Framework region

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The universal structure of antibody includes the constant regions part of the fragment crystallizable(Fc) region of the antibody (shown in dark blue). It also includes the fragment antigen binding which is composed of one heavy and one light chain (shown as L for light and H for heavy). Each heavy and light chain is composed of one variable region and one constant region (shown as V or C). The variable regions are composed of 7 amino acid segments; three of which are hypervariable regions or CDR (yellow) and four of which are FR(shown in green for heavy chains and pink for light chains). Antibody Structure and Antigen Binding Regions.jpg
The universal structure of antibody includes the constant regions part of the fragment crystallizable(Fc) region of the antibody (shown in dark blue). It also includes the fragment antigen binding which is composed of one heavy and one light chain (shown as L for light and H for heavy). Each heavy and light chain is composed of one variable region and one constant region (shown as V or C). The variable regions are composed of 7 amino acid segments; three of which are hypervariable regions or CDR (yellow) and four of which are FR(shown in green for heavy chains and pink for light chains).

In molecular biology, a framework region is a subdivision of the variable region (Fab) of the antibody. The variable region is composed of seven amino acid regions, four of which are framework regions and three of which are hypervariable regions. [1] The framework region makes up about 85% of the variable region. [2] Located on the tips of the Y-shaped molecule, the framework regions are responsible for acting as a scaffold for the complementarity determining regions (CDR), also referred to as hypervariable regions, of the Fab. These CDRs are in direct contact with the antigen and are involved in binding antigen, while the framework regions support the binding of the CDR to the antigen [3] and aid in maintaining the overall structure of the four variable domains on the antibody. [4] To increase its stability, the framework region has less variability in its amino acid sequences compared to the CDR. [2]

Contents

Function

The antibody has a three-dimensional structure with beta pleated sheet and alpha helices. [5] The antibody folds so the variable regions form three loops with the framework regions folded into one another and the CDR regions on the tips of each of these loops in direct contact with the antigen. [5] [6] [7] Residues are short amino acid sequences, residues of the framework region responsible for supporting the binding of the antigen to the antibody can be divided into two categories; residues that are in contact with the antigen and those not in contact with the antigen. Framework residues that come in contact with the antigen are a part of the antibody's binding site, and are located either close in sequence to the CDRs or in close proximity to the CDR when in the folded three dimensional structure. [4] Framework residues that do not come in contact with the antigen affect the binding indirectly by aiding in structural support for the CDR. This enables the CDR to take on the correct orientation and position so it is exposed on the surface of the chain ready to bind to an antigen. [2]

The framework regions are highly conserved regions of the variable portion of the antibody. The evolutionary reason for the conservation of these regions is to support proper folding of the antibody allowing the CDR regions to be stabilized. Folding in FR leads to antibody structure flexibility or rigidity of the binding region of the antibody. [8] [9]

Mutations

Mutations in the framework regions of antibodies occur in cells by somatic hypermutation and during affinity maturation of the antibody. In vitro, mutations of FR may occur by natural cause or by exposure to mutagens. [8] [9] Recent studies of framework mutations imply that the framework region flexibility or rigidity could alter the specificity of the antibody to its intended epitope. While the framework region doesn't directly interact with antigen, its structure determines whether the CDRs can interact with antigen. If the CDR regions have high affinity for the epitope of antigen, it has been found to be more effective to have a more rigid framework region. When CDR does not have high affinity for antigen, mutations in the FR that create a more flexible structure may allow for higher affinity maturation. [8]

Natural mutations in the variable region are typically due to activation-induced cytidine deaminase (AID). AID leads to deamination of cytosine to uracil in DNA and results in somatic hypermutation. This somatic hypermutation allows for immunoglobulin class switching but also results in affinity maturation of the antibody. The CDR are the areas of the variable regions in contact with antigen and thus we see the most mutation in these regions. Although, the framework regions of the antibody are also mutated. Studies have shown that when the CDR is blocked from mutation and only the FR is mutated, certain mutations can lead to increased expression and thermostability of the antibody as a whole. [9] Antibody humanization is an example of beneficial genetic engineering in medicine today. [10] Humanized antibody refers to the creation of non-human antibody in vivo and in response to antigen, then the isolation and humanization of the framework and constant regions. It has been discovered that while these antibodies remain relatively intact upon transition, these modifications can also lead to decreased binding affinity in the humanized framework regions and result in improper folding in humans. This observation is believed to be due to the framework region's role in antibody structure. [10]

also

Related Research Articles

<span class="mw-page-title-main">Antibody</span> Protein(s) forming a major part of an organisms immune system

