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The Inducible System: Antigens
Published in Julius P. Kreier, Infection, Resistance, and Immunity, 2022
An antigenic determinant is defined as a region of an antigenic molecule that fits into the combining site of an antibody. It comprises only a small part of the invading pathogen or molecuLe to which the immune system of the host has responded. The word determinant is usually used synonymously with the term epitope which literally means “surface shape” and refers to the site on the surface of the molecule to which the antibody binds. Short segments (i.e., polypeptides) of proteins or of polysaccharides may also serve as epitopes. Complex molecules such as proteins and polysaccharides may, therefore, have multiple determinants. The number of epitopes to which an animal responds, however, is usually fewer than the total number of potential epitopes of any protein or carbohydrate. At the same time, some epitopes are immunodominant and produce a stronger immune response than other epitopes on the same protein.
Immunochemical Approaches to the Diagnosis of Alzheimer Disease
Published in Robert E. Becker, Ezio Giacobini, Alzheimer Disease, 2020
Every immunologic test requires a target molecule, which the antibody will detect. This target molecule, such as ß-hCG in the pregnancy test, is termed the antigen. Often the antigen is a fairly large molecule such as a protein and the antibody only binds to one part of protein. The site on a molecule recognized by the antibody is termed an epitope. A large molecule such as a protein has many potential epitopes.
Introduction
Published in Arvind Kumar Bansal, Javed Iqbal Khan, S. Kaisar Alam, Introduction to Computational Health Informatics, 2019
Arvind Kumar Bansal, Javed Iqbal Khan, S. Kaisar Alam
In recent times, a variation of the approach is to use recombinant DNA techniques to integrate the epitope part of the pathogen with inactive DNA that can be used as vaccine. An epitope is the part of the pathogen that binds to the human cell in a host–pathogen interaction. It is around 8 amino-acid long. The epitope should come from those proteins that interact with the surface-proteins of the human cells. By deactivating the epitope binding, a pathogen can be made inactive. Recombinant DNA technology splices and integrates genes (or gene-domains) from two species to prepare a protein in a laboratory that does not exist in nature. When injected into the human body, the human immune system generates antibodies against the recombinant protein. These antibodies also can bind to pathogen epitopes making the pathogen inactive. By creating a library of epitopes found in pathogens, generic vaccines can be developed to inactivate multiple pathogens (disease-causing bacteria or virus).
Deciphering cross-species reactivity of LAMP-1 antibodies using deep mutational epitope mapping and AlphaFold
Published in mAbs, 2023
Tiphanie Pruvost, Magali Mathieu, Steven Dubois, Bernard Maillère, Emmanuelle Vigne, Hervé Nozach
We decided to generate structural and 3D modeling data to distinguish positions directly involved in the epitope from those affecting the overall conformation of the antigen and its folding, and ultimately refine the epitopes. We first solved the crystallographic structure of the complex between Fab B and an aglycosylated form of the first luminal domain of human LAMP-1 (Figure 4a). This domain adopts the same overall β-prism fold as murine LAMP-123 and DC-Lamp3.27 Most of the interaction between Fab B and LAMP-1 is mediated by amino acids in the heavy chain complementarity-determining regions (CDRs). Briefly, loop 82–86 of LAMP-1 interacts with CDRH1 and the FR3 loop from the Fab heavy chain. Loop 106–109 interacts with all heavy chain CDRs and loop 149–151 is in contact with CDRH3 and CDRL1. Lastly, loop 178–187 contacts both CDRH1 and CDRH3, along with CDRL1 and CDRL2. All LAMP-1 amino acids at the interface, i.e., at less than 4.5 Å from the Fab molecule are represented in yellow in Figure 4a and constitute what might be termed the ‘structural epitope’.
Recent trends in next generation immunoinformatics harnessed for universal coronavirus vaccine design
Published in Pathogens and Global Health, 2023
Chin Peng Lim, Boon Hui Kok, Hui Ting Lim, Candy Chuah, Badarulhisam Abdul Rahman, Abu Bakar Abdul Majeed, Michelle Wykes, Chiuan Herng Leow, Chiuan Yee Leow
An epitope is the part of an antigen that is recognized by the adaptive immune system. It binds to specific receptors including antibodies, MHC molecules and T-cell receptors [28]. The binding portion of an antibody is termed a paratope. Epitopes can be either continuous or discontinuous. A continuous or linear epitope is a relatively short (usually 5–6) amino acid sequences recognized by the paratope of a corresponding antibody. In contrast, a discontinuous epitope consists of non-adjacent segments of amino acids, not necessarily from one chain, which form a specific 3D structure, which can also be recognized by antibodies. Since discontinuous epitope arises from a specific 3D fold, it is also known as conformational epitope. Notably, epitopes recognized by B-cell epitopes may contain lipids, nucleic acids or carbohydrates, giving resultant antibodies a vast repertoire while T-cell epitopes are usually peptide fragments. The investigation, identification and development of epitopes are crucial in promoting the advancement of diagnostics and therapeutics [110].
The impact of the HLA DQB1 gene and amino acids on the development of narcolepsy
Published in International Journal of Neuroscience, 2022
Leila Kachooei-Mohaghegh-yaghoobi, Fatemeh Rezaei-Rad, Khosro Sadeghniiat-Haghighi, Mahdi Zamani
In the present study, the DQB1*06:02 allele displayed a negative effect by predisposing to the risk of developing Narcolepsy, whereas DQB1*03:05 demonstrated a positive impact by reducing the risk of Narcolepsy disease. This may be due to structural differences in the effectiveness of antigen presentation between the two HLA DQB1 alleles, especially in their epitope binding region. The epitopes are conformational amino acid arrangements of short segments of antigens that are recognized by antibodies, B cells, or T cells. Due to existence of polymorphic residues within these HLA receptor proteins (encoded by the HLA genes) binding to a particular antigen varies between the various subtypes of HLA molecules. Therefore, these polymorphic residues on HLA receptors have an important role in differentiating antigen binding and formation of complexes and HLA recognition by antibodies. Susceptible DQB1*06:02 allele contains amino acids serine at position 182 (DQB1Ser182) and threonine at position 185 (DQB1Thr185) both of which exhibit polymorphisms in the population that affect their epitopes. As compared with controls, DQB1*02:00 allele was more common among Iranian narcoleptic patient (Fr. in patients: 0.175 vs controls: 0.09), and also DQB1*06:02 allele (Pc = 1 × 10−14) contains the common Serine and Threonine AAs at the positions 182 and 185 respectively. Whereas, majority of the controls exhibit DQB1*03:05 and DQB1*03:01, 4 alleles with asparagine polymorphic residue in their epitopes at 182 AA position (DQB1Asn182).