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.