Dissociation of H-NS from different DNA sequences
Computational Chemistry, HIMS, University of Amsterdam
The Histone-like Nucleoid Structuring protein (H-NS) is a nucleoid-associated protein present in gram-negative bacteria where it is responsible for organizing the genomic DNA into the nucleoid. The association of H-NS to DNA is initiated by a conserved region in the protein known as the QGR motif. However, to this day the mechanism by which H-NS binds the DNA remains unknown.
With the aid of molecular dynamics and steered molecular dynamic simulations, the mechanism of dissociation from different DNA sequences was investigated. From the results, it could be concluded that the required work for the dissociation process is the highest for DNA with AT-rich domains and the lowest for the DNA sequences exclusively containing adenine.