Journal articles: 'Antigen-antibody complexes'

1

Davies, D. R., E. A. Padlan, and S. Sheriff. "Antibody-Antigen Complexes." Annual Review of Biochemistry 59, no. 1 (June 1990): 439–73. http://dx.doi.org/10.1146/annurev.bi.59.070190.002255.

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Davies, D. R., S. Sheriff, and E. A. Padlan. "Antibody-antigen complexes." Journal of Biological Chemistry 263, no. 22 (August 1988): 10541–44. http://dx.doi.org/10.1016/s0021-9258(18)38002-5.

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Manca, F., D. Fenoglio, G. Li Pira, A. Kunkl, and F. Celada. "Effect of antigen/antibody ratio on macrophage uptake, processing, and presentation to T cells of antigen complexed with polyclonal antibodies." Journal of Experimental Medicine 173, no. 1 (January 1, 1991): 37–48. http://dx.doi.org/10.1084/jem.173.1.37.

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Activation of a galactosidase-specific murine T hybridoma clone and of a human tetanus toxoid-specific T clone by antigen-presenting cells (APC) was used to evaluate the regulatory function of antibodies complexed with the relevant antigen. Complexed antigen, in fact, is taken up with high efficiency thanks to Fc receptors borne by APC. Antibody/antigen ratio in the complexes proved to be a critical parameter in enhancing antigen presentation. Complexes in moderate antibody excess provided optimal T cell activation independently of the physical state of the complexes (precipitated by a second antibody or solubilized by complement). Complexes in extreme antibody excess, on the contrary, did not yield T cell activation although taken up by APC efficiently. The effect of antibodies at extreme excess was observed with substimulatory dose of antigen (loss of potentiation) and with optimal dose of antigen (loss of stimulation). An excess of specific polyclonal antibodies hampers proteolytic degradation of antigen in vitro, supporting the view that a similar mechanism may operate within the APC that have internalized immune complexes in extreme antibody excess. The possibility that immune complex forming in extreme antibody excess may turn off the T cell response is proposed as a regulatory mechanism.

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Dixon, Frank J. "ANTIGEN-ANTIBODY COMPLEXES AND AUTOIMMUNITY*." Annals of the New York Academy of Sciences 124, no. 1 (December 16, 2006): 162–66. http://dx.doi.org/10.1111/j.1749-6632.1965.tb18954.x.

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Hilgartner, M. "Antigen-Antibody Complexes in Hemophilia." Scandinavian Journal of Haematology 33, S40 (April 24, 2009): 335–39. http://dx.doi.org/10.1111/j.1600-0609.1984.tb02582.x.

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Caulfield, M. J., and D. Shaffer. "Immunoregulation by antigen/antibody complexes. I. Specific immunosuppression induced in vivo with immune complexes formed in antibody excess." Journal of Immunology 138, no. 11 (June 1, 1987): 3680–83. http://dx.doi.org/10.4049/jimmunol.138.11.3680.

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Abstract Specific immune complexes, prepared at different ratios of antibody to antigen, were examined for their effects on the antibody response of BALB/c mice to the cell wall polysaccharide antigen (PnC) extracted from Streptococcus pneumonia R36a. Mice immunized with complexes formed in antigen excess developed a PnC-specific antibody response that was equivalent to that in mice injected with free antigen. On the other hand, mice injected with complexes formed in antibody excess developed very little PnC-specific antibody. Furthermore, administration of immune complexes (formed in antibody excess) resulted in suppression of the response to an immunogenic dose of PnC given concurrently or 1 day after injection of immune complexes but not when the antigen was given 1 day before injection of the immune complexes. Injections of free antibody (TEPC-15) also resulted in suppression of the response to antigenic challenge; however, suppression was greatest when the antibody was injected concurrently with the antigen, suggesting that the suppression was mediated through the formation of immune complexes in vivo. The suppression appears to be specific for the antigen (PnC), since in mice injected with TEPC-15/PnC complexes (formed in antibody excess) and challenged with PnC coupled to sheep RBC, only the response to PnC was suppressed.

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WINGREN, C., and U. ‐B HANSSON. "Surface Properties of Antigen–Antibody Complexes." Scandinavian Journal of Immunology 46, no. 2 (August 1997): 159–67. http://dx.doi.org/10.1046/j.1365-3083.1997.d01-106.x.

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Decanniere, K., T. R. Transue, A. Desmyter, D. Maes, S. Muyldermans, and L. Wyns. "Degenerate interfaces in antigen-antibody complexes." Journal of Molecular Biology 313, no. 3 (October 2001): 473–78. http://dx.doi.org/10.1006/jmbi.2001.5075.

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Randall, R. E., D. Young, T. Hanke, P. Szawlowski, and C. Botting. "Purification of antibody—antigen complexes containing recombinant SIV proteins: comparison of antigen and antibody—antigen complexes for immune priming." Vaccine 12, no. 4 (January 1994): 351–58. http://dx.doi.org/10.1016/0264-410x(94)90100-7.

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Bossi, Sergio, Benedetta Ferranti, Chiara Martinelli, Paola Capasso, and Ario de Marco. "Antibody-mediated purification of co-expressed antigen–antibody complexes." Protein Expression and Purification 72, no. 1 (July 2010): 55–58. http://dx.doi.org/10.1016/j.pep.2010.01.003.

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Penttinen, K., G. Myllylä, O. Mäkelä, and A. Vaheri. "SOLUBLE ANTIGEN-ANTIBODY COMPLEXES AND PLATELET AGGREGATION." Acta Pathologica Microbiologica Scandinavica 77, no. 2 (August 18, 2009): 309–17. http://dx.doi.org/10.1111/j.1699-0463.1969.tb04236.x.

