Insights from Ion Binding Site Network Analysis into Evolution and Functions of Proteins

Abstract

Many biological phenomena can be represented as complex networks. Using a protein binding site comparison approach, we generated a network of ion binding sites on the scale of all known protein structures from the Protein Data Bank. We found that this ion binding site similarity network is scale-free, indicating a network in which a few ion binding site scaffolds are the network hubs, and these are connected to hundreds of nodes, whereas the vast majority of nodes have only a few neighbors. Enrichment and statistical analysis of the network components and communities yielded insights into underlying processes from the functional and the structural perspective. Largest components and communities were observed to be closely related to basic metabolic processes and some of the most common structural folds, which, from the evolutionary point of view, indicates that they may be the oldest ones. Further, we derived the first comprehensive map of ion interchangeability, based on binding site similarity. Several highly interchangeable protein-ion binding site pairs emerged (e.g., Ca²⁺ and Mg²⁺ ), as well as structurally distinct ones. The constructed network of ion binding site similarities will aid in understanding the general principles of protein-ion binding sites structure, function and evolution. We demonstrate potential uses of the network on proteins involved in cancer development and immune response, where individual ions play prominent roles in disease development.

Keywords: binding site; evolution; function; ion network; protein similarity.