1
|
Lüking M, van der Spoel D, Elf J, Tribello GA. Can molecular dynamics be used to simulate biomolecular recognition? J Chem Phys 2023; 158:2889489. [PMID: 37158325 DOI: 10.1063/5.0146899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/19/2023] [Indexed: 05/10/2023] Open
Abstract
There are many problems in biochemistry that are difficult to study experimentally. Simulation methods are appealing due to direct availability of atomic coordinates as a function of time. However, direct molecular simulations are challenged by the size of systems and the time scales needed to describe relevant motions. In theory, enhanced sampling algorithms can help to overcome some of the limitations of molecular simulations. Here, we discuss a problem in biochemistry that offers a significant challenge for enhanced sampling methods and that could, therefore, serve as a benchmark for comparing approaches that use machine learning to find suitable collective variables. In particular, we study the transitions LacI undergoes upon moving between being non-specifically and specifically bound to DNA. Many degrees of freedom change during this transition and that the transition does not occur reversibly in simulations if only a subset of these degrees of freedom are biased. We also explain why this problem is so important to biologists and the transformative impact that a simulation of it would have on the understanding of DNA regulation.
Collapse
Affiliation(s)
- Malin Lüking
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, SE-75124 Uppsala, Sweden
| | - David van der Spoel
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, SE-75124 Uppsala, Sweden
| | - Johan Elf
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, SE-75124 Uppsala, Sweden
| | - Gareth A Tribello
- Centre for Quantum Materials and Technologies, School of Mathematics and Physics, Queen's University Belfast, Belfast BT7 1NN, United Kingdom
| |
Collapse
|
2
|
Li J, Pertsinidis A. Nanoscale nuclear environments, fine-scale 3D genome organization and transcription regulation. CURRENT OPINION IN SYSTEMS BIOLOGY 2022; 31:100436. [PMID: 37091742 PMCID: PMC10118054 DOI: 10.1016/j.coisb.2022.100436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Decades of in vitro biochemical reconstitution, genetics and structural biology studies have established a vast knowledge base on the molecular mechanisms of chromatin regulation and transcription. A remaining challenge is to understand how these intricate biochemical systems operate in the context of the 3D genome organization and in the crowded and compartmentalized nuclear milieu. Here we review recent progress in this area based on high-resolution imaging approaches.
Collapse
Affiliation(s)
- Jieru Li
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, NY 10065, USA
| | | |
Collapse
|
3
|
Misiura MM, Berezhkovskii AM, Bezrukov SM, Kolomeisky AB. Surface-facilitated trapping by active sites: From catalysts to viruses. J Chem Phys 2021; 155:184106. [PMID: 34773956 PMCID: PMC8730370 DOI: 10.1063/5.0069917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 10/20/2021] [Indexed: 11/14/2022] Open
Abstract
Trapping by active sites on surfaces plays important roles in various chemical and biological processes, including catalysis, enzymatic reactions, and viral entry into host cells. However, the mechanisms of these processes remain not well understood, mostly because the existing theoretical descriptions are not fully accounting for the role of the surfaces. Here, we present a theoretical investigation on the dynamics of surface-assisted trapping by specific active sites. In our model, a diffusing particle can occasionally reversibly bind to the surface and diffuse on it before reaching the final target site. An approximate theoretical framework is developed, and its predictions are tested by Brownian dynamics computer simulations. It is found that the surface diffusion can be crucial in mediating trapping by active sites. Our theoretical predictions work reasonably well as long as the area of the active site is much smaller than the overall surface area. Potential applications of our approach are discussed.
Collapse
Affiliation(s)
- Mikita M. Misiura
- Department of Chemistry and Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
| | - Alexander M. Berezhkovskii
- Mathematical and Statistical Computing Laboratory, Office of Intramural Research, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Sergey M. Bezrukov
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | | |
Collapse
|
4
|
Belotserkovskii BP. Effects of isolated nonspecific binders upon the search for specific targets: Absolute rates versus competition between the targets. Phys Rev E 2021; 103:022413. [PMID: 33735998 DOI: 10.1103/physreve.103.022413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 02/03/2021] [Indexed: 11/07/2022]
Abstract
Many biological processes involve macromolecules searching for their specific targets that are surrounded by other objects, and binding to these objects affects the target search. Acceleration of the target search by nonspecific binders was observed experimentally and analyzed theoretically, for example, for DNA-binding proteins. According to existing theories this acceleration requires continuous transfer between the nonspecific binders and the specific target. In contrast, our analysis predicts that (i) nonspecific binders could accelerate the search without continuous transfer to the specific target provided that the searching particle is capable of sliding along the binder; (ii) in some cases such binders could decelerate the target search, but provide an advantage in competition with the "binder-free" target; (iii) nonbinding objects decelerate the target search. We also show that although the target search in the presence of binders could be considered as diffusion in inhomogeneous media, in the general case it cannot be described by the effective diffusion coefficient.
Collapse
|
5
|
Xu X, Kim WK, Dzubiella J. Facilitating target search in polymer networks: Effects of target size and mixed one-dimensional and three-dimensional diffusion. Phys Rev E 2021; 103:032502. [PMID: 33862684 DOI: 10.1103/physreve.103.032502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 02/13/2021] [Indexed: 11/07/2022]
Abstract
We theoretically investigate the problem of diffusive target search and mean first passage times (MFPTs) of a tracer in a three-dimensional (3D) polymer network with a particular focus on the effects of combined one-dimensional (1D) diffusion along the polymer chains and 3D diffusion within the network. For this, we employ computer simulations as well as limiting theories of a single diffusive tracer searching for a spherical target fixed at a cross-link of a homogeneous 3D cubic lattice network. The free parameters are the target size, the ratio of the 1D and 3D friction constants, and the transition probabilities between bound and unbound states. For a very strongly bound tracer on the chains, the expected predominant set of 1D lattice diffusion (LD) is found. The MFPT in the LD process significantly depends on the target size, yielding two distinct scaling behaviors for target sizes smaller and larger than the network mesh size, respectively. In the limit of a pointlike target, the LD search becomes a random walk process on the lattice, which recovers the analytical solution for the MFPT previously reported by S. Condamin, O. Bénichou, and M. Moreau [Phys. Rev. Lett. 95, 260601 (2005)PRLTAO0031-900710.1103/PhysRevLett.95.260601]. For the very weakly bound tracer, the expected 3D free diffusion (FD) dominates, extrapolating to the well-known Smoluchowski limit. A critical target size is found above which the MFPT in the FD process is faster than in the LD process. For intermediate binding, i.e., a combination of LD and FD processes, the target search time can be minimized for an optimal range of target sizes and partitions between FD and LD, for which the MFPTs are substantially faster when compared to the limiting FD or LD processes. Our study may provide a theoretical basis to better understand and predict search and reaction processes in complex structured materials, thereby contributing to practical applications such as designing nanoreactors where catalytic targets are immobilized in polymer networks.
Collapse
Affiliation(s)
- Xiao Xu
- School of Chemical Engineering, Nanjing University of Science and Technology, 200 Xiao Ling Wei, Nanjing 210094, People's Republic of China
| | - Won Kyu Kim
- Korea Institute for Advanced Study, 85 Hoegiro, Seoul 02455, Republic of Korea
| | - Joachim Dzubiella
- Research Group for Simulations of Energy Materials, Helmholtz-Zentrum Berlin für Materialien und Energie, Hahn-Meitner-Platz 1, D-14109 Berlin, Germany.,Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder Strasse 3, D-79104 Freiburg, Germany
| |
Collapse
|
6
|
Felipe C, Shin J, Kolomeisky AB. DNA Looping and DNA Conformational Fluctuations Can Accelerate Protein Target Search. J Phys Chem B 2021; 125:1727-1734. [PMID: 33570939 DOI: 10.1021/acs.jpcb.0c09599] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Protein searching and binding to specific sites on DNA is a fundamentally important process that marks the beginning of all major cellular transformations. While the dynamics of protein-DNA interactions in in vitro settings is well investigated, the situation is much more complex for in vivo conditions because the DNA molecules in live cells are packed into chromosomal structures where they are undergoing strong dynamic and conformational fluctuations. In this work, we present a theoretical investigation on the role of DNA looping and DNA conformational fluctuations in the protein target search. It is based on a discrete-state stochastic analysis that allows for explicit calculations of dynamic properties, which is also supplemented by Monte Carlo computer simulations. It is found that for stronger nonspecific interactions between DNA and proteins the search occurs faster on the DNA looped conformation in comparison with the unlooped conformation, and the fastest search is observed when the loop is formed near the target site. It is also shown that DNA fluctuations between the looped and unlooped conformations influence the search dynamics, and this depends on the magnitude of conformational transition rates and on which conformation is more energetically stable. Physical-chemical arguments explaining these observations are presented. Our theoretical study suggests that the geometry and conformational changes in DNA are additional factors that might efficiently control the gene regulation processes.
