Signature of Pareto optimization in the Escherichia coli proteome

Abstract

Proteins have coevolved with cellular environments to improve or preserve their functions, maintaining at the same time the degree of hydrophobicity necessary to fold correctly and enough solubility to perform their biological roles. Here, we study the Escherichia coli proteome using a Pareto front analysis in the solubility-hydrophobicity space. The results indicate the existence of a Pareto optimal front, a triangle whose vertices correspond to archetypal proteins specialized in distinct tasks, such as regulatory processes, membrane transport, outer-membrane pore formation, catalysis, and binding. The vertices are further enriched with proteins that occupy different subcellular compartments, namely, cytoplasmic, inner membrane, outer membrane, and outer membrane bounded periplasmic space. The combination of various enriching features offers an interpretation of how bacteria use the physico-chemical properties of proteins, both to drive them into their final destination in the cell and to have their tasks accomplished.