Synthesis of immunoglobulin Fab fragments: Where can I learn about Fab?

Synthesis of immunoglobulin Fab fragments: Where can I learn about Fab?

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I wanted to know the chemical reaction involved in Fab synthesis. I looked everywhere for it. No luck. I know I will find it here.

All I know for now is:

Fab is a monovalent fragment that is produced from IgG and IgM, consisting of the VH, CH1 and VL, CL regions, linked by an intramolecular disulfide bond.

Molecular basis of Fab will make more sense.

For the generation of Fab-fragments antibodies, (possibly genetically modified) which can be made in large quantities by cells or animals, are used. Antibodies as a whole are not synthesized.

The Fab fragment is obtained from antibodies using the enzyme papain, which cleaves the antibody over the disulfide bonds in the hinge region. This results in two Fab fragments (which contain the antigen binding sites) and one Fc fragment (which contains the constant region of the antibody). See the image (from here):

If you want to go further into the topic, read one of the references below.

  1. Preparation and separation of Fab and Fc fragments from human immunoglobulin G with papain digestion
  2. Fragmentation of IgG Using Papain

FAbs are genetically engineered and not organically synthesized as such. This PNAS article nicely describes the construction of a phage (virus) library to generate a large amount of different FAbs and screen for FAbs with the wanted epitope (antigen) affinity:

Fab Abzyme Cutting Service

Creative Biolabs has established a technical platform to obtain antibody Fab fragments with the use of specific proteases, which can greatly satisfy your experimental research needs. We have many years of extensive experience in custom model organism antibdy production, from gene expression or peptide synthesis to antibody labeling and avi-tag biotinylated antibody service.

Enzyme Classification and Advantages

The Fab-Cutter A and Fab-B genes are both derived from Streptococcus pyogenes (S. pyogenes), expressed by E. coli, and obtained through multi-step purification. For different subtypes of human, mouse, sheep, goat, and other species, the enzyme can perform rapid single-point digestion of immunoglobulin IgG.

  • Fab-Cutter A
  • The enzyme cleavage site is located above the hinge region of the immunoglobulin IgG
  • Acquire Fab fragments and dimeric Fc fragments
  • Single enzyme cutting site, cutting fast
  • Fab-Cutter B
  • The enzyme cleavage site is located below the hinge region of the immunoglobulin IgG
  • Acquire F(ab')2 fragments and dimeric Fc fragments
  • Can also be applied to mouse IgG2a and IgG3
  • Single enzyme cutting site, cutting fast

Workflow of Our Service

Scientists at Creative Biolabs are dedicated to customizing a comprehensive project plan per your needs, allowing you to spend the least amount of time to achieve your expected results.

  • We provide a variety of antibodies for you to customize, just contact us for antibody resources
  • According to your application scenarios, we provide you with digestion solutions
  • We provide professional digestion experiment service

Features at Creative Biolabs

Creative Biolabs has extensive experience in Fab abzyme cutting service. Our scientific team is committed to studying in the field for many years, with rich experience. The digestion products we obtained have higher quality and can be used for pilot trials with a small amount of antibody.

Graphical Abstract

Disclosure: The authors declare the following competing financial interest(s): E.N., A.C.G., A.P. and A.C.P. filed for a patent to use the neck domain peptide in folate-targeted liposomes for specific drug delivery. M.R. is an employee of MC Toxicology Consulting. M.P. and M.S. are employees of EXBIO Praha.

Funding: This work has received funding from the European Union's Seventh Framework Program (FP7/2007-2013 grant agreement NMP4-LA-2009-228827 NANOFOL) and Horizon 2020 Research and Innovation Program (grant agreement No 683356 - FOLSMART), further from the Portuguese Foundation for Science and Technology under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684) and BioTecNorte operation (NORTE-01-0145-FEDER-000004) funded by the European Regional Development Fund under the scope of Norte2020.

Compared to whole IgG, Fab fragments can penetrate cells and tissues and bind antigens more easily thanks to their lower steric hindrance. Moreover, the absence of Fc region prevents Fab fragments from nonspecific binding to Fc receptors.

When the Fc fragment is of interest, papain is consequently the enzyme of choice. Papain is primarily used to generate Fab fragments, but it can also be used to generate F(ab&rsquo) 2 fragments when used in specific physico-chemical conditions.

Fab Antibody Production Service

Antigen binding fragments (Fab), are from the enzymatic or chemical digestion of a full size antibody (such as a IgG). These fragments are the antigen-binding domains of an antibody molecule, containing a variable region of heavy chain (VH), a variable region of light chain (VL), a constant region of heavy chain 1 (CH1) and a constant region of light chain (CL) [1]. Fab fragments can be obtained in two ways: via recombinant synthesis or enzymatic cleavage of the parent antibody [2].

