1
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Rogoulenko E, Levy Y. Skipping events impose repeated binding attempts: profound kinetic implications of protein-DNA conformational changes. Nucleic Acids Res 2024; 52:6763-6776. [PMID: 38721783 PMCID: PMC11229352 DOI: 10.1093/nar/gkae333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/09/2024] [Accepted: 04/16/2024] [Indexed: 07/09/2024] Open
Abstract
The kinetics of protein-DNA recognition, along with its thermodynamic properties, including affinity and specificity, play a central role in shaping biological function. Protein-DNA recognition kinetics are characterized by two key elements: the time taken to locate the target site amid various nonspecific alternatives; and the kinetics involved in the recognition process, which may necessitate overcoming an energetic barrier. In this study, we developed a coarse-grained (CG) model to investigate interactions between a transcription factor called the sex-determining region Y (SRY) protein and DNA, in order to probe how DNA conformational changes affect SRY-DNA recognition and binding kinetics. We find that, not only does a requirement for such a conformational DNA transition correspond to a higher energetic barrier for binding and therefore slower kinetics, it may further impede the recognition kinetics by increasing unsuccessful binding events (skipping events) where the protein partially binds its DNA target site but fails to form the specific protein-DNA complex. Such skipping events impose the need for additional cycles protein search of nonspecific DNA sites, thus significantly extending the overall recognition time. Our results highlight a trade-off between the speed with which the protein scans nonspecific DNA and the rate at which the protein recognizes its specific target site. Finally, we examine molecular approaches potentially adopted by natural systems to enhance protein-DNA recognition despite its intrinsically slow kinetics.
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Affiliation(s)
- Elena Rogoulenko
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yaakov Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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2
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Nordin A, Pagella P, Zambanini G, Cantù C. Exhaustive identification of genome-wide binding events of transcriptional regulators. Nucleic Acids Res 2024; 52:e40. [PMID: 38499482 PMCID: PMC11040144 DOI: 10.1093/nar/gkae180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/20/2024] [Accepted: 02/29/2024] [Indexed: 03/20/2024] Open
Abstract
Genome-wide binding assays aspire to map the complete binding pattern of gene regulators. Common practice relies on replication-duplicates or triplicates-and high stringency statistics to favor false negatives over false positives. Here we show that duplicates and triplicates of CUT&RUN are not sufficient to discover the entire activity of transcriptional regulators. We introduce ICEBERG (Increased Capture of Enrichment By Exhaustive Replicate aGgregation), a pipeline that harnesses large numbers of CUT&RUN replicates to discover the full set of binding events and chart the line between false positives and false negatives. We employed ICEBERG to map the full set of H3K4me3-marked regions, the targets of the co-factor β-catenin, and those of the transcription factor TBX3, in human colorectal cancer cells. The ICEBERG datasets allow benchmarking of individual replicates, comparing the performance of peak calling and replication approaches, and expose the arbitrary nature of strategies to identify reproducible peaks. Instead of a static view of genomic targets, ICEBERG establishes a spectrum of detection probabilities across the genome for a given factor, underlying the intrinsic dynamicity of its mechanism of action, and permitting to distinguish frequent from rare regulation events. Finally, ICEBERG discovered instances, undetectable with other approaches, that underlie novel mechanisms of colorectal cancer progression.
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Affiliation(s)
- Anna Nordin
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Pierfrancesco Pagella
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Gianluca Zambanini
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Claudio Cantù
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
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3
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Kim H, Pak Y. Three-State Diffusion Model of DNA Glycosylase Translocation along Stretched DNA as Revealed by Free Energy Landscapes at the All-Atom Level. J Chem Theory Comput 2024; 20:2666-2675. [PMID: 38451471 DOI: 10.1021/acs.jctc.4c00043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
DNA glycosylases play key roles in the maintenance of genomic integrity. These enzymes effectively find rare damaged sites in DNA and participate in subsequent base excision repair. Single-molecule and ensemble experiments have revealed key aspects of this damage-site searching mechanism and the involvement of facilitated diffusion. In this study, we describe free energy landscapes of enzyme translocation along nonspecific DNA obtained using a fully atomistic molecular dynamics (MD) simulation of a well-known DNA glycosylase, human 8-oxoguanine DNA glycosylase 1 (hOGG1). Based on an analysis of simulated free energy profiles, we propose a three-state model for the damage-site searching mechanism. In the three states, named the L1, L2, and L3 states, the L1 state is a helical sliding mode in close contact with DNA, whereas the L2 state is a major- or minor-groove tracking mode in loose contact with DNA and the L3 state is a two-dimensional freely diffusing mode during which hOGG1 is somewhat removed from the DNA surface (∼24 Å away from the surface). This three-state model well describes key experimental findings obtained from single-molecule and ensemble experiments and provides a unified molecular picture of the DNA lesion-searching mechanism of hOGG1.
