Crowding on DNA in Protein Search for Targets

Dynamics of the Protein Search for Targets on DNA in Quorum Sensing Cells

Quorum sensing (QS) is a bacterial cell-cell communication process that regulates gene expression. The search and binding of the AHL-bound LuxR-type proteins to specific sites on DNA in quorum sensing cells in Gram-negative bacteria is a complex process and has been theoretically investigated based on a discrete-state stochastic approach. It is shown that several factors such as the rate of formation of the AHL-bound LuxR protein within the cells and its dissociation to freely diffusing autoinducer molecule (AHL), the diffusion of the latter in and out of the cells, positive feedback loops, and the cell population density play an important role in the protein target search and can control the gene regulation processes. Physical-chemical arguments to explain these observations are presented. Our calculations of the dynamic properties are also supplemented by Monte Carlo computer simulations. Our theoretical model provides physical insights into the complex mechanisms of protein target search in quorum sensing cells.

Influence of Nonspecific Interactions between Proteins and In Vivo Cytoplasmic Crowders in Facilitated Diffusion of Proteins: Theoretical Insights

The binding of proteins to their respective specific sites on the DNA through facilitated diffusion serves as the initial step of various important biological processes. While this search process has been thoroughly investigated via in vitro studies, the cellular environment is complex and may interfere with the protein's search dynamics. The cytosol is heavily crowded, which can potentially modify the search by nonspecifically interacting with the protein that has been mostly overlooked. In this work, we probe the target search dynamics in the presence of explicit crowding agents that have an affinity toward the protein. We theoretically investigate the role of such protein-crowder associations in the target search process using a discrete-state stochastic framework that allows for the analytical description of dynamic properties. It is found that stronger nonspecific associations between the crowder and proteins can accelerate the facilitated diffusion of proteins in comparison with a purely inert, rather weakly interacting cellular environment. This effect depends on how strong these associations are, the spatial positions of the target with respect to the crowders, and the size of the crowded region. Our theoretical results are also tested with Monte Carlo computer simulations. Our predictions are in qualitative agreement with existing experimental observations and computational studies.

Tunable depletion force in active and crowded environments

We adopt two-dimensional Langevin dynamics simulations to study the effective interactions between two passive colloids in a bath crowded with active particles. We mainly pay attention to the significant effects of active particle size, crowding-activity coupling, and chirality. First, a transition of depletion force from repulsion to attraction is revealed by varying particle size. Moreover, larger active crowders with sufficient activity can generate strong attractive force, which is in contrast to the cage effect in passive media. It is interesting that the attraction induced by large active crowders follows a linear scaling with the persistence length of active particles. Second, the effective force also experiences a transition from repulsion to attraction as volume fraction increases, as a consequence of the competition between the two contrastive factors of activity and crowding. As bath volume fraction is relatively small, activity generates a dominant repulsion force, while as the bath becomes concentrated, crowding-induced attraction becomes overwhelming. Lastly, in a chiral bath, we observe a very surprising oscillation phenomenon of active depletion force, showing an evident quasiperiodic variation with increasing chirality. Aggregation of active particles in the vicinity of the colloids is carefully examined, which serves as a reasonable picture for our observations. Our findings provide an inspiring strategy for the tunable active depletion force by crowding, activity, and chirality.

Discrete-state stochastic kinetic models for target DNA search by proteins: Theory and experimental applications

To perform their functions, transcription factors and DNA-repair/modifying enzymes randomly search DNA in order to locate their specific targets on DNA. Discrete-state stochastic kinetic models have been developed to explain how the efficiency of the search process is influenced by the molecular properties of proteins and DNA as well as by other factors such as molecular crowding. These theoretical models not only offer explanations on the relation of microscopic processes to macroscopic behavior of proteins, but also facilitate the analysis and interpretation of experimental data. In this review article, we provide an overview on discrete-state stochastic kinetic models and explain how these models can be applied to experimental investigations using stopped-flow, single-molecule, nuclear magnetic resonance (NMR), and other biophysical and biochemical methods.

