title: Nonspecific DNA-protein interaction: why proteins can diffuse along DNA.
abstract: Recent single molecule experiments have reported that DNA binding proteins (DNA-BPs) can diffuse along DNA. This suggests that interactions between proteins and DNA play a role during the target search even far from their specific site on DNA. Here we show by means of Monte Carlo simulations and analytical calculations that there is a counterintuitive repulsion between the two oppositely charged macromolecules at a nanometer range. For the concave shape of DNA-BPs, and for realistic protein charge densities, we find that the DNA-protein interaction free energy has a minimum at a finite surface-to-surface separation, in which proteins can easily slide. When a protein encounters its target, the free energy barrier is completely counterbalanced by the H-bond interaction, thus enabling the sequence recognition.
authors: UPMC Université Paris 06, UMR 7195, PECSA, F-75005 Paris, France. vincent.dahirel@upmc.fr
authors: Vincent
authors: V
authors: Dahirel
authors: Fabien
authors: F
authors: Paillusson
authors: Marie
authors: M
authors: Jardat
authors: Maria
authors: M
authors: Barbi
authors: Jean-Marc
authors: JM
authors: Victor
mesh_terms: D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D004058:Diffusion; D011485:Protein Binding; D055672:Static Electricity; D013379:Substrate Specificity; D013816:Thermodynamics
chemical_list: D004268:DNA-Binding Proteins; D004247:DNA