With years of research experience in the field of recombinant antibody construction and expression, Biologics International Corp (BIC) offers antibody fragment production services, which include Fab, scFab, Fab’, F(ab’)2, scFv, diabody, triabody, minibody, and scFv-Fc production. Do not hesitate to get in touch for any further information regarding antibody fragments. We are always glad to assist you.

Fab fragments with a size of around 50 KDa are the antigen-binding domains of an antibody molecule, containing one constant and one variable domain of each of the heavy and the light chains. The fragments which contain disulfide bridge thiols are called Fab’ fragments, whereas those lacking the thiol functional group are termed Fab fragments [2]. Because of their small sizes, Fab/Fab’ can penetrate tissues more efficiently and be cleared from the blood more rapidly. As they do not have Fc fragments, Fab/Fab’ will not interfere with anti-Fc mediated antibody detection.

Fab Fragments Construction

To produce Fab fragments, two different methods can be employed. The primary method is via enzymatic/chemical cleavage of the whole antibody, in which the whole antibody is cleaved by enzyme (such as papain, pepsin, and ficin) to form F(ab’)2 fragments, followed by the reduction of those fragments to yield Fab fragments [2]. An alternative method is through the recombinant synthesis of F(ab’)2 antibody fragments, followed by chemical reduction of these fragments to yield Fab units.

Fab Antibody Library

Currently, most recombinant antibody fragments are generated by phage display antibody libraries [3]. Fab antibody library is advantageous in several important ways: first, compared with monoclonal antibodies, which is very laborious and time-consuming to produce, Fab antibody library can rapidly and efficiently select new antibodies that are difficult to gain through hybridoma technology. Second, like scFv antibodies, it could be easier to generate Fab antibodies with higher affinities. Third, advantages of Fab fragments are highly stable under long term storage [4] and are compatible with common detection antisera without the need for re-engineering. If you need an antibody against some unusual antigens, get in touch, our antibody library with rich diversity and large scale will help you to find an ideal antibody.

More Fab Formats

A F(ab')2 fragment, which retains a small part of the Fc hinge region, has two antigen binding regions that may increase the affinity to antigen. Reduction of F(ab')2 fragments produces two monovalent Fab' fragments, which have a free sulfhydryl group that is useful for conjugation with other molecules.

Although the utilization of enzymatic/chemical cleavage methods to generate Fab fragments is convenient and efficient, it requires a large quantity of monoclonal antibody as starting material. A single-chain Fab fragment (scFab) can lead to improved function and production of Fab fragments. According to some studies [3], scFab fragments show superior antigen-binding ability compared to Fab and compensate for some of the disadvantages of the soluble Fab production in E. coli.

Have some antibody formats in mind? Contact us with your ideas, let us see what we can do for you.

Basic Structure and Classes of Immunoglobulin

In this article we will discuss about the basic structure and classes of immunoglobulin.

Antibodies are the specific glycoproteins (Immunoglobulin) produced by cells in response to stimulation by an antigen (Immunogen) and capable of reacting specifically with that antigen. Every immunoglobulin (in short they are written as Ig) has the same basic structure made up of four polypeptide chains (two heavy chains and two light chains).

These chains are held together by non-covalent forces and covalent disulphide bridges. Each chain has a variable part and a constant part of amino acids (Fig. 10.3). By splitting the immunoglobulin molecule using different enzymes it has been possible to learn the functions of the different parts of the molecule.

The enzyme, Papain splits the molecule into two Fab-fragments (Fab = fragment antigen binding) and one Fc-fragment (Fc = fragment crystallizable), while enzyme, Pepsin splits the molecule into one F(ab)2 – fragment and several small and usually inactive peptides.

The differences in biological activities, together with distinct physico-chemical properties and different localizations have led to the division of antibodies into different classes and sub-classes.

The basic structure of Ig is illustrated below(Fig.10.3):

1. Basic Structure of Immuno­globulins:

A. Heavy and Light Chains:

All Igs have a four chain structure as their basic unit. One pair of the polypeptide chain contains approximately twice as many amino acids as the other pair. They are called heavy (H) chains (50-70 KDa.) and light (L) chains (25 KDa.) respectively.

B. Disulphide bonds:

1) Inter-Chain: The heavy chain and light chain and the two heavy chains are held together by inter-chain disulphide bonds.

