51
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Kolomeisky AB, Veksler A. How to accelerate protein search on DNA: location and dissociation. J Chem Phys 2012; 136:125101. [PMID: 22462896 DOI: 10.1063/1.3697763] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
One of the most important features of biological systems that controls their functioning is the ability of protein molecules to find and recognize quickly specific target sites on DNA. Although these phenomena have been studied extensively, detailed mechanisms of protein-DNA interactions during the search are still not well understood. Experiments suggest that proteins typically find their targets fast by combining three-dimensional and one-dimensional motions, and most of the searching time proteins are non-specifically bound to DNA. However these observations are surprising since proteins diffuse very slowly on DNA, and it seems that the observed fast search cannot be achieved under these conditions for single proteins. Here we propose two simple mechanisms that might explain some of these controversial observations. Using first-passage time analysis, it is shown explicitly that the search can be accelerated by changing the location of the target and by effectively irreversible dissociations of proteins. Our theoretical predictions are supported by Monte Carlo computer simulations.
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52
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Meyer B, Bénichou O, Kafri Y, Voituriez R. Geometry-induced bursting dynamics in gene expression. Biophys J 2012; 102:2186-91. [PMID: 22824283 PMCID: PMC3341560 DOI: 10.1016/j.bpj.2012.03.060] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 03/21/2012] [Accepted: 03/26/2012] [Indexed: 11/17/2022] Open
Abstract
In prokaryotes and eukaryotes, genes are transcribed stochastically according to various temporal patterns that range from simple first-order kinetics to marked bursts, resulting in temporal and cell-to-cell variations of mRNA and protein levels. Here, we consider the effect of the transport of regulatory molecules on the noise in gene expression by taking into account explicitly the dynamics of a finite number of transcription factors confined in the cell. We calculate analytically time-dependent correlation functions of mRNA levels for a wide range of transport mechanisms and find that in the limit of small-transcription-factor copy number, the results differ significantly from standard approaches, which ignore confinement. It is shown how such dynamical quantities, which can now be obtained experimentally, can be used to identify the underlying mechanisms of transcription. Of particular importance, it is demonstrated that the geometry of transcription-factor trajectories in the cellular environment plays a key role in transcription kinetics, and can intrinsically generate the observed various transcription patterns ranging from simple first-order kinetics to bursts.
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Affiliation(s)
- B. Meyer
- UMR 7600, Université Pierre et Marie Curie/CNRS, Paris, France
| | - O. Bénichou
- UMR 7600, Université Pierre et Marie Curie/CNRS, Paris, France
| | - Y. Kafri
- Department of Physics, Technion, Haifa, Israel
| | - R. Voituriez
- UMR 7600, Université Pierre et Marie Curie/CNRS, Paris, France
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53
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Normanno D, Dahan M, Darzacq X. Intra-nuclear mobility and target search mechanisms of transcription factors: a single-molecule perspective on gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:482-93. [PMID: 22342464 DOI: 10.1016/j.bbagrm.2012.02.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 01/26/2012] [Accepted: 02/03/2012] [Indexed: 12/26/2022]
Abstract
Precise expression of specific genes in time and space is at the basis of cellular viability as well as correct development of organisms. Understanding the mechanisms of gene regulation is fundamental and still one of the great challenges for biology. Gene expression is regulated also by specific transcription factors that recognize and bind to specific DNA sequences. Transcription factors dynamics, and especially the way they sample the nucleoplasmic space during the search for their specific target in the genome, are a key aspect for regulation and it has been puzzling researchers for forty years. The scope of this review is to give a state-of-the-art perspective over the intra-nuclear mobility and the target search mechanisms of specific transcription factors at the molecular level. Going through the seminal biochemical experiments that have raised the first questions about target localization and the theoretical grounds concerning target search processes, we describe the most recent experimental achievements and current challenges in understanding transcription factors dynamics and interactions with DNA using in vitro assays as well as in live prokaryotic and eukaryotic cells. This article is part of a Special Issue entitled: Nuclear Transport and RNA Processing.
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Affiliation(s)
- Davide Normanno
- Institut de Biologie de l'Ecole normale supérieure (IBENS), CNRS UMR 8197, Ecole normale supérieure, 46, Rue d'Ulm, 75005 Paris, France.
