Modeling Multivalent Ligand-Receptor Interactions with Steric Constraints on Configurations of Cell-Surface Receptor Aggregates

Kinet, 1999, The high-affinity IgE receptor (FcεRI): from physiology to pathology, Annu. Rev. Immunol., 17, 931, 10.1146/annurev.immunol.17.1.931 Kulczycki, 1974, The interaction of IgE with rat basophilic leukemia cells. II. Quantitative aspects of the binding reaction, J. Exp. Med., 140, 1676, 10.1084/jem.140.6.1676 Garman, 2000, Structure of the Fc fragment of human IgE bound to its high-affinity receptor FcεRIα, Nature, 406, 259, 10.1038/35018500 Metzger, 1992, Transmembrane signaling: the joy of aggregation, J. Immunol., 149, 1477, 10.4049/jimmunol.149.5.1477 Segal, 1977, Dimeric immunoglobulin E serves as a unit signal for mast cell degranulation, Proc. Natl. Acad. Sci. USA, 74, 2993, 10.1073/pnas.74.7.2993 Fewtrell, 1980, Larger oligomers of IgE are more effective than dimers in stimulating rat basophilic leukemia cells, J. Immunol., 125, 701, 10.4049/jimmunol.125.2.701 Conrad, 1983, Properties of two monoclonal antibodies directed against the Fc and Fab′ regions of rat IgE, Int. Arch. Allergy Appl. Immunol., 70, 352, 10.1159/000233347 Menon, 1986, Cross-linking of receptor-bound IgE to aggregates larger than dimers leads to rapid immobilization, J. Cell Biol., 102, 541, 10.1083/jcb.102.2.541 Ortega, 1988, Possible orientational constraints determine secretory signals induced by aggregation of IgE receptors on mast cells, EMBO J., 7, 4101, 10.1002/j.1460-2075.1988.tb03304.x Posner, 2004, Interaction of a monoclonal IgE-specific antibody with cell-surface IgE-FcεRI: characterization of equilibrium binding and secretory response, Biochemistry, 43, 11352, 10.1021/bi049686o Xu, 1998, Kinetics of multivalent antigen DNP-BSA binding to IgE-FcεRI in relationship to the stimulated tyrosine phosphorylation of FcεRI, J. Immunol., 160, 3225, 10.4049/jimmunol.160.7.3225 Hlavacek, 1999, Quantifying aggregation of IgE-FcεRI by multivalent antigen, Biophys. J., 76, 2421, 10.1016/S0006-3495(99)77397-2 Erickson, 1986, Cross-linking of IgE-receptor complexes at the cell surface: a fluorescence method for studying the binding of monovalent and bivalent haptens to IgE, Mol. Immunol., 23, 769, 10.1016/0161-5890(86)90089-1 Kane, 1986, Cross-linking of IgE-receptor complexes at the cell surface: synthesis and characterization of a long bivalent hapten that is capable of triggering mast cells and rat basophilic leukemia cells, Mol. Immunol., 23, 783, 10.1016/0161-5890(86)90090-8 Schweitzer-Stenner, 1987, Oligomerization and ring closure of immunoglobulin E class antibodies by divalent haptens, Biochemistry, 26, 3602, 10.1021/bi00386a053 Posner, 2002, A quantitative approach for studying IgE-FcεRI aggregation, Mol. Immunol., 38, 1221, 10.1016/S0161-5890(02)00067-6 Posner, 2007, Trivalent antigens for degranulation of mast cells, Org. Lett., 9, 3551, 10.1021/ol071175h Sil, 2007, Trivalent ligands with rigid DNA spacers reveal structural requirements for IgE receptor signaling in RBL mast cells, ACS Chem. Biol., 2, 674, 10.1021/cb7001472 Holowka, 2007, Insights into immunoglobulin E receptor signaling from structurally defined ligands, Immunol. Rev., 217, 269, 10.1111/j.1600-065X.2007.00517.x Posner, 1995, Simultaneous cross-linking by two nontriggering bivalent ligands causes synergistic signaling of IgE-FcεRI complexes, J. Immunol., 155, 3601, 10.4049/jimmunol.155.7.3601 Harris, 1997, Altered patterns of tyrosine phosphorylation and Syk activation for sterically restricted cyclic dimers of IgE-FcεRI, Biochemistry, 36, 2237, 10.1021/bi9619839 Baird, 2003, Highly effective poly(ethylene