2) Intra-Chain: Within each of the polypeptide chains, there are also intra-chain disulphide bonds.

C. Variable (V) and Constant (C) regions:

Both the H-chain and L-chain can be divided into two regions based on variability in the amino acid sequences.

1) Light Chain: Variable region, VL (110 amino acids) and constant region, CL (110 amino acids)

2) Heavy Chain: Variable region, VH (110 amino acids) and constant region, CH (330-440 amino acids).

The antibody (Ig) binds with the antigen through the V-region of the heavy and light chains, in other words a part of the Fab- fragment. The Fc – fragment is responsible for the biological activities.

The region of which the arms of the antibody molecule forms a ‘Y’ is called the hinge region, because there is some flexibility in the molecule at this point.

Ig molecule is folded into globular regions, each of which contains an intra-chain disulphide bond. These regions are called domains.

1) Light chain Domains – VL and CL

F. Oligosaccharides:

Carbohydrates are attached to the CH2 domain in most immunoglobulins.

Structure of the variable region:

A. Hypervariable regions (HVR) or Complementarity determining regions (CDR):

Comparison of the amino acid sequences of the variable regions of the Ig’s show that most of the variability resides in three regions (HVRI1, HVRI2, HVRI3) called the hypervariable region or the complementarity determining regions.

B. Frame work regions (FR):

The regions between the CDR’s in variable regions are called the frame work regions (FR1, FR2, FR3, FR4).

2. Immunoglobulin Classes and Sub-classes:

The Igs can be divided into five different classes in humans namely, IgA, IgD, IgE, IgG and IgM (Table 10.2). Among these IgA, IgD, IgE and IgG occur as monomers with the basic structure H2L2 i.e. two heavy and two light polypeptide chains. Serum IgA can polymerize to the dimeric (H2L2)2 and the oligomeric (H2L2)n forms.

IgA occurs mainly as a dimmer bound to a secretion component and to a polypeptide chain, the J-chain (J=join). IgM in serum occurs as pentamer (H2L2)S where the monomers are bound together by disulphide bridges and a J- chain. The classification of Igs is primarily based on the nature of H-chain and L-chain (Table 10.2).

The classes of Igs can be divided into sub­classes based on small differences in the amino acid sequences in the constant regions of the heavy chains. IgG is comprised of four sub­classes namely, IgGl (y-1 H-chain, 60-70% in serum), IgG2 (y-2 H-chain, 14-20% in serum), IgG3 (y-3 H-chain, 4-8% in serum) and IgG4 (y- 4 H-chain, 2-6% in serum). Among these IgG4 can bind to mast cells to accelerate allergic reaction in some cases.

IgA is comprised of two sub-classes namely IgAl (α-1 H-chain) and IgA2 (α-2 H-chain). IgE is involved in accelerating allergic reactions, though their concentration in serum is normally very low (0.001% of the total Igs). Elevated levels of IgE are found in the serum of patients suffering from allergic diseases. Certain cells like basophilic leukocytes and mast cells possess receptors for the Fc- fragment of IgE.

Synthesis of immunoglobulin Fab fragments: Where can I learn about Fab? - Biology

As well as altering the Fc portion of an antibody, the variable region of an immunoglobulin can be reformatted into a variety of different fragments such as Fab, F(ab)’2, scFv, VHH, and minibodies, or can be combined with a second specificity to make bispecific antibodies. The smaller antibody formats can be exploited for their improved tumour/tissue penetration and relative ease of expression in non-mammalian systems.

We can re-engineer antibodies and antibody fragments into virtually any format, some of which are shown below. Once produced, the antibodies can be characterised using an extensive suite of assays, such as ELISA, affinity determination using Biacore, or an appropriate biological assay.

F(ab)’2 retains the bivalent binding of an IgG without the Fc portion, that would otherwise be involved in the recruitment of effector functions through its interaction with Fcγ receptors.

Fabs are approximately a third of the size of a whole IgG and are monovalent. This smaller fragment has improved penetration into tissues and faster clearance from circulation, and can similarly benefit from the absence of Fcγ receptor-mediated effector functions. Fabs can easily be expressed in non-mammalian systems.

scFv are engineered by linking the variable domains of the heavy and light chains into a single chain molecule that is about a fifth of the size of a whole IgG. scFv are routinely used for phage display and can be expressed linked to a variety of fusion proteins for specific targeting.

VHH consist only of the variable domain of the heavy chain, and are about a tenth of the size of a whole IgG. Naturally found in camelids such as alpaca and llama, and also in sharks, VHH are highly stable and amenable to fusion with other proteins and can be linked to Fc domains to form heavy chain only antibodies.

