Comparative Analysis of Protein Charge Distribution in Genome Scale

Abstract

Biological cells are living in various environments: Halobacteria are in saturated salt solution and thermophilic bacteria are living at high temperature, while the environment of eukaryotic cells is kept constant by homeostasis. Therefore, each biological species is under the evolutionary pressure from its environment. It is well known that the amino acid sequence of each protein determines the 3D-structure, which is related to its biological function. For example, the amino acid sequence of membrane proteins have the specific hydrophobic distribution compared to soluble proteins and can be predicted [1]. The fraction of ORFs coding membrane proteins is 25% of total ORFs on whole genomes of 15 unicellular organisms [2]. Environments of living cells may not affect membrane proteins because this kind of protein is not subjected to cytoplasm. The environmental effect of all of ORFs on whole genomes has not been studied so far. In this work, we analyzed the electric net charge of total genomes for comparing the charge distribution among various biological organisms. Because the surface of proteins in aqueous solvent is mainly comprised of polar residues, the charge distribution of proteins has to be a good parameter to monitor the effect of environment on the physicochemical properties of proteins.