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Sundaram, S., C. M. Roth, and M. L. Yarmush. "Pressure-Induced Dissociation of Antigen-Antibody Complexes." Biotechnology Progress 14, no. 5 (October 2, 1998): 773–81. http://dx.doi.org/10.1021/bp980066m.

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Stura, Enrico A., Gail G. Fieser, and Ian A. Wilson. "Crystallization of Antibodies and Antibody-Antigen Complexes." ImmunoMethods 3, no. 3 (December 1993): 164–79. http://dx.doi.org/10.1006/immu.1993.1051.

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Roosnek, E., and A. Lanzavecchia. "Efficient and selective presentation of antigen-antibody complexes by rheumatoid factor B cells." Journal of Experimental Medicine 173, no. 2 (February 1, 1991): 487–89. http://dx.doi.org/10.1084/jem.173.2.487.

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Using Epstein-Barr virus B cell clones and antigen-specific T cell clones, we asked how antigen-antibody complexes are handled by B cells. We found that the only B cells capable of efficient presentation of antigen-antibody complexes are those that bind the complexes via membrane immunoglobulin, i.e., rheumatoid factor-producing B cells and, to a lower extent, antigen-specific B cells. On the contrary, nonspecific B cells, although capable of binding antigen-antibody complexes, fail to present them to T cells. Thus, rheumatoid factor B cells can present any antigen in the context of an immune complex and be triggered by T cells specific for a variety of foreign antigens. These results demonstrate a mechanism of intermolecular help that may be responsible for the production of rheumatoid factor and possibly of other types of autoantibodies.

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Fernández-Quintero, Monica L., Johannes R. Loeffler, Franz Waibl, Anna S. Kamenik, Florian Hofer, and Klaus R. Liedl. "Conformational selection of allergen-antibody complexes—surface plasticity of paratopes and epitopes." Protein Engineering, Design and Selection 32, no. 11 (November 2019): 513–23. http://dx.doi.org/10.1093/protein/gzaa014.

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Abstract Antibodies have the ability to bind various types of antigens and to recognize different antibody-binding sites (epitopes) of the same antigen with different binding affinities. Due to the conserved structural framework of antibodies, their specificity to antigens is mainly determined by their antigen-binding site (paratope). Therefore, characterization of epitopes in combination with describing the involved conformational changes of the paratope upon binding is crucial in understanding and predicting antibody-antigen binding. Using molecular dynamics simulations complemented with strong experimental structural information, we investigated the underlying binding mechanism and the resulting local and global surface plasticity in the binding interfaces of distinct antibody-antigen complexes. In all studied allergen-antibody complexes, we clearly observe that experimentally suggested epitopes reveal less plasticity, while non-epitope regions show high surface plasticity. Surprisingly, the paratope shows higher conformational diversity reflected in substantially higher surface plasticity, compared to the epitope. This work allows a visualization and characterization of antibody-antigen interfaces and might have strong implications for antibody-antigen docking and in the area of epitope prediction.

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Brenke, Ryan, David R. Hall, Gwo-Yu Chuang, Stephen R. Comeau, Tanggis Bohnuud, Dmitri Beglov, Ora Schueler-Furman, Sandor Vajda, and Dima Kozakov. "Application of asymmetric statistical potentials to antibody–protein docking." Bioinformatics 28, no. 20 (October 6, 2012): 2608–14. http://dx.doi.org/10.1093/bioinformatics/bts493.

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Abstract Motivation: An effective docking algorithm for antibody–protein antigen complex prediction is an important first step toward design of biologics and vaccines. We have recently developed a new class of knowledge-based interaction potentials called Decoys as the Reference State (DARS) and incorporated DARS into the docking program PIPER based on the fast Fourier transform correlation approach. Although PIPER was the best performer in the latest rounds of the CAPRI protein docking experiment, it is much less accurate for docking antibody–protein antigen pairs than other types of complexes, in spite of incorporating sequence-based information on the location of the paratope. Analysis of antibody–protein antigen complexes has revealed an inherent asymmetry within these interfaces. Specifically, phenylalanine, tryptophan and tyrosine residues highly populate the paratope of the antibody but not the epitope of the antigen. Results: Since this asymmetry cannot be adequately modeled using a symmetric pairwise potential, we have removed the usual assumption of symmetry. Interaction statistics were extracted from antibody–protein complexes under the assumption that a particular atom on the antibody is different from the same atom on the antigen protein. The use of the new potential significantly improves the performance of docking for antibody–protein antigen complexes, even without any sequence information on the location of the paratope. We note that the asymmetric potential captures the effects of the multi-body interactions inherent to the complex environment in the antibody–protein antigen interface. Availability: The method is implemented in the ClusPro protein docking server, available at http://cluspro.bu.edu. Contact: midas@bu.edu or vajda@bu.edu Supplementary information: Supplementary data are available at Bioinformatics online.

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Obmolova, Galina, Thomas J. Malia, Alexey Teplyakov, Raymond Sweet, and Gary L. Gilliland. "Promoting crystallization of antibody–antigen complexesviamicroseed matrix screening." Acta Crystallographica Section D Biological Crystallography 66, no. 8 (July 14, 2010): 927–33. http://dx.doi.org/10.1107/s0907444910026041.