Bispecific Antibodies

Bispecific antibodies consists of two binding domains that target separate antigens, enabling two antigens to be bound simultaneously by one construct. This can be especially useful when directing an effector cell to a target cell. Bispecific antibodies or antibody fragments can be made in a variety of different formats and can be tailored to your requirements, depending upon application.

The above examples provide a sample of Abzena’s capabilities and we can re-engineer antibodies and antibody fragments into virtually any format. Once produced, the antibodies can be characterised using an extensive suite of binding assays (such as using ELISA), Affinity determination using Biacore Surface Plasmon Resonance or in an appropriate biological assay.

Working with Abzena

Abzena’s services are tailored for each project to ensure that the objectives are met or exceeded. Experienced project teams are assigned to each study focusing on progressing projects through to results in the minimum amount of time. Our clients widely regard us as professional and attentive partners who deliver quality results.

To get more information, a quote or to schedule a teleconference please contact us.

Expression of actively soluble antigen-binding fragment (Fab) antibody and GFP fused Fab in the cytoplasm of the engineered Escherichia coli

The expression of recombinant antibody fragments in the cytoplasmic space of Escherichia coli and the refolding process for restoring the structure and activity of such antibodies are not efficient. Herein, fragment antigen-binding (Fab) antibodies against miroestrol and deoxymiroestrol (MD-Fab) and their fusions with a green fluorescent protein (GFP) were expressed. The reactive MD-Fabs were successfully expressed as soluble and active forms in the cytoplasm of the SHuffle® T7 E. coli strain. Regarding the construct of MD-Fab alone, VH–CH1 could associate VL–CL into Fab in the oxidizing cytoplasm of the E. coli strain, and no additional in vitro refolding was needed. In the case of the fusions with GFP, when the C-terminus of VH–CH1 was linked with the N-terminus of GFP, the MD-Fab binding reactivity was retained, but the fluorescent activity of GFP interfered. When the C-terminus of GFP was linked to the N-terminus of VL–CL, the binding activity of MD-Fab was not observed. The constructed MD-Fabs had higher specificity toward deoxymiroestrol than the parental monoclonal antibody clone 12G11. In conclusion, MD-Fabs could be expressed using SHuffle® T7 E. coli cells. This process could be considered an economical, productive, and effective method to produce antibody fragments for immunoassay techniques.

Immunoglobulin classes

There are 5 classes of immunoglobulins IgG, IgA, IgM, IgE and IgD as determined by the presence of unique amino acid sequences in the heavy chain constant regions. Basic structural properties of these immunoglobulin classes are discussed here briefly. General structure of five major classes of immunoglobulins (antibodies)
(Image source: Kubay Immunology)

Immunoglobulin G (IgG)

The IgG molecule consists of two γ heavy chains and two κ or two λ light chains. There are four human IgG subclasses, distinguished by differences in γ -chain sequence and numbered according to their decreasing average serum concentrations: IgG1, IgG2, IgG3, and IgG4. Find more about Immunoglobulin G (IgG) and its function here.

Immunoglobulin A (IgA)

The IgA molecule consists of two α heavy chains and two κ or two λ light chains.

IgA exists primarily as a monomer in serum but in external secretions, it (secretory IgA) is present as a dimer or tetramer linked by a J-chain polypeptide. Find more about immunoglobulin A and its function here.

Immunoglobulin M (IgM)

The IgM molecule consists of two μ heavy chains and two κ or two λ light chains. IgM has an “additional” heavy chain constant domain and absence of a hinge region in the μ-chain.

IgM has two forms monomeric IgM (membrane-bound on B cells) and pentameric IgM (secreted by plasma cells). In pentameric IgM, five monomer units are held together by disulfide bonds that link their carboxyl-terminal heavy chain domains (Cμ4/Cμ4) and their (Cμ3/Cμ3) domains held together by a Fc-linked polypeptide called the J (joining) chain. Find more about immunoglobulin M (IgM) and its functions here.

Immunoglobulin E (IgE)

The IgE molecule consists of two ε heavy chains and two κ or two λ light chains. IgE has an “additional” heavy chain constant domain and the absence of a hinge region in the ε-chain. Immunoglobulin E (IgE) is well known for its role in mediating immediate hypersensitivity reactions. More information about IgE will be published later in another blog post.

Immunoglobulin D (IgD)

The IgD molecule consists of two δ heavy chains and two κ or two λ light chains. IgD is typically coexpressed with IgM on the surface of mature B cells.

