Protein-DNA interaction in tight-binding paradigm

The interaction between protein and DNA across three distinct conformations of protein chains is examined in the framework of band structures and density of states analysis, utilizing a tight-binding Hamiltonian model in conjunction with Green's function technique. At a constant temperature and with a predetermined number of sub-sites on the DNA strand, the spectral diagrams reveal a flat energy dispersion curve for both the protein molecules and the DNA strand independently, demonstrating characteristics akin to those of semiconductors. An increase in the contact points between protein molecules and the DNA strand results in a transition from semiconducting to metallic properties, a change that is also affected by the hydrogen bonds contributed by the mutant protein at these contact points. The electronic characteristics of the protein-DNA system are modulated by the size of the DNA, leading to a conversion of localized states within the structures into less defined energy levels as the length of the DNA strand increases. The influence of temperature on the density of states causes variations in both the peak heights and their positions. The stretching effects of DNA influenced by the presence of protein molecules, result in modifications by redistributing spectral characteristics within the density of states. The interaction between protein and DNA is anticipated to have a direct impact on the electronic properties of DNA, which differ across various protein conformations, thus paving the way for new research opportunities with considerable biological significance.