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The application of microseed matrix screening to the crystallization of antibody–antigen complexes is described for a set of antibodies that include mouse anti-IL-13 antibody C836, its humanized version H2L6 and an affinity-matured variant of H2L6, M1295. The Fab fragments of these antibodies were crystallized in complex with the antigen human IL-13. The initial crystallization screening for each of the three complexes included 192 conditions. Only one hit was observed for H2L6 and none were observed for the other two complexes. Matrix self-microseeding using these microcrystals yielded multiple hits under various conditions that were further optimized to grow diffraction-quality H2L6 crystals. The same H2L6 seeds were also successfully used to promote crystallization of the other two complexes. The M1295 crystals appeared to be isomorphous to those of H2L6, whereas the C836 crystals were in a different crystal form. These results are consistent with the concept that the conditions that are best for crystal growth may be different from those that favor nucleation. Microseed matrix screening using either a self-seeding or cross-seeding approach proved to be a fast, robust and reliable method not only for the refinement of crystallization conditions but also to promote crystal nucleation and increase the hit rate.

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Coulie, P. G., and J. Van Snick. "Rheumatoid factor (RF) production during anamnestic immune responses in the mouse. III. Activation of RF precursor cells is induced by their interaction with immune complexes and carrier-specific helper T cells." Journal of Experimental Medicine 161, no. 1 (January 1, 1985): 88–97. http://dx.doi.org/10.1084/jem.161.1.88.

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IgG1 immune complexes were identified as the humoral stimuli responsible for the synthesis of IgG1-specific IgM rheumatoid factor (RF), which occurs in the mouse during the early stages of secondary immune responses to protein antigens. The specificity of this phenomenon was illustrated by the fact that complexes made with IgG1 F(ab')2 fragments or with antibodies of a different isotype failed to induce significant anti-IgG1 RF synthesis. The importance of immune complexes in the induction of RF was further underscored by the substantial increase in the titers of isotype-specific RF observed in the serum of mice immunized with IgG1- or IgG2a-complexed antigen rather than with antigen alone. The RF-inducing capacity of the complexes varied with the antigen/antibody ratio: it was maximal in antibody excess or at equivalence, but dramatically reduced in large antigen excess. The importance of T cell priming in RF precursor cell activation by immune complexes was demonstrated by the failure of T cell-deprived spleen cells to reconstitute the capability of irradiated mice to produce RF, and by the optimal RF responses observed after reconstitution of irradiated recipients with primed T cells and naive B cells. The involvement of T cells in this process could not be explained by the release of nonspecific B cell activators, because antigenic stimulation of primed T cells failed to enhance the activation of RF precursor cells by immune complexes of unrelated antigen.

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Miyata, Takashi. "Smart Hydrogels that Respond to Target Biomolecules." Advances in Science and Technology 57 (September 2008): 15–21. http://dx.doi.org/10.4028/www.scientific.net/ast.57.15.

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We have prepared a variety of biomolecule-responsive hydrogels by using biomolecular complexes as reversible crosslinking points. This paper describes two types of biomolecule-responsive hydrogels that undergo volume changes in response to target biomolecules, which were prepared using biomolecular complexes such as antigen-antibody complexes and saccharide-lectin complexes. One is a biomolecule-crosslinked hydrogel that can swell in response to a target biomolecule and the other is a biomolecule-imprinted hydrogel that can shrink. The antigen-responsive hydrogels as biomolecule-crosslinked hydrogels swelled in the presence of a target antigen due to the dissociation of antigen-antibody complexes that played a role as reversible crosslinking points. On the other hand, the tumor marker glycoprotein-responsive hydrogels as biomolecule-imprinted hydrogels shrank in response to a target glycoprotein due to the complex formation between ligands (lectin and antibody) and the target molecule (saccharide and peptide chains of glycoprotein). This paper focuses on synthetic strategy of the biomolecule-responsive hydrogels and their responsive behavior for target biomolecules.

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20

Haakenstad, A. O. "Removal of glomerular deposits induced by either preformed immune complexes or by a chronic immune complex model in NZB/W mice." Journal of Immunology 138, no. 12 (June 15, 1987): 4192–99. http://dx.doi.org/10.4049/jimmunol.138.12.4192.

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Abstract The solubilization and removal of defined glomerular immune complex deposits by excess antigen was examined in NZB/W female mice. Glomerular deposits were induced by administering preformed immune complexes to young (2 to 4 mo) mice before they naturally acquired deposits from endogenous disease and to old (7 mo) mice with deposits from naturally acquired disease. The administration of excess antigen specifically removed deposits of preformed immune complexes in both groups. This was associated with a reduction in circulating large latticed complexes containing more than two antigen and two antibody molecules (greater than Ag2Ab2). Established deposits in old mice therefore did not interfere with removal of newly induced deposits of preformed immune complexes. Glomerular deposits were also induced in young mice by a chronic human serum albumin (HSA) immune complex model. The antigen in immune deposits induced by 2 wk of chronic antigen administration was solubilized and was removed within 48 hr of administering excess antigen. Circulating antibodies to the antigen were also reduced by excess antigen. Glomerular deposits of mouse immunoglobulin and complement were not significantly reduced by excess antigen but remained more intense than in mice of comparable age given preformed complexes. Thus deposits of other antigen antibody systems and possibly endogenous disease were induced by the chronic HSA immune complex model in NZB/W mice. However, defined antigen deposits within deposits containing multiple antigen antibody systems can clearly be removed by administering excess antigen.

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Ambrosetti, Francesco, Brian Jiménez-García, Jorge Roel-Touris, and Alexandre M. J. J. Bonvin. "Modeling Antibody-Antigen Complexes by Information-Driven Docking." Structure 28, no. 1 (January 2020): 119–29. http://dx.doi.org/10.1016/j.str.2019.10.011.

