Influence of DNA stiffness in protein-DNA recognition

Protein-DNA recognition plays an essential role in the regulation of gene expression. The protein-DNA binding specificity is based on direct atomic contacts between protein and DNA and/or the conformational properties of DNA. In this work, we have analyzed the influence of DNA stiffness (E) to the specificity of protein-DNA complexes. The average DNA stiffness parameters for several protein-DNA complexes have been computed using the structure based sequence dependent stiffness scale. The relationship between DNA stiffness and experimental protein-DNA binding specificity has been brought out. We have investigated the importance of DNA stiffness with the aid of experimental free energy changes (ΔΔG) due to binding in several protein-DNA complexes, such as, ETS proteins, 434, λ, Mnt and trp repressors, 434 cro protein, EcoRV endonuclease V and zinc fingers. We found a correlation in the range 0.65-0.97 between ΔΔG and E in these examples. Further, we have qualitatively analyzed the effect of mutations in the target sequence of λ repressor and we observed that the DNA stiffness could correctly identify 70% of the correct bases among the considered nine positions.