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Journal articles on the topic 'FAB-ANTIGENS COMPLEX STRUCTURE'

Author: Grafiati

Published: 10 March 2023

Last updated: 31 July 2025

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1

Zimanyi, Marcell, Kaitlin Hulce, Charles Craik, and Yifan Cheng. "Cryo-EM Determines the Epitope of a 28 kD Viral Protease in Complex with an Antibody Fragment." Structural Dynamics 12, no. 2_Supplement (2025): A304. https://doi.org/10.1063/4.0000610.

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Cryo-Electron Microscopy (cryo-EM) is an enabling technology for structure-guided antibody drug design. The 50 kD antibody fragment antigen-binding (Fab) is particularly amenable to cryo-EM due to its clear features and its ability to make rigid complexes with antigens. However, the technical challenges of analyzing macromolecular complexes under 100 kD hinders the analysis of Fabs bound to a large portion of the druggable genome. We were able to determine the structure of a Fab in complex with a 28 kD viral protease where the entire Fab and its binding interface (epitope) are resolved below 3

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2

Yazaki, Shuma, Misaki Komatsu, Jinhua Dong, Hiroshi Ueda, and Ryoichi Arai. "Crystal Structures of Antigen-Binding Fragment of Anti-Osteocalcin Antibody KTM219." International Journal of Molecular Sciences 26, no. 2 (2025): 648. https://doi.org/10.3390/ijms26020648.

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Osteocalcin is a useful biomarker for bone formation and bone-related diseases. KTM219 is an anti-osteocalcin C-terminal peptide antibody. The single-chain variable region (scFv) and antigen-binding fragment (Fab) of KTM219 are applicable to the Quenchbody (Q-body) immunoassay. Q-body is a new type of fluorescent immunosensor, which is scFv or Fab labeled with a fluorescent dye. When Q-body binds to its antigen, the fluorescence intensity increases. The highly sensitive detection of antigens by changes in fluorescence intensity is performed in a single step by mixing the sample and reagent. In

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3

Panda, Abir Kumar, Kannan Natarajan, Surajit Sinha, et al. "Inhibition of Ly-49/LILRB-MHC-I interactions by anti-MHC-I augments innate and adaptive immunity." Journal of Immunology 210, no. 1_Supplement (2023): 169.14. http://dx.doi.org/10.4049/jimmunol.210.supp.169.14.

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Abstract Mouse NK cells recognize MHC-I antigens via stochastically expressed inhibitory Ly49 receptors. The loss of MHC-I expression on tumor cells (“missing self”) abrogates inhibitory signals, resulting in NK activation. We have identified an anti-mouse pan MHC-I mAb (M1/42), which blocks Ly49-MHC-I interactions but not TCR-MHC-I interactions. Administration of M1/42 in vivo markedly activated IFNg-producing NK cells that further drove the proliferation of NK cells and memory phenotype (MP) T cells and profoundly augmented adaptive immunity against viral infection and cancer metastasis. In

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4

Radwańska, Malwina J., Mateusz Jaskółowski, Elena Davydova, et al. "The structure of the C-terminal domain of the nucleoprotein from the Bundibugyo strain of the Ebola virus in complex with a pan-specific synthetic Fab." Acta Crystallographica Section D Structural Biology 74, no. 7 (2018): 681–89. http://dx.doi.org/10.1107/s2059798318007878.

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The vast majority of platforms for the detection of viral or bacterial antigens rely on immunoassays, typically ELISA or sandwich ELISA, that are contingent on the availability of suitable monoclonal antibodies (mAbs). This is a major bottleneck, since the generation and production of mAbs is time-consuming and expensive. Synthetic antibody fragments (sFabs) generated by phage-display selection offer an alternative with many advantages over Fabs obtained from natural antibodies using hybridoma technology. Unlike mAbs, sFabs are generated using phage display, allowing selection for binding to s

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5

Verdaguer, Nuria, Noemi Sevilla, Mari Luz Valero, et al. "A Similar Pattern of Interaction for Different Antibodies with a Major Antigenic Site of Foot-and-Mouth Disease Virus: Implications for Intratypic Antigenic Variation." Journal of Virology 72, no. 1 (1998): 739–48. http://dx.doi.org/10.1128/jvi.72.1.739-748.1998.

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ABSTRACT The three-dimensional structures of the Fab fragment of a neutralizing antibody raised against a foot-and-mouth disease virus (FMDV) of serotype C1, alone and complexed to an antigenic peptide representing the major antigenic site A (G-H loop of VP1), have been determined. As previously seen in a complex of the same antigen with another antibody which recognizes a different epitope within antigenic site A, the receptor recognition motif Arg-Gly-Asp and some residues from an adjacent helix participate directly in the interaction with the complementarity-determining regions of the antib

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6

Vukovich, Matthew J., Andrea R. Shiakolas, Jared Lindenberger, et al. "Isolation and characterization of IgG3 glycan-targeting antibodies with exceptional cross-reactivity for diverse viral families." PLOS Pathogens 20, no. 9 (2024): e1012499. http://dx.doi.org/10.1371/journal.ppat.1012499.