Collapse
Affiliation(s)
- Cayke Felipe
- Department of Physics and Astronomy, Rice University, Houston, Texas 77005, United States.,Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Jaeoh Shin
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States.,Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Anatoly B Kolomeisky
- Department of Physics and Astronomy, Rice University, Houston, Texas 77005, United States.,Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States.,Department of Chemistry, Rice University, Houston, Texas 77005, United States.,Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
| |
Collapse
|
7
|
Martini L, Brameyer S, Hoyer E, Jung K, Gerland U. Dynamics of chromosomal target search by a membrane-integrated one-component receptor. PLoS Comput Biol 2021; 17:e1008680. [PMID: 33539417 PMCID: PMC7888679 DOI: 10.1371/journal.pcbi.1008680] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 02/17/2021] [Accepted: 01/07/2021] [Indexed: 12/03/2022] Open
Abstract
Membrane proteins account for about one third of the cellular proteome, but it is still unclear how dynamic they are and how they establish functional contacts with cytoplasmic interaction partners. Here, we consider a membrane-integrated one-component receptor that also acts as a transcriptional activator, and analyze how it kinetically locates its specific binding site on the genome. We focus on the case of CadC, the pH receptor of the acid stress response Cad system in E. coli. CadC is a prime example of a one-component signaling protein that directly binds to its cognate target site on the chromosome to regulate transcription. We combined fluorescence microscopy experiments, mathematical analysis, and kinetic Monte Carlo simulations to probe this target search process. Using fluorescently labeled CadC, we measured the time from activation of the receptor until successful binding to the DNA in single cells, exploiting that stable receptor-DNA complexes are visible as fluorescent spots. Our experimental data indicate that CadC is highly mobile in the membrane and finds its target by a 2D diffusion and capture mechanism. DNA mobility is constrained due to the overall chromosome organization, but a labeled DNA locus in the vicinity of the target site appears sufficiently mobile to randomly come close to the membrane. Relocation of the DNA target site to a distant position on the chromosome had almost no effect on the mean search time, which was between four and five minutes in either case. However, a mutant strain with two binding sites displayed a mean search time that was reduced by about a factor of two. This behavior is consistent with simulations of a coarse-grained lattice model for the coupled dynamics of DNA within a cell volume and proteins on its surface. The model also rationalizes the experimentally determined distribution of search times. Overall our findings reveal that DNA target search does not present a much bigger kinetic challenge for membrane-integrated proteins than for cytoplasmic proteins. More generally, diffusion and capture mechanisms may be sufficient for bacterial membrane proteins to establish functional contacts with cytoplasmic targets. Adaptation to changing environments is vital to bacteria and is enabled by sophisticated signal transduction systems. While signal transduction by two-component systems is well studied, the signal transduction of membrane-integrated one-component systems, where one protein performs both sensing and response regulation, are insufficiently understood. How can a membrane-integrated protein bind to specific sites on the genome to regulate transcription? Here, we study the kinetics of this process, which involves both protein diffusion within the membrane and conformational fluctuations of the genomic DNA. A well-suited model system for this question is CadC, the signaling protein of the E. coli Cad system involved in pH stress response. Fluorescently labeled CadC forms visible spots in single cells upon stable DNA-binding, marking the end of the protein-DNA search process. Moreover, the start of the search is triggered by a medium shift exposing cells to pH stress. We probe the underlying mechanism by varying the number and position of DNA target sites. We combine these experiments with mathematical analysis and kinetic Monte Carlo simulations of lattice models for the search process. Our results suggest that CadC diffusion in the membrane is pivotal for this search, while the DNA target site is just mobile enough to reach the membrane.
Collapse
Affiliation(s)
- Linda Martini
- Physics of Complex Biosystems, Technical University of Munich, Garching, Germany
| | - Sophie Brameyer
- Microbiology, Ludwig-Maximilians-University Munich, Martinsried, Germany
| | - Elisabeth Hoyer
- Microbiology, Ludwig-Maximilians-University Munich, Martinsried, Germany
| | - Kirsten Jung
- Microbiology, Ludwig-Maximilians-University Munich, Martinsried, Germany
- * E-mail: (KJ); (UG)
| | - Ulrich Gerland
- Physics of Complex Biosystems, Technical University of Munich, Garching, Germany
- * E-mail: (KJ); (UG)
| |
Collapse
|
8
|
Jana T, Brodsky S, Barkai N. Speed-Specificity Trade-Offs in the Transcription Factors Search for Their Genomic Binding Sites. Trends Genet 2021; 37:421-432. [PMID: 33414013 DOI: 10.1016/j.tig.2020.12.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 12/17/2022]
Abstract
Transcription factors (TFs) regulate gene expression by binding DNA sequences recognized by their DNA-binding domains (DBDs). DBD-recognized motifs are short and highly abundant in genomes. The ability of TFs to bind a specific subset of motif-containing sites, and to do so rapidly upon activation, is fundamental for gene expression in all eukaryotes. Despite extensive interest, our understanding of the TF-target search process is fragmented; although binding specificity and detection speed are two facets of this same process, trade-offs between them are rarely addressed. In this opinion article, we discuss potential speed-specificity trade-offs in the context of existing models. We further discuss the recently described 'distributed specificity' paradigm, suggesting that intrinsically disordered regions (IDRs) promote specificity while reducing the TF-target search time.
Collapse
Affiliation(s)
- Tamar Jana
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sagie Brodsky
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
| |
Collapse
|
9
|
Ma P, Elber R, Makarov DE. Value of Temporal Information When Analyzing Reaction Coordinates. J Chem Theory Comput 2020; 16:6077-6090. [PMID: 32841001 PMCID: PMC7881391 DOI: 10.1021/acs.jctc.0c00678] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Reaction coordinates chart pathways from reactants to products of chemical reactions. Determination of reaction coordinates from ensembles of molecular trajectories has thus been the focus of many studies. A widely used and insightful choice of a reaction coordinate is the committor function, defined as the probability that a trajectory will reach the product before the reactant. Here, we consider alternatives to the committor function that add useful mechanistic information, the mean first passage time, and the exit time to the product. We further derive a simple relationship between the functions of the committor, the mean first passage time, and the exit time. We illustrate the diversity of mechanisms predicted by alternative reaction coordinates with several toy problems and with a simple model of protein searching for a specific DNA motif.
Collapse
Affiliation(s)
- Piao Ma
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Ron Elber
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
- Oden Institute for Computational Engineering and Sciences, Austin, Texas 78712, United States
| | - Dmitrii E Makarov
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
- Oden Institute for Computational Engineering and Sciences, Austin, Texas 78712, United States
| |
Collapse
|
10
|
Shin J, Kolomeisky AB. Target search on DNA by interacting molecules: First-passage approach. J Chem Phys 2019; 151:125101. [PMID: 31575173 DOI: 10.1063/1.5123988] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Gene regulation is one of the most important fundamental biological processes in living cells. It involves multiple protein molecules that locate specific sites on DNA and assemble gene initiation or gene repression multimolecular complexes. While the protein search dynamics for DNA targets has been intensively investigated, the role of intermolecular interactions during the genetic activation or repression remains not well quantified. Here, we present a simple one-dimensional model of target search for two interacting molecules that can reversibly form a dimer molecular complex, which also participates in the search process. In addition, the proteins have finite residence times on specific target sites, and the gene is activated or repressed when both proteins are simultaneously present at the target. The model is analyzed using first-passage analytical calculations and Monte Carlo computer simulations. It is shown that the search dynamics exhibit a complex behavior depending on the strength of intermolecular interactions and on the target residence times. We also found that the search time shows a nonmonotonic behavior as a function of the dissociation rate for the molecular complex. Physical-chemical arguments to explain these observations are presented. Our theoretical approach highlights the importance of molecular interactions in the complex process of gene activation/repression by multiple transcription factor proteins.