A lattice model on the rate of in vivo site-specific DNA-protein interactions

We develop a lattice model of site-specific DNA-protein interactions under in vivo conditions where DNA is modelled as a self-avoiding random walk that is embedded in a cubic lattice box resembling the living cell. The protein molecule searches for its cognate site on DNA via a combination of three dimensional (3D) and one dimensional (1D) random walks. Hopping and intersegmental transfers occur depending on the conformational state of DNA. Results show that the search acceleration ratio (= search time in pure 3D route/search time in 3D and 1D routes) asymptotically increases towards a limiting value as the dilution factor of DNA (= volume of the cell/the volume of DNA) tends towards infinity. When the dilution ratio is low, then hopping and intersegmental transfers significantly enhance the search efficiency over pure sliding. At high dilution ratio, hopping does not enhance the search efficiency much since under such situation DNA will be in a relaxed conformation that favors only sliding. In the absence of hopping and intersegmental transfers, there exists an optimum sliding time at which the search acceleration ratio attains a maximum in line with the current theoretical results. However, existence of such optimum sliding length disappears in the presence of hopping. When the DNA is confined in a small volume inside the cell resembling a natural cell system, then there exists an optimum dilution and compression ratios (= total cell volume/volume in which DNA is confined) at which the search acceleration factor attains a maximum especially in the presence of hopping and intersegmental transfers. These optimum values are consistent with the values observed in the Escherichia coli cell system. In the absence of confinement of DNA, position of the specific binding site on the genomic DNA significantly influences the search acceleration. However, such position dependent changes in the search acceleration ratio will be nullified in the presence of hopping and intersegmental transfers especially when the DNA is confined in a small volume that is embedded in an outer cell.

Lost in the Crowd: How Does Human 8-Oxoguanine DNA Glycosylase 1 (OGG1) Find 8-Oxoguanine in the Genome?

The most frequent DNA lesion resulting from an oxidative stress is 7,8-dihydro-8-oxoguanine (8-oxoG). 8-oxoG is a premutagenic base modification due to its capacity to pair with adenine. Thus, the repair of 8-oxoG is critical for the preservation of the genetic information. Nowadays, 8-oxoG is also considered as an oxidative stress-sensor with a putative role in transcription regulation. In mammalian cells, the modified base is excised by the 8-oxoguanine DNA glycosylase (OGG1), initiating the base excision repair (BER) pathway. OGG1 confronts the massive challenge that is finding rare occurrences of 8-oxoG among a million-fold excess of normal guanines. Here, we review the current knowledge on the search and discrimination mechanisms employed by OGG1 to find its substrate in the genome. While there is considerable data from in vitro experiments, much less is known on how OGG1 is recruited to chromatin and scans the genome within the cellular nucleus. Based on what is known of the strategies used by proteins searching for rare genomic targets, we discuss the possible scenarios allowing the efficient detection of 8-oxoG by OGG1.

Effect of DNA Conformation on the Protein Search for Targets on DNA: A Theoretical Perspective

Protein-DNA interactions are important for all biological processes and involve the process of proteins searching for and recognizing specific binding sites on the DNA. Many aspects of the mechanism of the protein search for targets on DNA are not well understood. One important problem is the effect of DNA conformation on the protein search dynamics. Using a theoretical method based on a discrete-state stochastic approach, we obtained an analytical description of the dynamic properties. We investigated a system with two DNA conformers. It was found that the average search time on one DNA conformer via 1D or 3D motions depended on the dynamics of the search process on the other DNA conformer.

The effect of obstacles in multi-site protein target search with DNA looping

Many fundamental biological processes are regulated by protein-DNA complexes called synaptosomes, which possess multiple interaction sites. Despite the critical importance of synaptosomes, the mechanisms of their formation are not well understood. Because of the multisite nature of participating proteins, it is widely believed that their search for specific sites on DNA involves the formation and breaking of DNA loops and sliding in the looped configurations. In reality, DNA in live cells is densely covered by other biological molecules that might interfere with the formation of synaptosomes. In this work, we developed a theoretical approach to evaluate the role of obstacles in the target search of multisite proteins when the formation of DNA loops and the sliding in looped configurations are possible. Our theoretical method is based on analysis of a discrete-state stochastic model that uses a master equations approach and extensive computer simulations. It is found that the obstacle slows down the search dynamics in the system when DNA loops are long-lived, but the effect is minimal for short-lived DNA loops. In addition, the relative positions of the target and the obstacle strongly influence the target search kinetics. Furthermore, the presence of the obstacle might increase the noise in the system. These observations are discussed using physical-chemical arguments. Our theoretical approach clarifies the molecular mechanisms of formation of protein-DNA complexes with multiple interactions sites.

