Journal articles: 'Protein-Antibody recognition'

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Addis, Philip W., Catherine J. Hall, Shaun Bruton, Vaclav Veverka, Ian C. Wilkinson, Frederick W. Muskett, Philip S. Renshaw, et al. "Conformational Heterogeneity in Antibody-Protein Antigen Recognition." Journal of Biological Chemistry 289, no. 10 (January 16, 2014): 7200–7210. http://dx.doi.org/10.1074/jbc.m113.492215.

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Ferrigno, Paul Ko. "Non-antibody protein-based biosensors." Essays in Biochemistry 60, no. 1 (June 30, 2016): 19–25. http://dx.doi.org/10.1042/ebc20150003.

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Biosensors that depend on a physical or chemical measurement can be adversely affected by non-specific interactions. For example, a biosensor designed to measure specifically the levels of a rare analyte can give false positive results if there is even a small amount of interaction with a highly abundant but irrelevant molecule. To overcome this limitation, the biosensor community has frequently turned to antibody molecules as recognition elements because they are renowned for their exquisite specificity. Unfortunately antibodies can often fail when immobilised on inorganic surfaces, and alternative biological recognition elements are needed. This article reviews the available non-antibody-binding proteins that have been successfully used in electrical and micro-mechanical biosensor platforms.

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Pierce, Brian G., Zhen-Yong Keck, Patrick Lau, Catherine Fauvelle, Ragul Gowthaman, Thomas F. Baumert, Thomas R. Fuerst, Roy A. Mariuzza, and Steven K. H. Foung. "Global mapping of antibody recognition of the hepatitis C virus E2 glycoprotein: Implications for vaccine design." Proceedings of the National Academy of Sciences 113, no. 45 (October 26, 2016): E6946—E6954. http://dx.doi.org/10.1073/pnas.1614942113.

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The E2 envelope glycoprotein is the primary target of human neutralizing antibody response against hepatitis C virus (HCV), and is thus a major focus of vaccine and immunotherapeutics efforts. There is emerging evidence that E2 is a highly complex, dynamic protein with residues across the protein that are modulating antibody recognition, local and global E2 stability, and viral escape. To comprehensively map these determinants, we performed global E2 alanine scanning with a panel of 16 human monoclonal antibodies (hmAbs), resulting in an unprecedented dataset of the effects of individual alanine substitutions across the E2 protein (355 positions) on antibody recognition. Analysis of shared energetic effects across the antibody panel identified networks of E2 residues involved in antibody recognition and local and global E2 stability, as well as predicted contacts between residues across the entire E2 protein. Further analysis of antibody binding hotspot residues defined groups of residues essential for E2 conformation and recognition for all 14 conformationally dependent E2 antibodies and subsets thereof, as well as residues that enhance antibody recognition when mutated to alanine, providing a potential route to engineer E2 vaccine immunogens. By incorporating E2 sequence variability, we found a number of E2 polymorphic sites that are responsible for loss of neutralizing antibody binding. These data and analyses provide fundamental insights into antibody recognition of E2, highlighting the dynamic and complex nature of this viral envelope glycoprotein, and can serve as a reference for development and rational design of E2-targeting vaccines and immunotherapeutics.

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Huang, Jiachen, Darren Diaz, and Jarrod J. Mousa. "Antibody recognition of the Pneumovirus fusion protein trimer interface." PLOS Pathogens 16, no. 10 (October 9, 2020): e1008942. http://dx.doi.org/10.1371/journal.ppat.1008942.

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Wang, Meryl, David Zhu, Jianwei Zhu, Ruth Nussinov, and Buyong Ma. "Local and global anatomy of antibody-protein antigen recognition." Journal of Molecular Recognition 31, no. 5 (December 8, 2017): e2693. http://dx.doi.org/10.1002/jmr.2693.

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Margulies, David, and Andrew D. Hamilton. "Combinatorial protein recognition as an alternative approach to antibody-mimetics." Current Opinion in Chemical Biology 14, no. 6 (December 2010): 705–12. http://dx.doi.org/10.1016/j.cbpa.2010.07.017.

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Kanaujia, G. V., S. Motzel, M. A. Garcia, P. Andersen, and M. L. Gennaro. "Recognition of ESAT-6 Sequences by Antibodies in Sera of Tuberculous Nonhuman Primates." Clinical Diagnostic Laboratory Immunology 11, no. 1 (January 2004): 222–26. http://dx.doi.org/10.1128/cdli.11.1.222-226.2004.

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ABSTRACT Previous work in our laboratory showed that the ESAT-6 protein of Mycobacterium tuberculosis and Mycobacterium bovis induces strong antibody responses in a large proportion (∼90%) of experimentally or naturally infected nonhuman primates. Here, the antibody response to ESAT-6 in tuberculous monkeys was characterized at the epitope level by measuring antibodies to overlapping, synthetic peptides spanning the ESAT-6 sequence. The antibody response against the COOH-terminal portion of the protein was the strongest in both experimentally and naturally infected animals. Moreover, these antibodies became detectable the earliest during experimental infection, suggesting an ordered expansion of ESAT-6-specific B-cell clones in the course of infection. The data support use of synthetic peptides in lieu of the full-length ESAT-6 protein in diagnostic antibody detection assays.

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Fuchs, Stephen M., Krzysztof Krajewski, Richard W. Baker, Victoria L. Miller, and Brian D. Strahl. "Influence of Combinatorial Histone Modifications on Antibody and Effector Protein Recognition." Current Biology 21, no. 1 (January 2011): 53–58. http://dx.doi.org/10.1016/j.cub.2010.11.058.

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Lak, Parnian, Spandana Makeneni, Robert J. Woods, and Todd L. Lowary. "Specificity of Furanoside-Protein Recognition through Antibody Engineering and Molecular Modeling." Chemistry - A European Journal 21, no. 3 (November 20, 2014): 1138–48. http://dx.doi.org/10.1002/chem.201405259.

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Otlewski, J., and W. Apostoluk. "Structural and energetic aspects of protein-protein recognition." Acta Biochimica Polonica 44, no. 3 (September 30, 1997): 367–87. http://dx.doi.org/10.18388/abp.1997_4392.