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Broadly reactive antibodies that target sequence-diverse antigens are of interest for vaccine design and monoclonal antibody therapeutic development because they can protect against multiple strains of a virus and provide a barrier to evolution of escape mutants. Using LIBRA-seq (linking B cell receptor to antigen specificity through sequencing) data for the B cell repertoire of an individual chronically infected with human immunodeficiency virus type 1 (HIV-1), we identified a lineage of IgG3 antibodies predicted to bind to HIV-1 Envelope (Env) and influenza A Hemagglutinin (HA). Two lineage

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7

Pan, Jingxi, and Sara Zhang. "Antibody epitope mapping at single residue resolution for unpurified antigens." Journal of Immunology 202, no. 1_Supplement (2019): 131.36. http://dx.doi.org/10.4049/jimmunol.202.supp.131.36.

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Abstract The vast majority of antigen-antibody interactions rely upon binding to conformational epitopes, which are composed of amino acids that are discontinuous in the protein sequence but are brought together upon three-dimensional protein folding. This character has made conformational epitopes particularly difficult to map because they are only formed in the native structure of the antigen protein. X-ray crystallography is a gold-standard method for mapping conformational epitopes at high-resolution, but it only works for highly purified antigens and is time consuming, and is not applicab

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8

Mitropoulou, Alkistis N., Holly Bowen, Tihomir S. Dodev, et al. "Structure of a patient-derived antibody in complex with allergen reveals simultaneous conventional and superantigen-like recognition." Proceedings of the National Academy of Sciences 115, no. 37 (2018): E8707—E8716. http://dx.doi.org/10.1073/pnas.1806840115.

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Antibodies classically bind antigens via their complementarity-determining regions, but an alternative mode of interaction involving V-domain framework regions has been observed for some B cell “superantigens.” We report the crystal structure of an antibody employing both modes of interaction simultaneously and binding two antigen molecules. This human antibody from an allergic individual binds to the grass pollen allergen Phl p 7. Not only are two allergen molecules bound to each antibody fragment (Fab) but also each allergen molecule is bound by two Fabs: One epitope is recognized classicall

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9

Onuoha, Shimobi, Mathieu Ferrari, Anna Bulek, et al. "Structure Guided Engineering of Highly Specific Chimeric Antigen Receptors for the Treatment of T Cell Lymphomas." Blood 132, Supplement 1 (2018): 1661. http://dx.doi.org/10.1182/blood-2018-99-119564.

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Abstract Introduction Mature T cell lymphomas are aggressive, treatment resistant cancers that are associated with poor prognosis. Clinical application of immunotherapeutic approaches has been limited by a lack of target antigens that discriminate malignant from healthy T cells. Unlike B cell depletion, pan-T cell aplasia is prohibitively toxic. Previously we reported a targeting strategy based on the mutually exclusive expression of T cell receptor beta-chain constant domains 1 and 2 (TRBC1 and TRBC2). We identified an antibody with unique TRBC1 specificity and demonstrated that anti TRBC1 ch

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10

Danska, J. S., A. M. Livingstone, V. Paragas, T. Ishihara, and C. G. Fathman. "The presumptive CDR3 regions of both T cell receptor alpha and beta chains determine T cell specificity for myoglobin peptides." Journal of Experimental Medicine 172, no. 1 (1990): 27–33. http://dx.doi.org/10.1084/jem.172.1.27.

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The T cell receptor alpha/beta (TCR-alpha/beta) is encoded by variable (V), diversity (D), joining (J), and constant (C) segments assembled by recombination during thymocyte maturation to produce a heterodimer that imparts antigenic specificity to the T cell. Unlike immunoglobulins (Igs), which bind free antigen, the ligands of TCR-alpha/beta are cell surface complexes of intracellularly degraded antigens (i.e., peptides) bound to and presented by polymorphic products of the major histocompatibility complex (MHC). Therefore, antigen recognition by T cells is defined as MHC restricted. A model

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11

Darowski, Diana, Mohamed-Reda Benmebarek, Christian Jost, et al. "Abstract 570: Developing a novel adaptor CAR-T cell platform based on the recognition of the P329G Fc mutation in therapeutic IgG1 antibodies for adoptive T cell therapy." Cancer Research 82, no. 12_Supplement (2022): 570. http://dx.doi.org/10.1158/1538-7445.am2022-570.

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Abstract Chimeric antigen receptor (CAR) T cells have shown promising results for the treatment of blood cancers and various CAR-T cell approaches are in development for use in different tumor indications. Universal or modular CARs do not directly recognize the tumor target antigen, but bind via an adaptor molecule to their respective tumor target. We describe the P329G-CAR-T platform as a novel modular CAR-T cell platform that recognizes the P329G mutation in the Fc portion of IgG1 antibodies, a mutation frequently applied to abolish the Fc immune effector function of therapeutic antibodies.