Collapse
Affiliation(s)
- Jaeoh Shin
- Department of Chemistry, Rice University, Houston, Texas 77005, USA
| | | |
Collapse
|
11
|
Cencini M, Pigolotti S. Energetic funnel facilitates facilitated diffusion. Nucleic Acids Res 2019; 46:558-567. [PMID: 29216364 PMCID: PMC5778461 DOI: 10.1093/nar/gkx1220] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 11/24/2017] [Indexed: 01/25/2023] Open
Abstract
Transcription factors (TFs) are able to associate to their binding sites on DNA faster than the physical limit posed by diffusion. Such high association rates can be achieved by alternating between three-dimensional diffusion and one-dimensional sliding along the DNA chain, a mechanism-dubbed facilitated diffusion. By studying a collection of TF binding sites of Escherichia coli from the RegulonDB database and of Bacillus subtilis from DBTBS, we reveal a funnel in the binding energy landscape around the target sequences. We show that such a funnel is linked to the presence of gradients of AT in the base composition of the DNA region around the binding sites. An extensive computational study of the stochastic sliding process along the energetic landscapes obtained from the database shows that the funnel can significantly enhance the probability of TFs to find their target sequences when sliding in their proximity. We demonstrate that this enhancement leads to a speed-up of the association process.
Collapse
Affiliation(s)
- Massimo Cencini
- Istituto dei Sistemi Complessi, Consiglio Nazionale delle Ricerche, via dei Taurini 19, 00185 Rome, Italy
| | - Simone Pigolotti
- Biological Complexity Unit, Okinawa Institute of Science and Technology and Graduate University, Onna, Okinawa 904-0495, Japan.,Max Planck Institute for the Physics of Complex Systems, Nöthnitzerstraße 38, 01187 Dresden, Germany.,Departament de Fisica, Universitat Politecnica de Catalunya Edif. GAIA, Rambla Sant Nebridi 22, 08222 Terrassa, Barcelona, Spain
| |
Collapse
|
12
|
Barel I, Reich NO, Brown FLH. Integrated rate laws for processive and distributive enzymatic turnover. J Chem Phys 2019; 150:244120. [PMID: 31255081 DOI: 10.1063/1.5097576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Recently derived steady-state differential rate laws for the catalytic turnover of molecules containing two substrate sites are reformulated as integrated rate laws. The analysis applies to a broad class of Markovian dynamic models, motivated by the varied and often complex mechanisms associated with DNA modifying enzymes. Analysis of experimental data for the methylation kinetics of DNA by Dam (DNA adenine methyltransferase) is drastically improved through the use of integrated rate laws. Data that are too noisy for fitting to differential predictions are reliably interpreted through the integrated rate laws.
Collapse
Affiliation(s)
- Itay Barel
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
| | - Norbert O Reich
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
| | - Frank L H Brown
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
| |
Collapse
|
13
|
Leven I, Levy Y. Quantifying the two-state facilitated diffusion model of protein-DNA interactions. Nucleic Acids Res 2019; 47:5530-5538. [PMID: 31045207 PMCID: PMC6582340 DOI: 10.1093/nar/gkz308] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 04/13/2019] [Accepted: 04/17/2019] [Indexed: 01/13/2023] Open
Abstract
The current report extends the facilitated diffusion model to account for conflict between the search and recognition binding modes adopted by DNA-binding proteins (DBPs) as they search DNA and subsequently recognize and bind to their specific binding site. The speed of the search dynamics is governed by the energetic ruggedness of the protein-DNA landscape, whereas the rate for the recognition process is mostly dictated by the free energy barrier for the transition between the DBP's search and recognition binding modes. We show that these two modes are negatively coupled, such that fast 1D sliding and rapid target site recognition probabilities are unlikely to coexist. Thus, a tradeoff occurs between optimizing the timescales for finding and binding the target site. We find that these two kinetic properties can be balanced to produce a fast timescale for the total target search and recognition process by optimizing frustration. Quantification of the facilitated diffusion model by including a frustration term enables it to explain several experimental observations concerning search and recognition speeds. The extended model captures experimental estimate of the energetic ruggedness of the protein-DNA landscape and predicts how various molecular properties of protein-DNA binding affect recognition kinetics. Particularly, point mutations may change the frustration and so affect protein association with DNA, thus providing a means to modulate protein-DNA affinity by manipulating the protein's association or dissociation reactions.
Collapse
Affiliation(s)
- Itai Leven
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| |
Collapse
|
14
|
Mechanisms of Protein Search for Targets on DNA: Theoretical Insights. Molecules 2018; 23:molecules23092106. [PMID: 30131459 PMCID: PMC6225296 DOI: 10.3390/molecules23092106] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 08/13/2018] [Accepted: 08/17/2018] [Indexed: 11/17/2022] Open
Abstract
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.
Collapse
|
15
|
Hettich J, Gebhardt JCM. Transcription factor target site search and gene regulation in a background of unspecific binding sites. J Theor Biol 2018; 454:91-101. [PMID: 29870697 PMCID: PMC6103292 DOI: 10.1016/j.jtbi.2018.05.037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/29/2018] [Accepted: 05/30/2018] [Indexed: 11/02/2022]
Abstract
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.
Collapse
Affiliation(s)
- J Hettich
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, Ulm 89081, Germany
| | - J C M Gebhardt
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, Ulm 89081, Germany.
| |
Collapse
|
16
|
Amitai A. Chromatin Configuration Affects the Dynamics and Distribution of a Transiently Interacting Protein. Biophys J 2018; 114:766-771. [PMID: 29395046 DOI: 10.1016/j.bpj.2017.12.037] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/13/2017] [Accepted: 12/27/2017] [Indexed: 01/20/2023] Open
Affiliation(s)
- Assaf Amitai
- Department of Chemical Engineering, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts; Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts.
| |
Collapse
|
17
|
Barel I, Naughton B, Reich NO, Brown FLH. Specificity versus Processivity in the Sequential Modification of DNA: A Study of DNA Adenine Methyltransferase. J Phys Chem B 2018; 122:1112-1120. [DOI: 10.1021/acs.jpcb.7b10349] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Itay Barel
- Department
of Chemistry and Biochemistry, University of California, Santa
Barbara, California 93106, United States
- Department
of Physics, University of California, Santa Barbara, California 93106, United States
| | - Brigitte Naughton
- Department
of Chemistry and Biochemistry, University of California, Santa
Barbara, California 93106, United States
| | - Norbert O. Reich
- Department
of Chemistry and Biochemistry, University of California, Santa
Barbara, California 93106, United States
| | - Frank L. H. Brown
- Department
of Chemistry and Biochemistry, University of California, Santa
Barbara, California 93106, United States
- Department
of Physics, University of California, Santa Barbara, California 93106, United States
| |
Collapse
|
18
|
Kar P, Cherstvy AG, Metzler R. Acceleration of bursty multiprotein target search kinetics on DNA by colocalisation. Phys Chem Chem Phys 2018; 20:7931-7946. [DOI: 10.1039/c7cp06922g] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
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.
