Description of nonspecific DNA-protein interaction and facilitated diffusion with a dynamical model.

摘要: We propose a dynamical model for nonspecific DNA-protein interaction, which is based on the “bead-spring” previously developed by other groups, and investigate its properties using Brownian dynamics simulations. show that successfully reproduces some of observed real systems predictions kinetic models. For example, sampling DNA sequence protein proceeds via succession three-dimensional motion in solvent, one-dimensional sliding along sequence, short hops between neighboring sites, intersegmental transfers. Moreover, facilitated diffusion takes place certain range values effective charge, is, combination leads to faster than pure motion. At last, number base pairs visited during event comparable deduced from single-molecule experiments. also point out discuss discrepancies this recent experimental results as well hypotheses