Target Search of N Sliding Proteins on a DNA

Nucleic acids research, 2015

DNA-binding proteins (DBPs) rapidly search and specifically bind to their target sites on genomic DNA in order to trigger many cellular regulatory processes. It has been suggested that the facilitation of search dynamics is achieved by combining 3D diffusion with one-dimensional sliding and hopping dynamics of interacting proteins. Although, recent studies have advanced the knowledge of molecular determinants that affect one-dimensional search efficiency, the role of DNA molecule is poorly understood. In this study, by using coarse-grained simulations, we propose that dynamics of DNA molecule and its degree of confinement due to cellular crowding concertedly regulate its groove geometry and modulate the inter-communication with DBPs. Under weak confinement, DNA dynamics promotes many short, rotation-decoupled sliding events interspersed by hopping dynamics. While this results in faster 1D diffusion, associated probability of missing targets by jumping over them increases. In contras...

Biophysical Journal, 2004

Recognition and binding of specific sites on DNA by proteins is central for many cellular functions such as transcription, replication, and recombination. In the process of recognition, a protein rapidly searches for its specific site on a long DNA molecule and then strongly binds this site. Here we aim to find a mechanism that can provide both a fast search (1-10 s) and high stability of the specific protein-DNA complex (K d ¼ 10 ÿ15 -10 ÿ8 M). Earlier studies have suggested that rapid search involves sliding of the protein along the DNA. Here we consider sliding as a one-dimensional diffusion in a sequencedependent rough energy landscape. We demonstrate that, despite the landscape's roughness, rapid search can be achieved if one-dimensional sliding is accompanied by three-dimensional diffusion. We estimate the range of the specific and nonspecific DNA-binding energy required for rapid search and suggest experiments that can test our mechanism. We show that optimal search requires a protein to spend half of its time sliding along the DNA and the other half diffusing in three dimensions. We also establish that, paradoxically, realistic energy functions cannot provide both rapid search and strong binding of a rigid protein. To reconcile these two fundamental requirements we propose a search-and-fold mechanism that involves the coupling of protein binding and partial protein folding. The proposed mechanism has several important biological implications for search in the presence of other proteins and nucleosomes, simultaneous search by several proteins, etc. The proposed mechanism also provides a new framework for interpretation of experimental and structural data on protein-DNA interactions.

2010

Gene regulatory proteins find their target sites on DNA remarkably quickly; the experimental binding rate for lac repressor is orders-of-magnitude higher than predicted by free diffusion alone. It has been proposed that nonspecific binding aids the search by allowing proteins to slide and hop along DNA. We develop a reaction-diffusion theory of protein translocation that accounts for transport both on and off the strand and incorporates the physical conformation of DNA. For linear DNA modeled as a wormlike chain, the distribution of hops available to a protein exhibits long, power-law tails that make the long-time displacement along the strand superdiffusive. Our analysis predicts effective superdiffusion coefficients for given nonspecific binding and unbinding rate parameters. Translocation rate exhibits a maximum at intermediate values of the binding rate constant, while search efficiency is optimized at larger binding rate constant values. Thus, our theory predicts a region of values of the nonspecific binding and unbinding rate parameters that balance the protein translocation rate and the efficiency of the search. Published data for several proteins falls within this predicted region of parameter values.

Journal of Physics A: Mathematical and Theoretical, 2009

A number of vital biological processes rely on fast and precise recognition of a specific DNA sequence (site) by a protein. How can a protein find its site on a long DNA molecule among 10 6 -10 9 decoy sites? Here, we present our recent studies of the protein-DNA search problem. Seminal biophysical works suggested that the protein-DNA search is facilitated by 1D diffusion of the protein along DNA (sliding). We present a simple framework to calculate the mean search time and focus on several new aspects of the process such as the roles of DNA sequence and protein conformational flexibility. We demonstrate that coupling of DNA recognition with conformational transition within the protein-DNA complex is essential for fast search. To approach the complexity of the in vivo environment, we examine how the search can proceed at realistic DNA concentrations and binding constants. We propose a new mechanism for local distance-dependent search that is likely essential in bacteria. Simulations of the search on tightly packed DNA and crowded DNA demonstrate that our theoretical framework can be extended to correctly predicts search time in such complicated environments. We relate our findings to a broad range of experiments and summarize the results of our recent singlemolecule studies of a eukaryotic protein (p53) sliding along DNA.

