Beyond Diffusion-Controlled Kinetics: How a Protein Implements a Fast Search on DNA to Get to its Specific Binding Site

Abstract

There are a wide number of proteins that initiate and regulate the transcription of genes. All have DNA-binding domains that give them the ability to bind specific sequences. Classical binding reactions are controlled by diffusion limit. In those cases, association rate for binding doesn’t exceed 108 M−1S−1 and then, for high affinity binding (nM), dissociation rate would expands dozens of seconds. Find a short target sequence within the enormous pool provided by genomic DNA requires protein moving fast towards the specific binding site (fast association and dissociation while searching). Before reaching their targets, DNA-binding proteins encounter nonspecific DNA first and bind to it, although with weaker affinity than DNA specific sequence. As observed first in 1970, DNA binding proteins binds its target ∼100 times faster than allowed by the 3D diffusion limit. This faster-than-diffusion binding was explained by the facilitated-diffusion model, in which a DNA-binding protein interacts with nonspecific DNA before reaching its target by three main mechanism: sliding, where protein slides in 1D along nonspecific DNA; hopping, where the protein dissociates from DNA briefly, performing free 3D diffusion, and lands back on DNA at other close location; and jumping, where the protein's DNA landing location is not correlated to the dissociation site. Facilitate diffusion has been studied theoretically, computationally and experimentally. However, very little is known from the protein viewpoint, and how protein and DNA dialogue in an efficient manner. We are using the DNA-binding engrailed homeodomain module that binds with high affinity to DNA sequence TAATTA/G. In the present work we will analyze how DNA sequence seems to have evolved towards an organization that ensures biologically precise gene expression. Combination of specific sequence binding, degenerated sequence binding and nonspecific binding could promote an antenna effect for guiding the protein to the specific site. Mechanical statistical models help us to confirm the experimental data and shed light on this fundamental and multifactorial biological problem.