Non-specific DNA-protein interaction: Why proteins can diffuse along DNA

Details Non-specific DNA-protein interaction: Why proteins can diffuse along DNA Non-specific DNA-protein interaction: Why proteins can diffuse along DNA

2009-02-16

arxiv.org/abs/0902.2708v1

Biology

Quantitative Biology

Biomolecules

4 pages, 4 figures, submitted to PRL

Scientific paper

The structure of DNA Binding Proteins enables a strong interaction with their specific target site on DNA. However, recent single molecule experiment reported that proteins can diffuse on DNA. This suggests that the interactions between proteins and DNA play a role during the target search even far from the specific site. It is unclear how these non-specific interactions optimize the search process, and how the protein structure comes into play. Each nucleotide being negatively charged, one may think that the positive surface of DNA-BPs should electrostatically collapse onto DNA. Here we show by means of Monte Carlo simulations and analytical calculations that a counter-intuitive repulsion between the two oppositely charged macromolecules exists at a nanometer range. We also show that this repulsion is due to a local increase of the osmotic pressure exerted by the ions which are trapped at the interface. For the concave shape of DNA-BPs, and for realistic protein charge densities, we find that the repulsion pushes the protein in a free energy minimum at a distance from DNA. As a consequence, a favourable path exists along which proteins can slide without interacting with the DNA bases. When a protein encounters its target, the osmotic barrier is completely counter-balanced by the H-bond interaction, thus enabling the sequence recognition.

Affiliated with

Also associated with

No associations

Rating

Non-specific DNA-protein interaction: Why proteins can diffuse along DNA does not yet have a rating. At this time, there are no reviews or comments for this scientific paper.

If you have personal experience with Non-specific DNA-protein interaction: Why proteins can diffuse along DNA, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Non-specific DNA-protein interaction: Why proteins can diffuse along DNA will most certainly appreciate the feedback.

Rate now

Comments { 0 }

Profile ID: LFWR-SCP-O-463379