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Specific recognition between proteins plays a crucial role in a great number of vital processes. In this review different types of protein-protein complexes are analyzed on the basis of their three-dimensional structures which became available in recent years. The complexes which are analyzed include: those resulting from different types of recognition between proteinase and protein inhibitor (canonical inhibitors of serine proteinases, hirudin, inhibitors of cysteine proteinases, carboxypeptidase inhibitor), barnase-barstar, human growth hormone-receptor and antibody-antigen. It seems obvious that specific and strong protein-protein recognition is achieved in many different ways. To further explore this question, the structural information was analyzed together with kinetic and thermodynamic data available for the respective complexes. It appears that the energy and rates of specific recognition of proteins are influenced by many different factors, including: area of interacting surfaces; complementarity of shapes, charges and hydrogen bonds; water structure at the interface; conformational changes; additivity and cooperativity of individual interactions, steric effects and various (conformational, hydration) entropy changes.

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Wong, Hing C., Robert G. Newman, Warren D. Marcus, Bai Liu, Emily K. Jeng, Sarah Alter, and Peter R. Rhode. "Novel antibody-like single-chain TCR antibody Fc fusion protein." Journal of Immunology 198, no. 1_Supplement (May 1, 2017): 120.9. http://dx.doi.org/10.4049/jimmunol.198.supp.120.9.

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Abstract We have previously reported the construction of a fusion protein composed of a soluble single-chain T cell receptor genetically linked to the constant domain of the human IgG1 heavy chain (TCR-Ig). The antigen recognition portion of the protein binds to an unmutated peptide derived from human p53 (amino acids 264–272) presented in the context of HLA-A2.1, whereas the IgG1 Fc provides effector functions. The protein is capable of forming dimers, specifically staining tumor cells, and promoting target and effector cell conjugation. The protein also has potent antitumor effects against p53+/HLA-A2.1+ human tumor xenografts in athymic nude mice and can mediate cell killing by antibody-dependent cellular cytotoxicity. Therefore, TCR-Ig behaves like an antibody, but possesses the ability to recognize antigens derived from intracellular targets. To test TCR-Ig in fully immunocompetent models, we have generated murine tumor cells stably expressing the human p53 epitope by constructing a single chain trimer composed of the human p53 peptide genetically linked to murine beta 2 microglobulin genetically linked to HLA-A2.1, with the inclusion of a disulfide trap to enhance stability. Utilizing haNK (NK-92 cells stably expressing high affinity Fc receptor and IL-2) as effector cells in the presence of TCR-Ig we demonstrated specific killing of murine single chain trimer expressing tumor cells. We are currently evaluating the antitumor activities and vaccinal effects of TCR-Ig in an HLA-A2.1 transgenic mouse model. TCR-Ig may represent a novel group of immunotherapeutics that has the potential to expand the range of tumors available for targeted therapies beyond those currently addressed by conventional antibody-based approaches.

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Branco, Ricardo J. F., Ana M. G. C. Dias, and Ana C. A. Roque. "Understanding the molecular recognition between antibody fragments and protein A biomimetic ligand." Journal of Chromatography A 1244 (June 2012): 106–15. http://dx.doi.org/10.1016/j.chroma.2012.04.071.

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Huang, Ao, Luning Zhang, Weiwei Li, Zeyu Ma, Shi Shuo, and Tianming Yao. "Controlled fluorescence quenching by antibody-conjugated graphene oxide to measure tau protein." Royal Society Open Science 5, no. 4 (April 2018): 171808. http://dx.doi.org/10.1098/rsos.171808.

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We report an ultrasensitive immunoassay for tau protein—a key marker of Alzheimer's disease. This sensing platform relies on graphene oxide (GO) surfaces conjugated with anti-human tau antibody to provide quantitative binding sites for the tau protein. The GO quenches standard fluorescein isothiocyanate labelled tau (tau-FITC) when tau protein and tau-FITC are both present and compete for the binding sites. This change in fluorescence signal can be used to quantitate tau protein. In contrast with traditional enzyme-linked immunosorbent assay (ELISA), our method does not require enzyme-linked secondary antibodies for protein recognition nor does it require an enzyme substrate for optical signal generation. This requires fewer reagents and has less systematic error than the antigen–antibody recognition steps in ELISA. Our method has a tau protein detection limit of 0.14 pmol ml −1 in buffer. This approach could be developed into a promising biosensor for the detection of tau protein and may be useful in the clinical diagnosis of tau-induced neurodegeneration syndromes.

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Zhang, Zulei, Xingdi Zhang, Dechao Niu, Yongsheng Li, and Jianlin Shi. "Large-pore, silica particles with antibody-like, biorecognition sites for efficient protein separation." Journal of Materials Chemistry B 5, no. 22 (2017): 4214–20. http://dx.doi.org/10.1039/c7tb00886d.

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Liu, Hejun, Meng Yuan, Chang-Chun D. Lee, Nicholas C. Wu, and Ian A. Wilson. "Cross-neutralizing antibody recognition of sarbecoviruses." Journal of Immunology 206, no. 1_Supplement (May 1, 2021): 114.02. http://dx.doi.org/10.4049/jimmunol.206.supp.114.02.

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Abstract The ongoing COVID-19 pandemic has been devasting to public health and global economy, with more than 82 million confirmed cases and 1.8 million deaths in 2020. Vaccines and antibody therapies are currently under emergency use authorization and provide hope to slow down and eventually stop the spread of SARS-CoV-2 infection. However, the continued identification of SARS-CoV-2 mutants as well as reciprocal transmission between human and farmed mink raise concerns on antigenic drift of SARS-CoV-2 and potential escape from current vaccines. Despite potent and versatile antibody responses to the receptor binding site of the SARS-CoV-2 spike protein, cross-neutralizing antibodies isolated from COVID-19 patients are relatively rare. We have been characterizing these rare cross-neutralizing antibodies using high-resolution X-ray crystallography, as well as other biophysical methods. These antibodies neutralize SARS-CoV-2 and SARS-CoV pseudotyped viruses and are cross-reactive with the receptor binding domain of several sarbecoviruses tested. Our structures have revealed the location of the conserved epitopes that lead to cross-neutralization and the different neutralization mechanisms used by these antibodies. Our findings provide insights for developing more universal SARS-like coronavirus vaccines and therapies to combat antigenic drift in SARS-CoV-2 as well as potential epidemics of other zoonotic coronaviruses.