Advances in protein chemistry and structural biology, 2013

Gene expression and regulation rely on an apparently finely tuned set of reactions between some proteins and DNA. Such DNA-binding proteins have to find specific sequences on very long DNA molecules and they mostly do so in the absence of any active process. It has been rapidly recognized that, to achieve this task, these proteins should be efficient at both searching (i.e., sampling fast relevant parts of DNA) and finding (i.e., recognizing the specific site). A two-mode search and variants of it have been suggested since the 1970s to explain either a fast search or an efficient recognition. Combining these two properties at a phenomenological level is, however, more difficult as they appear to have antagonist roles. To overcome this difficulty, one may simply need to drop the dichotomic view inherent to the two-mode search and look more thoroughly at the set of interactions between DNA-binding proteins and a given DNA segment either specific or nonspecific. This chapter demonstrat...

Nucleic Acids Research

Target search models of DNA-binding proteins in cells typically consider search mechanisms that include 3D diffusion and 1D sliding, which can be characterized by single-molecule tracking on DNA. However, the finding of liquid droplets of DNA and nuclear components in cells cast doubt on extrapolation from the behavior in ideal non-condensed DNA conditions to those in cells. In this study, we investigate the target search behavior of DNA-binding proteins in reconstituted DNA-condensed droplets using single-molecule fluorescence microscopy. To mimic nuclear condensates, we reconstituted DNA-condensed droplets using dextran and PEG polymers. In the DNA-condensed droplets, we measured the translational movement of four DNA-binding proteins (p53, Nhp6A, Fis and Cas9) and p53 mutants possessing different structures, sizes, and oligomeric states. Our results demonstrate the presence of fast and slow mobility modes in DNA-condensed droplets for the four DNA-binding proteins. The slow mobil...

Biophysical Journal, 2006

It is known since the early days of molecular biology that proteins locate their specific targets on DNA up to two orders-of-magnitude faster than the Smoluchowski three-dimensional diffusion rate. An accepted explanation of this fact is that proteins are nonspecifically adsorbed on DNA, and sliding along DNA provides for the faster one-dimensional search. Surprisingly, the role of DNA conformation was never considered in this context. In this article, we explicitly address the relative role of three-dimensional diffusion and one-dimensional sliding along coiled or globular DNA and the possibility of correlated readsorption of desorbed proteins. We have identified a wealth of new different scaling regimes. We also found the maximal possible acceleration of the reaction due to sliding. We found that the maximum on the rate-versus-ionic strength curve is asymmetric, and that sliding can lead not only to acceleration, but also in some regimes to dramatic deceleration of the reaction.

Physical Review E, 2015

DNA-binding protein searches for its target, a specific site on DNA, by means of diffusion. The search process consists of many recurrent steps of one-dimensional diffusion (sliding) along DNA chain and three-dimensional diffusion (hopping) after dissociation of a protein from DNA chain. Here we propose a computational method that allows extracting the contribution of sliding and hopping to the search process in vivo from the measurements of the kinetics of the target search by lac repressor in Escherichia coli (Hammar et al. (2012). Science, 336, 1595). The method combines lattice Monte Carlo simulations with the Brownian excursion theory and includes explicitly steric constraints for hopping due to the helical structure of DNA. The simulation results including all experimental data revealed that the in vivo target search is dominated by sliding. The short-range hopping to the same base pair interrupts one-dimensional sliding while long-range hopping does not contribute significantly to the kinetics of the search of the target in vivo. I.

Biophysical Journal, 2017

Physical Review E, 2005

We study the size fluctuations of a local denaturation zone in a DNA molecule, in the presence of proteins that exclusively bind to single-stranded DNA, based on a (2 + 1)-dimensional master equation governing the time evolution of the probability distribution P (m, n, t) to find a bubble of size m with n bound proteins. In particular, by tuning the physical parameters we can drive the system from undisturbed bubble fluctuations to full, binding protein-induced denaturation. Moreover, we determine the effective free energy landscape of the DNA-bubble and its lifetime. 87.14.Gg Under physiological conditions, the Watson-Crick double-helix is the thermodynamically stable configuration of a DNA molecule. This stability is effected by the specific Watson-Crick H-bonding, whose key-lock principle guarantees the high level of fidelity during replication and transcription; and by the stronger base-stacking between neighboring base-pairs causing hydrophobic interactions between the planar aromatic bases .