The Role of First and Second Shell Interactions in Phosphate Binding Proteins

Abstract

The phosphate anion is involved in a wide range of processes ranging from cell signaling to energy storage in cells. It can interact with proteins in different modes, where its interactions range from being covalently bound to the protein to coordinating metal sites in enzymes. The motif for coordinating or binding the phosphate depends on its functional usage, e.g. a structural motif known as the P loop is often found. In this work, we survey phosphate-binding proteins with emphasis on the molecular recognition of the first- and second-shell interactions between anion and amino acid residues. To characterize the binding sites, we optimize the geometries by using density functional theory calculations. From the optimized geometries, we calculate the charge transfer and force constants between the first shell interactions and the phosphate moiety as well as the interaction between the first- and second shell of the protein. The results serve to describe the strength of the first shell interaction, where positive amino acids and metals are often observed. Results also show the importance of the second shell interactions to support the binding motif. Our approach can provide basic insight into the high specificity amino acid interactions with phosphate seen in phosphate binding proteins. This knowledge is of importance in understanding phosphate-binding proteins and in the development of biomimetic sustainable phosphate biosensors.