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54
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Haeusler AR, Goodson KA, Lillian TD, Wang X, Goyal S, Perkins NC, Kahn JD. FRET studies of a landscape of Lac repressor-mediated DNA loops. Nucleic Acids Res 2012; 40:4432-45. [PMID: 22307389 PMCID: PMC3378866 DOI: 10.1093/nar/gks019] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
DNA looping mediated by the Lac repressor is an archetypal test case for modeling protein and DNA flexibility. Understanding looping is fundamental to quantitative descriptions of gene expression. Systematic analysis of LacI•DNA looping was carried out using a landscape of DNA constructs with lac operators bracketing an A-tract bend, produced by varying helical phasings between operators and the bend. Fluorophores positioned on either side of both operators allowed direct Förster resonance energy transfer (FRET) detection of parallel (P1) and antiparallel (A1, A2) DNA looping topologies anchored by V-shaped LacI. Combining fluorophore position variant landscapes allows calculation of the P1, A1 and A2 populations from FRET efficiencies and also reveals extended low-FRET loops proposed to form via LacI opening. The addition of isopropyl-β-d-thio-galactoside (IPTG) destabilizes but does not eliminate the loops, and IPTG does not redistribute loops among high-FRET topologies. In some cases, subsequent addition of excess LacI does not reduce FRET further, suggesting that IPTG stabilizes extended or other low-FRET loops. The data align well with rod mechanics models for the energetics of DNA looping topologies. At the peaks of the predicted energy landscape for V-shaped loops, the proposed extended loops are more stable and are observed instead, showing that future models must consider protein flexibility.
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Affiliation(s)
- Aaron R Haeusler
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742-2021, USA
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55
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Sheinman M, Bénichou O, Kafri Y, Voituriez R. Classes of fast and specific search mechanisms for proteins on DNA. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2012; 75:026601. [PMID: 22790348 DOI: 10.1088/0034-4885/75/2/026601] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Problems of search and recognition appear over different scales in biological systems. In this review we focus on the challenges posed by interactions between proteins, in particular transcription factors, and DNA and possible mechanisms which allow for fast and selective target location. Initially we argue that DNA-binding proteins can be classified, broadly, into three distinct classes which we illustrate using experimental data. Each class calls for a different search process and we discuss the possible application of different search mechanisms proposed over the years to each class. The main thrust of this review is a new mechanism which is based on barrier discrimination. We introduce the model and analyze in detail its consequences. It is shown that this mechanism applies to all classes of transcription factors and can lead to a fast and specific search. Moreover, it is shown that the mechanism has interesting transient features which allow for stability at the target despite rapid binding and unbinding of the transcription factor from the target.
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Affiliation(s)
- M Sheinman
- Department of Physics and Astronomy, Vrije Universiteit, Amsterdam, The Netherlands
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56
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Towards a molecular view of transcriptional control. Curr Opin Struct Biol 2012; 22:160-7. [PMID: 22296921 DOI: 10.1016/j.sbi.2012.01.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Revised: 01/06/2012] [Accepted: 01/09/2012] [Indexed: 11/21/2022]
Abstract
The accumulation of experimental data over recent years has fueled theoretical work on how transcription factors (TFs) search for and recognise their DNA target sites, how they interact with one another, or with other DNA-binding proteins, and how they cope with the compaction of DNA within bacterial nucleoids or within eukaryotic chromatin. Many models have been built to study the kinetic, thermodynamic and mechanistic aspects of these questions. In some cases they have resulted in a relatively clear consensus view, but a number of questions remain controversial. We present an overview of recent work, with an emphasis on models that provide, or can inspire, a better understanding of transcriptional control at a detailed molecular level.
