Structure of DPS Protein Complexes with DNA

Abstract

The mechanisms of interaction of DPS protein molecules (DNA-binding protein from starved cells) with DNA, which are important for understanding the protection of the genetic material of bacteria under stress, were examined. The results of studies of molecular dynamics studies of the complexes of E. coli DPS proteins with DNA showed that the main role in the binding of DNA molecules to DPS molecules is played by the amino acid residues Lys8 and Lys10 located in the disordered part of N-termini of DPS, and Lys27 in its ordered part. The pair of Asp23–Ser24 residues exerts a coordinating effect. A strong redistribution of Na+ ions from the outer part of the computational cell into DPS molecules and their preferential binding to His63 and Glu82 amino acid residues coordinating the binding site of the ferroxidase center, which can reduce the efficiency of binding of iron ions by this center, were found. A study of the recently understood three-dimensional crystal structure of E. coli DPS protein crystals (PDB ID: 6GCM) shows the presence of three types of mutually orthogonal channels: a wide channel and two narrow ones. The presence of DNA in the wide channels, unlike narrow ones, does not destroy but stabilizes the crystal. Crystal stabilization occurs due to the formation of additional interactions between the N-terminal regions of one DPS molecule with DNA and with another DPS molecule.