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Affiliation(s)
- Hyeonjun Kim
- Department of Chemistry and Institute of Functional Materials, Pusan National University, Busan 46241, South Korea
| | - Youngshang Pak
- Department of Chemistry and Institute of Functional Materials, Pusan National University, Busan 46241, South Korea
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4
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Bebon R, Godec A. Controlling Uncertainty of Empirical First-Passage Times in the Small-Sample Regime. PHYSICAL REVIEW LETTERS 2023; 131:237101. [PMID: 38134782 DOI: 10.1103/physrevlett.131.237101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 10/18/2023] [Accepted: 10/31/2023] [Indexed: 12/24/2023]
Abstract
We derive general bounds on the probability that the empirical first-passage time τ[over ¯]_{n}≡∑_{i=1}^{n}τ_{i}/n of a reversible ergodic Markov process inferred from a sample of n independent realizations deviates from the true mean first-passage time by more than any given amount in either direction. We construct nonasymptotic confidence intervals that hold in the elusive small-sample regime and thus fill the gap between asymptotic methods and the Bayesian approach that is known to be sensitive to prior belief and tends to underestimate uncertainty in the small-sample setting. We prove sharp bounds on extreme first-passage times that control uncertainty even in cases where the mean alone does not sufficiently characterize the statistics. Our concentration-of-measure-based results allow for model-free error control and reliable error estimation in kinetic inference, and are thus important for the analysis of experimental and simulation data in the presence of limited sampling.
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Affiliation(s)
- Rick Bebon
- Mathematical bioPhysics Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Aljaž Godec
- Mathematical bioPhysics Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
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5
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Al Masri C, Wan B, Yu J. Nonspecific vs. specific DNA binding free energetics of a transcription factor domain protein. Biophys J 2023; 122:4476-4487. [PMID: 37897044 PMCID: PMC10722393 DOI: 10.1016/j.bpj.2023.10.025] [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: 03/06/2023] [Revised: 07/06/2023] [Accepted: 10/20/2023] [Indexed: 10/29/2023] Open
Abstract
Transcription factor (TF) proteins regulate gene expression by binding to specific sites on the genome. In the facilitated diffusion model, an optimized search process is achieved by the TF alternating between 3D diffusion in the bulk and 1D diffusion along DNA. While undergoing 1D diffusion, the protein can switch from a search mode for fast diffusion along nonspecific DNA to a recognition mode for stable binding to specific DNA. It was recently noticed that, for a small TF domain protein, reorientations on DNA happen between the nonspecific and specific DNA binding. We here conducted all-atom molecular dynamics simulations with steering forces to reveal the protein-DNA binding free energetics, confirming that the search and recognition modes are distinguished primarily by protein orientations on the DNA. As the binding free energy difference between the specific and nonspecific DNA system slightly deviates from that being estimated directly from dissociation constants on 15-bp DNA constructs, we hypothesize that the discrepancy can come from DNA sequences flanking the 6-bp central binding sites that impact on the dissociation kinetics measurements. The hypothesis is supported by a simplified spherical protein-DNA model along with stochastic simulations and kinetic modeling.
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Affiliation(s)
- Carmen Al Masri
- Department of Physics and Astronomy, University of California, Irvine, California
| | - Biao Wan
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China
| | - Jin Yu
- Department of Physics and Astronomy, University of California, Irvine, California; Department of Physics and Astronomy, Department of Chemistry, NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, California.
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6
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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.
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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
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7
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Dutta P, Roy P, Sengupta N. Effects of External Perturbations on Protein Systems: A Microscopic View. ACS OMEGA 2022; 7:44556-44572. [PMID: 36530249 PMCID: PMC9753117 DOI: 10.1021/acsomega.2c06199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Protein folding can be viewed as the origami engineering of biology resulting from the long process of evolution. Even decades after its recognition, research efforts worldwide focus on demystifying molecular factors that underlie protein structure-function relationships; this is particularly relevant in the era of proteopathic disease. A complex co-occurrence of different physicochemical factors such as temperature, pressure, solvent, cosolvent, macromolecular crowding, confinement, and mutations that represent realistic biological environments are known to modulate the folding process and protein stability in unique ways. In the current review, we have contextually summarized the substantial efforts in unveiling individual effects of these perturbative factors, with major attention toward bottom-up approaches. Moreover, we briefly present some of the biotechnological applications of the insights derived from these studies over various applications including pharmaceuticals, biofuels, cryopreservation, and novel materials. Finally, we conclude by summarizing the challenges in studying the combined effects of multifactorial perturbations in protein folding and refer to complementary advances in experiment and computational techniques that lend insights to the emergent challenges.