Synthesis of immunoglobulin Fab fragments: Where can I learn about Fab? - Biology

Here we present an in-depth description of antibody structure and various antibody fragments. We discuss major applications of antibodies as well as advantages and disadvantages of using full-size antibodies versus fragments. We then provide an overview of studies using antibody fragments and a discussion of antibody receptors called Fc receptors.

Antibodies are immunoglobulin (Ig) glycoproteins produced by plasma cells (B cells) in response to foreign antigenic molecules (immunogens). The primary function of antibodies is to bind specifically to these foreign antigens to disable them and/or mark them for destruction by the immune system, thereby protecting the host from infection. There are several classes of antibodies. The first portion of this summary focuses on conventional full-size antibodies, the IgG and IgM class antibodies, which are heavily utilized in a multitude of research, diagnostic and therapeutic biomedical applications.

The basic unit of a conventional antibody is a four polypeptide unit consisting of two identical heavy chains and two identical light chains held together by disulfide bonds. The light chains are shorter, with lower molecular weights than the heavy chains. The general shape of an antibody is a Y, with a flexible hinge (interdomain) region at the center of the Y. The flexibility of the interdomain hinge region is important for the bivalent binding of an antibody [2], allowing the two binding pockets to interact with antigenic sites at variable distances. Each polypeptide chain has a constant region, which does not vary significantly among antibodies, and a variable region, which is specific to each particular antibody. The common notation for the light chain variable region is VL and for the light chain constant region is CL (Figure 1). The notation is similar for the heavy chain variable (VH) and constant regions (CH) with CH1, CH2, and CH3 denoting the different constant region domains of the heavy chain. Carbohydrates are normally attached to the CH2 domains of the heavy chains. The fragment crystallizable (Fc) region contains only constant regions from the heavy chains (CH), but the fragment antigen-binding region (Fab) includes both a constant domain and the variable domains of both the heavy and light chains (VH and CL). The fragment variable region FV region contains only the two variable domains (Figure 1). See mouse antibody for discussion on immunoglobulin isotypes, subclasses, and the number of immunoglobulin domains.

Each complete antibody has two antigen-binding pockets, located in the FV regions, and can bind to two antigens (bivalent binding). However, if the two antigens are too close (≤3 nm), or too far apart (≥29nm), the antibody can only bind to one antigen (monovalent binding) [2]. There is a significant affinity change between monovalent and bivalent bindings with a 1,500-fold change in Kd values [2].

The structure of specific antibodies is available from the Structural Antibody Database (SAbDab), a curated database of publicly available antibody structures, as well as structural modelling tools, which is updated weekly from the Protein Data Bank (PDB) [3].

Conventional full-size antibodies have been utilized in research for protein detection via Western blot analyses [4], immunohistochemistry [5], and enzyme-linked immunosorbent assays (ELISA) [6] for decades. Full-size antibodies have also been developed for diagnostic applications such as pregnancy tests and detection of bacteria and viruses in blood, such as an ELISA that detects HIV. Additionally, conventional full-size antibodies are used commonly in disease therapeutics. For example, Infliximab is one antibody of many available that recognize tumor necrosis factor alpha (TNFα) and it is used in the treatment of Crohn's disease and rheumatoid arthritis [7, 8]. Trastuzumab, or Herceptin, is an antibody that binds to epidermal growth factor receptor 2 and is used in the treatment of metastatic breast cancer [9]. There are also several antibody-based therapies, including Muromonab [10], given to transplant recipients to prevent allograft rejection.

Though conventional full-size antibodies may both be used for therapeutic applications, there are advantages and disadvantages to using the complete antibody. An important advantage of conventional antibodies is the fact the Fc region engages the body's immune response, and can target bound antigens for destruction. This Fc region can also be a disadvantage in some clinical applications because the immune response that it typically elicits may be detrimental to the patient's health. Additionally, full-size antibodies cannot penetrate well into certain tissues due to their relatively large size [11]. In some cases, when using full-size antibodies for diagnostic applications the Fc domain can cause significant nonspecific binding, which may impair detection applications.

For many applications antibody fragments are preferable. Antibody fragments can be produced through chemical or genetic mechanisms. Chemical fragmentation utilizes reducing agents to break the disulfide bonds within the hinge region and digestion of the antibody with proteases including pepsin, papain, and ficin. Genetic construction of fragments offers the ability to create a multitude of fragment-containing molecules, each with unique binding and functional characteristics.