Collapse
Affiliation(s)
- Prathitha Kar
- Dept of Inorganic and Physical Chemistry
- Indian Institute of Science
- Bengaluru
- India
- Institute for Physics & Astronomy
| | - Andrey G. Cherstvy
- Institute for Physics & Astronomy
- University of Potsdam
- 14476 Potsdam-Golm
- Germany
| | - Ralf Metzler
- Institute for Physics & Astronomy
- University of Potsdam
- 14476 Potsdam-Golm
- Germany
| |
Collapse
|
19
|
Zhou M, Dick JE, Bard AJ. Electrodeposition of Isolated Platinum Atoms and Clusters on Bismuth-Characterization and Electrocatalysis. J Am Chem Soc 2017; 139:17677-17682. [PMID: 29131602 DOI: 10.1021/jacs.7b10646] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We describe a method for the electrodeposition of an isolated single Pt atom or small cluster, up to 9 atoms, on a bismuth ultramicroelectrode (UME). This deposition was immediately followed by electrochemical characterization via the hydrogen evolution reaction (HER) that occurs readily on the electrodeposited Pt but not on Bi. The observed voltammetric current plateau, even for a single atom, which behaves as an electrode, allows the estimation of deposit size. Pt was plated from solutions of femtomolar PtCl62-, which allowed precise control of the arrival of ions and thus the plating rate on the Bi UME, to one ion every few seconds. This allowed the atom-by-atom fabrication of isolated platinum deposits, ranging from single atoms to 9-atom clusters. The limiting currents in voltammetry gave the size and number of atoms of the clusters. Given the stochasticity of the plating process, we show that the number of atoms plated over a given time (10 and 20 s) follows a Poisson distribution. Taking the potential at a certain current density as a measure of the relative rate of the HER, we found that the potential shifted positively as the size increased, with single atoms showing the largest overpotentials compared to bulk Pt.
Collapse
Affiliation(s)
- Min Zhou
- Center for Electrochemistry, Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Jeffrey E Dick
- Center for Electrochemistry, Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Allen J Bard
- Center for Electrochemistry, Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| |
Collapse
|
20
|
Vijaykumar A, Ten Wolde PR, Bolhuis PG. The magnitude of the intrinsic rate constant: How deep can association reactions be in the diffusion limited regime? J Chem Phys 2017; 147:184108. [PMID: 29141426 DOI: 10.1063/1.5009547] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Intrinsic and effective rate constants have an important role in the theory of diffusion-limited reactions. In a previous paper, we provide detailed microscopic expressions for these intrinsic rates [A. Vijaykumar, P. G. Bolhuis, and P. R. ten Wolde, Faraday Discuss. 195, 421 (2016)], which are usually considered as abstract quantities and assumed to be implicitly known. Using these microscopic expressions, we investigate how the rate of association depends on the strength and the range of the isotropic potential and the strength of the non-specific attraction in case of the anisotropic potential. In addition, we determine the location of the interface where these expressions become valid for anisotropic potentials. In particular, by investigating the particles' orientational distributions, we verify whether the interface at which these distributions become isotropic agrees with the interface predicted by the effective association rate constant. Finally, we discuss how large the intrinsic association rate can become, and what are the consequences for the existence of the diffusion limited regime.
Collapse
Affiliation(s)
- Adithya Vijaykumar
- FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | | | - Peter G Bolhuis
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, The Netherlands
| |
Collapse
|
21
|
Liu L, Chen W, Chen J. Shape and Diffusion of Circular Polyelectrolytes in Salt-Free Dilute Solutions and Comparison with Linear Polyelectrolytes. Macromolecules 2017. [DOI: 10.1021/acs.macromol.7b00189] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lijun Liu
- State Key Laboratory
of Polymer
Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Wenduo Chen
- State Key Laboratory
of Polymer
Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Jizhong Chen
- State Key Laboratory
of Polymer
Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| |
Collapse
|
22
|
Chow E, Skolnick J. DNA Internal Motion Likely Accelerates Protein Target Search in a Packed Nucleoid. Biophys J 2017; 112:2261-2270. [PMID: 28591599 DOI: 10.1016/j.bpj.2017.04.049] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 04/17/2017] [Accepted: 04/28/2017] [Indexed: 12/18/2022] Open
Abstract
Transcription factors must diffuse through densely packed and coiled DNA to find their binding sites. Using a coarse-grained model of DNA and lac repressor (LacI) in the Escherichia coli nucleoid, simulations were performed to examine how LacI diffuses in such a space. Despite the canonical picture of LacI diffusing rather freely, in reality the DNA is densely packed, is not rigid but highly mobile, and the dynamics of DNA dictates to a great extent the LacI motion. A possibly better picture of unbound LacI motion is that of gated diffusion, where DNA confines LacI in a cage, but LacI can move between cages when hindering DNA strands move out of the way. Three-dimensional diffusion constants for unbound LacI computed from simulations closely match those for unbound LacI in vivo reported in the literature. The internal motions of DNA appear to be governed by strong internal forces arising from being crowded into the small space of the nucleoid. A consequence of the DNA internal motion is that protein target search may be accelerated.
Collapse
Affiliation(s)
- Edmond Chow
- School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia.
| | - Jeffrey Skolnick
- Center for the Study of Systems Biology, School of Biosciences, Georgia Institute of Technology, Atlanta, Georgia
| |
Collapse
|
23
|
Yesudhas D, Batool M, Anwar MA, Panneerselvam S, Choi S. Proteins Recognizing DNA: Structural Uniqueness and Versatility of DNA-Binding Domains in Stem Cell Transcription Factors. Genes (Basel) 2017; 8:genes8080192. [PMID: 28763006 PMCID: PMC5575656 DOI: 10.3390/genes8080192] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/22/2017] [Accepted: 07/25/2017] [Indexed: 12/17/2022] Open
Abstract
Proteins in the form of transcription factors (TFs) bind to specific DNA sites that regulate cell growth, differentiation, and cell development. The interactions between proteins and DNA are important toward maintaining and expressing genetic information. Without knowing TFs structures and DNA-binding properties, it is difficult to completely understand the mechanisms by which genetic information is transferred between DNA and proteins. The increasing availability of structural data on protein-DNA complexes and recognition mechanisms provides deeper insights into the nature of protein-DNA interactions and therefore, allows their manipulation. TFs utilize different mechanisms to recognize their cognate DNA (direct and indirect readouts). In this review, we focus on these recognition mechanisms as well as on the analysis of the DNA-binding domains of stem cell TFs, discussing the relative role of various amino acids toward facilitating such interactions. Unveiling such mechanisms will improve our understanding of the molecular pathways through which TFs are involved in repressing and activating gene expression.
Collapse
Affiliation(s)
- Dhanusha Yesudhas
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
| | - Maria Batool
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
| | - Muhammad Ayaz Anwar
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
| | - Suresh Panneerselvam
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
| |
Collapse
|
24
|
Chen Y, Gao T, Wang Y, Yang G. Investigating the Influence of Magnesium Ions on p53-DNA Binding Using Atomic Force Microscopy. Int J Mol Sci 2017; 18:ijms18071585. [PMID: 28754018 PMCID: PMC5536072 DOI: 10.3390/ijms18071585] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 07/10/2017] [Accepted: 07/18/2017] [Indexed: 12/22/2022] Open
Abstract
p53 is a tumor suppressor protein that plays a significant role in apoptosis and senescence, preserving genomic stability, and preventing oncogene expression. Metal ions, such as magnesium and zinc ions, have important influences on p53–DNA interactions for stabilizing the structure of the protein and enhancing its affinity to DNA. In the present study, we systematically investigated the interaction of full length human protein p53 with DNA in metal ion solution by atomic force microscopy (AFM). The p53–DNA complexes at various p53 concentrations were scanned by AFM and their images are used to measure the dissociation constant of p53–DNA binding by a statistical method. We found that the dissociation constant of p53 binding DNA is 328.02 nmol/L in physiological buffer conditions. The influence of magnesium ions on p53–DNA binding was studied by AFM at various ion strengths through visualization. We found that magnesium ions significantly stimulate the binding of the protein to DNA in a sequence-independent manner, different from that stimulated by zinc. Furthermore, the high concentrations of magnesium ions can promote p53 aggregation and even lead to the formation of self-assembly networks of DNA and p53 proteins. We propose an aggregation and self-assembly model based on the present observation and discuss its biological meaning.
