Molecular dynamics of DNA-binding protein and its 2D-crystals

Abstract

Abstract In this work the dodecamers and the two-dimensional crystals of DNA-binding protein from starved cells (DPS) of Escherichia coli bacteria were investigated. The DPS monomer contains 167 amino acids residues. It can form dimers, trimers, and dodecamers. The versatility of the DPS protein structure can be used to design nanomaterials with structures and functions not found in living nature. The ability of this protein to self-assemble into complex shapes and structures defined on the nanometer scale can make them highly demanded for various technological applications. It was used all-atom classical molecular dynamics simulation on 0.1 microsecond scale to obtain the spatial and energy characteristics of the proteins and the components of the simulation box. The fluctuation mobility of DPS protein at various temperatures was discussed. The diffusion of ions in the presence of dodecamers and 2D crystals was compared. It has been shown that this protein retains its ability to accumulate ions in a wide range of biological temperatures from 277 to 369K. It also retains the mobility of key amino acid residues involved in the formation of nanocrystals and the transport of ions into the cavity, even at low physiological temperatures.