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Novotny, Jiri, and Kim Sharp. "Electrostatic fields in antibodies and antibody/antigen complexes." Progress in Biophysics and Molecular Biology 58, no. 3 (January 1992): 203–24. http://dx.doi.org/10.1016/0079-6107(92)90006-r.

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Yarmush, David M., Regina M. Murphy, Clark K. Colton, Michael Fisch, and Martin L. Yarmush. "Quasi-elastic light scattering of antigen-antibody complexes." Molecular Immunology 25, no. 1 (January 1988): 17–32. http://dx.doi.org/10.1016/0161-5890(88)90086-7.

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Cheung, Charles Y., David J. Green, Gerald J. Litt, and James A. Laugharn. "High-pressure-mediated dissociation of immune complexes demonstrated in model systems." Clinical Chemistry 44, no. 2 (February 1, 1998): 299–303. http://dx.doi.org/10.1093/clinchem/44.2.299.

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Abstract The use of pressure to disrupt immune complexes was demonstrated in two model systems: prostate-specific antigen (PSA) and anti-PSA antibody; and epiglycanin, a mucin glycoprotein, and an antibody specific to that protein. Dissociation of the anti-PSA antibody from the immobilized PSA antigen was observed when pressures of 415 MPa and 550 MPa (1 MPa ∼144 psi) were applied at room temperature (∼21 °C). Application of pressures ranging from 140 MPa to 550 MPa resulted in dissociation of antibody from epiglycanin. In both cases, the rebinding of dissociated antibody to immobilized antigen indicated that the effect of high pressure on the binding of the immune complexes was reversible. These findings suggest that application of high hydrostatic pressure has the potential to be used to significantly improve the sensitivity and specificity of clinical assays.

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Uher, F., and H. B. Dickler. "Cooperativity between B lymphocyte membrane molecules: independent ligand occupancy and cross-linking of antigen receptors and Fc gamma receptors down-regulates B lymphocyte function." Journal of Immunology 137, no. 10 (November 15, 1986): 3124–29. http://dx.doi.org/10.4049/jimmunol.137.10.3124.

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Abstract IgG antibody-antigen complexes bound to B lymphocyte Fc gamma receptor (Fc gamma R) but not surface immunoglobulin inhibit the antibody-forming cell response but not proliferation of these cells in response to F(ab')2 anti-mu and lymphokines. The role of B lymphocyte antigen receptors in B lymphocyte Fc gamma R-mediated inhibition was evaluated. With the use of several different antigen receptor-dependent plaque-forming cell (PFC) responses, it was found that inhibition occurred irrespective of the type of stimulatory signal used, or whether antigen receptors were bound by antibody or occupied by nominal antigen. The degree of inhibition appeared to be directly related to the extent of antigen receptor cross-linking. Maximal inhibition only occurred if both antigen receptors and Fc gamma R were occupied by their respective ligands simultaneously during the early hours of activation. In contrast, antigen receptor-independent PFC responses to the mitogen lipopolysaccharide (LPS) were not inhibited by complexes. However, the antigen-independent TNP-specific PFC response to LPS was inhibited by the combination of IgG antibody-antigen complexes and the hapten, but by neither alone. These results suggest that a down-regulatory signal is generated by functional cooperation between Fc gamma R and antigen receptors. Generation of this inhibiting signal could be mediated by the previously described physical interaction between these two receptors, and interactions between membrane receptors may be a general mechanism utilized by lymphocytes for the integration of multiple signals.

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Chu, C. T., T. D. Oury, J. J. Enghild, and S. V. Pizzo. "Adjuvant-free in vivo targeting. Antigen delivery by alpha 2-macroglobulin enhances antibody formation." Journal of Immunology 152, no. 4 (February 15, 1994): 1538–45. http://dx.doi.org/10.4049/jimmunol.152.4.1538.

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Abstract The proteinase "inhibitor" alpha 2-macroglobulin (alpha 2M) is able to entrap and form covalent linkages with diverse proteins during a transient proteinase-activated state. These complexes are rapidly endocytosed after binding to receptors present on macrophages and other cells. We have previously shown that compared to free hen egg lysozyme (HEL), alpha 2M-complexed HEL undergoes enhanced macrophage uptake, processing, and presentation to T hybridoma clones in vitro. Inasmuch as it is not clear whether T hybridoma responses accurately reflect primary immune responses in vivo, we studied antibody production in rabbits using two Ag complexed with either human alpha 2M (H alpha 2M) or a homologous protein purified from rabbit plasma, alpha 1-macroglobulin (R alpha 1M). Pathogen-free NZW rabbits received s.c. injections with adjuvant-free preparations of free HEL or porcine pancreatic elastase (PPE), H alpha 2M-HEL-PPE complexes, R alpha 1M-HEL-PPE complexes, or mixtures of the uncomplexed proteins. Complexing the Ag to alpha 2M resulted in 10 to 500-fold higher IgG titers compared to uncomplexed controls. Injection of Ag complexed to either H alpha 2M or R alpha 1M resulted in levels of anti-HEL IgG comparable to those elicited by emulsification in CFA. Inasmuch as inflammatory proteinases such as neutrophil elastase can initiate covalent complex formation with alpha 2M, we propose that "proteinase-activated" alpha 2M may mediate receptor-enhanced Ag uptake by macrophages, resulting in augmented Ag processing and antibody production.

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Goins, Chelsey L., Craig P. Chappell, Shashidhara Murthy, Periasamy Selvaraj, and Joshy Jacob. "Naive B cells participate in secondary antibody response via immune complex mediated activation (84.6)." Journal of Immunology 182, no. 1_Supplement (April 1, 2009): 84.6. http://dx.doi.org/10.4049/jimmunol.182.supp.84.6.