Collapse
Affiliation(s)
- Yang Chen
- School of Physics and Electronic Information, Wenzhou University, Wenzhou 325035, China.
| | - Tianyong Gao
- School of Physics and Electronic Information, Wenzhou University, Wenzhou 325035, China.
| | - Yanwei Wang
- School of Physics and Electronic Information, Wenzhou University, Wenzhou 325035, China.
| | - Guangcan Yang
- School of Physics and Electronic Information, Wenzhou University, Wenzhou 325035, China.
| |
Collapse
|
25
|
Kochugaeva MP, Shvets AA, Kolomeisky AB. On the Mechanism of Homology Search by RecA Protein Filaments. Biophys J 2017; 112:859-867. [PMID: 28297645 DOI: 10.1016/j.bpj.2017.01.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 01/20/2017] [Accepted: 01/24/2017] [Indexed: 10/20/2022] Open
Abstract
Genetic stability is a key factor in maintaining, survival, and reproduction of biological cells. It relies on many processes, but one of the most important is a homologous recombination, in which the repair of breaks in double-stranded DNA molecules is taking place with a help of several specific proteins. In bacteria, this task is accomplished by RecA proteins that are active as nucleoprotein filaments formed on single-stranded segments of DNA. A critical step in the homologous recombination is a search for a corresponding homologous region on DNA, which is called a homology search. Recent single-molecule experiments clarified some aspects of this process, but its molecular mechanisms remain not well understood. We developed a quantitative theoretical approach to analyze the homology search. It is based on a discrete-state stochastic model that takes into account the most relevant physical-chemical processes in the system. Using a method of first-passage processes, a full dynamic description of the homology search is presented. It is found that the search dynamics depends on the degree of extension of DNA molecules and on the size of RecA nucleoprotein filaments, in agreement with experimental single-molecule measurements of DNA pairing by RecA proteins. Our theoretical calculations, supported by extensive Monte Carlo computer simulations, provide a molecular description of the mechanisms of the homology search.
Collapse
Affiliation(s)
- Maria P Kochugaeva
- Department of Chemistry, Rice University, Houston, Texas; Center for Theoretical Biological Physics, Rice University, Houston, Texas
| | - Alexey A Shvets
- Department of Chemistry, Rice University, Houston, Texas; Center for Theoretical Biological Physics, Rice University, Houston, Texas
| | - Anatoly B Kolomeisky
- Department of Chemistry, Rice University, Houston, Texas; Center for Theoretical Biological Physics, Rice University, Houston, Texas.
| |
Collapse
|
26
|
Liu L, Cherstvy AG, Metzler R. Facilitated Diffusion of Transcription Factor Proteins with Anomalous Bulk Diffusion. J Phys Chem B 2017; 121:1284-1289. [DOI: 10.1021/acs.jpcb.6b12413] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Lin Liu
- CAS
Key Laboratory of Soft Matter Chemistry, Dept. of Polymer Science
and Engineering, University of Science and Technology of China, Hefei, Anhui Province 230026, China
- Institute for Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Andrey G. Cherstvy
- Institute for Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Ralf Metzler
- Institute for Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
| |
Collapse
|
27
|
Rad4 recognition-at-a-distance: Physical basis of conformation-specific anomalous diffusion of DNA repair proteins. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2016; 127:93-104. [PMID: 27939760 DOI: 10.1016/j.pbiomolbio.2016.12.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 12/06/2016] [Indexed: 11/20/2022]
Abstract
Since Robert Brown's first observations of random walks by pollen particles suspended in solution, the concept of diffusion has been subject to countless theoretical and experimental studies in diverse fields from finance and social sciences, to physics and biology. Diffusive transport of macromolecules in cells is intimately linked to essential cellular functions including nutrient uptake, signal transduction, gene expression, as well as DNA replication and repair. Advancement in experimental techniques has allowed precise measurements of these diffusion processes. Mathematical and physical descriptions and computer simulations have been applied to model complicated biological systems in which anomalous diffusion, in addition to simple Brownian motion, was observed. The purpose of this review is to provide an overview of the major physical models of anomalous diffusion and corresponding experimental evidence on the target search problem faced by DNA-binding proteins, with an emphasis on DNA repair proteins and the role of anomalous diffusion in DNA target recognition.
Collapse
|
28
|
Krepel D, Gomez D, Klumpp S, Levy Y. Mechanism of Facilitated Diffusion during a DNA Search in Crowded Environments. J Phys Chem B 2016; 120:11113-11122. [DOI: 10.1021/acs.jpcb.6b07813] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Dana Krepel
- Department
of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - David Gomez
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany
| | - Stefan Klumpp
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany
- Institute
for Nonlinear Dynamics, Georg-August University Göttingen, Friedrich-Hund-Platz
1, 37077 Göttingen, Germany
| | - Yaakov Levy
- Department
of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| |
Collapse
|
29
|
Isom CE, Menon SK, Thomas LM, West AH, Richter-Addo GB, Karr EA. Crystal structure and DNA binding activity of a PadR family transcription regulator from hypervirulent Clostridium difficile R20291. BMC Microbiol 2016; 16:231. [PMID: 27716049 PMCID: PMC5050560 DOI: 10.1186/s12866-016-0850-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 09/24/2016] [Indexed: 01/05/2023] Open
Abstract
Background Clostridium difficile is a spore-forming obligate anaerobe that can remain viable for extended periods, even in the presence of antibiotics, which contributes to the persistence of this bacterium as a human pathogen during host-to-host transmission and in hospital environments. We examined the structure and function of a gene product with the locus tag CDR20291_0991 (cdPadR1) as part of our broader goal aimed at elucidating transcription regulatory mechanisms involved in virulence and antibiotic resistance of the recently emergent hypervirulent C. difficile strain R20291. cdPadR1 is genomically positioned near genes that are involved in stress response and virulence. In addition, it was previously reported that cdPadR1 and a homologue from the historical C. difficile strain 630 (CD630_1154) were differentially expressed when exposed to stressors, including antibiotics. Results The crystal structure of cdPadR1 was determined to 1.9 Å resolution, which revealed that it belongs to the PadR-s2 subfamily of PadR transcriptional regulators. cdPadR1 binds its own promoter and other promoter regions from within the C. difficile R20291 genome. DNA binding experiments demonstrated that cdPadR1 binds a region comprised of inverted repeats and an AT-rich core with the predicted specific binding motif, GTACTAT(N2)ATTATA(N)AGTA, within its own promoter that is also present in 200 other regions in the C. difficile R20291 genome. Mutation of the highly conserved W in α4 of the effector binding/oligomerization domain, which is predicted to be involved in multi-drug recognition and dimerization in other PadR-s2 proteins, resulted in alterations of cdPadR1 binding to the predicted binding motif, potentially due to loss of higher order oligomerization. Conclusions Our results indicate that cdPadR1 binds a region within its own promoter consisting of the binding motif GTACTAT(N2)ATTATA(N)AGTA and seems to associate non-specifically with longer DNA fragments in vitro, which may facilitate promoter and motif searching. This suggests that cdPadR1 acts as a transcriptional auto-regulator, binding specific sites within its own promoter, and is part of a broad gene regulatory network involved, in part, with environmental stress response, antibiotic resistance and virulence. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0850-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Catherine E Isom
- Price Family Foundation Institute of Structural Biology and Department of Microbiology and Plant Biology, University of Oklahoma, 770 Van Vleet Oval, Norman, OK, 73019, USA.,Price Family Foundation Institute of Structural Biology and Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Smita K Menon
- Price Family Foundation Institute of Structural Biology and Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Leonard M Thomas
- Price Family Foundation Institute of Structural Biology and Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Ann H West
- Price Family Foundation Institute of Structural Biology and Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - George B Richter-Addo
- Price Family Foundation Institute of Structural Biology and Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Elizabeth A Karr
- Price Family Foundation Institute of Structural Biology and Department of Microbiology and Plant Biology, University of Oklahoma, 770 Van Vleet Oval, Norman, OK, 73019, USA.
| |
Collapse
|
30
|
Shvets AA, Kolomeisky AB. Sequence heterogeneity accelerates protein search for targets on DNA. J Chem Phys 2016; 143:245101. [PMID: 26723711 DOI: 10.1063/1.4937938] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The process of protein search for specific binding sites on DNA is fundamentally important since it marks the beginning of all major biological processes. We present a theoretical investigation that probes the role of DNA sequence symmetry, heterogeneity, and chemical composition in the protein search dynamics. Using a discrete-state stochastic approach with a first-passage events analysis, which takes into account the most relevant physical-chemical processes, a full analytical description of the search dynamics is obtained. It is found that, contrary to existing views, the protein search is generally faster on DNA with more heterogeneous sequences. In addition, the search dynamics might be affected by the chemical composition near the target site. The physical origins of these phenomena are discussed. Our results suggest that biological processes might be effectively regulated by modifying chemical composition, symmetry, and heterogeneity of a genome.