Chemical and protease digestion of full-size IgG or IgM antibodies yield antigen-binding fragments (Fab Figure 1), and Fc fragments, comprised only of the heavy chain CH2, and CH3 domains. Biochemical methods of generating antibody fragments produce useful tools for diagnostic and therapeutic applications, but it is quite laborious and requires a large quantity of antibody starting material.

The antigen-binding fragments produced by biochemical digestion include Fab, (Fab')2, Fab', and FV, all of which lack the Fc region. Monovalent F(ab) fragments have one antigen-binding site, whereas divalent (Fab')2 fragments have two antigen-binding regions that are linked by disulfide bonds. Two individual F(ab) fragments are produced when a full-size antibody is digested with papain enzyme. A F(ab')2 fragment, which retains a portion of the hinge region, is produced by pepsin digestion of IgG or IgM antibodies. Reduction of F(ab')2 fragments produces 2 monovalent Fab' fragments, which have a free sulfhydryl group that is useful for conjugation to other molecules. FV fragments are the smallest fragment made from enzymatic cleavage of IgG and IgM class antibodies (Figure 1). FV fragments have the antigen-binding site made of the VH and VL regions, but they lack the constant regions of Fab (CH1 and CL) regions (Figure 1, right panel). The VH and VL are held together in FV fragments by non-covalent interactions. The fragments can be generated through commercially available kits, for example, F(ab')2 Fragmentation Kit from G-Biosciences [12].

Genetic engineering methods allow the production of single chain variable fragments (scFv), which are FV type fragments that consist of the VH and VL domains linked by an engineered flexible linker peptide (Figure 1) [13]. Manipulation of the orientation of the V-domains and the linker length creates different forms of FV molecules [14]. When the linker is at least 12 residues long, the scFv fragments are primarily monomeric (as shown in Figure 1) [14]. Linkers that are 3-11 residues long yield scFv molecules that are unable to fold into a functional FV domain. These molecules associate with a second scFv molecule, which creates a bivalent diabody [15]. If the linker length is less than three residues, scFv molecules associate into triabodies or tetrabodies [14]. For example, Tao Y et al generated a VH-VL diabody with a short GGGGS linker and scFv with a long GTTAASGSSGGSSSGA linker [16]. Multivalent scFvs possess greater functional binding affinity to their target antigens as a result of having two more target antigen binding sites, which reduces the off-rate of the antibody fragment [17]. Minibodies are scFv-CH3 fusion proteins that assemble into bivalent dimers [18]. Small scFv fragments with two different variable domains can be generated to produce bispecific bis-scFv fragments capable of binding two different epitopes concurrently [19]. Genetic methods are also used to create bispecific Fab dimers (Fab2) and trispecific Fab trimers (Fab3) [19]. These antibody fragments are capable of simultaneously binding 2 or 3 different antigens, respectively. Researchers often use scFv fragments to stabilize protein complexes in protein structure studies [20].

In addition to conventional antibodies, camelid and shark (squalidae) species contain a subset of peculiar Heavy Chain Antibodies (hcAb) exclusively composed by heavy chain homodimers lacking light chains [21, 22]. The Fab portions of these antibodies, called VHH in camelids and VNAR in sharks, are the smallest antigen-binding regions naturally found [23]. Nanobodies are VHH-derived recombinant domains able to bind antigens, often cloned from VHH phage libraries such as those against betacoronarivus S proteins [24] or against SARS-CoV-2 spike protein RBD domain [25]. Their binding thermodynamics and structures have been studied ( [26] and reference therein). Nanobodies are very stable and can be easily produced in huge quantity by using common simple protein expression systems such as bacteria (functional conventional full-size antibodies are difficult to express properly in a bacterial system), thus representing a promising tool for research and therapeutic purposes, especially in the areas of super-resolution microscopy, mass spectrometry, and targeted protein degradation [27]. Nanobodies can also be delivered inside living cells through conjugated with peptides [28, 29], or in vivo [30], or expressed directly in vivo and recognize its targets in vivo. Nanobodies against RFP or GFP, when conjugated with far-red Atto dyes, attained 118-fold magnification of fluorescent signals over GFP or RFP, and were used to generate whole-body mouse neuronal connectivity [31]. They have also been used to stabilize the active state of proteins in structural studies [32]. An expression system with multiple concatenated nanobodies against different influenza strains is being examined as a means to generate a universal flu vaccine [33]. Recombinant anti-IgG secondary nanobodies have great potential to replace widely used polyclonal secondary antibodies produced using animals [34].