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Affiliation(s)
- Pallab Dutta
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
| | - Priti Roy
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
- Department
of Chemistry, Oklahoma State University, Stillwater, Oklahoma74078, United States
| | - Neelanjana Sengupta
- Department
of Biological Sciences, Indian Institute
of Science Education and Research (IISER) Kolkata, Mohanpur741246, India
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8
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Mondal A, Bhattacherjee A. Understanding protein diffusion on force-induced stretched DNA conformation. Front Mol Biosci 2022; 9:953689. [PMID: 36545509 PMCID: PMC9760818 DOI: 10.3389/fmolb.2022.953689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 11/22/2022] [Indexed: 12/11/2022] Open
Abstract
DNA morphology is subjected to environmental conditions and is closely coupled with its function. For example, DNA experiences stretching forces during several biological processes, including transcription and genome transactions, that significantly alter its conformation from that of B-DNA. Indeed, a well-defined 1.5 times extended conformation of dsDNA, known as Σ-DNA, has been reported in DNA complexes with proteins such as Rad51 and RecA. A striking feature in Σ-DNA is that the nucleobases are partitioned into triplets of three locally stacked bases separated by an empty rise gap of ∼ 5 Å. The functional role of such a DNA base triplet was hypothesized to be coupled with the ease of recognition of DNA bases by DNA-binding proteins (DBPs) and the physical origin of three letters (codon/anti-codon) in the genetic code. However, the underlying mechanism of base-triplet formation and the ease of DNA base-pair recognition by DBPs remain elusive. To investigate, here, we study the diffusion of a protein on a force-induced stretched DNA using coarse-grained molecular dynamics simulations. Upon pulling at the 3' end of DNA by constant forces, DNA exhibits a conformational transition from B-DNA to a ladder-like S-DNA conformation via Σ-DNA intermediate. The resulting stretched DNA conformations exhibit non-uniform base-pair clusters such as doublets, triplets, and quadruplets, of which triplets are energetically more stable than others. We find that protein favors the triplet formation compared to its unbound form while interacting non-specifically along DNA, and the relative population of it governs the ruggedness of the protein-DNA binding energy landscape and enhances the efficiency of DNA base recognition. Furthermore, we analyze the translocation mechanism of a DBP under different force regimes and underscore the significance of triplet formation in regulating the facilitated diffusion of protein on DNA. Our study, thus, provides a plausible framework for understanding the structure-function relationship between triplet formation and base recognition by a DBP and helps to understand gene regulation in complex regulatory processes.
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9
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Li S, Chen L, Gui X, He D, Hu J, Huang Z, Lin S, Tu Y, Dong Y. Molecular Dynamics Simulation for Thiolated Poly(ethylene glycol) at Low‐Temperature Based on the Density Functional Tight‐Binding Method. ADVANCED THEORY AND SIMULATIONS 2022. [DOI: 10.1002/adts.202200281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Shi Li
- Guangzhou Institute of Chemistry Chinese Academy of Sciences Guangzhou 510650 P. R. China
- School of Chemical and Environmental Engineering Anhui Polytechnic University Wuhu 241000 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Lei Chen
- Guangzhou Institute of Chemistry Chinese Academy of Sciences Guangzhou 510650 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Xuefeng Gui
- Guangzhou Institute of Chemistry Chinese Academy of Sciences Guangzhou 510650 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
- Guangdong Provincial Key Laboratory of Organic Polymer Materials for Electronics Guangzhou 510650 P. R. China
- CAS Engineering Laboratory for Special Fine Chemicals Guangzhou 510650 P. R. China
- Incubator of Nanxiong CAS Co. Ltd. Nanxiong 512400 P. R. China
| | - Daguang He
- Guangzhou Institute of Chemistry Chinese Academy of Sciences Guangzhou 510650 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Jiwen Hu
- Guangzhou Institute of Chemistry Chinese Academy of Sciences Guangzhou 510650 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
- Guangdong Provincial Key Laboratory of Organic Polymer Materials for Electronics Guangzhou 510650 P. R. China
- CAS Engineering Laboratory for Special Fine Chemicals Guangzhou 510650 P. R. China
- Incubator of Nanxiong CAS Co. Ltd. Nanxiong 512400 P. R. China
| | - Zhenzhu Huang
- Guangzhou Institute of Chemistry Chinese Academy of Sciences Guangzhou 510650 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
- Guangdong Provincial Key Laboratory of Organic Polymer Materials for Electronics Guangzhou 510650 P. R. China
- CAS Engineering Laboratory for Special Fine Chemicals Guangzhou 510650 P. R. China
- Incubator of Nanxiong CAS Co. Ltd. Nanxiong 512400 P. R. China
| | - Shudong Lin
- Guangzhou Institute of Chemistry Chinese Academy of Sciences Guangzhou 510650 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
- Guangdong Provincial Key Laboratory of Organic Polymer Materials for Electronics Guangzhou 510650 P. R. China
- CAS Engineering Laboratory for Special Fine Chemicals Guangzhou 510650 P. R. China
- Incubator of Nanxiong CAS Co. Ltd. Nanxiong 512400 P. R. China
| | - Yuanyuan Tu