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57
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Vuzman D, Levy Y. Intrinsically disordered regions as affinity tuners in protein–DNA interactions. ACTA ACUST UNITED AC 2012; 8:47-57. [DOI: 10.1039/c1mb05273j] [Citation(s) in RCA: 154] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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58
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Eliazar I. Langevin dynamics, entropic crowding, and stochastic cloaking. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 84:061132. [PMID: 22304065 DOI: 10.1103/physreve.84.061132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2011] [Indexed: 05/31/2023]
Abstract
We consider a pack of independent probes--within a spatially inhomogeneous thermal bath consisting of a vast number of randomly moving particles--which are subjected to an external force. The stochastic dynamics of the probes are governed by Langevin's equation. The probes attain a steady state distribution which, in general, is different than the concentration of the particles in the spatially inhomogeneous thermal bath. In this paper we explore the state of "entropic crowding" in which the probes' distribution and the particles' concentration coincide--thus yielding maximal relative entropies of one with respect to the other. Entropic crowding can be attained by two scenarios which are analyzed in detail: (i) "entropically crowding thermal baths"--in which the particles crowd uniformly around the probes; (ii) "entropically crowding Langevin forces"--in which the probes crowd uniformly amongst the particles. Entropic crowding is equivalent to the optimal stochastic cloaking of the probes within the spatially inhomogeneous thermal bath.
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Affiliation(s)
- Iddo Eliazar
- Department of Technology Management, Holon Institute of Technology, PO Box 305, Holon 58102, Israel.
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59
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Mayo ML, Perkins EJ, Ghosh P. First-passage time analysis of a one-dimensional diffusion-reaction model: application to protein transport along DNA. BMC Bioinformatics 2011; 12 Suppl 10:S18. [PMID: 22165905 PMCID: PMC3236840 DOI: 10.1186/1471-2105-12-s10-s18] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Proteins search along the DNA for targets, such as transcription initiation sequences, according to one-dimensional diffusion, which is interrupted by micro- and macro-hopping events and intersegmental transfers that occur under close packing conditions. RESULTS A one-dimensional diffusion-reaction model in the form of difference-differential equations is proposed to analyze the nonequilibrium protein sliding kinetics along a segment of bacterial DNA. A renormalization approach is used to derive an expression for the mean first-passage time to arrive at sites downstream of the origin from the occupation probabilities given by the individual transport equations. Monte Carlo simulations are employed to assess the validity of the proposed approach, and all results are interpreted within the context of bacterial transcription. CONCLUSIONS Mean first-passage times decrease with increasing reaction rates, indicating that, on average, surviving proteins more rapidly locate downstream targets than their reaction-free counterparts, but at the price of increasing rarity. Two qualitatively different screening regimes are identified according to whether the search process operates under "small" or "large" values for the dissociation rate of the protein-DNA complex. Lower bounds are placed on the overall search time for varying reactive conditions. Good agreement with experimental estimates requires the reaction rate reside near the transition between both screening regimes, suggesting that biology balances a need for rapid searches against maximum exploration during each round of the sliding phase.
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Affiliation(s)
- Michael L Mayo
- Environemental Laboratory, US Army Engineer Research and Development Center, Vicksburg, MS 39180, USA.
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60
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Sanchez H, Suzuki Y, Yokokawa M, Takeyasu K, Wyman C. Protein-DNA interactions in high speed AFM: single molecule diffusion analysis of human RAD54. Integr Biol (Camb) 2011; 3:1127-34. [PMID: 21986699 DOI: 10.1039/c1ib00039j] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
High-speed AFM (atomic force microscopy also called scanning force microscopy) provides nanometre spatial resolution and sub-second temporal resolution images of individual molecules. We exploit these features to study diffusion and motor activity of the RAD54 DNA repair factor. Human RAD54 functions at critical steps in recombinational-DNA repair. It is a member of the Swi2/Snf2 family of chromatin remodelers that translocate on DNA using ATP hydrolysis. A detailed single molecular description of DNA-protein interactions shows intermediate states and distribution of variable states, usually hidden by ensemble averaging. We measured the motion of individual proteins using single-particle tracking and observed that random walks were affected by imaging-buffer composition. Non-Brownian diffusion events were characterized in the presence and in the absence of nucleotide cofactors. Double-stranded DNA immobilized on the surface functioned as a trap reducing Brownian motion. Distinct short range slides and hops on DNA were visualized by high-speed AFM. These short-range interactions were usually inaccessible by other methods based on optical resolution. RAD54 monomers displayed a diffusive behavior unrelated to the motor activity.
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Affiliation(s)
- Humberto Sanchez
- Department of Cell Biology and Genetics, Cancer Genomics Center, Erasmus MC, PO Box 2040, 3000 CA Rotterdam, The Netherlands.
