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.
Norberg
Jan
J
Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168 St., New York, NY 10032, USA. Jan.Norberg@biosci.ki.se
D000469:Alkaline Phosphatase; D020816:Amino Acid Motifs; D001665:Binding Sites; D003461:Crystallography; D018844:Cyclin-Dependent Kinases / Q000737:chemistry / Q000378:metabolism; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D015245:Deoxyribonuclease BamHI / Q000737:chemistry / Q000378:metabolism; D018257:Helix-Loop-Helix Motifs; D006860:Hydrogen Bonding; D008958:Models, Molecular; D017570:MyoD Protein / Q000737:chemistry / Q000378:metabolism; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D012492:Salts; D055672:Static Electricity; D014867:Water
D017570:MyoD Protein; D011506:Proteins; D012492:Salts; D014867:Water; D004247:DNA; D018844:Cyclin-Dependent Kinases; D015245:Deoxyribonuclease BamHI; D000469:Alkaline Phosphatase