Predicting the mechanisms of H-NS – DNA assembly

Bacterial chromosomal DNA is organized within a structure called the nucleoid, which is distinctly different from the rest of the cytoplasm. Bacteria have a number of nucleoid-associated proteins (NAPs) that influence the organization of the nucleoid by bending, wrapping or bridging DNA. The Histone-like Nucleoid Structuring protein H-NS can bridge DNA by binding to two separate DNA duplexes, or shield the DNA by binding to distant sites on the same duplex, depending on external conditions. H-NS occurs in Gram-negative enterobacteria and silences genes involved in bacterial virulence and antibiotic resistance. The current view reflects that the formation of an H-NS ? DNA assembly starts with the initial binding of an H-NS dimer to a specific nucleotide sequence, followed by additional H-NS dimers interacting with bound H-NS and binding to adjacent sites on DNA. Several nucleotide sequences have been identified to which H-NS binds strongly. Despite enormous progress in methods aimed at resolving molecular structures, which resulted in resolving the structures of the dimerization domain and the DNA binding domain, it is still impossible to experimentally obtain detailed structural information of the entire complex, whereas dynamic properties are even harder to investigate in experiments. Molecular simulation can complement experiments by modeling the dynamical time evolution of biomolecular systems in atomistic detail. The recent advances in molecular simulation of biological systems all heavily rely on molecular dynamics (MD). We used conventional molecular dynamics (MD) simulations to determine the stability of various conformations of H-NS. By using adaptive potentials in the metadynamics approach we were able to obtain a preliminary estimate of the free energies related to H-NS binding to different nucleotide sequences. Also, we have developed a coarse grained model to study the effect of different binding modes of H-NS on the compaction of DNA.}, time={11:30am