Structural Basis of Enhanced Facilitated Diffusion of DNA-Binding Protein in Crowded Cellular Milieu

Although the fast association between DNA-binding proteins (DBPs) and DNA is explained by a facilitated diffusion mechanism, in which DBPs adopt a weighted combination of three-dimensional diffusion and one-dimensional (1D) sliding and hopping modes of transportation, the role of cellular environment that contains many nonspecifically interacting proteins and other biomolecules is mostly overlooked. By performing large-scale computational simulations with an appropriately tuned model of protein and DNA in the presence of nonspecifically interacting bulk and DNA-bound crowders (genomic crowders), we demonstrate the structural basis of the enhanced facilitated diffusion of DBPs inside a crowded cellular milieu through, to our knowledge, novel 1D scanning mechanisms. In this one-dimensional scanning mode, the protein can float along the DNA under the influence of nonspecific interactions of bulk crowder molecules. The search mode is distinctly different compared to usual 1D sliding and hopping dynamics in which protein diffusion is regulated by the DNA electrostatics. In contrast, the presence of genomic crowders expedites the target search process by transporting the protein over DNA segments through the formation of a transient protein-crowder bridged complex. By analyzing the ruggedness of the associated potential energy landscape, we underpin the molecular origin of the kinetic advantages of these search modes and show that they successfully explain the experimentally observed acceleration of facilitated diffusion of DBPs by molecular crowding agents and crowder-concentration-dependent enzymatic activity of transcription factors. Our findings provide crucial insights into gene regulation kinetics inside the crowded cellular milieu.

Biologically motivated three-species exclusion model: Effects of leaky scanning and overlapping genes on initiation of protein synthesis

The totally asymmetric simple exclusion process was originally introduced as a model for the trafficlike collective movement of ribosomes on a messenger RNA (mRNA) that serves as the track for the motorlike forward stepping of individual ribosomes. In each step, a ribosome elongates a protein by a single unit using the track also as a template for protein synthesis. But, prefabricated functionally competent ribosomes are not available to begin synthesis of protein; a subunit directionally scans the mRNA in search of the predesignated site where it is supposed to bind with the other subunit and begin the synthesis of the corresponding protein. However, because of "leaky" scanning, a fraction of the scanning subunits miss the target site and continue their search beyond the first target. Sometimes such scanners successfully identify the site that marks the site for initiation of the synthesis of a different protein. In this paper, we develop an exclusion model with three interconvertible species of hard rods to capture some of the key features of these biological phenomena and study the effects of the interference of the flow of the different species of rods on the same lattice. More specifically, we identify the mean time for the initiation of protein synthesis as appropriate mean first-passage time that we calculate analytically using the formalism of backward master equations. Despite the approximations made, our analytical predictions are in reasonably good agreement with the numerical data that we obtain by performing Monte Carlo simulations.

Theory of Site-Specific DNA-Protein Interactions in the Presence of Nucleosome Roadblocks

We show that nucleosomes exert a maximal amount of hindrance to the one-dimensional diffusion of transcription factors (TFs) when they are present between TFs and their cognate sites on DNA. The effective one-dimensional diffusion coefficient of TFs (χ_TF) decreases with a rise in the free-energy barrier (μ_NU) of the sliding of nucleosomes as χ_TF∝exp(-μ_NU). The average time (η_L) required by TFs to slide over L sites on DNA increases with μ_NU as η_L∝exp(μ_NU). When TFs move close to nucleosomes, then they exhibit typical subdiffusion. Nucleosomes can enhance the search dynamics of TFs when TFs are present between nucleosomes and TF binding sites. These results suggest that nucleosome-depleted regions around the cognate sites of TFs are mandatory for efficient site-specific binding of TFs. Remarkably, the genome-wide in vivo positioning pattern of TFs shows a maximum at their specific binding sites where the occupancy of nucleosomes shows a minimum. This could be a consequence of an increasing level of breathing dynamics of nucleosome cores and decreasing levels of fluctuations in the DNA binding domains of TFs as they move across TF binding sites. The dynamics of TFs becomes slow as they approach their cognate sites so that TFs form a tight site-specific complex, whereas the dynamics of nucleosomes becomes rapid so that they quickly pass through the cognate sites of TFs. Several in vivo data sets on the genome-wide positioning pattern of nucleosomes and TFs agree well with our arguments. The retarding effects of nucleosomes can be minimized when the degree of condensation of DNA is such that it can permit a jump size associated with the dynamics of TFs beyond ∼160-180 bp.

