title: Cooperativity in Binding Processes: New Insights from Phenomenological Modeling.
abstract: Cooperative binding is one of the most interesting and not fully understood phenomena involved in control and regulation of biological processes. Here we analyze the simplest phenomenological model that can account for cooperativity (i.e. ligand binding to a macromolecule with two binding sites) by generating equilibrium binding isotherms from deterministically simulated binding time courses. We show that the Hill coefficients determined for cooperative binding, provide a good measure of the Gibbs free energy of interaction among binding sites, and that their values are independent of the free energy of association for empty sites. We also conclude that although negative cooperativity and different classes of binding sites cannot be distinguished at equilibrium, they can be kinetically differentiated. This feature highlights the usefulness of pre-equilibrium time-resolved strategies to explore binding models as a key complement of equilibrium experiments. Furthermore, our analysis shows that under conditions of strong negative cooperativity, the existence of some binding sites can be overlooked, and experiments at very high ligand concentrations can be a valuable tool to unmask such sites.
authors.affiliation: Laboratorio de Biofísica Molecular, Instituto de Química y Fisicoquímica Biológicas, Universidad de Buenos Aires - CONICET, Buenos Aires, Argentina.|Centre de Biochimie Structurale, Université de Montpellier 1 and 2, Montpellier, France.
authors.forename: Diego I
authors.initials: DI
authors.lastname: Cattoni
authors.affiliation: Institute of Physics of Liquids and Biological Systems (IFLYSIB), University of La Plata - CONICET, La Plata, Argentina.|Center for Information Services and High Performance Computing, Technische Universität Dresden, Dresden, Germany.
authors.forename: Osvaldo
authors.initials: O
authors.lastname: Chara
authors.affiliation: Laboratorio de Biofísica Molecular, Instituto de Química y Fisicoquímica Biológicas, Universidad de Buenos Aires - CONICET, Buenos Aires, Argentina.
authors.forename: Sergio B
authors.initials: SB
authors.lastname: Kaufman
authors.affiliation: Laboratorio de Biofísica Molecular, Instituto de Química y Fisicoquímica Biológicas, Universidad de Buenos Aires - CONICET, Buenos Aires, Argentina.
authors.forename: F Luis
authors.initials: FL
authors.lastname: González Flecha
mesh_terms: D001665:Binding Sites; D004734:Energy Metabolism; D007700:Kinetics; D008024:Ligands; D046911:Macromolecular Substances / Q000378:metabolism; D008954:Models, Biological; D011485:Protein Binding; D013997:Time Factors
chemical_list: D008024:Ligands; D046911:Macromolecular Substances