Conformation Of DNA Effect On Dynamics Of Proteins Search For Its Targets And Superselective Adsorption Of Multivalent Polymer Chains To A Surface With Receptors

The search of DNA-binding proteins for their target sites positioned on DNA plays a very important role in many cellular processes. We use theoretical analysis and 3D Langevin dynamics simulations to explore how the conformation of single-strand DNA affect the search of a protein for a specific binding site on DNA. In the facilitated diffusion model, the search process consists of cycling through the 3D excursions in the bulk solution and one dimensional (1D) sliding along the DNA chain.We clearly observe that, with the increasing the interaction strength, the search time get a minimum. The search process is more dependent on 1D sliding than 3D excursions, due to the times of jumping decrease to a stable value. We also found that the conformation of single-strand DNA actually influence the search time. With the increasing of the end to end distance of DNA single strand, the distance of jumping decrease, which potentially reduce the search efficiency. As the previous experiments show, the ratio of 3D excursions and 1D sliding is the key of improving the effectiveness of search. More 3D excursions may lead to repeatedly searching on DNA sites, while more 1D sliding may result in deficiently searching for target. The balance of jumping times and jumping distance make the existing of minimum search time reasonable.Multivalent interactions exist widely in nature, which play a crucial role in many biological processes, including the adhesion of virus to cells, cell recognition and cell signaling. Interactions between multiple ligands on a biological entity and multiple receptors on another one are considered to be multivalent. While the local dynamics of multivalent polymers targeting to cell surface receptors is evidently important for practical applications, it is still obscure and rather difficult to assess experimentally. In the present work, we use 3D Langevin dynamics simulations to investigate the properties of multivalent polymer chain-surface binding systems.In this work, we have performed 3D Langevin dynamics simulations to investigate the adsorption of multivalent polymer chains to surface receptors. We show that multivalent polymer chains display superselective behaviors when they bind to surface receptors. Superselectivity is an important feature of multivalency, which implies that the number of ligands that are bound to the surface increases faster than linearly with the density of receptors. Furthermore, the range of the density of surface receptors φ where a multivalent polymer chain displays the superselective behavior narrows down for chains with higher density of ligands φ. While the optimal density of receptors where the highest superselectivity is achieved decreases with the increasing the density of ligands. These results provide a rule of thumb to design multivalent polymer chains when it is expected to achieve a balance between the φ region that achieves the superselectivity and the optimal φ realizing the highest superselectivity.By checking the conformations of bound multivalent polymer chains, we find that soft films are formed on the surfaces. Interestingly, the equilibrium radius of gyration and its horizontal component have a maximum as a function of the density of surface receptors.