Experimental and theoretical high pressure strategies for investigating protein–nucleic acid assemblies

A method was developed to investigate the stability of protein–nucleic acid complexes using hydrostatic pressure during electrophoretic gel mobility shift analysis. The initial system probed by this technique was the well-characterized cognate BamHI–DNA complex. Band shift analysis at several elevated pressures found the equilibrium dissociation (K_d) constant to be dependent on pressure, which allowed the volume change of dissociation (ΔV) to be calculated. In order to describe the effects of pressure on the specific BamHI–DNA complex at the molecular level, molecular dynamics simulations at both ambient and elevated pressure was performed. Comparison of the simulation trajectories identified several individual BamHI–DNA contacts that are disrupted due to pressure. The disruption of these contacts can be attributed to an observed pressure-induced increase in hydration at the protein–DNA interface during the elevated pressure simulation.