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Zhu, Jing, and Gang Sun. "Bio-functionalized nanofibrous membranes as a hybrid platform for selective antibody recognition and capturing." RSC Advances 5, no. 36 (2015): 28115–23. http://dx.doi.org/10.1039/c5ra01140j.

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Jian, Jhih-Wei, Hong-Sen Chen, Yi-Kai Chiu, Hung-Pin Peng, Chao-Ping Tung, Ing-Chien Chen, Chung-Ming Yu, et al. "Effective binding to protein antigens by antibodies from antibody libraries designed with enhanced protein recognition propensities." mAbs 11, no. 2 (January 9, 2019): 373–87. http://dx.doi.org/10.1080/19420862.2018.1550320.

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Hui, G. S., S. P. Chang, H. Gibson, A. Hashimoto, C. Hashiro, P. J. Barr, and S. Kotani. "Influence of adjuvants on the antibody specificity to the Plasmodium falciparum major merozoite surface protein, gp195." Journal of Immunology 147, no. 11 (December 1, 1991): 3935–41. http://dx.doi.org/10.4049/jimmunol.147.11.3935.

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Abstract The effect of adjuvants on the specificity of immune responses to the Plasmodium falciparum gp195 protein was investigated using adjuvant formulations based on synthetic muramyl dipeptide and monophosphoryl lipid A derivatives, in parallel with CFA and alum. Although these immunomodulators were as effective as CFA in inducing an antibody response to gp195, there were distinct differences in the recognition of B cell epitopes by these antibody populations. We have also demonstrated that MHC control of antibody specificity can be related to the adjuvant used for immunization. In general, the potency of adjuvants, their ability to induce antibodies of a particular specificity, or their ability to overcome MHC control of immune responsiveness varied independently. These findings suggest a critical role of adjuvants in the determination of the specificity of the immune response to protein Ag. Thus, the influence of adjuvants should be a major consideration in studies on immunologic recognition, as well as in the design of modern subunit vaccines.

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Lyashchenko, Konstantin, Roberto Colangeli, Michel Houde, Hamdan Al Jahdali, Dick Menzies, and Maria Laura Gennaro. "Heterogeneous Antibody Responses in Tuberculosis." Infection and Immunity 66, no. 8 (August 1, 1998): 3936–40. http://dx.doi.org/10.1128/iai.66.8.3936-3940.1998.

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ABSTRACT Antibody responses during tuberculosis were analyzed by an enzyme-linked immunosorbent assay with a panel of 10 protein antigens of Mycobacterium tuberculosis. It was shown that serum immunoglobulin G antibodies were produced against a variety of M. tuberculosis antigens and that the vast majority of sera from tuberculosis patients contained antibodies against one or more M. tuberculosis antigens. The number and the species of serologically reactive antigens varied greatly from individual to individual. In a given serum, the level of specific antibodies also varied with the antigen irrespective of the total number of antigens recognized by that particular serum. These findings indicate that person-to-person heterogeneity of antigen recognition, rather than recognition of particular antigens, is a key attribute of the antibody response in tuberculosis.

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Ramsden, J. J., and P. Schneider. "Membrane insertion and antibody recognition of a glycosylphosphatidylinositol-anchored protein: an optical study." Biochemistry 32, no. 2 (January 19, 1993): 523–29. http://dx.doi.org/10.1021/bi00053a017.

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Kang, Hyo Jin, Young Ji Kang, Young-Mi Lee, Hyun-Hee Shin, Sang J. Chung, and Sebyung Kang. "Developing an antibody-binding protein cage as a molecular recognition drug modular nanoplatform." Biomaterials 33, no. 21 (July 2012): 5423–30. http://dx.doi.org/10.1016/j.biomaterials.2012.03.055.

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Pantophlet, Ralph, Meng Wang, Rowena O. Aguilar-Sino, and Dennis R. Burton. "The Human Immunodeficiency Virus Type 1 Envelope Spike of Primary Viruses Can Suppress Antibody Access to Variable Regions." Journal of Virology 83, no. 4 (November 26, 2008): 1649–59. http://dx.doi.org/10.1128/jvi.02046-08.

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ABSTRACT The human immunodeficiency virus type 1 (HIV-1) envelope spike is a heavily glycosylated trimeric structure in which protein surfaces conserved between different HIV-1 isolates are particularly well hidden from antibody recognition. However, even variable regions on the spike tend to be less antigenic and immunogenic than one might have anticipated for external structures. Here we show that the envelope spike of primary viruses has an ability to restrict antibody recognition of variable regions. We show that access to an artificial epitope, introduced at multiple positions across the spike, is frequently limited, even though the epitope has been inserted at surface-exposed regions on the spike. Based on the data, we posit that restricted antibody access may be the result, at least in part, of a rigidification of the epitope sequence in the context of the spike and/or a highly effective flexible arrangement of the glycan shield on primary viruses. Evolution of the HIV envelope structure to incorporate extra polypeptide sequences into nominally accessible regions with limited antibody recognition may contribute to reducing the magnitude of antibody responses during infection and allow the virus to replicate unhindered by antibody pressure for longer periods.

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Moraes, Adolfo H., Luca Simonelli, Mattia Pedotti, Fabio C. L. Almeida, Luca Varani, and Ana P. Valente. "Antibody Binding Modulates Conformational Exchange in Domain III of Dengue Virus E Protein." Journal of Virology 90, no. 4 (December 4, 2015): 1802–11. http://dx.doi.org/10.1128/jvi.02314-15.