An antibody (Ab), also known as an immunoglobulin (Ig), is a large, Y-shaped protein used by the immune system to identify and neutralize foreign objects such as pathogenic bacteria and viruses. The antibody recognizes a unique molecule of the pathogen, called an antigen. Each tip of the "Y" of an antibody contains a paratope that is specific for one particular epitope on an antigen, allowing these two structures to bind together with precision. Using this binding mechanism, an antibody can tag a microbe or an infected cell for attack by other parts of the immune system, or can neutralize it directly.

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 are also epitopes.

<span class="mw-page-title-main">Memory B cell</span> Cell of the adaptive immune system

In immunology, a memory B cell (MBC) is a type of B lymphocyte that forms part of the adaptive immune system. These cells develop within germinal centers of the secondary lymphoid organs. Memory B cells circulate in the blood stream in a quiescent state, sometimes for decades. Their function is to memorize the characteristics of the antigen that activated their parent B cell during initial infection such that if the memory B cell later encounters the same antigen, it triggers an accelerated and robust secondary immune response. Memory B cells have B cell receptors (BCRs) on their cell membrane, identical to the one on their parent cell, that allow them to recognize antigen and mount a specific antibody response.

<span class="mw-page-title-main">Single-chain variable fragment</span> Fragment

A single-chain variable fragment (scFv) is not actually a fragment of an antibody, but instead is a fusion protein of the variable regions of the heavy (VH) and light chains (VL) of immunoglobulins, connected with a short linker peptide of ten to about 25 amino acids. The linker is usually rich in glycine for flexibility, as well as serine or threonine for solubility, and can either connect the N-terminus of the VH with the C-terminus of the VL, or vice versa. This protein retains the specificity of the original immunoglobulin, despite removal of the constant regions and the introduction of the linker. The image to the right shows how this modification usually leaves the specificity unaltered.

In immunology, affinity maturation is the process by which TFH cell-activated B cells produce antibodies with increased affinity for antigen during the course of an immune response. With repeated exposures to the same antigen, a host will produce antibodies of successively greater affinities. A secondary response can elicit antibodies with several fold greater affinity than in a primary response. Affinity maturation primarily occurs on membrane immunoglobulin of germinal center B cells and as a direct result of somatic hypermutation (SHM) and selection by TFH cells.

<span class="mw-page-title-main">T-cell receptor</span> Protein complex on the surface of T cells that recognises antigens

The T-cell receptor (TCR) is a protein complex found on the surface of T cells, or T lymphocytes, that is responsible for recognizing fragments of antigen as peptides bound to major histocompatibility complex (MHC) molecules. The binding between TCR and antigen peptides is of relatively low affinity and is degenerate: that is, many TCRs recognize the same antigen peptide and many antigen peptides are recognized by the same TCR.

<span class="mw-page-title-main">Epitope mapping</span> Identifying the binding site of an antibody on its target antigen

In immunology, epitope mapping is the process of experimentally identifying the binding site, or epitope, of an antibody on its target antigen. Identification and characterization of antibody binding sites aid in the discovery and development of new therapeutics, vaccines, and diagnostics. Epitope characterization can also help elucidate the binding mechanism of an antibody and can strengthen intellectual property (patent) protection. Experimental epitope mapping data can be incorporated into robust algorithms to facilitate in silico prediction of B-cell epitopes based on sequence and/or structural data.

<span class="mw-page-title-main">Activation-induced cytidine deaminase</span> Enzyme that creates mutations in DNA

Activation-induced cytidine deaminase, also known as AICDA, AID and single-stranded DNA cytosine deaminase, is a 24 kDa enzyme which in humans is encoded by the AICDA gene. It creates mutations in DNA by deamination of cytosine base, which turns it into uracil. In other words, it changes a C:G base pair into a U:G mismatch. The cell's DNA replication machinery recognizes the U as a T, and hence C:G is converted to a T:A base pair. During germinal center development of B lymphocytes, AID also generates other types of mutations, such as C:G to A:T. The mechanism by which these other mutations are created is not well understood. It is a member of the APOBEC family.