Collapse
Affiliation(s)
- Alexey A Shvets
- Department of Chemistry and Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
| | - Anatoly B Kolomeisky
- Department of Chemistry and Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
| |
Collapse
|
31
|
Stratmann SA, Morrone SR, van Oijen AM, Sohn J. The innate immune sensor IFI16 recognizes foreign DNA in the nucleus by scanning along the duplex. eLife 2015; 4:e11721. [PMID: 26673078 PMCID: PMC4829420 DOI: 10.7554/elife.11721] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 12/15/2015] [Indexed: 12/31/2022] Open
Abstract
The ability to recognize foreign double-stranded (ds)DNA of pathogenic origin in the intracellular environment is an essential defense mechanism of the human innate immune system. However, the molecular mechanisms underlying distinction between foreign DNA and host genomic material inside the nucleus are not understood. By combining biochemical assays and single-molecule techniques, we show that the nuclear innate immune sensor IFI16 one-dimensionally tracks long stretches of exposed foreign dsDNA to assemble into supramolecular signaling platforms. We also demonstrate that nucleosomes represent barriers that prevent IFI16 from targeting host DNA by directly interfering with these one-dimensional movements. This unique scanning-assisted assembly mechanism allows IFI16 to distinguish friend from foe and assemble into oligomers efficiently and selectively on foreign DNA.
Collapse
Affiliation(s)
| | - Seamus R Morrone
- Johns Hopkins University School of Medicine, Baltimore, United States
| | - Antoine M van Oijen
- University of Groningen, Groningen, Netherlands.,University of Wollongong, Wollongong, Australia
| | - Jungsan Sohn
- Johns Hopkins University School of Medicine, Baltimore, United States
| |
Collapse
|
32
|
Shvets A, Kochugaeva M, Kolomeisky AB. Role of Static and Dynamic Obstacles in the Protein Search for Targets on DNA. J Phys Chem B 2015; 120:5802-9. [DOI: 10.1021/acs.jpcb.5b09814] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Alexey Shvets
- Department of Chemistry and
Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Maria Kochugaeva
- Department of Chemistry and
Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Anatoly B. Kolomeisky
- Department of Chemistry and
Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| |
Collapse
|
33
|
Barel I, Reich NO, Brown FLH. Extracting enzyme processivity from kinetic assays. J Chem Phys 2015; 143:224115. [DOI: 10.1063/1.4937155] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Itay Barel
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
- Department of Physics, University of California, Santa Barbara, California 93106, USA
| | - Norbert O. Reich
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
| | - Frank L. H. Brown
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
- Department of Physics, University of California, Santa Barbara, California 93106, USA
| |
Collapse
|
34
|
Turkin A, van Oijen AM, Turkin AA. Theory of bimolecular reactions in a solution with linear traps: Application to the problem of target search on DNA. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:052703. [PMID: 26651719 DOI: 10.1103/physreve.92.052703] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Indexed: 06/05/2023]
Abstract
One-dimensional sliding along DNA as a means to accelerate protein target search is a well-known phenomenon occurring in various biological systems. Using a biomimetic approach, we have recently demonstrated the practical use of DNA-sliding peptides to speed up bimolecular reactions more than an order of magnitude by allowing the reactants to associate not only in the solution by three-dimensional (3D) diffusion, but also on DNA via one-dimensional (1D) diffusion [A. Turkin et al., Chem. Sci. (2015)]. Here we present a mean-field kinetic model of a bimolecular reaction in a solution with linear extended sinks (e.g., DNA) that can intermittently trap molecules present in a solution. The model consists of chemical rate equations for mean concentrations of reacting species. Our model demonstrates that addition of linear traps to the solution can significantly accelerate reactant association. We show that at optimum concentrations of linear traps the 1D reaction pathway dominates in the kinetics of the bimolecular reaction; i.e., these 1D traps function as an assembly line of the reaction product. Moreover, we show that the association reaction on linear sinks between trapped reactants exhibits a nonclassical third-order behavior. Predictions of the model agree well with our experimental observations. Our model provides a general description of bimolecular reactions that are controlled by a combined 3D+1D mechanism and can be used to quantitatively describe both naturally occurring as well as biomimetic biochemical systems that reduce the dimensionality of search.
Collapse
Affiliation(s)
- Alexander Turkin
- Single-Molecule Biophysics, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen 9747 AG, Netherlands
| | - Antoine M van Oijen
- Single-Molecule Biophysics, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen 9747 AG, Netherlands
| | - Anatoliy A Turkin
- National Science Center "Kharkiv Institute of Physics & Technology," Akademichna street 1, Kharkiv 61108, Ukraine
| |
Collapse
|
35
|
Kemme CA, Esadze A, Iwahara J. Influence of quasi-specific sites on kinetics of target DNA search by a sequence-specific DNA-binding protein. Biochemistry 2015; 54:6684-91. [PMID: 26502071 PMCID: PMC4642223 DOI: 10.1021/acs.biochem.5b00967] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Functions
of transcription factors require formation of specific
complexes at particular sites in cis-regulatory elements of genes.
However, chromosomal DNA contains numerous sites that are similar
to the target sequences recognized by transcription factors. The influence
of such “quasi-specific” sites on functions of the transcription
factors is not well understood at present by experimental means. In
this work, using fluorescence methods, we have investigated the influence
of quasi-specific DNA sites on the efficiency of target location by
the zinc finger DNA-binding domain of the inducible transcription
factor Egr-1, which recognizes a 9 bp sequence. By stopped-flow assays,
we measured the kinetics of Egr-1’s association with a target
site on 143 bp DNA in the presence of various competitor DNAs, including
nonspecific and quasi-specific sites. The presence of quasi-specific
sites on competitor DNA significantly decelerated the target association
by the Egr-1 protein. The impact of the quasi-specific sites depended
strongly on their affinity, their concentration, and the degree of
their binding to the protein. To quantitatively describe the kinetic
impact of the quasi-specific sites, we derived an analytical form
of the apparent kinetic rate constant for the target association and
used it for fitting to the experimental data. Our kinetic data with
calf thymus DNA as a competitor suggested that there are millions
of high-affinity quasi-specific sites for Egr-1 among the 3 billion
bp of genomic DNA. This study quantitatively demonstrates that naturally
abundant quasi-specific sites on DNA can considerably impede the target
search processes of sequence-specific DNA-binding proteins.
Collapse
Affiliation(s)
- Catherine A Kemme
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch , Galveston, Texas 77555, United States
| | - Alexandre Esadze
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch , Galveston, Texas 77555, United States
| | - Junji Iwahara
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch , Galveston, Texas 77555, United States
| |
Collapse
|
36
|
Mondal A, Bhattacherjee A. Searching target sites on DNA by proteins: Role of DNA dynamics under confinement. Nucleic Acids Res 2015; 43:9176-86. [PMID: 26400158 PMCID: PMC4627088 DOI: 10.1093/nar/gkv931] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 08/15/2015] [Accepted: 09/07/2015] [Indexed: 02/07/2023] Open
Abstract
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 contrast, strong confinement favours rotation-coupled sliding to locate targets but lacks structural flexibility to achieve desired specificity. By testing under physiological crowding, our study provides a plausible mechanism on how DNA molecule may help in maintaining an optimal balance between fast hopping and rotation-coupled sliding dynamics, to locate target sites rapidly and form specific complexes precisely.