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ABSTRACTDomain III of dengue virus E protein (DIII) participates in the recognition of cell receptors and in structural rearrangements required for membrane fusion and ultimately viral infection; furthermore, it contains epitopes for neutralizing antibodies and has been considered a potential vaccination agent. In this work, we addressed various structural aspects of DIII and their relevance for both the dengue virus infection mechanism and antibody recognition. We provided a dynamic description of DIII at physiological and endosomal pHs and in complex with the neutralizing human antibody DV32.6. We observed conformational exchange in the isolated DIII, in regions important for the packing of E protein dimers on the virus surface. This conformational diversity is likely to facilitate the partial detachment of DIII from the other E protein domains, which is required to achieve fusion to the host cellular membranes and to expose the epitopes of many anti-DIII antibodies. A comparison of DIII of two dengue virus serotypes revealed many common features but also some possibly unexpected differences. Antibody binding to DIII of dengue virus serotype 4 attenuated the conformational exchange in the epitope region but, surprisingly, generated exchange in other parts of DIII through allosteric effects.IMPORTANCEMany studies have provided extensive structural information on the E protein and particularly on DIII, also in complex with antibodies. However, there is very scarce information regarding the molecular dynamics of DIII, and almost nothing is available on the dynamic effect of antibody binding, especially at the quantitative level. This work provides one of the very rare descriptions of the effect of antibody binding on antigen dynamics.

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Easton, Donna M., Adam Smith, Sara Gomez Gallego, A. Ruth Foxwell, Allan W. Cripps, and Jennelle M. Kyd. "Characterization of a Novel Porin Protein from Moraxella catarrhalis and Identification of an Immunodominant Surface Loop." Journal of Bacteriology 187, no. 18 (September 15, 2005): 6528–35. http://dx.doi.org/10.1128/jb.187.18.6528-6535.2005.

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ABSTRACT Moraxella catarrhalis is a gram-negative bacterium that is mainly responsible for respiratory tract infections. In this study we report a novel outer membrane protein (OMP), designated M35, with a molecular mass of 36.1 kDa. This protein was structurally homologous to classic gram-negative porins, such as OMP C from Escherichia coli and OMP K36 from Klebsiella pneumoniae, with a predicted structure of 8 surface loops and 16 antiparallel β-sheets. The DNA sequences of the genes from 18 diverse clinical isolates showed that the gene was highly conserved (99.6 to 100% of nucleotides), with only one isolate (ID78LN266) having base variations that resulted in amino acid substitutions. Electrophoresis and analysis of recognition of the protein using mouse anti-M35 sera showed that M35 was expressed on the bacterial surface and constitutively expressed across M. catarrhalis isolates, with only ID78LN266 showing poor antibody recognition. Our results showed that the single amino acid mutation in loop 3 significantly affected antibody recognition, indicating that loop 3 appeared to contain an immunodominant B-cell epitope. The antibody specificity to loop 3 may be a potential mechanism for evasion of host immune responses targeted to M35, since loop 3 should theoretically orientate into the porin channel. Thus, M35 is a highly conserved, surface-expressed protein that is of significance for its potential functional role as an M. catarrhalis porin and is of interest as a vaccine candidate.

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Tokatlian, Talar, Benjamin J. Read, Christopher A. Jones, Daniel W. Kulp, Sergey Menis, Jason Y. H. Chang, Jon M. Steichen, et al. "Innate immune recognition of glycans targets HIV nanoparticle immunogens to germinal centers." Science 363, no. 6427 (December 20, 2018): 649–54. http://dx.doi.org/10.1126/science.aat9120.

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In vaccine design, antigens are often arrayed in a multivalent nanoparticle form, but in vivo mechanisms underlying the enhanced immunity elicited by such vaccines remain poorly understood. We compared the fates of two different heavily glycosylated HIV antigens, a gp120-derived mini-protein and a large, stabilized envelope trimer, in protein nanoparticle or “free” forms after primary immunization. Unlike monomeric antigens, nanoparticles were rapidly shuttled to the follicular dendritic cell (FDC) network and then concentrated in germinal centers in a complement-, mannose-binding lectin (MBL)–, and immunogen glycan–dependent manner. Loss of FDC localization in MBL-deficient mice or via immunogen deglycosylation significantly affected antibody responses. These findings identify an innate immune–mediated recognition pathway promoting antibody responses to particulate antigens, with broad implications for humoral immunity and vaccine design.

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Rauch, J., and AS Janoff. "Antibodies against Phospholipids other than Cardiolipin: Potential Roles for Both Phospholipid and Protein." Lupus 5, no. 5 (October 1996): 498–502. http://dx.doi.org/10.1177/096120339600500534.

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Autoantibodies to phospholipids other than cardiolipin have received less attention, to date, than anti-cardiolipin antibodies. This review focuses on these antibodies and potential roles for both phospholipid and protein in their reactivity. We review data in the literature indicating that antibodies to phosphatidylethanolamine and some lupus anticoagulant antibodies recognize phospholipid-binding proteins in association with phospholipid. Kininogens appear to be involved in the binding of antibodies to phosphatidylethanolamine, while phosphatidylserine-binding proteins, such as prothrombin and annexin V, have been implicated in lupus anticoagulant antibody recognition. These proteins bind to phospholipids that normally reside in the inner monolayer of the cell membrane, suggesting that exposure of these lipids is necessary for protein binding and antibody recognition to occur. In contrast, other autoantibodies, in particular those reactive with erythrocytes, appear to be directed at phospholipids that normally occur in the outer membrane leaflet, such as phosphatidylcholine. In summary, there is clearly accumulating evidence that antibodies to phospholipids other than cardiolipin recognize epitopes on phospholipid-binding proteins. It is not clear whether recognition of these epitopes is due to an increase in antigen density or a change in the protein or phospholipid structure, but it is likely that both protein and phospholipid structure play an important role in the in vivo interactions of these antibodies.

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Nicholls, Ian A., and Jesper G. Wiklander. "Towards Peptide and Protein Recognition by Antibody Mimicking Synthetic Polymers – Background, State of the Art, and Future Outlook." Australian Journal of Chemistry 73, no. 4 (2020): 300. http://dx.doi.org/10.1071/ch20020.

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Antibody–peptide/protein interactions are instrumental for many processes in the pharmaceutical and biotechnology industries and as tools for biomedical and biochemical research. The recent development of molecularly imprinted polymer nanoparticles displaying antibody-like recognition of peptides and proteins offers the possibility for substituting antibodies with these robust materials for applications where the structural integrity and function of antibodies is compromised by temperature, pH, solvent, etc. The background to the development of this class of antibody-mimicking material and the state-of-the-art in their synthesis and application is presented in this review.