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61
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Chechkin AV, Zaid IM, Lomholt MA, Sokolov IM, Metzler R. Effective surface motion on a reactive cylinder of particles that perform intermittent bulk diffusion. J Chem Phys 2011; 134:204116. [PMID: 21639433 DOI: 10.1063/1.3593198] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In many biological and small scale technological applications particles may transiently bind to a cylindrical surface. In between two binding events the particles diffuse in the bulk, thus producing an effective translation on the cylindrical surface. We here derive the effective motion on the surface allowing for additional diffusion on the cylindrical surface itself. We find explicit solutions for the number of adsorbed particles at one given instant, the effective surface displacement, as well as the surface propagator. In particular sub- and superdiffusive regimes are found, as well as an effective stalling of diffusion visible as a plateau in the mean squared displacement. We also investigate the corresponding first passage problem.
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Affiliation(s)
- Aleksei V Chechkin
- Institute for Theoretical Physics NSC KIPT, Akademicheskaya St.1, 61108 Kharkov, Ukraine
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62
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Tafvizi A, Mirny LA, van Oijen AM. Dancing on DNA: kinetic aspects of search processes on DNA. Chemphyschem 2011; 12:1481-9. [PMID: 21560221 DOI: 10.1002/cphc.201100112] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2011] [Indexed: 11/12/2022]
Abstract
Recognition and binding of specific sites on DNA by proteins is central for many cellular functions such as transcription, replication, and recombination. In the search for its target site, the DNA-associated protein is facing both thermodynamic and kinetic difficulties. The thermodynamic challenge lies in recognizing and tightly binding a cognate (specific) site among the billions of other (non-specific) sequences on the DNA. The kinetic difficulty lies in finding a cognate site in mere seconds amidst the crowded cellular environment that is filled with other DNA sequences and proteins. Herein, we discuss the history of the DNA search problem, the theoretical background and the various experimental methods used to study the kinetics of proteins searching for target sites on DNA.
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Affiliation(s)
- Anahita Tafvizi
- Dept. of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
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63
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Meyer B, Chevalier C, Voituriez R, Bénichou O. Universality classes of first-passage-time distribution in confined media. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 83:051116. [PMID: 21728499 DOI: 10.1103/physreve.83.051116] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Indexed: 05/31/2023]
Abstract
We study the first-passage time (FPT) distribution to a target site for a random walker evolving in a bounded domain. We show that in the limit of large volume of the confining domain, this distribution falls into universality classes indexed by the walk dimension d(w) and the fractal dimension d(f) of the medium, which have been recently identified previously [Bénichou et al., Nat. Chem. 2, 472 (2010)]. We present in this paper a complete derivation of these universal distributions, discuss extensively the range of applicability of the results, and extend the method to continuous-time random walks. This analysis puts forward the importance of the geometry, and in particular the position of the starting point, in first-passage statistics. Analytical results are validated by numerical simulations, applied to various models of transport in disordered media, which illustrate the universality classes of the FPT distribution.
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Affiliation(s)
- B Meyer
- Laboratoire de Physique Théorique de la matière Condensée (UMR 7600), Université Paris 6, Paris, France
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64
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Bonnet I, Desbiolles P. The diffusion constant of a labeled protein sliding along DNA. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2011; 34:25. [PMID: 21400049 DOI: 10.1140/epje/i2011-11025-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Accepted: 02/11/2011] [Indexed: 05/30/2023]
Abstract
Long ago inferred by biochemists, the linear diffusion of proteins along DNA has recently been observed at a single-molecule level using fluorescence microscopy. This imaging technique requires labeling the protein of interest with a fluorophore, usually an organic nanosized dye that is not supposed to impact the dynamics of the protein. Yet individual proteins can also be tracked using much larger labels, like quantum dots or beads. We investigate here the impact of such a large label on the protein diffusion along DNA. Solving a Fokker-Planck equation, we estimate the diffusion constant of a protein-label complex diffusing in a periodic potential that mimics the DNA-protein interaction, the link between the protein and the label being modeled as a Hookean spring. Our results indicate that the diffusion constant can generally be calculated by considering that the motion of the protein in the DNA potential is decoupled from the Brownian motion of the label. Our conclusions are in good agreement with the experimental results we obtained with the restriction enzyme EcoRV, assuming a rotation-coupled diffusion of the enzyme along DNA.
