title: Influence of DNA stiffness in protein-DNA recognition.
abstract: 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 (DeltaDeltaG) due to binding in several protein-DNA complexes, such as, ETS proteins, 434, lambda, 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 DeltaDeltaG and E in these examples. Further, we have qualitatively analyzed the effect of mutations in the target sequence of lambda repressor and we observed that the DNA stiffness could correctly identify 70% of the correct bases among the considered nine positions.
authors.affiliation: Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan. michael-gromiha@aist.go.jp
authors.forename: M Michael
authors.initials: MM
authors.lastname: Gromiha
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry*; D004548:Elasticity; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D017422:Sequence Analysis, DNA / Q000379:methods*; D013329:Structure-Activity Relationship
chemical_list: D004268:DNA-Binding Proteins; D004247:DNA