Nanobodies have the unique ability to cross the blood-brain barrier [35, 36] however, nanobodies tend to be processed and cleared very quickly from the body [37]. Nanobodies can be used for methods like immunoprecipitation, for example, RFP-Trap MA from Chromotek [38], or coupled to fluorescent proteins to track intracellular targets in live cells in real-time [39].

About 10% of bovine immunoglobulins contain an unusually long third heavy-chain complementarity-determining region (CDR 3H) with a large number of cysteine residues [40-42]. These cysteines pair to form disulfide bonds which leads to a stalk-and-knob like structure in the antigen binding domain [42]. This exceptionally long CDR3H domain with the long-stalk contributes to the diversity of bovine antibody specificity.

Intrabodies, or intracellular antibodies, refer to antibodies or their fragments (usually of scFv design) expressed directly inside cells or in animals in vivo through an expression vector. For example, Dong JX et al developed several nanobodies against neuronal proteins for intracellular expression as intrabodies [43]. One important consideration/caveat is the reducing intracellular environment which diminishes the affinity of an antibody or antibody fragment whose binding with the antigen is dependent on intradomain disulfide bonds. Another consideration is that intrabodies tend to aggregate. Kabayama H et al designed intrabodies with a net engative charge even at the lowest cytoplasmic pH 6.6 to generate ultra-stable cytoplasmic antibodies [44]. Intrabodies are used as alternatives to pharmacological inhibitors to target specific endocytic participants. For instances, expression of a single-chain variable fragment (scFv) derived from the 3B12A monoclonal antibody against the TDP-43 nuclear export signal in HEK293A cells or after in utero electroporation of its expression vector promoted the proteolysis of TDP-43 aggregates in cultured cells and embryonic mouse brain [45]. Virus-mediated delivery into the nervous system of an scFv antibody against the RNA recognition motif 1 of TDP-43 reduced microgliosis in a mouse model of acute neuroinflammation and mitigated cognitive impairment, motor defects, TDP-43 proteinopathy, and neuroinflammation in transgenic mice expressing TDP-43 mutations linked to amyotrophic lateral sclerosis [46]. The potential of intrabodies as a therapeutical modality remains to emerge.

An antibody fragment can also be linked with a cell-import tag, such as an IPTD tag [47], to facilitate its entry into cells.

Antibody fragments offer certain advantages over a full-size antibody for some applications. This topic was reviewed by Nelson [48]. One advantage of fragments over full-size antibodies is that antibody fragments are smaller than conventional antibodies and generally lack glycosylation, allowing their production in prokaryotic expression systems, which provide time and cost savings. Additionally, fragments are small enough to infiltrate into some tissues that full-size antibodies are unable to penetrate, which aids in many therapeutic and immunohistochemical procedures [11]. Furthermore, the lack of Fc domain is a substantial advantage for primary antibodies used in immunohistochemistry and other detection applications because they have greatly reduced non-specific binding to the Fc receptor. One scFv that is commonly used in diagnostics is the NC10 antibody against influenza neuraminidase. The MOC-31 antibody against epithelial cell adhesion molecule Ep-CAM is an scFv commonly used in as a cancer therapy. Diabodies, triabodies and tetrabodies have potential uses in applications such as radioimmunotherapy and diagnostic in vivo imaging [49]. However, fragments that lack the Fc domain are degraded in the body much more rapidly than conventional antibodies [50], and are unable to elicit Fc-mediated cytotoxic processes unless they are conjugated to an effector moiety [51], which requires further optimization for antibody fragment-based therapeutics.

Although various antibody fragments offer certain advantages, they are not commonly utilized in experiments. In the more than 60,000 articles manually curated by Labome only a few articles cited applications of antibody Fab fragments. The Roche anti-digoxigenin Fab antibody fragments ( 11093274910) and anti-fluorescein Fab antibody fragments ( 11426338910) are generated in sheep and produced through digestion with papain. Anti-digoxigenin Fab fragments were used for in situ hybridizations since the RNA probes are labeled with digoxigenin [52-54]. They were also used to perform protein folding analysis to study the process of single calmodulin molecule folding through single-molecule force spectroscopy [55]. F(ab) fragments of anti-mouse secondary antibodies are often used to block endogenous mouse Ig during immunostaining, for example, AffiniPure Fab fragment Donkey antimouse IgG from Biozol (JIM-715-007-003) [56].

