title: A general framework improving teaching ligand binding to a macromolecule.
abstract: The interaction of a ligand with a macromolecule has been modeled following different theories. The tenants of the induced fit model consider that upon ligand binding, the protein-ligand complex undergoes a conformational change. In contrast, the allosteric model assumes that only one among different coexisting conformers of a given protein is suitable to bind the ligand optimally. In the present paper, we propose a general framework to model the binding of ligands to a macromolecule. Such framework built on the binding polynomial allows opening new ways to teach in a unified manner ligand binding, enzymology and receptor binding in pharmacology. Moreover, we have developed simple software that allows building the binding polynomial from the schematic description of the biological system under study. Taking calmodulin as a canonical example, we show here that the proposed tool allows the easy retrieval of previously experimental and computational reports. This article is part of a Special Issue entitled: Calcium Signaling in Health and Disease. Guest Editors: Geert Bultynck, Jacques Haiech, Claus W. Heizmann, Joachim Krebs, and Marc Moreau.
authors.affiliation: LIT, Therapeutic Innovation Laboratory, UMR7200 CNRS, University of Strasbourg, Faculty of Pharmacy, Illkirch, France. Electronic address: haiech@unistra.fr.
authors.forename: Jacques
authors.initials: J
authors.lastname: Haiech
authors.affiliation: ICube, Engineering, Computer and Imaging Science Laboratory, UMR7357 CNRS, University of Strasbourg, Telecom - Strasbourg, France.
authors.forename: Yves
authors.initials: Y
authors.lastname: Gendrault
authors.affiliation: LIT, Therapeutic Innovation Laboratory, UMR7200 CNRS, University of Strasbourg, Faculty of Pharmacy, Illkirch, France.
authors.forename: Marie-Claude
authors.initials: MC
authors.lastname: Kilhoffer
authors.affiliation: LIT, Therapeutic Innovation Laboratory, UMR7200 CNRS, University of Strasbourg, Faculty of Pharmacy, Illkirch, France.
authors.forename: Raoul
authors.initials: R
authors.lastname: Ranjeva
authors.affiliation: ICube, Engineering, Computer and Imaging Science Laboratory, UMR7357 CNRS, University of Strasbourg, Telecom - Strasbourg, France.
authors.forename: Morgan
authors.initials: M
authors.lastname: Madec
authors.affiliation: ICube, Engineering, Computer and Imaging Science Laboratory, UMR7357 CNRS, University of Strasbourg, Telecom - Strasbourg, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Lallement
mesh_terms: D000465:Algorithms; D000495:Allosteric Site; D002118:Calcium / Q000737:chemistry / Q000378:metabolism*; D002147:Calmodulin / Q000737:chemistry / Q000378:metabolism*; D006801:Humans; D007700:Kinetics; D008024:Ligands; D015233:Models, Statistical; D011485:Protein Binding; D012984:Software
chemical_list: D002147:Calmodulin; D008024:Ligands; D002118:Calcium
keywords: Adair–Klotz model; Allostery; Binding model; Binding polynomial; Calmodulin; Enzymology; Induced fit