Nonspecific DNA-Protein Interaction: Why Proteins Can Diffuse along DNA

Abstract

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 favorable 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.DNA stores the genetic material of all living cells and viruses. This huge amount of information is effective only if DNA binding proteins (DNA-BPs) manipulates DNA in very specific locations. When the protein finds its DNA target, the shape complementarity of DNA Binding Proteins and their specific DNA sequence enables to maximize the number of hydrogen bonds, thus leading to a strong protein-DNA association [1,2,3,4,5,6]. The rate of protein-DNA association is however not controlled by the association step itself, but by the whole searching process. It is well established now that DNA-BPs diffuse along DNA before they reach their specific site [7]. During this search, the only interactions between protein and DNA which can play a role are non sequence-specific. Those non-specific interactions between protein and DNA remain poorly documented. Altough the predominance of electrostatics is unquestionable [1,2,3,4,5,6], it remains unclear how the protein structure comes into play [5,6,7]. Does the typical concavity of DNA-BPs which favors the specific association also influence the non-specific electrostatic interaction? In DNA-protein complexes, the mean charge of the protein residues located at the interface is positive [1,2]. Nevertheless, structural studies of non-specific complexes have shown that the protein atoms and the DNA atoms are weakly packed together at the interface [1,2,3,5,6], thus suggesting that a force counterbalances the electrostatic attraction. In this letter, our purpose is to establish the general mechanisms that control the mean force between protein and DNA and that are applicable to a wide variety of DNA-BPs. That goal in mind, we design coarse-grained D...

Protein–DNA Electrostatics

“…Proteins that bind to DNA are most often positively charged. More precisely, positively charged patches are observed in the region which faces the DNA when the specific complex is formed, an effect which can be accounted for by evaluating the propensity of positive residues to occurs more frequently in a DNA-binding interface [14,15,65,66,67,68,25].…”

“…They can cover the DNA molecule by using up to 35 % of their surface [14]. Averaging over different types of proteins, one obtains for the average surface of the interface a value of S prot ∼ 15 nm 2 [14,15,65,25]. Generally, and particularly for enzymes, electrostatic patches and significant protein concavities often overlap, so that DNA is "inserted" in this concavities leading to a quite typical enveloping or complementary shape [14,65] (Figure 13).…”

“…The complete comparison of the different protein models have been presented in Ref. [25]. The main result of this analysis is presented in Figure 14, where the free energy profiles obtained with the spherical and complementary shapes shown in Figure ??…”

“…We have shown indeed that a charged convex body (like DNA) counter-intuitively repels an oppositely charged concave body (like DNA-binding proteins), provided the two bodies do not exactly neutralize each other [25,26]. In the following, we will describe how to obtain this result, and discuss its implications on the search mechanism.…”

“…Mirny and co-workers proposed that the protein could undergo conformational changes between a search state and a recognition state, in an intermittent way [23,24]. We have proposed an alternative mechanism, where the key parameter will be the distance between the protein and the DNA [25,26].…”