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Abstract The adaptive immune system confers survival advantage to the host by its inherent ability to respond to a plethora of pathogens and its ability to never forget an antigenic insult. In the case of humoral immune responses, repeat antigenic exposure leads to a secondary antibody response that is 2-3 orders of magnitude greater than the primary. This increased efficacy is due to the production of amplified levels of antigen-specific antibody, as well as the accelerated kinetics of their production. Current dogma holds that this response results from activation of memory B cells, which are formed following primary exposure and can rapidly produce large quantities of specific antibody upon secondary exposure. Our research, however, suggest that memory B cells may not be the chief source of antibody during the secondary response. Using a hapten model system we have shown that the phenomena associated with secondary responses - increased antibody levels and accelerated kinetics of antibody production - can be recapitulated by primary immunization with immune complexes. This suggests that immune complexes are able to activate antigen-inexperienced naive B cells in such a manner that their response mirrors a secondary response. Additionally we have found that blocking the Fc receptor binding activity of immune complexes inhibits the secondary antibody response. We propose that immune complexes are formed upon secondary antigen exposure, and that these complexes enhance the secondary antibody response through naive B cell activation.

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Nemazee, D. A. "Immune complexes can trigger specific, T cell-dependent, autoanti-IgG antibody production in mice." Journal of Experimental Medicine 161, no. 1 (January 1, 1985): 242–56. http://dx.doi.org/10.1084/jem.161.1.242.

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Immunization of mice with a combination of passively administered syngeneic IgG (anti-p-azophenylarsonate [anti-Ars]) antibody and a soluble, multivalent form of the antibody's corresponding antigen (Limulus polyphemus hemocyanin conjugated with Ars [Lph-Ars]) resulted in specific autoanti-IgG Fc (rheumatoid factor) production. The response was rapid and only anti-IgG of the IgM isotype is found. Because immunization with either the IgG antibody or the antigen alone did not result in rheumatoid antibody production, immune complexes appear to be the active form of the immunogens. Antibody/antigen ratios that resulted in maximal anti-IgG antibody responses were the same as those required for peak in vitro immunoprecipitation, i.e., equivalence. Previous exposure of the mice to the exogenously supplied antigen was not required for the response. The response to immune complexes is specific because mice immunized with IgG2a-containing complexes produced autoanti-IgG2a, while mice immunized with IgG1-containing complexes produced anti-IgG1 with little reactivity to other IgG isotypes. IgG2a blocked in its complement-fixing capacity was more effective in eliciting the anti-IgG2a response than native IgG2a, suggesting a possible role for the complement system in modulating the anti-IgG2a response. Induction of rheumatoid factor production by immune complexes could be induced in xid mice but not in nu/nu mice, indicating T lymphocyte dependence of the response. In contrast, the B lymphocyte activator lipopolysaccharide was able to elicit vigorous rheumatoid factor production in both nu/nu and normal mice, demonstrating that nu/nu mice contain B cells capable of making the response. Rheumatoid antibody produced in the immune complex- or LPS-induced responses is Fc specific and has relatively low affinity for IgG that is not bound to antigen.

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Gonzalez, Tawny R., Kyle P. Martin, Jonathan E. Barnes, Jagdish Suresh Patel, and F. Marty Ytreberg. "Assessment of software methods for estimating protein-protein relative binding affinities." PLOS ONE 15, no. 12 (December 21, 2020): e0240573. http://dx.doi.org/10.1371/journal.pone.0240573.

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A growing number of computational tools have been developed to accurately and rapidly predict the impact of amino acid mutations on protein-protein relative binding affinities. Such tools have many applications, for example, designing new drugs and studying evolutionary mechanisms. In the search for accuracy, many of these methods employ expensive yet rigorous molecular dynamics simulations. By contrast, non-rigorous methods use less exhaustive statistical mechanics, allowing for more efficient calculations. However, it is unclear if such methods retain enough accuracy to replace rigorous methods in binding affinity calculations. This trade-off between accuracy and computational expense makes it difficult to determine the best method for a particular system or study. Here, eight non-rigorous computational methods were assessed using eight antibody-antigen and eight non-antibody-antigen complexes for their ability to accurately predict relative binding affinities (ΔΔG) for 654 single mutations. In addition to assessing accuracy, we analyzed the CPU cost and performance for each method using a variety of physico-chemical structural features. This allowed us to posit scenarios in which each method may be best utilized. Most methods performed worse when applied to antibody-antigen complexes compared to non-antibody-antigen complexes. Rosetta-based JayZ and EasyE methods classified mutations as destabilizing (ΔΔG < -0.5 kcal/mol) with high (83–98%) accuracy and a relatively low computational cost for non-antibody-antigen complexes. Some of the most accurate results for antibody-antigen systems came from combining molecular dynamics with FoldX with a correlation coefficient (r) of 0.46, but this was also the most computationally expensive method. Overall, our results suggest these methods can be used to quickly and accurately predict stabilizing versus destabilizing mutations but are less accurate at predicting actual binding affinities. This study highlights the need for continued development of reliable, accessible, and reproducible methods for predicting binding affinities in antibody-antigen proteins and provides a recipe for using current methods.

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Greenfield, Edward A., James DeCaprio, and Mohan Brahmandam. "Making Weak Antigens Strong: Preparing Immune Complexes for Injection." Cold Spring Harbor Protocols 2021, no. 9 (September 2021): pdb.prot099978. http://dx.doi.org/10.1101/pdb.prot099978.

