Principles Governing Anion Selectivity in Proteins

Abstract

The highly selective anion binding by proteins is essential for a number of biological processes including normal renal function and maintenance of blood acidity. Various transport systems are at the core of anion homeostasis in living cells, by binding selectively a range of substrates such as chloride (Cl-), bromide (Br-), fluoride (F -), carbonate (CO32-), and bicarbonate (HCO3-), among others. The efficient binding requires a high specificity recognition of anions by the protein host. However, the detailed molecular-level understanding of general anion recognition across protein sites is lacking as most of the studies are focusing only on a specific protein. In the present work, we use high-resolution crystal structures of proteins with known specificity sequence such as haloalkane dehalogenase (DhlA), the human anion exchanger 1 (hAE1), and the Cl-/F- antiporter from the CLC family to identify the thermodynamical underpinnings of anion selectivity as a first step to the rational design of anion-selective proteins. To that end, we employ a combination of in-vacuum and implicit solvent QM calculations to evaluate the binding free energies of a set of binding site models interacting with different inorganic anions including Cl-, F-, HCO3-, and CO32-. We place our findings in a broader context of anion-selective binding sites by comparison to the statistical distribution of amino acid topology and organization in various anion binding proteins available in the Protein Data Bank. The analysis involved 30 proteins structures binding F-, 67 CO32--binding proteins and 49 structures that bind HCO3-. Our results can inform the rational design of anion-moving and anion-binding systems including applications of membrane proteins to desalination and biosensing.