Disparity in anomalous diffusion of proteins searching for their target DNA sites in a crowded medium is controlled by the size, shape and mobility of macromolecular crowders

Using extensive computer simulations, we analyzed the role of physical properties of molecular crowding agents such as size, shape and mobility in the target search dynamics of DNA binding proteins. Our main result is that the sub-diffusive dynamics of a protein inside a crowded medium strongly depends on the crowder properties and also on the protein's mode of diffusion. For instance, while scanning the DNA one-dimensionally, the protein dynamics does not vary with the change in crowder properties. Conversely, the diffusion exponent varies non-monotonically during 3D diffusion and is maximally affected when the crowders match the protein physically. The investigation shows that the effect stems from the ruggedness of the associated potential energy landscape, which is regulated by the protein-crowder and DNA-crowder interactions. Our findings have broad significance in understanding the target search dynamics of proteins on DNA in crowded cellular milieu and selecting appropriate crowding agents when designing in vitro experiments.

Mechanisms of Protein Search for Targets on DNA: Theoretical Insights

Protein-DNA interactions are critical for the successful functioning of all natural systems. The key role in these interactions is played by processes of protein search for specific sites on DNA. Although it has been studied for many years, only recently microscopic aspects of these processes became more clear. In this work, we present a review on current theoretical understanding of the molecular mechanisms of the protein target search. A comprehensive discrete-state stochastic method to explain the dynamics of the protein search phenomena is introduced and explained. Our theoretical approach utilizes a first-passage analysis and it takes into account the most relevant physical-chemical processes. It is able to describe many fascinating features of the protein search, including unusually high effective association rates, high selectivity and specificity, and the robustness in the presence of crowders and sequence heterogeneity.

Aptasensor designed via the stochastic tunneling-basin hopping method for biosensing of vascular endothelial growth factor

The Systematic Evolution Ligands by Exponential Enrichment (SELEX) is common used for selection of high affinity single-stranded DNA (ssDNA) aptamer with target protein. However, we do not know what the most stable configuration of the selected aptamer bound with target protein is. Therefore, a systematic search process using the stochastic tunneling-basin hopping (STUN-BH) method is proposed to find the most stable configuration of the ssDNA aptamer specific for vascular endothelial growth factor (VEGF) capture (Apt_VEGF; 5'-TGTGGGGGTGGACGGGCCGGGTAGA-3'). After the most stable configuration was obtained by the STUN-BH method, molecular dynamics (MD) simulation was carried out to investigate the thermal stability of Apt_VEGF/VEGF at 300 K in both vacuum and water. All molecular simulations were conducted with the large-scale atomic/molecular massively parallel simulator (LAMMPS), and the AMBER99SB force field was used to describe the atomic interactions for the current Apt_VEGF/VEGF system. The three most stable Apt_VEGF/VEGF configurations obtained by the STUN-BH method indicated that Apt_VEGF residues exhibit greater affinity for VEGF surface loop fragments as compared with surface alpha helix and beta sheet fragments. Results indicated that after the first Apt_VEGF (Apt_VEGF I) occupies most of the VEGF loop fragment, the second Apt_VEGF (Apt_VEGF II) is adsorbed by the rest of the VEGF loop fragment and the VEGF Chain B beta sheet fragment, resulting in a 24.8% reduction in binding strength as compared to that of Apt_VEGF I. Furthermore, when Apt_VEGF I and Apt_VEGF II chains were stably adsorbed by VEGF, the third Apt_VEGF (Apt_VEGF III) chain can only partially attach to VEGF, as confirmed by real Apt_VEGF-VEGF binding experiments. Lastly, we demonstrated that the aptasensor constructed according to MD simulation is highly sensitive for VEGF with a linear detection range of 10 pg/mL-10 ng/mL.

Transcription factor target site search and gene regulation in a background of unspecific binding sites

Response time and transcription level are vital parameters of gene regulation. They depend on how fast transcription factors (TFs) find and how efficient they occupy their specific target sites. It is well known that target site search is accelerated by TF binding to and sliding along unspecific DNA and that unspecific associations alter the occupation frequency of a gene. However, whether target site search time and occupation frequency can be optimized simultaneously is mostly unclear. We developed a transparent and intuitively accessible state-based formalism to calculate search times to target sites on and occupation frequencies of promoters of arbitrary state structure. Our formalism is based on dissociation rate constants experimentally accessible in live cell experiments. To demonstrate our approach, we consider promoters activated by a single TF, by two coactivators or in the presence of a competitive inhibitor. We find that target site search time and promoter occupancy differentially vary with the unspecific dissociation rate constant. Both parameters can be harmonized by adjusting the specific dissociation rate constant of the TF. However, while measured DNA residence times of various eukaryotic TFs correspond to a fast search time, the occupation frequencies of target sites are generally low. Cells might tolerate low target site occupancies as they enable timely gene regulation in response to a changing environment.

