Asymmetric DNA-Search Dynamics by Symmetric Dimeric Proteins

Abstract

We focus on dimeric DNA-binding proteins from two well-studied families: orthodox type II restriction endonucleases (REs) and transcription factors (TFs). Interactions of the protein's recognition sites with the DNA and, particularly, the contribution of each of the monomers to one-dimensional (1D) sliding along nonspecific DNA were studied using computational tools. Coarse-grained molecular dynamics simulations of DNA scanning by various TFs and REs provide insights into how the symmetry of a homodimer can be broken while they nonspecifically interact with DNA. The characteristics of protein sliding along DNA, such as the average sliding length, partitioning between 1D and 3D search, and the one-dimensional diffusion coefficient D1, strongly depend on the salt concentration, which in turn affects the probability of the two monomers adopting a cooperative symmetric sliding mechanism. Indeed, we demonstrate that maximal DNA search efficiency is achieved when the protein adopts an asymmetric search mode in which one monomer slides while its partner hops. We find that proteins classified as TFs have a higher affinity for the DNA, longer sliding lengths, and an increased probability of symmetric sliding in comparison with REs. Moreover, TFs can perform their biological function over a much wider range of salt concentrations than REs. Our results demonstrate that the different biological functions of DNA-binding proteins are related to the different nonspecific DNA search mechanisms they adopt.

Search by proteins for their DNA target site: 1. The effect of DNA conformation on protein sliding

“…One should note that due to the coarse-grained nature of the model, the distances between the charged beads of the protein and of the DNA are longer compared to the fully atomistic models. The effective electrostatic interactions are therefore weaker in our model and correspondingly the effective range of salt concentration (0.01–0.05 M) that allows the protein to interact strongly with the DNA molecule is typically lower compared to the physiological salt conditions (0.1–0.15 M) (32,65,66). Nevertheless, the model has been proven to successfully capture key characteristics of protein search modes on DNA (25,27,29) at salt conditions ranging from 0.01 to 0.2 M. We used a dielectric constant of 70–80, because the protein–DNA interface is much more hydrated in the non-specific complex than in the specific complex (39).…”

“…Of course, the relative weights of the various search mechanisms are also dependent on the sequence composition and structural features of DBPs (28,32,81). Our results suggest that, for a given DBP, the rotation-coupled sliding dynamics is precluded in highly curved DNA because of the large electrostatic energy barrier between the inside and outside of the DNA molecule.…”

Probing the effect of promoters on noise in gene expression using thousands of designed sequences

“…Transcription factors are known to search for their sites through some combination of nonspecific DNA binding via threedimensional (3D) diffusion and subsequent sliding across the DNA via one-dimensional (1D) diffusion (Hammar et al 2012;Khazanov et al 2013). However, the extent to which these mechanisms affect transcriptional regulation is not well understood.…”

The “Monkey‐Bar” Mechanism for Searching for the DNA Target Site: The Molecular Determinants

“…It has been suggested that intersegment transfer significantly accelerates the search for a specific target site on DNA under conditions where the protein is adsorbed onto the DNA most of the time, as it is in vivo. [44] The interactions of tetrameric proteins, such as p53, with nonspecific DNA contrast sharply with those of mono-or dimeric p53. Describing the molecular aspects of DNA search is essential for understanding the interplay between the structural architecture of proteins or DNA and the efficiency of the DNA search.…”

“…Homodimeric proteins may slide very differently than their monomeric variants. [44] The interactions of tetrameric proteins, such as p53, with nonspecific DNA contrast sharply with those of mono-or dimeric p53. Compared with single-domain proteins, proteins composed of several domains may also show unique biophysical characteristics when interacting with DNA.…”