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12

Templeton, Douglas M., and Kerstin Moehle. "Structural aspects of molecular recognition in the immune system. Part I: Acquired immunity (IUPAC Technical Report)." Pure and Applied Chemistry 86, no. 10 (2014): 1435–81. http://dx.doi.org/10.1515/pac-2013-1020.

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Abstract Humoral immunity allows the body to mount a defense against pathogens and foreign substances, and to respond with memory to subsequent exposures. The molecular participants may also recognize self-structures, leading to attack on the body and autoimmune disease. The main players in humoral immunity are antibody-producing B lymphocytes, and several classes of T lymphocytes. This review deals with the molecular details of recognition of antigens by soluble antibodies, and of substances presented to receptors on the surfaces of T cells (TCRs). The prototype antibody consists of a dimer o

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13

Alonso, G., and P. Siaud. "Combined use of immunoperoxidase and radioimmunocytochemistry for double immunocytochemical labeling of neurons at light and electron microscopic level." Journal of Histochemistry & Cytochemistry 37, no. 12 (1989): 1799–809. http://dx.doi.org/10.1177/37.12.2573630.

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Complexes formed by binding 125I- or 3H-labeled neuropeptides to one of the two binding sites of their specific antibodies allowed specific and sensitive labeling of various peptidergic neurons, which could be detected by classical autoradiographic methods. To visualize two neuronal antigens on the same material at both light and electron microscopic level, we used a new technique of double immunocytochemical labeling, combining immunoperoxidase and radioimmunocytochemistry. The main steps of the process included: (a) indirect labeling of the first antigen by its specific antibody and by a per

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14

Fernandez-Martinez, David, Mark D. Tully, Gordon Leonard, Magali Mathieu, and Eaazhisai Kandiah. "Structural insights into the bi-specific cross-over dual variable antibody architecture by cryo-EM." Scientific Reports 13, no. 1 (2023). http://dx.doi.org/10.1038/s41598-023-35678-4.

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AbstractMulti-specific antibodies (msAbs) are being developed as next generation antibody-based therapeutics. Knowledge of the three-dimensional structures, in the full antibody context, of their fragment antigen-binding (Fab) moieties with or without bound antigens is key to elucidating their therapeutic efficiency and stability. However, the flexibility of msAbs, a feature essential for their multi specificity, has hindered efforts in this direction. Cross-Over Dual Variable immunoglobulin (CODVIg) is a promising bispecific antibody format, designed to simultaneously target the interleukins

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15

"Studies of structure and specificity of some antigen-antibody complexes." Philosophical Transactions of the Royal Society of London. B, Biological Sciences 323, no. 1217 (1989): 487–94. http://dx.doi.org/10.1098/rstb.1989.0026.

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By using X -ray diffraction and immunochemical techniques, we have exploited the use of monoclonal antibodies raised against hen egg lysozyme (HEL) to study systematically those factors responsible for the high specificity of antigen -antibody interactions. HEL was chosen for our investigations because its three-dimensional structure and immunochemistry have been well characterized and because naturally occurring sequence variants from different avian species are readily available to test the fine specificity of the antibodies. The X-ray crystal structure of a complex formed between HEL and th

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16

Makabe, Koki, Takeshi Yokoyama, Shiro Uehara, et al. "Anti-EGFR antibody 528 binds to domain III of EGFR at a site shifted from the cetuximab epitope." Scientific Reports 11, no. 1 (2021). http://dx.doi.org/10.1038/s41598-021-84171-3.

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AbstractAntibodies have been widely used for cancer therapy owing to their ability to distinguish cancer cells by recognizing cancer-specific antigens. Epidermal growth factor receptor (EGFR) is a promising target for the cancer therapeutics, against which several antibody clones have been developed and brought into therapeutic use. Another antibody clone, 528, is an antagonistic anti-EGFR antibody, which has been the focus of our antibody engineering studies to develop cancer drugs. In this study, we explored the interaction of 528 with the extracellular region of EGFR (sEGFR) via binding ana

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17

Argiriadi, Maria A., Kangwen Deng, David Egan, et al. "The use of cyclic peptide antigens to generate LRP8 specific antibodies." Frontiers in Drug Discovery 2 (January 12, 2023). http://dx.doi.org/10.3389/fddsv.2022.1093153.

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LRP8 is a member of the LDLR-like protein family. It is a transport receptor, which can be used in the design of antibodies specific for investigating increasing exposure to therapeutics with respect to the blood brain barrier (BBB). In this study, a LRP8 peptide immunization strategy was implemented to generate antibodies to a specific epitope of the CR1 domain of LRP8 that could enable transport function and cross-react in mice, cynomolgus monkeys and humans. Additionally, a cyclized peptide immunogen was designed to conserve the structural β-hairpin element observed in a previously solved c

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