Single-Molecule Titration in a Protein Nanoreactor Reveals the Protonation/Deprotonation Mechanism of a C:C Mismatch in DNA

Measurement of single-molecule reactions can elucidate microscopic mechanisms that are often hidden from ensemble analysis. Herein, we report the acid-base titration of a single DNA duplex confined within the wild-type α-hemolysin (α-HL) nanopore for up to 3 h, while monitoring the ionic current through the nanopore. Modulation between two states in the current-time trace for duplexes containing the C:C mismatch in proximity to the latch constriction of α-HL is attributed to the base flipping of the C:C mismatch. As the pH is lowered, the rate for the C:C mismatch to flip from the intra-helical state to the extra-helical state ( k_intra-extra) decreases, while the rate for base flipping from the extra-helical state to the intra-helical state ( k_extra-intra) remains unchanged. Both k_intra-extra and k_extra-intra are on the order of 1 × 10^-2 s^-1 to 1 × 10^-1 s^-1 and remain stable over the time scale of the measurement (several hours). Analysis of the pH-dependent kinetics of base flipping using a hidden Markov kinetic model demonstrates that protonation/deprotonation occurs while the base pair is in the intra-helical state. We also demonstrate that the rate of protonation is limited by transport of H⁺ into the α-HL nanopore. Single-molecule kinetic isotope experiments exhibit a large kinetic isotope effect (KIE) for k_intra-extra ( k_H/ k_D ≈ 5) but a limited KIE for k_extra-intra ( k_H/ k_D ≈ 1.3), supporting our model. Our experiments correspond to the longest single-molecule measurements performed using a nanopore, and demonstrate its application in interrogating mechanisms of single-molecule reactions in confined geometries.

Intersegmental transfer of proteins between DNA regions in the presence of crowding

Intersegmental transfer that involves direct relocation of a DNA-binding protein from one nonspecific DNA site to another was previously shown to contribute to speeding up the identification of the DNA target site. This mechanism is promoted when the protein is composed of at least two domains that have different DNA binding affinities and thus show a degree of mobility. In this study, we investigate the effect of particle crowding on the ability of a multi-domain protein to perform intersegmental transfer. We show that although crowding conditions often favor 1D diffusion of proteins along DNA over 3D diffusion, relocation of one of the tethered domains to initiate intersegmental transfer is possible even under crowding conditions. The tendency to perform intersegmental transfer by a multi-domain protein under crowding conditions is much higher for larger crowding particles than smaller ones and can be even greater than under no-crowding conditions. We report that the asymmetry of the two domains is even magnified by the crowders. The observations that crowding supports intersegmental transfer serve as another example that in vivo complexity does not necessarily slow down DNA search kinetics by proteins.

Acceleration of bursty multiprotein target search kinetics on DNA by colocalisation

Proteins are capable of locating specific targets on DNA by employing a facilitated diffusion process with intermittent 1D and 3D search steps. We here uncover the implications of colocalisation of protein production and DNA binding sites via computer simulations.

Measurement of nanoscale DNA translocation by uracil DNA glycosylase in human cells

DNA ‘sliding’ by human repair enzymes is considered to be important for DNA damage detection. Here, we transfected uracil-containing DNA duplexes into human cells and measured the probability that nuclear human uracil DNA glycosylase (hUNG2) excised two uracil lesions spaced 10–80 bp apart in a single encounter without escaping the micro-volume containing the target sites. The two-site transfer probabilities were 100% and 54% at a 10 and 40 bp spacing, but dropped to only 10% at 80 bp. Enzyme trapping experiments suggested that site transfers over 40 bp followed a DNA ‘hopping’ pathway in human cells, indicating that authentic sliding does not occur even over this short distance. The transfer probabilities were much greater than observed in aqueous buffers, but similar to in vitro measurements in the presence of polymer crowding agents. The findings reveal a new role for the crowded nuclear environment in facilitating DNA damage detection.