Collapse
Affiliation(s)
- Anupam Mondal
- Center for Computational Biology, Indraprastha Institute of Information Technology (IIIT) Delhi, New Delhi-110020, India
| | - Arnab Bhattacherjee
- Center for Computational Biology, Indraprastha Institute of Information Technology (IIIT) Delhi, New Delhi-110020, India
| |
Collapse
|
37
|
Lange M, Kochugaeva M, Kolomeisky AB. Dynamics of the Protein Search for Targets on DNA in the Presence of Traps. J Phys Chem B 2015; 119:12410-6. [PMID: 26328804 DOI: 10.1021/acs.jpcb.5b07303] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Protein search for specific binding sites on DNA is a fundamental biological phenomenon associated with the beginning of most major biological processes. It is frequently found that proteins find and recognize their specific targets quickly and efficiently despite the complex nature of protein-DNA interactions in living cells. Although significant experimental and theoretical efforts were made in recent years, the mechanisms of these processes remain not well-clarified. We present a theoretical study of the protein target search dynamics in the presence of semispecific binding sites which are viewed as traps. Our theoretical approach employs a discrete-state stochastic method that accounts for the most important physical and chemical processes in the system. It also leads to a full analytical description for all dynamic properties of the protein search. It is found that the presence of traps can significantly modify the protein search dynamics. This effect depends on the spatial positions of the targets and traps, on distances between them, on the average sliding length of the protein along the DNA, and on the total length of DNA. Theoretical predictions are discussed using simple physical-chemical arguments, and they are also validated with extensive Monte Carlo computer simulations.
Collapse
Affiliation(s)
- Martin Lange
- Department of Chemistry, Rice University , Houston, Texas 77005, United States.,Johannes Gutenberg University , Mainz 55122, Germany
| | - Maria Kochugaeva
- Department of Chemistry, Rice University , Houston, Texas 77005, United States.,Center for Theoretical Biological Physics, Rice University , Houston, Texas 77005, United States
| | - Anatoly B Kolomeisky
- Department of Chemistry, Rice University , Houston, Texas 77005, United States.,Center for Theoretical Biological Physics, Rice University , Houston, Texas 77005, United States
| |
Collapse
|
38
|
Tabaka M, Burdzy K, Hołyst R. Method for the analysis of contribution of sliding and hopping to a facilitated diffusion of DNA-binding protein: Application to in vivo data. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:022721. [PMID: 26382446 DOI: 10.1103/physreve.92.022721] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Indexed: 06/05/2023]
Abstract
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 the DNA chain and three-dimensional diffusion (hopping) after dissociation of a protein from the 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 the lac repressor in Escherichia coli [P. Hammar et al., Science 336, 1595 (2012)]. 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 reveal 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.
Collapse
Affiliation(s)
- Marcin Tabaka
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Krzysztof Burdzy
- Department of Mathematics, University of Washington, Box 354350, Seattle, Washington 98195, USA
| | - Robert Hołyst
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| |
Collapse
|
39
|
Cartailler J, Reingruber J. Facilitated diffusion framework for transcription factor search with conformational changes. Phys Biol 2015. [PMID: 26200216 DOI: 10.1088/1478-3975/12/4/046012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Cellular responses often require the fast activation or repression of specific genes, which depends on transcription factors (TFs) that have to quickly find the promoters of these genes within a large genome. TFs search for their DNA promoter target by alternating between bulk diffusion and sliding along the DNA, a mechanism known as facilitated diffusion. We study a facilitated diffusion framework with switching between three search modes: a bulk mode and two sliding modes triggered by conformational changes between two protein conformations. In one conformation (search mode) the TF interacts unspecifically with the DNA backbone resulting in fast sliding. In the other conformation (recognition mode) it interacts specifically and strongly with DNA base pairs leading to slow displacement. From the bulk, a TF associates with the DNA at a random position that is correlated with the previous dissociation point, which implicitly is a function of the DNA structure. The target affinity depends on the conformation. We derive exact expressions for the mean first passage time (MFPT) to bind to the promoter and the conditional probability to bind before detaching when arriving at the promoter site. We systematically explore the parameter space and compare various search scenarios. We compare our results with experimental data for the dimeric Lac repressor search in E. coli bacteria. We find that a coiled DNA conformation is absolutely necessary for a fast MFPT. With frequent spontaneous conformational changes, a fast search time is achieved even when a TF becomes immobilized in the recognition state due to the specific bindings. We find a MFPT compatible with experimental data in presence of a specific TF-DNA interaction energy that has a Gaussian distribution with a large variance.
Collapse
|
40
|
Real sequence effects on the search dynamics of transcription factors on DNA. Sci Rep 2015; 5:10072. [PMID: 26154484 PMCID: PMC5507490 DOI: 10.1038/srep10072] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 03/30/2015] [Indexed: 11/15/2022] Open
Abstract
Recent experiments show that transcription factors (TFs) indeed use the facilitated diffusion mechanism to locate their target sequences on DNA in living bacteria cells: TFs alternate between sliding motion along DNA and relocation events through the cytoplasm. From simulations and theoretical analysis we study the TF-sliding motion for a large section of the DNA-sequence of a common E. coli strain, based on the two-state TF-model with a fast-sliding search state and a recognition state enabling target detection. For the probability to detect the target before dissociating from DNA the TF-search times self-consistently depend heavily on whether or not an auxiliary operator (an accessible sequence similar to the main operator) is present in the genome section. Importantly, within our model the extent to which the interconversion rates between search and recognition states depend on the underlying nucleotide sequence is varied. A moderate dependence maximises the capability to distinguish between the main operator and similar sequences. Moreover, these auxiliary operators serve as starting points for DNA looping with the main operator, yielding a spectrum of target detection times spanning several orders of magnitude. Auxiliary operators are shown to act as funnels facilitating target detection by TFs.
Collapse
|
41
|
Godec A, Metzler R. Signal focusing through active transport. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:010701. [PMID: 26274108 DOI: 10.1103/physreve.92.010701] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Indexed: 06/04/2023]
Abstract
The accuracy of molecular signaling in biological cells and novel diagnostic devices is ultimately limited by the counting noise floor imposed by the thermal diffusion. Motivated by the fact that messenger RNA and vesicle-engulfed signaling molecules transiently bind to molecular motors and are actively transported in biological cells, we show here that the random active delivery of signaling particles to within a typical diffusion distance to the receptor generically reduces the correlation time of the counting noise. Considering a variety of signaling particle sizes from mRNA to vesicles and cell sizes from prokaryotic to eukaryotic cells, we show that the conditions for active focusing-faster and more precise signaling-are indeed compatible with observations in living cells. Our results improve the understanding of molecular cellular signaling and novel diagnostic devices.
Collapse
Affiliation(s)
- Aljaž Godec
- Institute of Physics & Astronomy, University of Potsdam, D-14476 Potsdam-Golm, Germany
- Laboratory for Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Ralf Metzler
- Institute of Physics & Astronomy, University of Potsdam, D-14476 Potsdam-Golm, Germany
- Department of Physics, Tampere University of Technology, FI-33101 Tampere, Finland
| |
Collapse
|
42
|
Smrek J, Grosberg AY. Facilitated diffusion of proteins through crumpled fractal DNA globules. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:012702. [PMID: 26274198 DOI: 10.1103/physreve.92.012702] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Indexed: 06/04/2023]
Abstract
We explore how the specific fractal globule conformation, found for the chromatin fiber of higher eukaryotes and topologically constrained dense polymers, affects the facilitated diffusion of proteins in this environment. Using scaling arguments and supporting Monte Carlo simulations, we relate DNA looping probability distribution, fractal dimension, and protein nonspecific affinity for the DNA to the effective diffusion parameters of the proteins. We explicitly consider correlations between subsequent readsorption events of the proteins, and we find that facilitated diffusion is faster for the crumpled globule conformation with high intersegmental surface dimension than in the case of dense fractal conformations with smooth surfaces. As a byproduct, we obtain an expression for the macroscopic conductivity of a hypothetic material consisting of conducting fractal nanowires immersed in a weakly conducting medium.
