Association of protein–DNA recognition complexes: electrostatic and nonelectrostatic effects

In this study the electrostatic and nonelectrostatic contributions to the binding free energy of a number of different protein–DNA recognition complexes are investigated. To determine the electrostatic effects in the protein–DNA association the Poisson–Boltzmann approach was applied. Overall the salt-dependent electrostatic free energy opposed binding in all protein–DNA complexes except one, and the salt-independent electrostatic contribution favored binding in more than half of the complexes. Further the salt-dependent electrostatic free energy increased with higher ionic concentrations and therefore complex association is stronger opposed at higher ionic concentrations. The hydrophobic effect in the protein–DNA complexes was determined from the buried accessible surface area and the surface tension. A majority of the complexes showed more polar than nonpolar buried accessible surface area. Interestingly the buried DNA-accessible surface area was preferentially hydrophilic, only in one complex a slightly more hydrophobic buried accessible surface area was observed. A quite sophisticated balance between several different free energy components seems to be responsible for determining the free energy of binding in protein–DNA systems.