" shape, the immunoglobulin fold, held together by a disulfide bond.[35][36]

Antibody complexes

Secreted antibodies can occur as a single Y-shaped unit, a monomer. However, some antibody classes also form dimers with two Ig units (as with IgA), tetramers with four Ig units (like teleost fish IgM), or pentamers with five Ig units (like shark IgW or mammalian IgM, which occasionally forms hexamers as well, with six units).[37] IgG can also form hexamers, though no J chain is required.[38] IgA tetramers and pentamers have also been reported.[39]

Antibodies also form complexes by binding to antigen: this is called an antigen-antibody complex or immune complex. Small antigens can cross-link two antibodies, also leading to the formation of antibody dimers, trimers, tetramers, etc. Multivalent antigens (e.g., cells with multiple epitopes) can form larger complexes with antibodies. An extreme example is the clumping, or agglutination, of red blood cells with antibodies in blood typing to determine blood groups: the large clumps become insoluble, leading to visually apparent precipitation.[40][41][42]