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Affiliation(s)
- I Bonnet
- Laboratoire Kastler Brossel, ENS, UPMC-Paris, CNRS UMR, France
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65
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DeSantis MC, Li JL, Wang YM. Protein sliding and hopping kinetics on DNA. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 83:021907. [PMID: 21405863 PMCID: PMC3683889 DOI: 10.1103/physreve.83.021907] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Indexed: 05/16/2023]
Abstract
Using Monte Carlo simulations, we deconvolved the sliding and hopping kinetics of GFP-LacI proteins on elongated DNA from their experimentally observed seconds-long diffusion trajectories. Our simulations suggest the following results: (i) in each diffusion trajectory, a protein makes on average hundreds of alternating slides and hops with a mean sliding time of several tens of milliseconds; (ii) sliding dominates the root-mean-square displacement of fast diffusion trajectories, whereas hopping dominates slow ones; (iii) flow and variations in salt concentration have limited effects on hopping kinetics, while in vivo DNA configuration is not expected to influence sliding kinetics; and (iv) the rate of occurrence for hops longer than 200 nm agrees with experimental data for EcoRV proteins.
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Affiliation(s)
- Michael C DeSantis
- Department of Physics, Washington University in St. Louis, St. Louis, Missouri 63130, USA
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66
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Bénichou O, Chevalier C, Meyer B, Voituriez R. Facilitated diffusion of proteins on chromatin. PHYSICAL REVIEW LETTERS 2011; 106:038102. [PMID: 21405302 DOI: 10.1103/physrevlett.106.038102] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2010] [Indexed: 05/30/2023]
Abstract
We present a theoretical model of facilitated diffusion of proteins in the cell nucleus. This model, which takes into account the successive binding and unbinding events of proteins to DNA, relies on a fractal description of the chromatin which has been recently evidenced experimentally. Facilitated diffusion is shown quantitatively to be favorable for a fast localization of a target locus by a transcription factor and even to enable the minimization of the search time by tuning the affinity of the transcription factor with DNA. This study shows the robustness of the facilitated diffusion mechanism, invoked so far only for linear conformations of DNA.
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Affiliation(s)
- O Bénichou
- Laboratoire de Physique Théorique de la Matière Condensée CNRS-UPMC, 4 Place Jussieu, 75255 Paris Cedex, France
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67
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Paillusson F, Dahirel V, Jardat M, Victor JM, Barbi M. Effective interaction between charged nanoparticles and DNA. Phys Chem Chem Phys 2011; 13:12603-13. [DOI: 10.1039/c1cp20324j] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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68
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Vuzman D, Polonsky M, Levy Y. Facilitated DNA search by multidomain transcription factors: cross talk via a flexible linker. Biophys J 2010; 99:1202-11. [PMID: 20713004 DOI: 10.1016/j.bpj.2010.06.007] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Revised: 05/30/2010] [Accepted: 06/02/2010] [Indexed: 10/19/2022] Open
Abstract
More than 70% of eukaryotic proteins are composed of multiple domains. However, most studies of the search for DNA focus on individual protein domains and do not consider potential cross talk within a multidomain transcription factor. In this study, the molecular features of the DNA search mechanism were explored for two multidomain transcription factors: human Pax6 and Oct-1. Using a simple computational model, we compared a DNA search of multidomain proteins with a search of isolated domains. Furthermore, we studied how manipulating the binding affinity of a single domain to DNA can affect the overall DNA search of the multidomain protein. Tethering the two domains via a flexible linker increases their affinity to the DNA, resulting in a higher propensity for sliding along the DNA, which is more significant for the domain with the weaker DNA-binding affinity. In this case, the domain that binds DNA more tightly anchors the multidomain protein to the DNA and, via the linker, increases the local concentration of the weak DNA-binding domain (DBD). The tethered domains directly exchange between two parallel DNA molecules via a bridged intermediate, where intersegmental transfer is promoted by the weaker DBD. We found that, in general, the relative affinity of the two domains can significantly affect the cross talk between them and thus their overall capability to search DNA efficiently. The results we obtained by examining various multidomain DNA-binding proteins support the necessity of discrepancies between the DNA-binding affinities of the constituent domains.