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If antibodies against a particular antigen are available, that antigen can be purified and used for further immunizations, and antigens thus purified can show enhanced immunogenicity. Purified immune complexes can be injected directly, or while coupled to beads; the presence of antibodies and/or beads stimulates phagocytosis and usually will not influence the response. This method provides a useful means of antigen enrichment for a variety of applications, such as using antibodies raised against a denatured antigen to harvest a native protein for further immunizations, or when using a monoclonal antibody as an intermediate to the preparation of polyclonal antisera. Injecting antibody-coated antigens has also been used to mask a particularly immunodominant epitope on an antigen, and thereby develop a response against other epitopes. The amount of antigen needed to elicit a strong response using immune complexes will vary from one compound to another. Doses as low as 50 ng of antigen have been used successfully when delivered this way.

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Mongi, A. O., S. Z. Shapiro, J. J. Doyle, and M. P. Cunningham. "Immunization of rabbits with Rhipicephalus appendiculatus antigen–antibody complexes." International Journal of Tropical Insect Science 7, no. 04 (August 1986): 471–77. http://dx.doi.org/10.1017/s1742758400009681.

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Murphy, Regina M., Richard A. Chamberlin, Peter Schurtenberger, Clark K. Colton, and Martin L. Yarmush. "Size and structure of antigen-antibody complexes: thermodynamic parameters." Biochemistry 29, no. 49 (December 1990): 10889–99. http://dx.doi.org/10.1021/bi00501a005.

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Boulot, G., V. Guillon, R. A. Mariuzza, R. J. Poljak, M. M. Riottot, H. Souchon, S. Spinelli, and D. Tello. "Crystallization of antibody fragments and their complexes with antigen." Journal of Crystal Growth 90, no. 1-3 (July 1988): 213–21. http://dx.doi.org/10.1016/0022-0248(88)90318-1.

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Green, E. A., C. Botting, H. M. Webb, T. R. Hirst, and R. E. Randall. "Construction, purification and immunogenicity of antigen-antibody-LTB complexes." Vaccine 14, no. 10 (July 1996): 949–58. http://dx.doi.org/10.1016/0264-410x(96)00039-4.

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Bandehpour, Mojgan, Shahrzad Ahangarzadeh, Fatemeh Yarian, Arezou Lari, and Poopak Farnia. "In silicoevaluation of the interactions among two selected single chain variable fragments (scFvs) and ESAT-6 antigen ofMycobacterium tuberculosis." Journal of Theoretical and Computational Chemistry 16, no. 08 (December 2017): 1750069. http://dx.doi.org/10.1142/s0219633617500699.

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Nowadays antibody engineering is an important approach in the design and manufacture of therapeutic and diagnostic antibodies. The study of interactions between antibodies and antigens is the critical step in the design of antibodies with desirable properties. Computational docking is a useful tool for structural characterization of bimolecular interactions. Docking is the process of predicting bound conformations and binding enthalpy of antibody–antigen complexes. In this study, the three-dimensional structures of two ribosome displayed-selected scFv antibodies were constructed by Kotai Antibody Builder. By using ClusPro 2.0 web server, the ESAT-6 antigen (a tuberculosis-specific antigen) structure was docked to both scFv models to obtain the structures of the binding complexes and molecular dynamics (MD) simulations were performed using GROMACS 4.5.3 package. By analyzing of the ESAT-scFv complexes, important amino acids involved in antigen–antibody interactions were identified which were Asn164 in VL3, Ser164 in VL7 and Asn55 in VH7. All three amino acids belonged to the CDRs. In conclusion, results achieved from this bioinformatics study can help in the design and development of novel antibodies with improved affinities for tuberculosis diagnosis.

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Dewerchin, Hannah L., Els Cornelissen, Evelien Van Hamme, Kaatje Smits, Bruno Verhasselt, and Hans J. Nauwynck. "Surface-expressed viral proteins in feline infectious peritonitis virus-infected monocytes are internalized through a clathrin- and caveolae-independent pathway." Journal of General Virology 89, no. 11 (November 1, 2008): 2731–40. http://dx.doi.org/10.1099/vir.0.2008/002212-0.

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Infection with feline infectious peritonitis virus (FIPV), a feline coronavirus, frequently leads to death in spite of a strong humoral immune response. In previous work, we reported that infected monocytes, the in vivo target cells of FIPV, express viral proteins in their plasma membranes. These proteins are quickly internalized upon binding of antibodies. As the cell surface is cleared from viral proteins, internalization might offer protection against antibody-dependent cell lysis. Here, the internalization and subsequent trafficking of the antigen–antibody complexes were characterized using biochemical, cell biological and genetic approaches. Internalization occurred through a clathrin- and caveolae-independent pathway that did not require dynamin, rafts, actin or rho-GTPases. These findings indicate that the viral antigen–antibody complexes were not internalized through any of the previously described pathways. Further characterization showed that this internalization process was independent from phosphatases and tyrosine kinases but did depend on serine/threonine kinases. After internalization, the viral antigen–antibody complexes passed through the early endosomes, where they resided only briefly, and accumulated in the late endosomes. Between 30 and 60 min after antibody addition, the complexes left the late endosomes but were not degraded in the lysosomes. This study reveals what is probably a new internalization pathway into primary monocytes, confirming once more the complexity of endocytic processes.

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Cosio, F. G., D. J. Birmingham, D. J. Sexton, and L. A. Hebert. "Interactions between precipitating and nonprecipitating antibodies in the formation of immune complexes." Journal of Immunology 138, no. 8 (April 15, 1987): 2587–92. http://dx.doi.org/10.4049/jimmunol.138.8.2587.

