Nonspecific DNA-protein interaction: why proteins can diffuse along DNA.
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.
Dahirel
Vincent
V
UPMC Université Paris 06, UMR 7195, PECSA, F-75005 Paris, France. vincent.dahirel@upmc.fr
Paillusson
Fabien
F
Jardat
Marie
M
Barbi
Maria
M
Victor
Jean-Marc
JM
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
D004268:DNA-Binding Proteins; D004247:DNA