title: Ion binding sites and their representations by reduced models.
abstract: The binding of small metal ions to complex macromolecular structures is typically dominated by strong local interactions of the ion with its nearest ligands. Progress in understanding the molecular determinants of ion selectivity can often be achieved by considering simplified reduced models comprised of only the most important ion-coordinating ligands. Although the main ingredients underlying simplified reduced models are intuitively clear, a formal statistical mechanical treatment is nonetheless necessary in order to draw meaningful conclusions about complex macromolecular systems. By construction, reduced models only treat the ion and the nearest coordinating ligands explicitly. The influence of the missing atoms from the protein or the solvent is incorporated indirectly. Quasi-chemical theory offers one example of how to carry out such a separation in the case of ion solvation in bulk liquids, and in several ways, a statistical mechanical formulation of reduced binding site models for macromolecules is expected to follow a similar route. However, there are also important differences when the ion-coordinating moieties are not solvent molecules from a bulk phase but are molecular ligands covalently bonded to a macromolecular structure. Here, a statistical mechanical formulation of reduced binding site models is elaborated to address these issues. The formulation provides a useful framework to construct reduced binding site models, and define the average effect from the surroundings on the ion and the nearest coordinating ligands.
authors.affiliation: Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago, Chicago, Illinois 60637, USA. roux@uchicago.edu
authors.forename: Benoît
authors.initials: B
authors.lastname: Roux
mesh_terms: D001665:Binding Sites; D007477:Ions / Q000737:chemistry; D008024:Ligands; D046911:Macromolecular Substances / Q000737:chemistry*; D008670:Metals / Q000737:chemistry*; D008958:Models, Molecular; D011789:Quantum Theory; D013816:Thermodynamics
chemical_list: D007477:Ions; D008024:Ligands; D046911:Macromolecular Substances; D008670:Metals