<span class="mw-page-title-main">Immunoglobulin heavy chain</span> Large polypeptide subunit of an antibody

The immunoglobulin heavy chain (IgH) is the large polypeptide subunit of an antibody (immunoglobulin). In human genome, the IgH gene loci are on chromosome 14.

<span class="mw-page-title-main">Germinal center</span> Lymphatic tissue structure

Germinal centers or germinal centres (GCs) are transiently formed structures within B cell zone (follicles) in secondary lymphoid organs – lymph nodes, ileal Peyer's patches, and the spleen – where mature B cells are activated, proliferate, differentiate, and mutate their antibody genes during a normal immune response; most of the germinal center B cells (BGC) are removed by tingible body macrophages. There are several key differences between naive B cells and GC B cells, including level of proliferative activity, size, metabolic activity and energy production. The B cells develop dynamically after the activation of follicular B cells by T-dependent antigen. The initiation of germinal center formation involves the interaction between B and T cells in the interfollicular area of the lymph node, CD40-CD40L ligation, NF-kB signaling and expression of IRF4 and BCL6.

Humanized antibodies are antibodies from non-human species whose protein sequences have been modified to increase their similarity to antibody variants produced naturally in humans. The process of "humanization" is usually applied to monoclonal antibodies developed for administration to humans. Humanization can be necessary when the process of developing a specific antibody involves generation in a non-human immune system. The protein sequences of antibodies produced in this way are partially distinct from homologous antibodies occurring naturally in humans, and are therefore potentially immunogenic when administered to human patients. The International Nonproprietary Names of humanized antibodies end in -zumab, as in omalizumab.

A hypervariable region (HVR) is a location within nuclear DNA or the D-loop of mitochondrial DNA in which base pairs of nucleotides repeat or have substitutions. Changes or repeats in the hypervariable region are highly polymorphic.

<span class="mw-page-title-main">Complementarity-determining region</span> Part of the variable chains in immunoglobulins and T cell receptors

Complementarity-determining regions (CDRs) are part of the variable chains in immunoglobulins (antibodies) and T cell receptors, generated by B-cells and T-cells respectively, where these molecules bind to their specific antigen. A set of CDRs constitutes a paratope. As the most variable parts of the molecules, CDRs are crucial to the diversity of antigen specificities generated by lymphocytes.

<span class="mw-page-title-main">Polyclonal B cell response</span> Immune response by adaptive immune system

Polyclonal B cell response is a natural mode of immune response exhibited by the adaptive immune system of mammals. It ensures that a single antigen is recognized and attacked through its overlapping parts, called epitopes, by multiple clones of B cell.

<span class="mw-page-title-main">Idiotype</span>

In immunology, an idiotype is a shared characteristic between a group of immunoglobulin or T-cell receptor (TCR) molecules based upon the antigen binding specificity and therefore structure of their variable region. The variable region of antigen receptors of T cells (TCRs) and B cells (immunoglobulins) contain complementarity-determining regions (CDRs) with unique amino acid sequences. They define the surface and properties of the variable region, determining the antigen specificity and therefore the idiotope of the molecule. Immunoglobulins or TCRs with a shared idiotope are the same idiotype. Antibody idiotype is determined by:

<span class="mw-page-title-main">Immunoglobulin heavy constant alpha 1</span> Gene in the species Homo sapiens

Immunoglobulin heavy constant alpha 1 is a immunoglobulin gene with symbol IGHA1. It encodes a constant (C) segment of Immunoglobulin A heavy chain. Immunoglobulin A is an antibody that plays a critical role in immune function in the mucous membranes. IgA shows the same typical structure of other antibody classes, with two heavy chains and two light chains, and four distinct domains: one variable region, and three variable regions. As a major class of immunoglobulin in body secretions, IgA plays a role in defending against infection, as well as preventing the access of foreign antigens to the immunologic system.