B Shen et al performed whole mount staining of mouse half bones with Alexa Fluor 647-AffiniPure F(ab')2 fragment donkey anti-chicken IgY at 1:250, Alexa Fluor 488-AffiniPure F(ab')2 fragment donkey anti-rabbit IgG at 1:250, Alexa Fluor 488-AffiniPure F(ab')2 fragment donkey anti-rabbit IgG (at 1:250 (all from Jackson ImmunoResearch) [57]. Invitrogen Alexa Fluor 546-conjugated goat anti-rabbit IgG F(ab')2 fragment was used to perform immunohistochemistry to investigate the role of sFLT-1 in the maintenance of the avascular photoreceptor layer in mouse models [58] and Invitrogen Alexa Fluor 488 (Fab')2 fragment of rabbit anti-goat IgG (H+L) was used in immunohistochemistry to investigate the mechanism of tip link regeneration in auditory hair cells [59].

Fc receptors (FcRs) are molecules expressed primarily on/in innate immune cells, that recognize and bind the Fc domain of antibodies and thereby initiate a cell-based immune response. The diverse functions of FcRs reflect the wide range of protective or modulating roles of antibodies, including mediating the neutralization and clearance of targeted substrates, as well as the programming of adaptive immunity [60]. The biological functions of FcRs are regulated by immunoreceptor tyrosine-based activation motifs (ITAMs) and immunoreceptor tyrosine-based inhibitory motifs (ITIMs), that act as the receptor’s interface with activating and inhibitory signaling pathways, respectively. Thus, signaling by ITAMs can elicit cell activation, phagocytosis and endocytosis, whereas signaling by ITIMs has an inhibitory effect on cell activation [61]. FcRs have been described for all classes of immunoglobulins and some of them are discussed below.

This family includes FcγRI, FcγRII, FcγRIII and their isoforms. They are responsible for antibody-dependent cell-mediated cytotoxicity (ADCC) and antibody-dependent cell-mediated phagocytosis (ACDP) [60].

Another receptor that binds IgG is neonatal Fc receptor (FcRn), which is involved in the transfer of passive humoral immunity from a mother to her fetus. FcRn also protects IgG from degradation in vivo, explaining their long half-life in the serum [62]. This phenomenon has led to the development of better therapeutic antibodies by introducing alterations in the Fc region to promote the Fc-FcRn interaction.

They include the high-affinity FcεRI, which is capable of binding monomeric IgE, and the low-affinity C-type lectin FcεRII, which interacts preferentially with complex IgE. FcεRI mediates the immediate hypersensitivity response of many allergic reactions by stimulating degranulation and the release of a range of inflammatory mediators on mast cells and basophils [63]. FcεRII exists both in a membrane-bound form that delivers a downregulating signal for IgE synthesis [63], as well as soluble fragments that generate an opposing upregulation on IgE synthesis [64]. Its role in transcytosis of IgE-allergen complexes in human airway and the intestinal epithelium is actively being investigated as a potential target for allergic airway inflammation as a result of food allergies [65, 66].

The sole member of the IgA receptor group, FcαRI, is expressed only in cells of the myeloid lineage. It plays a role in both pro- and anti-inflammatory responses depending on the state of the IgA bound. While binding of secretory IgA (SIgA) present at mucosal sites has anti-inflammatory effects including prevention of pathogen invasion, binding of serum IgA leads to inflammatory responses. FcαRI also regulates neutrophil viability depending on the inflammatory microenvironment [67].

TRIM21 can be distinguished from other FcRs as it shows a broad antibody specificity. It can bind IgG, IgM and IgA [68-70]. It is also expressed by cells of most histogenic lineages [71]. TRIM21 participates in antibody-mediated interference of viral replication by targeting cytosolic virus-antibody complexes for proteasomal degradation.

Binding of Fc domains to FcRs can have undesired effects in monoclonal antibody-based analytical methods such as immunohistochemistry (IHC), fluorescence activated cell sorting (FACS) and chromatin immunoprecipitation (ChIP). Non-specific binding to FcRs may introduce background noise that can lead to detection of false positives. Solutions to deal with this problem include the use of (i) isotype controls for gating, (ii) serum to broadly compete for the receptors involved in non‐specific binding, or (iii) purified IgG to block Fc receptors specifically [72]. Innovex Fc Receptor blocker #NB309 can be used to block paraffin or frozen sections during IHC or IC experiments [73] or BD Biosciences #553142 [73, 74], Miltenyi Biotec Fc receptor block [75, 76] for flow cytometry. For example, Chopra S et al blocked FcγR binding with 5 μg/ml TruStain fcX (anti-mouse CD16/32, clone 93) from BioLegend during flow cytometry and cell sorting [77].

Dr. Macarena Fritz Kelly from São José dos Campos, SP, Brazil, contributed the section about Fc receptors in September, 2018.