Interaction investigations of HipA binding to HipB dimer and HipB dimer plus DNA complex: a molecular dynamics simulation study

We carried out molecular dynamics simulations and free energy calculations for a series of ternary and diplex models for the HipA protein, HipB dimer, and DNA molecule to address the mechanism of HipA sequestration and the binding order of events from apo HipB/HipA to 2HipA+HipB dimer+DNA complex. The results revealed that the combination of DNA with the HipB dimer is energetically favorable for the combination of HipB dimer with HipA protein. The binding of DNA to HipB dimer induces a long-range allosteric communication from the HipB(2)-DNA interface to the HipA-HipB(2) interface, which involves the closeness of 1 helices of HipB dimer to HipA protein and formations of extra hydrogen bonds in the HipA-HipB(2) interface through the extension of 2/3 helices in the HipB dimer. These simulated results suggested that the DNA molecule, as a regulative media, modulates the HipB dimer conformation, consequently increasing the interactions of HipB dimer with the HipA proteins, which explains the mechanism of HipA sequestration reported by the previous experiment. Simultaneously, these simulations also explored that the thermodynamic binding order in a simulated physiological environment, that is, the HipB dimer first bind to DNA to form HipB dimer+DNA complex, then capturing strongly the HipA proteins to form a ternary complex, 2HipA+HipB dimer+DNA, for sequestrating HipA in the nucleoid. Copyright (c) 2013 John Wiley & Sons, Ltd.