Somatic hypermutation is a cellular mechanism by which the immune system adapts to the new foreign elements that confront it, as seen during class switching. A major component of the process of affinity maturation, SHM diversifies B cell receptors used to recognize foreign elements (antigens) and allows the immune system to adapt its response to new threats during the lifetime of an organism. Somatic hypermutation involves a programmed process of mutation affecting the variable regions of immunoglobulin genes. Unlike germline mutation, SHM affects only an organism's individual immune cells, and the mutations are not transmitted to the organism's offspring. Because this mechanism is merely selective and not precisely targeted, somatic hypermutation has been strongly implicated in the development of B-cell lymphomas and many other cancers.

Ocaratuzumab is a humanized monoclonal antibody designed for the treatment of cancer and autoimmune disorders. The antibody is engineered for enhanced affinity to the CD20 antigen on B-lymphocytes, increased antibody-dependent cell-mediated cytotoxicity (ADCC), and for improved treatment of low-affinity FcγRIIIa allotypes.

J. (Joseph) Donald Capra was an American immunologist, physician-scientist, and was the 4th full-time president (1997–2007) and later, president emeritus, of the Oklahoma Medical Research Foundation (OMRF) in Oklahoma City, OK. While president, he helped to raise over $100 million and spearheaded major research growth in grants funded and faculty recruited to the institution.

Antigen-antibody interaction, or antigen-antibody reaction, is a specific chemical interaction between antibodies produced by B cells of the white blood cells and antigens during immune reaction. The antigens and antibodies combine by a process called agglutination. It is the fundamental reaction in the body by which the body is protected from complex foreign molecules, such as pathogens and their chemical toxins. In the blood, the antigens are specifically and with high affinity bound by antibodies to form an antigen-antibody complex. The immune complex is then transported to cellular systems where it can be destroyed or deactivated.

References

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  2. 1 2 3 Elgert, Klaus (1998). Immunology: Understanding the Immune System. John Wiley & Sons, Inc. p. 63.
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  4. 1 2 Sela-Culang, Inbal; Kunik, Vered; Ofran, Yanay (2013-10-08). "The Structural Basis of Antibody-Antigen Recognition". Frontiers in Immunology. 4: 302. doi: 10.3389/fimmu.2013.00302 . ISSN   1664-3224. PMC   3792396 . PMID   24115948.
  5. 1 2 Zhu, Kai; Day, Tyler; Warshaviak, Dora; Murrett, Colleen; Friesner, Richard; Pearlman, David (2014-08-01). "Antibody structure determination using a combination of homology modeling, energy-based refinement, and loop prediction". Proteins: Structure, Function, and Bioinformatics. 82 (8): 1646–1655. doi:10.1002/prot.24551. ISSN   1097-0134. PMC   5282925 . PMID   24619874.
  6. ↑ Stanfield, Robyn L.; Wilson, Ian A. (2015-01-01). "Antibody Structure". In Crowe; Boraschi; Rappuoli (eds.). Antibodies for Infectious Diseases. pp. 49–62. doi:10.1128/9781555817411. ISBN   9781555817350.
  7. ↑ Charles A Janeway, Jr; Travers, Paul; Walport, Mark; Shlomchik, Mark J. (2001). "The structure of a typical antibody molecule".{{cite journal}}: Cite journal requires |journal= (help)
  8. 1 2 3 Ovchinnikov, Victor; Louveau, Joy E; Barton, John P; Karplus, Martin; Chakraborty, Arup K (2018-02-14). "Role of framework mutations and antibody flexibility in the evolution of broadly neutralizing antibodies". eLife. 7. doi: 10.7554/elife.33038 . ISSN   2050-084X. PMC   5828663 . PMID   29442996.
  9. 1 2 3 Lombana, T. Noelle; Dillon, Michael; III, Jack Bevers; Spiess, Christoph (2015-12-03). "Optimizing antibody expression by using the naturally occurring framework diversity in a live bacterial antibody display system". Scientific Reports. 5 (1): 17488. Bibcode:2015NatSR...517488L. doi:10.1038/srep17488. ISSN   2045-2322. PMC   4668361 . PMID   26631978.
  10. 1 2 Caldas, Cristina; Coelho, Verônica; Kalil, Jorge; Moro, Ana Maria; Maranhão, Andrea Q; Brı́gido, Marcelo M (2003). "Humanization of the anti-CD18 antibody 6.7: an unexpected effect of a framework residue in binding to antigen". Molecular Immunology. 39 (15): 941–952. doi:10.1016/s0161-5890(03)00022-1. PMID   12695120.
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