Semantic resources project/Antibodies/Preliminary work/Definitions

Definitions
Antibody

Any of a large variety of proteins normally present in the body or produced in response to an antigen, which it neutralizes, thus producing an immune response (WordNet 3.0)

Antigen

An antigen is any substance that can bind to a specific antibody. All antigens have the potential to elicit specific antibodies, but some need to be attached to an immunogen to do so (Immunobiology, Janeway, Travers, Walport, Shlomchik, 2001). Antigens are usually proteins or polysaccharides. This includes parts (coats, capsules, cell walls, flagella, fimbrae, and toxins) of bacteria, viruses, and other microorganisms. Lipids and nucleic acids are antigenic only when combined with proteins and polysaccharides (Wikipedia)

Immunogen and Antigen

Immunogens are those substances that elicit a response from the immune system, whereas antigens are defined as substances that bind to specific antibodies. Not all antigens produce an immunogenic response (i.e. not all antigens are immunogenes), but all immunogens are antigens (Immunobiology, Janeway, Travers, Walport, Shlomchik, 2001)

Adjuvants (see Appendix A)

An adjuvant is any substance that enhances the immunogenicity of substances mixed with it.

Monoclonal Antibodies (see Appendix B)

Monoclonal antibodies are monospecific antibodies that are identical because they are produced by one type of immune cell that are all clones of a single parent cell. Given almost any substance, it is possible to create monoclonal antibodies that specifically bind to that substance; they can then serve to detect or purify that substance (Wikipedia).

Clone number

Monoclonal antibody are normally identified by a number given once the individual cell is identified as producing a monoclonal antibody that recognizes the antigen of interest.

Polyclonal Antibodies

Polyclonal antibodies (or antisera) are antibodies that are derived from different B cell lines. They are a mixture of immunoglobulin molecules secreted against a specific antigen, each recognizing a different epitope. These antibodies are typically produced by immunization of a suitable mammal, such as a mouse, rabbit or goat. Larger mammals (like horses) are often preferred as the amount of serum that can be collected is greater. An antigen is injected into the mammal. This induces the B-lymphocytes to produce IgG immunoglobulins specific for the antigen. This polyclonal IgG is polyclonal purified from the mammal’s serum (Wikipedia)

Specificity

Specificity determines the ability of the antibody to distinguish the immunogen from other antigens (Immunobiology, Janeway, Travers, Walport, Shlomchik, 2001). Specificity is dependent on chemical composition, physical forces, and molecular structure at the binding site (Source: CRISP)

Specificity and mono-/poly- clonal

Specificity depends on the antibody. If you have a high-specificity monoclonal, it could be more specific than a polyclonal (and often cleaner in western blot due to the lack of "contaminating" antibodies in polyclonal sera that are not directed against your protein of interest). However, many proteins do not lend themselves to good monoclonal generation, either because they are highly conserved, or otherwise are poorly immunogenic. In this case, a polyclonal can be a better choice, as the aggregate "avidity" of the polyclonal serum is higher than any single antibody. Another case where polyclonals are helpful is if your protein of interest occurs in many forms. In this case, change in protein conformation, phosphorylation, ubiquitinylation, etc., can mask the epitope that the monoclonal antibody binds, and you'll lose reactivity. In this case, you should have "coverage" in a polyclonal, due to the multiple epitopes the polyclonal antibodies recognize. (Source http://www.madsci.org/posts/archives/2004-08/1092972216.Im.r.html)

Epitopes (see Appendix C)

An antibody generally recognizes only a small region on the surface of a large molecule such as a polysaccharide or protein. The structure recognized by an antibody is called an antigenic determinant or epitope (Immunobiology, Janeway, Travers, Walport, Shlomchik, 2001).

Isotypes (see Appendix D)

In immunology, the "immunoglobulin isotype" refers to the genetic variations or differences in the constant region of the heavy chain of the Ig (immunoglobulins) classes and sub-classes (from Wikipedia).

Appendix A – Adjuvants
Most proteins are poorly immunogenic or non-immunogenic when administered by themselves. Strong adaptive immune responses to protein antigens almost always require that the antigen be injected in a mixture known as an adjuvant. Adjuvants differ from protein carriers in that they do not form stable linkages with the immunogen. Furthermore, adjuvants are needed primarily for initial immunizations, whereas carriers are required to elicit not only primary but also subsequent responses to haptens.

Appendix B – Monoclonal Antibodies
A monoclonal antibody is the result of a single B-cell - cancer-cell fusion, that is grown up into a clonal population (thus mono-clonal). The important thing here is that the monoclonal antibody produced will have identical idiotype/specificity (it is lots of one antibody). Monoclonals are usually produced by immunizing an animal, then removing the spleen and fusing it with a non-immunoglobin- producing B-cell cancer cell, forming a hybridoma. If the hybridoma makes antibody, the antibody-producing genes are from the spleen B cell, not the cancer B cell, but the cells will grow indefinitely in culture due to the transformed nature of the cancer B cell. The hybridomas are then cloned by limiting dilution or FACS-based single cell sorting and screened for desirable antibody production. So that's a monoclonal antibody. (Source http://www.madsci.org/posts/archives/2004-08/1092972216.Im.r.html). Interesting animation explaining monoclonal antibodies production.

Appendix C – Epitopes
Some of the most important pathogens are polysaccharide coats, and antibodies that recognize epitopes formed by the sugar subunits of these molecules are essential in providing immune protection from such pathogens. For example, protective antibodies against viruses recognize viral coat proteins. In many cases, however, the antigens that provoke an immune response are proteins. In such cases, the structures recognized by the antibodies are located on the surface of the protein. Such sites are likely to be composed of amino acids from different parts of the polypeptide chain that have been brought together by protein folding. Antigenic determinants of this kind are known as conformational or discontinuous epitopes because the structure recognized is composed of segments of the protein that are discontinuous in the amino acid sequence of the antigen but are brought together in the three-dimensional structure. In contrast, an epitope composed of a single segment of polypeptide chain is termed a continuous or linear epitope (Immunobiology, Janeway, Travers, Walport, Shlomchik, 2001).

The part of an antibody that recognizes the epitope is called a paratope. Epitopes are sometimes cross-reactive. This property is exploited by the immune system in regulation by anti-idiotypic antibodies (originally proposed by Nobel laureate Niels Kaj Jerne). If an antibody binds to an antigen's epitope, the paratope could become the epitope for another antibody that will then bind to it. If this second antibody is of IgM class, its binding can upregulate the immune response; if the second antibody is of IgG class, its binding can downregulate the immune response (Wikipedia)

Appendix D – Heavy and light chains
A heavy chain is the large polypeptide subunit of a protein complex, such as a motor protein (e.g. myosin, kinesin, or dynein) or antibody (or immunoglobulin). It commonly refers to the immunoglobulin heavy chain. Each heavy chain has two regions, the constant region and the variable region. The constant region is identical in all antibodies of the same isotype, but differs in antibodies of different isotypes. Heavy chains γ, α and δ have a constant region composed of three tandem (in a line) Ig domains, and a hinge region for added flexibility; heavy chains μ and ε have a constant region composed of four immunoglobulin domains. The variable region of the heavy chain differs in antibodies produced by different B cells, but is the same for all antibodies produced by a single B cell or B cell clone. The variable region of each heavy chain is approximately 110 amino acids long and is composed of a single Ig domain.