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Kumar, Vasanthi U., S. Shishupala, H. S. Shetty, and S. Umesh-Kumar. "Serological evidence for the occurrence of races in Sclerospora graminicola and identification of a race-specific surface protein involved in host recognition." Canadian Journal of Botany 71, no. 11 (November 1, 1993): 1467–71. http://dx.doi.org/10.1139/b93-177.

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A protein specific to a virulent pathotype of the downy mildew pathogen Sclerospora graminicola was identified on the Western transfers using the cross-adsorbed antibody. This protein was approximately 90 kDa and without subunits. Serological agglutination studies localized the protein on the cell wall surfaces. Enzyme linked immunosorbent assay and dot blotting using the specific antibodies identified distinct races of the pathogen. Immunofluorescence studies and enzyme linked immunosorbent assay using suspension cultures of host cells showed that the protein bound to the cells of susceptible cultivar but not to those of resistant cultivar. These results suggested that this protein may be involved in host recognition. Key words: Sclerospora graminicola, Pennisetum glaucum, host–pathogen recognition.

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Crispin, Max, Andrew B. Ward, and Ian A. Wilson. "Structure and Immune Recognition of the HIV Glycan Shield." Annual Review of Biophysics 47, no. 1 (May 20, 2018): 499–523. http://dx.doi.org/10.1146/annurev-biophys-060414-034156.

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Vaccine design efforts against the human immunodeficiency virus (HIV) have been greatly stimulated by the observation that many infected patients eventually develop highly potent broadly neutralizing antibodies (bnAbs). Importantly, these bnAbs have evolved to recognize not only the two protein components of the viral envelope protein (Env) but also the numerous glycans that form a protective barrier on the Env protein. Because Env is heavily glycosylated compared to host glycoproteins, the glycans have become targets for the antibody response. Therefore, considerable efforts have been made in developing and validating biophysical methods to elucidate the complex structure of the Env-spike glycoprotein, with its combination of glycan and protein epitopes. We illustrate here how the application of robust biophysical methods has transformed our understanding of the structure and function of the HIV Env spike and stimulated innovation in vaccine design strategies that takes into account the essential glycan components.

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Lyashchenko, Konstantin P., John M. Pollock, Roberto Colangeli, and Maria Laura Gennaro. "Diversity of Antigen Recognition by Serum Antibodies in Experimental Bovine Tuberculosis." Infection and Immunity 66, no. 11 (November 1, 1998): 5344–49. http://dx.doi.org/10.1128/iai.66.11.5344-5349.1998.

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ABSTRACT Tuberculosis in cattle remains a major zoonotic and economic problem in many countries. The standard diagnostic assay for bovine tuberculosis, the intradermal tuberculin test, has low accuracy. Therefore, alternative immunodiagnostic methods, such as serological assays, are needed for detection of infected animals. Development of an accurate serodiagnostic test requires a detailed understanding of the humoral immune responses during bovine tuberculosis and, in particular, identification of the key antigens of Mycobacterium bovisinvolved in antibody production. In this study, we characterized antibody responses in cattle experimentally infected with M. bovis. Sequential serum samples were collected every 3 to 4 weeks for up to 27 months postinfection. Circulating immunoglobulin G antibody levels were measured by an enzyme-linked immunosorbent assay using 12 highly purified recombinant proteins of M. bovis. Six proteins, ESAT-6, 14-kDa protein, MPT63, MPT70, MPT51, and MPT32, were identified as major seroreactive antigens in bovine tuberculosis. A remarkable animal-to-animal variation of antigen recognition by serum antibodies was observed. Kinetic analyses of the antibody production to individual antigens during infection revealed that the heterogeneous antigen recognition profile changed markedly in a given infected animal as disease progressed.

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Huang, Fei, Xu Liu, Yongjing Cheng, Xiaolin Sun, Yingni Li, Jing Zhao, Di Cao, et al. "Antibody to peptidoglycan recognition protein (PGLYRP)-2 as a novel biomarker in rheumatoid arthritis." Clinical and Experimental Rheumatology 39, no. 5 (August 31, 2021): 988–94. http://dx.doi.org/10.55563/clinexprheumatol/vlvlqu.

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Oyen, David, Jonathan L. Torres, Ulrike Wille-Reece, Christian F. Ockenhouse, Daniel Emerling, Jacob Glanville, Wayne Volkmuth, et al. "Structural basis for antibody recognition of the NANP repeats in Plasmodium falciparum circumsporozoite protein." Proceedings of the National Academy of Sciences 114, no. 48 (November 14, 2017): E10438—E10445. http://dx.doi.org/10.1073/pnas.1715812114.

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Acquired resistance against antimalarial drugs has further increased the need for an effective malaria vaccine. The current leading candidate, RTS,S, is a recombinant circumsporozoite protein (CSP)-based vaccine against Plasmodium falciparum that contains 19 NANP repeats followed by a thrombospondin repeat domain. Although RTS,S has undergone extensive clinical testing and has progressed through phase III clinical trials, continued efforts are underway to enhance its efficacy and duration of protection. Here, we determined that two monoclonal antibodies (mAbs 311 and 317), isolated from a recent controlled human malaria infection trial exploring a delayed fractional dose, inhibit parasite development in vivo by at least 97%. Crystal structures of antibody fragments (Fabs) 311 and 317 with an (NPNA)3 peptide illustrate their different binding modes. Notwithstanding, one and three of the three NPNA repeats adopt similar well-defined type I β-turns with Fab311 and Fab317, respectively. Furthermore, to explore antibody binding in the context of P. falciparum CSP, we used negative-stain electron microscopy on a recombinant shortened CSP (rsCSP) construct saturated with Fabs. Both complexes display a compact rsCSP with multiple Fabs bound, with the rsCSP–Fab311 complex forming a highly organized helical structure. Together, these structural insights may aid in the design of a next-generation malaria vaccine.

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Thielges, Megan C., Jörg Zimmermann, Wayne Yu, Masayuki Oda, and Floyd E. Romesberg. "Exploring the Energy Landscape of Antibody−Antigen Complexes: Protein Dynamics, Flexibility, and Molecular Recognition." Biochemistry 47, no. 27 (July 2008): 7237–47. http://dx.doi.org/10.1021/bi800374q.

