Abstract

The DNA architectural proteins, which are responsible for DNA compaction, play crucial roles in packaging the bacterial nucleoid into a cell. HU, one of the most abundant prokaryotic DNA binding proteins, binds double stranded DNA preferentially to the intrinsically curved regions and stabilizes the bent structure of DNA, which is important in many processes such as nucleoid packaging, replication, transcription, and DNA repairing. Despite the physiological importance, the sliding and recognition mechanism of HU and the relationship between HU binding and DNA bending is still unclear. Here we use coarse-grained molecular dynamics simulations to investigate the binding, sliding and searching process of HU on DNA. Our results provide new insights into the mechanism of non-sequence-specific protein-DNA interactions, and the coupling between protein binding and DNA curvature.