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Abstract In the present study, we used monoclonal antidinitrophenol (DNP) antibodies to determine certain of the biophysical characteristics of precipitating and nonprecipitating antibodies. In addition, we studied the dynamics of immune complex (IC) formation when precipitating antibodies react with antigen in the presence of nonprecipitating antibodies. The antigen utilized in these studies was DNP-bovine serum albumin. All isolated nonprecipitating anti-DNP antibodies were of the IgG2b isotype, whereas all antibodies with other isotypes (IgG1, IgG3, IgM, IgA and IgE) were precipitating. Nonprecipitating antibodies did not differ significantly from precipitating antibodies in affinity, valence, or isoelectric point. Nonprecipitating antibodies inhibited the formation of precipitable IC between antigen and precipitating antibodies. In addition, preformed IC precipitates were solubilized by nonprecipitating antibodies. The solubilization of IC precipitates was influenced by the isotype of the precipitating antibody and by the antibody:antigen ratio in the IC precipitate. By isokinetic sucrose density centrifugation, we determined that solubilization of IC precipitates by nonprecipitating antibodies was associated with release of free precipitating antibody and formation of soluble IC between the antigen and the nonprecipitating antibody. In conclusion, in this study the nonprecipitating property of mouse anti-DNP antibodies is isotype-specific. Nonprecipitating antibodies compete and displace precipitating antibodies from the antigen, resulting in inhibition of IC precipitation and in IC solubilization. On the basis of the present results, we postulate that antibody-antibody interactions are important determinants of precipitating ability, and that these interactions are a characteristic of antibody isotype.

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Jemmerson, R., and Y. Paterson. "Mapping epitopes on a protein antigen by the proteolysis of antigen-antibody complexes." Science 232, no. 4753 (May 23, 1986): 1001–4. http://dx.doi.org/10.1126/science.2422757.

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Mannik, M., V. J. Gauthier, S. A. Stapleton, and L. Y. Agodoa. "Immune complexes with cationic antibodies deposit in glomeruli more effectively than cationic antibodies alone." Journal of Immunology 138, no. 12 (June 15, 1987): 4209–17. http://dx.doi.org/10.4049/jimmunol.138.12.4209.

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Abstract In previously published studies, highly cationized antibodies alone and in immune complexes bound to glomeruli by charge-charge interaction, but only immune complexes persisted in glomeruli. Because normal IgG does not deposit in glomeruli, studies were conducted to determine whether cationized antibodies can be prepared which deposit in glomeruli when bound to antigen but not when free in circulation. A series of cationized rabbit antiHSA was prepared with the number of added amino groups ranging from 13.3 to 60.2 per antibody molecule. Antibodies alone or in preformed soluble immune complexes, prepared at fivefold or 50-fold antigen excess, were administered to mice. With the injection of a fixed dose of 100 micrograms per mouse, antibodies alone did not deposit in glomeruli with less than 29.6 added amino groups by immunofluorescence microscopy. In contrast, 100 micrograms of antibodies with 23.5 added amino groups in immune complexes, made at fivefold antigen excess, formed immune deposits in glomeruli. With selected preparations of cationized, radiolabeled antibodies, deposition in glomeruli was quantified by isolation of mouse glomeruli. These quantitative data were in good agreement with the results of immunofluorescence microscopy. Immune complexes made at 50-fold antigen excess, containing only small-latticed immune complexes with no more than two antibody molecules per complex, deposited in glomeruli similar to antibodies alone. Selected cationized antibodies alone or in immune complexes were administered to mice in varying doses. In these experiments, glomerular deposition of immune complexes, made at fivefold antigen excess, was detected with five- to 10-fold smaller doses than the deposition of the same antibodies alone. These studies demonstrate that antibody molecules in immune complexes are more likely to deposit in glomeruli by charge-charge interactions than antibodies alone.

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Greenfield, Edward A. "Hybridoma Screening by Antibody Capture: A High-Throughput Western Blot Assay." Cold Spring Harbor Protocols 2021, no. 11 (November 2021): pdb.prot103069. http://dx.doi.org/10.1101/pdb.prot103069.

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Antibody capture assays are often the easiest and most convenient of the hybridoma screening methods. In this procedure, proteins in solution or in a cell lysate are separated according to size by gel electrophoresis and then transferred by blotting to a nitrocellulose sheet. Antigen bound to the solid substrate is incubated with the primary antibody, and the resultant antibody–antigen complexes are detected by a horseradish peroxidase (HRP)–conjugated secondary antibody and a chemiluminescent substrate for HRP.

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Gill, Jasmita, Praapti Jayaswal, and Dinakar M. Salunke. "Antigen exposure leads to rigidification of germline antibody combining site." Journal of Bioinformatics and Computational Biology 12, no. 03 (June 2014): 1450006. http://dx.doi.org/10.1142/s0219720014500061.

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Immune complexes involving diverse antigens and corresponding antibodies were analyzed for mapping conformational transitions of an antibody before antigen binding, upon antigen binding and after antigen release. Molecular dynamics simulations of the two comprehensive datasets consisting of the antigen-free and antigen-bound structures of the germline antibodies 36-65 and BBE6.12H3 provided mechanistic model of antigen encounter by primary antibodies. While native germline antibodies exhibit substantial mobility in the antigen-combining sites, their antigen-bound states exhibit relatively rigid conformations, even in the absence of the antigen suggesting preservation of the structural state after antigen release. It is proposed that acquired rigidity by a germline antibody upon antigen binding may be the first step in affinity maturation in favor of that antigen.

