Multiple-binding-site mechanism explains concentration-dependent unbinding rates of DNA-binding proteins

Charles E Sing,John F Marko,Monica Olvera De La Cruz

doi:10.1093/nar/gkt1327

Abstract

Recent work has demonstrated concentration-dependent unbinding rates of proteins from DNA, using fluorescence visualization of the bacterial nucleoid protein Fis [Graham et al. (2011) (Concentration-dependent exchange accelerates turnover of proteins bound to double-stranded DNA. Nucleic Acids Res., 39:2249)]. The physical origin of this concentration-dependence is unexplained. We use a combination of coarse-grained simulation and theory to demonstrate that this behavior can be explained by taking into account the dimeric nature of the protein, which permits partial dissociation and exchange with other proteins in solution. Concentration-dependent unbinding is generated by this simple model, quantitatively explaining experimental data. This effect is likely to play a major role in determining binding lifetimes of proteins in vivo where there are very high concentrations of solvated molecules.

Highlights

The kinetics of DNA–protein interactions control all aspects of gene expression and cell function, and are of strong biological and biophysical interest
Experimental work on DNA-binding proteins Fis, HU and NHP6A has recently demonstrated the appearance of concentration-dependent unbinding [16], with similar behaviors observed in other systems [22]
This behavior does not occur in usual models of protein–DNA interactions widely used to fit kinetic data where there is by construction a concentration-independent off-rate

Summary

Introduction

The kinetics of DNA–protein interactions control all aspects of gene expression and cell function, and are of strong biological and biophysical interest. Recent experimental studies of the proteins Fis [9,11,12,13], NHP6A [10] and others [14,15] have used novel single-molecule methods to probe unbinding dynamics These in vitro experiments directly visualize the presence of binding proteins using fluorescence microscopy or DNA force spectroscopy measurements [16,17,18,19,20,21], and have demonstrated an unexpected concentration-dependent off-rate koff, of the form [16]: koff 1⁄4 k0+k1 c ð1Þ where k0 is the bare zero-concentration reaction constant and k1 is a coefficient that incorporates a linear dependence of off-rate to concentration c [16]. Analogies can be drawn to classical reaction-rate descriptions of chemical processes, where interplays exist between kinetics and molecular structure [26]

Methods

Results

Conclusion