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Watanabe, Masato, Masatoshi Hagiwara, Koji Onoda, and Hiroyoshi Hidaka. "Monoclonal antibody recognition of two subtype forms of protein kinase C in human platelets." Biochemical and Biophysical Research Communications 152, no. 2 (April 1988): 642–48. http://dx.doi.org/10.1016/s0006-291x(88)80087-1.

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Justice, John M., M. Michael Bliziotes, Linda A. Stevens, Joel Moss, and Martha Vaughan. "Involvement ofN-Myristoylation in Monoclonal Antibody Recognition Sites on Chimeric G Protein α Subunits." Journal of Biological Chemistry 270, no. 12 (March 24, 1995): 6436–39. http://dx.doi.org/10.1074/jbc.270.12.6436.

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Hamuro, Yoshitomo, Mercedes Crego Calama, Hyung Soon Park, and Andrew D. Hamilton. "A Calixarene with Four Peptide Loops: An Antibody Mimic for Recognition of Protein Surfaces." Angewandte Chemie International Edition in English 36, no. 23 (December 15, 1997): 2680–83. http://dx.doi.org/10.1002/anie.199726801.

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Windberg, Emôke, Katalin Uray, Eszter Illyés, Zsolt Skribanek, Michael R. Price, Ferenc Sebestyén, and Ferenc Hudecz. "Heteroclitic recognition of combinatorial TX1TX2T peptide mixtures by mucin-2 protein specific monoclonal antibody." Journal of Peptide Science 10, no. 1 (January 2004): 56–65. http://dx.doi.org/10.1002/psc.483.

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Liley, Martha, Jacques Bouvier, and Horst Vogel. "Incorporation and Antibody Recognition of a Lipid-Anchored Membrane Protein in Supported Lipid Layers." Journal of Colloid and Interface Science 194, no. 1 (October 1997): 53–58. http://dx.doi.org/10.1006/jcis.1997.5111.

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Kamata, Teddy, Mohan Natesan, Kelly Warfield, M. Javad Aman, and Robert G. Ulrich. "Determination of Specific Antibody Responses to the Six Species of Ebola and Marburg Viruses by Multiplexed Protein Microarrays." Clinical and Vaccine Immunology 21, no. 12 (September 17, 2014): 1605–12. http://dx.doi.org/10.1128/cvi.00484-14.

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ABSTRACTInfectious hemorrhagic fevers caused by the Marburg and Ebola filoviruses result in human mortality rates of up to 90%, and there are no effective vaccines or therapeutics available for clinical use. The highly infectious and lethal nature of these viruses highlights the need for reliable and sensitive diagnostic methods. We assembled a protein microarray displaying nucleoprotein (NP), virion protein 40 (VP40), and glycoprotein (GP) antigens from isolates representing the six species of filoviruses for use as a surveillance and diagnostic platform. Using the microarrays, we examined serum antibody responses of rhesus macaques vaccinated with trivalent (GP, NP, and VP40) virus-like particles (VLP) prior to infection with the Marburg virus (MARV) (i.e.,Marburg marburgvirus) or the Zaire virus (ZEBOV) (i.e.,Zaire ebolavirus). The microarray-based assay detected a significant increase in antigen-specific IgG resulting from immunization, while a greater level of antibody responses resulted from challenge of the vaccinated animals with ZEBOV or MARV. Further, while antibody cross-reactivities were observed among NPs and VP40s of Ebola viruses, antibody recognition of GPs was very specific. The performance of mucin-like domain fragments of GP (GP mucin) expressed inEscherichia coliwas compared to that of GP ectodomains produced in eukaryotic cells. Based on results with ZEBOV and MARV proteins, antibody recognition of GP mucins that were deficient in posttranslational modifications was comparable to that of the eukaryotic cell-expressed GP ectodomains in assay performance. We conclude that the described protein microarray may translate into a sensitive assay for diagnosis and serological surveillance of infections caused by multiple species of filoviruses.

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Guo, Xin-Yu, Xiao-Dong Gao, and Morihisa Fujita. "Sulfation of a FLAG tag mediated by SLC35B2 and TPST2 affects antibody recognition." PLOS ONE 16, no. 5 (May 5, 2021): e0250805. http://dx.doi.org/10.1371/journal.pone.0250805.

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A FLAG tag consisting of DYKDDDDK is an epitope tag that is frequently and widely used to detect recombinant proteins of interest. In this study, we performed a CRISPR-based genetic screening to identify factors involved in the detection of a FLAG-tagged misfolded model protein at the cell surface. In the screening, SLC35B2, which encodes 3’-phosphoadenosine-5’-phosphosulfate transporter 1, was identified as the candidate gene. The detection of FLAG-tagged misfolded proteins at the cell surface was significantly increased in SLC35B2-knockout cells. Furthermore, protein tyrosine sulfation mediated by tyrosyl-protein sulfotransferase 2 (TPST2) suppressed FLAG-tagged protein detection. Localization analysis of the FLAG-tagged misfolded proteins confirmed that defects in tyrosine sulfation are only responsible for enhancing anti-FLAG staining on the plasma membrane but not inducing the localization change of misfolded proteins on the plasma membrane. These results suggest that a FLAG tag on the misfolded protein would be sulfated, causing a reduced detection by the M2 anti-FLAG antibody. Attention should be required when quantifying the FLAG-tagged proteins in the secretory pathway.

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Milich, D. R., A. McLachlan, F. V. Chisari, and G. B. Thornton. "Nonoverlapping T and B cell determinants on an hepatitis B surface antigen pre-S(2) region synthetic peptide." Journal of Experimental Medicine 164, no. 2 (August 1, 1986): 532–47. http://dx.doi.org/10.1084/jem.164.2.532.

