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] Individual residues in the framework region can be divided into two categories, depending on whether they are in direct 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

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<span class="mw-page-title-main">Antigen</span> Molecule triggering an immune response (antibody production) in the host

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.

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

An antibody (Ab) is the secreted form of a B cell receptor; the term immunoglobulin (Ig) can refer to either the membrane-bound form or the secreted form of the B cell receptor, but they are, broadly speaking, the same protein, and so the terms are often treated as synonymous. Antibodies are large, Y-shaped proteins belonging to the immunoglobulin superfamily which are used by the immune system to identify and neutralize antigens such as bacteria and viruses, including those that cause disease. Antibodies can recognize virtually any size antigen with diverse chemical compositions from molecules. Each antibody recognizes one or more specific antigens. Antigen literally means "antibody generator", as it is the presence of an antigen that drives the formation of an antigen-specific antibody. Each tip of the "Y" of an antibody contains a paratope that specifically binds to one particular epitope on an antigen, allowing the two molecules to bind together with precision. Using this mechanism, antibodies can effectively "tag" a microbe or an infected cell for attack by other parts of the immune system, or can neutralize it directly.

<span class="mw-page-title-main">B cell</span> Type of white blood cell

B cells, also known as B lymphocytes, are a type of white blood cell of the lymphocyte subtype. They function in the humoral immunity component of the adaptive immune system. B cells produce antibody molecules which may be either secreted or inserted into the plasma membrane where they serve as a part of B-cell receptors. When a naïve or memory B cell is activated by an antigen, it proliferates and differentiates into an antibody-secreting effector cell, known as a plasmablast or plasma cell. In addition, B cells present antigens and secrete cytokines. In mammals, including marsupials B cells mature in the bone marrow, which is at the core of most bones. In birds, B cells mature in the bursa of Fabricius, a lymphoid organ where they were first discovered by Chang and Glick, which is why the B stands for bursa and not bone marrow, as commonly believed.

<span class="mw-page-title-main">Superantigen</span> Antigen which strongly activates the immune system

Superantigens (SAgs) are a class of antigens that result in excessive activation of the immune system. Specifically they cause non-specific activation of T-cells resulting in polyclonal T cell activation and massive cytokine release. Superantigens act by binding to the MHC proteins on antigen-presenting cells (APCs) and to the TCRs on their adjacent helper T-cells, bringing the signaling molecules together, and thus leading to the activation of the T-cells, regardless of the peptide displayed on the MHC molecule. SAgs are produced by some pathogenic viruses and bacteria most likely as a defense mechanism against the immune system. Compared to a normal antigen-induced T-cell response where 0.0001-0.001% of the body's T-cells are activated, these SAgs are capable of activating up to 20% of the body's T-cells. Furthermore, Anti-CD3 and Anti-CD28 antibodies (CD28-SuperMAB) have also shown to be highly potent superantigens.

<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.

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 recognizes 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">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, error-prone DNA repair following AID action also generates other types of mutations, such as C:G to A:T. AID 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.

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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

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<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>

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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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  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)
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  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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