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Affiliation(s)
- Dana Vuzman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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69
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Kolomeisky AB. Physics of protein-DNA interactions: mechanisms of facilitated target search. Phys Chem Chem Phys 2010; 13:2088-95. [PMID: 21113556 DOI: 10.1039/c0cp01966f] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
One of the most critical aspects of protein-DNA interactions is the ability of protein molecules to quickly find and recognize specific target sequences on DNA. Experimental measurements indicate that the corresponding association rates to few specific sites among large number of non-specific sites are typically large. For some proteins they might be even larger than maximal allowed three-dimensional diffusion rates. Although significant progress in understanding protein search and recognition of targets on DNA has been achieved, detailed mechanisms of these processes are still strongly debated. Here we present a critical review of current theoretical approaches and some experimental observations in this area. Specifically, the role of lowering dimensionality, non-specific interactions, diffusion along the DNA molecules, protein and target sites concentrations, and electrostatic effects are critically analyzed. Possible future directions and outstanding problems are also presented and discussed.
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70
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DNA search efficiency is modulated by charge composition and distribution in the intrinsically disordered tail. Proc Natl Acad Sci U S A 2010; 107:21004-9. [PMID: 21078959 DOI: 10.1073/pnas.1011775107] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Intrinsically disordered tails are common in DNA-binding proteins and can affect their search efficiency on nonspecific DNA by promoting the brachiation dynamics of intersegment transfer. During brachiation, the protein jumps between distant DNA regions via an intermediate state in which the tail and globular moieties are bound to different DNA segments. While the disordered tail must be long and positively charged to facilitate DNA search, the effect of its residue sequence on brachiation is unknown. We explored this issue using the NK-2 and Antp homeodomain transcription factors. We designed 566 NK-2 tail-variants and 55 Antp tail-variants having different net charges and positive charge distributions and studied their dynamics and DNA search efficiencies using coarse-grained molecular dynamics simulations. More intersegment transfers occur when the tail is moderately positively charged and the positive charges are clustered together in the middle of the tail or towards its N terminus. The presence of a negatively charged residue does not significantly affect protein brachiation, although it is likely that the presence of many negatively charged residues will complicate the DNA search mechanism. A bioinformatic analysis of 1,384 wild-type homeodomains illustrates that the charge composition and distribution in their N-tail sequences are consistent with an optimal charge pattern to promote intersegment transfer. Our study thus indicates that the residue sequence of the disordered tails of DNA-binding proteins has unique characteristics that were evolutionarily selected to achieve optimized function and suggests that the sequence-structure-function paradigm known for structured proteins is valid for intrinsically disordered proteins as well.
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71
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Tejedor V, Bénichou O, Voituriez R, Jungmann R, Simmel F, Selhuber-Unkel C, Oddershede LB, Metzler R. Quantitative analysis of single particle trajectories: mean maximal excursion method. Biophys J 2010; 98:1364-72. [PMID: 20371337 DOI: 10.1016/j.bpj.2009.12.4282] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Revised: 11/19/2009] [Accepted: 12/02/2009] [Indexed: 11/26/2022] Open
Abstract
An increasing number of experimental studies employ single particle tracking to probe the physical environment in complex systems. We here propose and discuss what we believe are new methods to analyze the time series of the particle traces, in particular, for subdiffusion phenomena. We discuss the statistical properties of mean maximal excursions (MMEs), i.e., the maximal distance covered by a test particle up to time t. Compared to traditional methods focusing on the mean-squared displacement we show that the MME analysis performs better in the determination of the anomalous diffusion exponent. We also demonstrate that combination of regular moments with moments of the MME method provides additional criteria to determine the exact physical nature of the underlying stochastic subdiffusion processes. We put the methods to test using experimental data as well as simulated time series from different models for normal and anomalous dynamics such as diffusion on fractals, continuous time random walks, and fractional Brownian motion.
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Affiliation(s)
- Vincent Tejedor
- Physics Department, Technical University of Munich, Garching, Germany
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de la Rosa MAD, Koslover EF, Mulligan PJ, Spakowitz AJ. Dynamic strategies for target-site search by DNA-binding proteins. Biophys J 2010; 98:2943-53. [PMID: 20550907 DOI: 10.1016/j.bpj.2010.02.055] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Revised: 02/01/2010] [Accepted: 02/12/2010] [Indexed: 10/19/2022] Open
Abstract
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.