Collapse
Affiliation(s)
- Jan Smrek
- Center for Soft Matter Research and Department of Physics, New York University, New York, New York 10003, USA
| | - Alexander Y Grosberg
- Center for Soft Matter Research and Department of Physics, New York University, New York, New York 10003, USA
| |
Collapse
|
43
|
Buechner CN, Maiti A, Drohat AC, Tessmer I. Lesion search and recognition by thymine DNA glycosylase revealed by single molecule imaging. Nucleic Acids Res 2015; 43:2716-29. [PMID: 25712093 PMCID: PMC4357730 DOI: 10.1093/nar/gkv139] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The ability of DNA glycosylases to rapidly and efficiently detect lesions among a vast excess of nondamaged DNA bases is vitally important in base excision repair (BER). Here, we use single molecule imaging by atomic force microscopy (AFM) supported by a 2-aminopurine fluorescence base flipping assay to study damage search by human thymine DNA glycosylase (hTDG), which initiates BER of mutagenic and cytotoxic G:T and G:U mispairs in DNA. Our data reveal an equilibrium between two conformational states of hTDG–DNA complexes, assigned as search complex (SC) and interrogation complex (IC), both at target lesions and undamaged DNA sites. Notably, for both hTDG and a second glycosylase, hOGG1, which recognizes structurally different 8-oxoguanine lesions, the conformation of the DNA in the SC mirrors innate structural properties of their respective target sites. In the IC, the DNA is sharply bent, as seen in crystal structures of hTDG lesion recognition complexes, which likely supports the base flipping required for lesion identification. Our results support a potentially general concept of sculpting of glycosylases to their targets, allowing them to exploit the energetic cost of DNA bending for initial lesion sensing, coupled with continuous (extrahelical) base interrogation during lesion search by DNA glycosylases.
Collapse
Affiliation(s)
- Claudia N Buechner
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Atanu Maiti
- Department of Biochemistry and Molecular Biology and Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Alexander C Drohat
- Department of Biochemistry and Molecular Biology and Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Ingrid Tessmer
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| |
Collapse
|
44
|
Abstract
I present a review of the theoretical and computational methodologies that have been used to model the assembly of viral capsids. I discuss the capabilities and limitations of approaches ranging from equilibrium continuum theories to molecular dynamics simulations, and I give an overview of some of the important conclusions about virus assembly that have resulted from these modeling efforts. Topics include the assembly of empty viral shells, assembly around single-stranded nucleic acids to form viral particles, and assembly around synthetic polymers or charged nanoparticles for nanotechnology or biomedical applications. I present some examples in which modeling efforts have promoted experimental breakthroughs, as well as directions in which the connection between modeling and experiment can be strengthened.
Collapse
|
45
|
Colomb W, Sarkar SK. Extracting physics of life at the molecular level: A review of single-molecule data analyses. Phys Life Rev 2015; 13:107-37. [PMID: 25660417 DOI: 10.1016/j.plrev.2015.01.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 01/09/2015] [Indexed: 12/31/2022]
Abstract
Studying individual biomolecules at the single-molecule level has proved very insightful recently. Single-molecule experiments allow us to probe both the equilibrium and nonequilibrium properties as well as make quantitative connections with ensemble experiments and equilibrium thermodynamics. However, it is important to be careful about the analysis of single-molecule data because of the noise present and the lack of theoretical framework for processes far away from equilibrium. Biomolecular motion, whether it is free in solution, on a substrate, or under force, involves thermal fluctuations in varying degrees, which makes the motion noisy. In addition, the noise from the experimental setup makes it even more complex. The details of biologically relevant interactions, conformational dynamics, and activities are hidden in the noisy single-molecule data. As such, extracting biological insights from noisy data is still an active area of research. In this review, we will focus on analyzing both fluorescence-based and force-based single-molecule experiments and gaining biological insights at the single-molecule level. Inherently nonequilibrium nature of biological processes will be highlighted. Simulated trajectories of biomolecular diffusion will be used to compare and validate various analysis techniques.
Collapse
Affiliation(s)
- Warren Colomb
- Department of Physics, Colorado School of Mines, Golden, CO 80401, United States
| | - Susanta K Sarkar
- Department of Physics, Colorado School of Mines, Golden, CO 80401, United States.
| |
Collapse
|
46
|
Bhattacherjee A, Levy Y. Search by proteins for their DNA target site: 1. The effect of DNA conformation on protein sliding. Nucleic Acids Res 2014; 42:12404-14. [PMID: 25324308 PMCID: PMC4227778 DOI: 10.1093/nar/gku932] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The recognition of DNA-binding proteins (DBPs) to their specific site often precedes by a search technique in which proteins slide, hop along the DNA contour or perform inter-segment transfer and 3D diffusion to dissociate and re-associate to distant DNA sites. In this study, we demonstrated that the strength and nature of the non-specific electrostatic interactions, which govern the search dynamics of DBPs, are strongly correlated with the conformation of the DNA. We tuned two structural parameters, namely curvature and the extent of helical twisting in circular DNA. These two factors are mutually independent of each other and can modulate the electrostatic potential through changing the geometry of the circular DNA conformation. The search dynamics for DBPs on circular DNA is therefore markedly different compared with linear B-DNA. Our results suggest that, for a given DBP, the rotation-coupled sliding dynamics is precluded in highly curved DNA (as well as for over-twisted DNA) because of the large electrostatic energy barrier between the inside and outside of the DNA molecule. Under such circumstances, proteins prefer to hop in order to explore interior DNA sites. The change in the balance between sliding and hopping propensities as a function of DNA curvature or twisting may result in different search efficiency and speed.
Collapse
Affiliation(s)
- Arnab Bhattacherjee
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| |
Collapse
|
47
|
Abstract
Until now, it has been reasonably assumed that specific base-pair recognition is the only mechanism controlling the specificity of transcription factor (TF)-DNA binding. Contrary to this assumption, here we show that nonspecific DNA sequences possessing certain repeat symmetries, when present outside of specific TF binding sites (TFBSs), statistically control TF-DNA binding preferences. We used high-throughput protein-DNA binding assays to measure the binding levels and free energies of binding for several human TFs to tens of thousands of short DNA sequences with varying repeat symmetries. Based on statistical mechanics modeling, we identify a new protein-DNA binding mechanism induced by DNA sequence symmetry in the absence of specific base-pair recognition, and experimentally demonstrate that this mechanism indeed governs protein-DNA binding preferences.
Collapse
|
48
|
DNA Looping Provides for “Intersegmental Hopping” by Proteins: A Mechanism for Long-Range Site Localization. J Mol Biol 2014; 426:3539-52. [DOI: 10.1016/j.jmb.2014.08.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 07/30/2014] [Accepted: 08/04/2014] [Indexed: 11/22/2022]
|
49
|
Paijmans J, ten Wolde PR. Lower bound on the precision of transcriptional regulation and why facilitated diffusion can reduce noise in gene expression. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:032708. [PMID: 25314474 DOI: 10.1103/physreve.90.032708] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Indexed: 06/04/2023]
Abstract
The diffusive arrival of transcription factors at the promoter sites on DNA sets a lower bound on how accurately a cell can regulate its protein levels. Using results from the literature on diffusion-influenced reactions, we derive an analytical expression for the lower bound on the precision of transcriptional regulation. In our theory, transcription factors can perform multiple rounds of one-dimensional (1D) diffusion along the DNA and 3D diffusion in the cytoplasm before binding to the promoter. Comparing our expression for the lower bound on the precision against results from Green's function reaction dynamics simulations shows that the theory is highly accurate under biologically relevant conditions. Our results demonstrate that, to an excellent approximation, the promoter switches between the transcription-factor bound and unbound state in a Markovian fashion. This remains true even in the presence of sliding, i.e., with 1D diffusion along the DNA. This has two important implications: (1) Minimizing the noise in the promoter state is equivalent to minimizing the search time of transcription factors for their promoters; (2) the complicated dynamics of 3D diffusion in the cytoplasm and 1D diffusion along the DNA can be captured in a well-stirred model by renormalizing the promoter association and dissociation rates, making it possible to efficiently simulate the promoter dynamics using Gillespie simulations. Based on the recent experimental observation that sliding can speed up the promoter search by a factor of 4, our theory predicts that sliding can enhance the precision of transcriptional regulation by a factor of 2.
Collapse
Affiliation(s)
- Joris Paijmans
- FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | | |
Collapse
|
50
|
|