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Chargelegue, Daniel, Pascal M. W. Drake, Patricia Obregon, Alessandra Prada, Neil Fairweather, and Julian K.-C. Ma. "Highly Immunogenic and Protective Recombinant Vaccine Candidate Expressed in Transgenic Plants." Infection and Immunity 73, no. 9 (September 2005): 5915–22. http://dx.doi.org/10.1128/iai.73.9.5915-5922.2005.

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ABSTRACT Vaccine development has been hampered by difficulties in developing new and safe adjuvants, so alternative technologies that offer new avenues forward are urgently needed. The goal of this study was to express a monoclonal recombinant immune complex in a transgenic plant. A recombinant protein consisting of a tetanus toxin C fragment-specific monoclonal antibody fused with the tetanus toxin C fragment was designed and expressed. Immune complex formation occurred between individual fusion proteins to form immune complex-like aggregates that bound C1q and FcγRIIa receptor and could be targeted to antigen-presenting cells. Unlike antigen alone, the recombinant immune fusion complexes were highly immunogenic in mice and did not require coadministration of an adjuvant (when injected subcutaneously). Indeed, these complexes elicited antibody titers that were more than 10,000 times higher than those observed in animals immunized with the antigen alone. Furthermore, animals immunized with only 1 μg of recombinant immune complex without adjuvant were fully protected against lethal challenge. This the first report on the use of a genetic fusion between antigen and antibody to ensure an optimal expression ratio between the two moieties and to obtain fully functional recombinant immune complexes as a new vaccine model.

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Bandehpour, Mojgan, Fatemeh Yarian, and Shahrzad Ahangarzadeh. "Bioinformatics evaluation of novel ribosome display-selected single chain variable fragment (scFv) structure with factor H binding protein through docking." Journal of Theoretical and Computational Chemistry 16, no. 03 (April 18, 2017): 1750021. http://dx.doi.org/10.1142/s0219633617500213.

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Antibodies play a significant role in the immunotherapy, basic research and the pharmaceutical industry. Nowadays, both DNA recombinant technology and antibody engineering technology are widely used in many fields such as diagnostics, therapeutics, drug targeted delivery, and research reagents. Computational docking of antigen-antibody complexes and analysis of atomic interactions are important to find effective B-cell epitopes and new antibodies with appropriate properties. In the present study, by using ClusPro 2.0 webserver, docking the antigen (factor H binding protein (fHbp)) to the novel-selected scFv antibody was performed. By analyzing the fHbp-scFv complexes, important amino acids were identified. After docking, peptides Ala192-His198, Asp 211-216, and Gly229-Ser228 of the fHbp antigen were recognized as essential interactive regions to the scFv antibody. Results obtained from our bioinformatics study are important and give us the basis for the favored designs of new molecules such as effective B-cell epitopes targeted by neutralizing antibodies for vaccine design.

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Weis, J. H., C. C. Morton, G. A. Bruns, J. J. Weis, L. B. Klickstein, W. W. Wong, and D. T. Fearon. "A complement receptor locus: genes encoding C3b/C4b receptor and C3d/Epstein-Barr virus receptor map to 1q32." Journal of Immunology 138, no. 1 (January 1, 1987): 312–15. http://dx.doi.org/10.4049/jimmunol.138.1.312.

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Abstract The alternative or classical pathways for complement system component C3 may be triggered by microorganisms and antigen-antibody complexes. In particular, an activated fragment of C3, C3b, covalently attaches to microorganisms or antigen-antibody complexes, which in turn bind to the C3b receptor, also known as complement receptor 1. The genes encoding the proteins that constitute the C3-activating enzymes have been cloned and mapped to a "complement activation" locus in the major histocompatibility complex, and we demonstrate in this study such a locus on the long arm of chromosome 1 at band 1q32.

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Suttorp-Schulten, Maria S. A., Bob Nunes-Cardozo, Adrian C. Breebaart, and Aize Kijlstra. "The fate of antigen-antibody complexes in the rabbit cornea." Current Eye Research 10, no. 8 (January 1991): 773–78. http://dx.doi.org/10.3109/02713689109013871.

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Pedersen, B. K., B. S. Thomsen, and H. Nielsen. "Inhibition of Natural Killer Cell Activity by Antigen-Antibody Complexes." Allergy 41, no. 8 (November 1986): 568–74. http://dx.doi.org/10.1111/j.1398-9995.1986.tb00348.x.

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Leroy, B., J. M. Lachapelle, M. G. Jacquemin, and J. M. R. Saint-Remy. "Immunotherapy of Atopic Dermatitis by Injections of Antigen-Antibody Complexes." Dermatology 186, no. 4 (1993): 276–77. http://dx.doi.org/10.1159/000247374.

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Venkatesh, N., and G. S. Murthy. "Dissociation of monoclonal antibody-antigen complexes: implications for ELISA procedures." Journal of Immunological Methods 199, no. 2 (December 1996): 167–74. http://dx.doi.org/10.1016/s0022-1759(96)00179-2.

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Lee, Cheng S., Ping Yu Huang, and David M. Ayres. "Induced electrostatic potentials on antigen-antibody complexes for bioanalytical applications." Analytical Chemistry 63, no. 5 (March 1991): 464–67. http://dx.doi.org/10.1021/ac00005a016.

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Mummert, Mark E., and Edward W. Voss. "Transition-State Theory and Secondary Forces in Antigen−Antibody Complexes." Biochemistry 35, no. 25 (January 1996): 8187–92. http://dx.doi.org/10.1021/bi9604791.

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Journal articles on the topic 'Antigen-antibody complexes'

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