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73
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Searching DNA via a "Monkey Bar" mechanism: the significance of disordered tails. J Mol Biol 2009; 396:674-84. [PMID: 19958775 DOI: 10.1016/j.jmb.2009.11.056] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Revised: 11/23/2009] [Accepted: 11/24/2009] [Indexed: 11/22/2022]
Abstract
The search through nonspecific DNA for a specific site by proteins is known to be facilitated by sliding, hopping, and intersegment transfer between separate DNA strands, yet the driving forces of these protein dynamics from the molecular perspective are unclear. In this study, molecular features of the DNA search mechanism were explored for three homologous proteins (the HoxD9, Antp, and NK-2 homeodomains) using a simple computational model in which protein-DNA interactions are represented solely by electrostatic forces. In particular, we studied the impact that disordered N-terminal tails (N-tails), which are more common in DNA-binding proteins than in other proteins, have on the efficiency of DNA search. While the three homeodomain proteins were found to use similar binding interfaces in specific and nonspecific interactions with DNAs, their different electrostatic potentials affect the nature of their sliding dynamics. The different lengths and net charges of the N-tails of the homeodomains affect their motion along the DNA. The presence of an N-tail increases sliding propensity but slows linear diffusion along the DNA. When the search is performed in the presence of two parallel DNA molecules, a direct transfer, which is facilitated by the protein tail, from one nonspecific DNA to another occurs. The tailed proteins jump between two DNA molecules through an intermediate in which the recognition helix of the protein is adsorbed to one DNA fragment and the N-tail is adsorbed to the second, suggesting a "monkey bar" mechanism. Our study illustrates how the molecular architecture of proteins controls the efficiency of DNA scanning.
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74
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Bénichou O, Kafri Y, Sheinman M, Voituriez R. Searching fast for a target on DNA without falling to traps. PHYSICAL REVIEW LETTERS 2009; 103:138102. [PMID: 19905543 DOI: 10.1103/physrevlett.103.138102] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2009] [Indexed: 05/28/2023]
Abstract
Genomic expression depends critically on both the ability of regulatory proteins to locate specific target sites on DNA within seconds and on the formation of long-lived (many minutes) complexes between these proteins and the DNA. Equilibrium experiments show that indeed regulatory proteins bind tightly to their target site. However, they also find strong binding to other nonspecific sites which act as traps that can dramatically increase the time needed to locate the target. This gives rise to a conflict between the speed and stability requirements. Here we suggest a simple mechanism which can resolve this long-standing paradox.
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Affiliation(s)
- O Bénichou
- UMR 7600, Université Pierre et Marie Curie/CNRS, 75255 Paris Cedex 05, France
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Loverdo C, Bénichou O, Moreau M, Voituriez R. Robustness of optimal intermittent search strategies in one, two, and three dimensions. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009; 80:031146. [PMID: 19905101 DOI: 10.1103/physreve.80.031146] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Indexed: 05/28/2023]
Abstract
Search problems at various scales involve a searcher, be it a molecule before reaction or a foraging animal, which performs an intermittent motion. Here we analyze a generic model based on such type of intermittent motion, in which the searcher alternates phases of slow motion allowing detection and phases of fast motion without detection. We present full and systematic results for different modeling hypotheses of the detection mechanism in space in one, two, and three dimensions. Our study completes and extends the results of our recent letter [Loverdo, Nat. Phys. 4, 134 (2008)] and gives the necessary calculation details. In addition, another modeling of the detection case is presented. We show that the mean target detection time can be minimized as a function of the mean duration of each phase in one, two, and three dimensions. Importantly, this optimal strategy does not depend on the details of the modeling of the slow detection phase, which shows the robustness of our results. We believe that this systematic analysis can be used as a basis to study quantitatively various real search problems involving intermittent behaviors.
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Affiliation(s)
- C Loverdo
- Laboratoire de Physique Théorique de la Matière Condensée, UMR CNRS 7600, Université Pierre et Marie Curie, 4 Place Jussieu, 75252 Paris, France
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