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We have examined T cell recognition of a hepatitis B surface antigen (HBsAg), pre-S(2)-region synthetic peptide, p120-145, in terms of fine specificity, H-2-linked genetic influences, comparison to antibody binding, and relevance to T cell recognition of the native protein. We showed that the immune response to the synthetic peptide is regulated by H-2-linked genes, but that the pattern of H-2 restriction differed from that observed for the native anti-pre-S(2) response. Dominant and nonoverlapping T cell and B cell recognition sites were identified on the synthetic peptide p120-145. T cell recognition is focussed on the NH2-terminal sequence, and antibody (B cell) recognition is focussed on the COOH-terminal sequence. The fine specificity of T cell recognition of p120-145 was defined by a single, subtype-dependent amino acid substitution. With respect to the immunogenicity of p120-145, the synthetic peptide containing both T and B cell determinants is highly immunogenic in responder strains, whereas separate T or B cell peptide determinants are minimally immunogenic. Furthermore, the synthetic T cell recognition site can prime T cell help for antibody production to the synthetic B cell site, which is crossreactive with the native pre-S(2) region of HBsAg/p33 particles. This system provides evidence that totally synthetic T cell and B cell recognition sites can be combined to yield a functional immunogen.

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Lee, Bok-Soo, Michelle Connole, Zuoquin Tang, Nancy L. Harris, and Jae U. Jung. "Structural Analysis of the Kaposi's Sarcoma-Associated Herpesvirus K1 Protein." Journal of Virology 77, no. 14 (July 15, 2003): 8072–86. http://dx.doi.org/10.1128/jvi.77.14.8072-8086.2003.

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ABSTRACT The K1 protein of Kaposi's sarcoma-associated herpesvirus (KSHV) efficiently transduces extracellular signals to elicit cellular activation events through its cytoplasmic immunoreceptor tyrosine-based activation motif (ITAM). In addition, the extracellular domain of K1 demonstrates regional homology with the immunoglobulin (Ig) family and contains conserved regions (C1 and C2) and variable regions (V1 and V2). To generate mouse monoclonal antibodies directed against the KSHV K1 protein, BALB/c mice were primed and given boosters with K1 protein purified from mammalian cells. Twenty-eight hybridomas were tested for reactivity with K1 protein by enzyme-linked immunosorbent assay, immunofluorescence, flow cytometry, immunohistochemistry, and immunoblotting. Deletion mutants of the K1 extracellular domain were used to map the epitope of each antibody. All antibodies were directed to the Ig, C1, and C2 regions of K1. Furthermore, antibody recognition of a short sequence (amino acids 92 to 125) of the C2 region overlapping with the Ig region of K1 efficiently induced intracellular free calcium mobilization; antibody recognition of the other regions of K1 did not. The efficient signal transduction of K1 induced by antibody stimulation required both the ITAM sequence of the cytoplasmic domain and the normal structure of the extracellular domain. Finally, immunological assays showed that K1 was expressed during the early lytic cycle of viral replication in primary effusion lymphoma cells. K1 was readily detected in multicentric Castleman's disease tissues, whereas it was not detected in Kaposi's sarcoma lesions, suggesting that K1 is preferentially expressed in lymphoid cells. Thus, these results indicate that the conserved regions, particularly the Ig and C2 regions, of the K1 extracellular domain are exposed on the outer surface and play an important role in K1 structure and signal transduction, whereas the variable regions of K1 appear to be away from the surface.

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Velappan, Nileena, Fortunato Ferrara, Sara D’Angelo, Devin Close, Leslie Naranjo, Madeline R. Bolding, Sarah C. Mozden, et al. "Direct selection of functional fluorescent-protein antibody fusions by yeast display." PLOS ONE 18, no. 2 (February 24, 2023): e0280930. http://dx.doi.org/10.1371/journal.pone.0280930.

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Antibodies are important reagents for research, diagnostics, and therapeutics. Many examples of chimeric proteins combining the specific target recognition of antibodies with complementing functionalities such as fluorescence, toxicity or enzymatic activity have been described. However, antibodies selected solely on the basis of their binding specificities are not necessarily ideal candidates for the construction of chimeras. Here, we describe a high throughput method based on yeast display to directly select antibodies most suitable for conversion to fluorescent chimera. A library of scFv binders was converted to a fluorescent chimeric form, by cloning thermal green protein into the linker between VH and VL, and directly selecting for both binding and fluorescent functionality. This allowed us to directly identify antibodies functional in the single chain TGP format, that manifest higher protein expression, easier protein purification, and one-step binding assays.

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Xainli, Jia, Jennifer L. Cole-Tobian, Moses Baisor, Will Kastens, Moses Bockarie, Syed Shams Yazdani, Chetan E. Chitnis, John H. Adams, and Christopher L. King. "Epitope-Specific Humoral Immunity to Plasmodium vivax Duffy Binding Protein." Infection and Immunity 71, no. 5 (May 2003): 2508–15. http://dx.doi.org/10.1128/iai.71.5.2508-2515.2003.

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ABSTRACT Erythrocyte invasion by Plasmodium vivax is completely dependent on binding to the Duffy blood group antigen by the parasite Duffy binding protein (DBP). The receptor-binding domain of this protein lies within a cysteine-rich region referred to as region II (DBPII). To examine whether antibody responses to DBP correlate with age-acquired immunity to P. vivax, antibodies to recombinant DBP (rDBP) were measured in 551 individuals residing in a village endemic for P. vivax in Papua New Guinea, and linear epitopes mapped in the critical binding region of DBPII. Antibody levels to rDBPII increased with age. Four dominant linear epitopes were identified, and the number of linear epitopes recognized by semiimmune individuals increased with age, suggesting greater recognition with repeated infection. Some individuals had antibodies to rDBPII but not to the linear epitopes, indicating the presence of conformational epitopes. This occurred in younger individuals or subjects acutely infected for the first time with P. vivax, indicating that repeated infection is required for recognition of linear epitopes. All four dominant B-cell epitopes contained polymorphic residues, three of which showed variant-specific serologic responses in over 10% of subjects examined. In conclusion, these results demonstrate age-dependent and variant-specific antibody responses to DBPII and implicate this molecule in partial acquired immunity to P. vivax in populations in endemic areas.

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Giannoccaro, Maria Pia, Sarah J. Crisp, and Angela Vincent. "Antibody-mediated central nervous system diseases." Brain and Neuroscience Advances 2 (January 2018): 239821281881749. http://dx.doi.org/10.1177/2398212818817497.