glycol) architectures for specific inhibition of immune receptor activation, Biochemistry, 42, 12739, 10.1021/bi034884l Goldstein, 1984, Equilibrium theory for the clustering of bivalent cell surface receptors by trivalent ligands. Application to histamine release from basophils, Biophys. J., 45, 1109, 10.1016/S0006-3495(84)84259-9 Hlavacek, 2006, Rules for modeling signal-transduction systems, Sci. STKE, 2006, re6, 10.1126/stke.3442006re6 Yang, 2008, Kinetic Monte Carlo method for rule-based modeling of biochemical networks, Phys. Rev. E Stat. Nonlin. Soft Matter Phys., 78, 031910, 10.1103/PhysRevE.78.031910 Perelson, 1980, Receptor clustering on a cell surface. I. Theory of receptor cross-linking by ligands bearing two chemically identical functional groups, Math. Biosci., 48, 71, 10.1016/0025-5564(80)90017-6 Dembo, 1978, A thermodynamic model of binding of flexible bivalent haptens to antibody, Immunochemistry, 15, 307, 10.1016/0161-5890(78)90091-3 DeLisi, 1980, The biophysics of ligand-receptor interactions, Q. Rev. Biophys., 13, 201, 10.1017/S0033583500001657 Schweitzer-Stenner, 1992, Dimerization kinetics of the IgE-class antibodies by divalent haptens. I. The Fab-hapten interactions, Biophys. J., 63, 551, 10.1016/S0006-3495(92)81609-0 Hlavacek, 1999, Steric effects on multivalent ligand-receptor binding: exclusion of ligand sites by bound cell surface receptors, Biophys. J., 76, 3031, 10.1016/S0006-3495(99)77456-4 Faeder, 2009, Rule-based modeling of biochemical systems with BioNetGen, Methods Mol. Biol., 500, 113, 10.1007/978-1-59745-525-1_5 Feret, 2009, Internal coarse-graining of molecular systems, Proc. Natl. Acad. Sci. USA, 106, 6453, 10.1073/pnas.0809908106 Danos, 2007, Scalable simulation of cellular signaling networks, Lect. Notes Comput. Sci., 4807, 139, 10.1007/978-3-540-76637-7_10 Colvin, 2009, Simulation of large-scale rule-based models, Bioinformatics, 25, 910, 10.1093/bioinformatics/btp066 Guo, 1999, A thermodynamic model for receptor clustering, Biophys. J., 77, 2358, 10.1016/S0006-3495(99)77073-6 Barisas, 2003, Aggregation and gelation of divalent cell surface receptors by rigid polyvalent ligands: examination by theoretical, kinetic and thermodynamic techniques, Thermochim. Acta, 400, 1, 10.1016/S0040-6031(02)00403-3 Nag, 2009, Aggregation of membrane proteins by cytosolic cross-linkers: theory and simulation of the LAT-Grb2-SOS1 system, Biophys. J., 96, 2604, 10.1016/j.bpj.2009.01.019 Bilgiçer, 2007, A synthetic trivalent hapten that aggregates anti-2,4-DNP IgG into bicyclic trimers, J. Am. Chem. Soc., 129, 3722, 10.1021/ja067159h Liu, 1980, Monoclonal dinitrophenyl-specific murine IgE antibody: preparation, isolation, and characterization, J. Immunol., 124, 2728, 10.4049/jimmunol.124.6.2728 Faeder, 2003, Investigation of early events in FcεRI-mediated signaling using a detailed mathematical model, J. Immunol., 170, 3769, 10.4049/jimmunol.170.7.3769 Holowka, 1982, Further characterization of the β-component of the receptor for immunoglobulin E, Mol. Immunol., 19, 219, 10.1016/0161-5890(82)90334-0 Barsumian, 1981, IgE-induced histamine release from rat basophilic leukemia cell lines: isolation of releasing and nonreleasing clones, Eur. J. Immunol., 11, 317, 10.1002/eji.1830110410 Erickson, 1987, The effect of receptor density on the forward rate constant for binding of ligands to cell surface receptors, Biophys. J., 52, 657, 10.1016/S0006-3495(87)83258-7 Becker, 1973, Surface IgE on human basophils during histamine release, J. Exp. Med., 138, 394, 10.1084/jem.138.2.394 Metzger, 2002, Molecular versatility of antibodies, Immunol. Rev., 185, 186, 10.1034/j.1600-065X.2002.18516.x