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Antibody-mediated central nervous system diseases are a relatively new area of clinical neuroscience with growing impact. Their recognition has challenged the dogma of the blood–brain barrier preventing antibody access into the central nervous system. The antibodies discovered so far are mainly against neurotransmitter receptors (e.g. N-methyl-d-aspartate and glycine receptors) and ion channel–associated proteins (leucine-rich glioma inactivated protein 1 and contactin-associated protein 2) and are expressed on the surface of neuronal synapses and elsewhere. The disorders are reversible with immunotherapies that reduce antibody levels. Although rare, the identification of these disorders in clinical practice has made central nervous system autoimmune diseases a consideration in the differential diagnoses of many clinical presentations. There is still much to learn about the aetiology of the diseases and the mechanisms by which the antibodies act, the neuronal and glial changes that follow antibody-attack, and the compensatory changes that may be required to ensure good recovery.

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Reza, Farooq, Koji Igarashi, Shigeru Tokita, Kenji Asai, Junken Aoki, Yoshinori Asaoka, Masato Umeda, and Keizo Inoue. "Anti-idiotypic monoclonal antibody recognizes a consensus recognition site for phosphatidylserine in phosphatidylserine-specific monoclonal antibody and protein kinase C." FEBS Letters 339, no. 3 (February 21, 1994): 229–33. http://dx.doi.org/10.1016/0014-5793(94)80421-4.

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Ntchobo, Hyacinthe, Holly Rothermel, Wambui Chege, Allen C. Steere, and Jenifer Coburn. "Recognition of Multiple Antibody Epitopes throughout Borrelia burgdorferi p66, a Candidate Adhesin, in Patients with Early or Late Manifestations of Lyme Disease." Infection and Immunity 69, no. 3 (March 1, 2001): 1953–56. http://dx.doi.org/10.1128/iai.69.3.1953-1956.2001.

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ABSTRACT Antibody responses to p66, a candidate integrin ligand ofBorrelia burgdorferi, were studied in 79 patients with early or late manifestations of Lyme disease. The central portion of p66 was previously shown to contain all of the information required for specific recognition of β3-chain integrins, but work by others had suggested that the C-terminal portion of the protein contains a single surface-exposed, immunodominant loop. In examining antibody responses to full-length p66 and to three overlapping fragments of the protein, we found that the majority of Lyme disease patients had immunoglobulin M (IgM) and/or IgG responses to p66 and that, particularly early in the disease, epitopes throughout p66 were recognized. Among patients with later manifestations of the illness, antibody responses to the C-terminal portion of the protein were more prominent. These results demonstrate that Lyme disease patient sera recognize epitopes throughout p66.

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Hartshorn, Kevan L., Mitchell R. White, Michael Rynkiewicz, Grith Sorensen, Uffe Holmskov, James Head, and Erika C. Crouch. "Monoclonal antibody-assisted structure-function analysis of the carbohydrate recognition domain of surfactant protein D." American Journal of Physiology-Lung Cellular and Molecular Physiology 299, no. 3 (September 2010): L384—L392. http://dx.doi.org/10.1152/ajplung.00096.2010.

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Surfactant protein D (SP-D) plays important roles in host defense against a variety of pathogens including influenza A virus (IAV). Ligand binding by SP-D is mediated by the trimeric neck and carbohydrate recognition domain (NCRD). We used monoclonal antibodies (mAbs) against human SP-D and a panel of mutant collectin NCRD constructs to identify functionally and structurally important epitopes. The ability of SP-D to bind to IAV and mannan involved partially overlapping binding sites that are distinct from those involved in binding to the glycoprotein-340 (gp-340) scavenger receptor protein. A species-specific motif (D324,D325,R343), which has been implicated in the specific binding of several ligands, contributes to recognition by mAbs that block antiviral or mannan binding activity. D325, in particular, is involved in the epitopes of these blocking mAbs. Conversely, the interspecies substitution of arginine for Lys343 in the rat NCRD (rK343R) conferred binding to two of the mAbs. The single site substitution of alanine for R349 or E347 resulted in highly selective alterations in mAb binding and caused decreased antiviral activity. Mutations at Glu333 (E333A), Trp340 (W340F), and Phe335 (F335A), which abrogated antiviral activity, were associated with decreased binding to multiple blocking mAbs, consistent with critical structural roles. More conservative substitutions at 335, which showed a significant increase in neutralization activity, caused selective loss of binding to one mAb. The analysis reveals, for the first time, an extended binding site for IAV; calcium-dependent antiviral activity involves residues flanking the primary carbohydrate binding site as well as more remote residues displayed on the carbohydrate recognition domain surface.

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Rauch, J. "Lupus anticoagulant antibodies: Recognition of phospholipid-binding protein complexes." Lupus 7, no. 2_suppl (February 1998): 29–31. http://dx.doi.org/10.1177/096120339800700207.

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Lupus anticoagulant antibodies form a heterogeneous group of antiphospholipid antibodies with rather poorly defined antigens. The role that phospholipid-binding proteins play in lupus anticoagulant antibody activity is a subject of current investigation. Several candidate proteins have been proposed, including β2-glycoprotein I (β2GPI), prothrombin, and annexin V. As β2GPI-dependent lupus anticoagulants will be reviewed elsewhere in this issue, this paper will focus on the involvement of prothrombin and annexin V in lupus anticoagulant activity. Evidence for a role for these proteins in the reactivity and induction of lupus anticoagulant antibodies will be discussed, as well as an apparent requirement for both phospholipid and phospholipid-binding protein. The data presented here suggest that some lupus anticoagulant antibodies recognize and may be induced by complexes of phospholipid and phospholipid-binding proteins, in particular, phospholipid and prothrombin or annexin V.

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Lafont, Virginie, Michael Schaefer, Roland H. Stote, Danièle Altschuh, and Annick Dejaegere. "Protein-protein recognition and interaction hot spots in an antigen-antibody complex: Free energy decomposition identifies “efficient amino acids”." Proteins: Structure, Function, and Bioinformatics 67, no. 2 (January 26, 2007): 418–34. http://dx.doi.org/10.1002/prot.21259.

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Journal articles on the topic 'Protein-Antibody recognition'

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