- Guangzhou Institute of Chemistry Chinese Academy of Sciences Guangzhou 510650 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
- Guangdong Provincial Key Laboratory of Organic Polymer Materials for Electronics Guangzhou 510650 P. R. China
- CAS Engineering Laboratory for Special Fine Chemicals Guangzhou 510650 P. R. China
- Incubator of Nanxiong CAS Co. Ltd. Nanxiong 512400 P. R. China
| | - Yonglu Dong
- Guangzhou Institute of Chemistry Chinese Academy of Sciences Guangzhou 510650 P. R. China
- Incubator of Nanxiong CAS Co. Ltd. Nanxiong 512400 P. R. China
- Management Committee of Shaoguan NanXiong Hi‐Tech Industry Development Zone Nanxiong 512400 P. R. China
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10
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Felipe C, Shin J, Kolomeisky AB. How Pioneer Transcription Factors Search for Target Sites on Nucleosomal DNA. J Phys Chem B 2022; 126:4061-4068. [PMID: 35622093 DOI: 10.1021/acs.jpcb.2c01931] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
All major biological processes start after protein molecules known as transcription factors detect specific regulatory sequences on DNA and initiate genetic expression by associating to them. But in eukaryotic cells, much of the DNA is covered by nucleosomes and other chromatin structures, preventing transcription factors from binding to their targets. At the same time, experimental studies show that there are several classes of proteins, called "pioneer transcription factors", that are able to reach the targets on nucleosomal DNA; however, the underlying microscopic mechanisms remain not well understood. We propose a new theoretical approach that might explain how pioneer transcription factors can find their targets. It is argued that pioneer transcription factors might weaken the interactions between the DNA and nucleosome by substituting them with similar interactions between transcription factors and DNA. Using this idea, we develop a discrete-state stochastic model that allows for exact calculations of target search dynamics on nucleosomal DNA using first-passage probabilities approach. It is found that the target search on nuclesomal DNA for pioneer transcription factors might be significantly accelerated while the search is slower on naked DNA in comparison with normal transcription factors. Our theoretical predictions are supported by Monte Carlo computer simulations, and they also agree with available experimental observations.
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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
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11
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Garcia DA, Fettweis G, Presman DM, Paakinaho V, Jarzynski C, Upadhyaya A, Hager GL. Power-law behavior of transcription factor dynamics at the single-molecule level implies a continuum affinity model. Nucleic Acids Res 2021; 49:6605-6620. [PMID: 33592625 DOI: 10.1093/nar/gkab072] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/13/2021] [Accepted: 02/11/2021] [Indexed: 12/11/2022] Open
Abstract
Single-molecule tracking (SMT) allows the study of transcription factor (TF) dynamics in the nucleus, giving important information regarding the diffusion and binding behavior of these proteins in the nuclear environment. Dwell time distributions obtained by SMT for most TFs appear to follow bi-exponential behavior. This has been ascribed to two discrete populations of TFs-one non-specifically bound to chromatin and another specifically bound to target sites, as implied by decades of biochemical studies. However, emerging studies suggest alternate models for dwell-time distributions, indicating the existence of more than two populations of TFs (multi-exponential distribution), or even the absence of discrete states altogether (power-law distribution). Here, we present an analytical pipeline to evaluate which model best explains SMT data. We find that a broad spectrum of TFs (including glucocorticoid receptor, oestrogen receptor, FOXA1, CTCF) follow a power-law distribution of dwell-times, blurring the temporal line between non-specific and specific binding, suggesting that productive binding may involve longer binding events than previously believed. From these observations, we propose a continuum of affinities model to explain TF dynamics, that is consistent with complex interactions of TFs with multiple nuclear domains as well as binding and searching on the chromatin template.
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Affiliation(s)
- David A Garcia
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA.,Department of Physics, University of Maryland, College Park, MD 20742, USA
| | - Gregory Fettweis
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA
| | - Diego M Presman
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA.,Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, C1428EGA, Buenos Aires, Argentina
| | - Ville Paakinaho
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA.,Institute of Biomedicine, University of Eastern Finland, Kuopio, PO Box 1627, FI-70211 Kuopio, Finland
| | - Christopher Jarzynski
- Department of Physics, University of Maryland, College Park, MD 20742, USA.,Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA.,Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - Arpita Upadhyaya
- Department of Physics, University of Maryland, College Park, MD 20742, USA.,Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA
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12
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Corbella M, Liao Q, Moreira C, Parracino A, Kasson PM, Kamerlin SCL. The N-terminal Helix-Turn-Helix Motif of Transcription Factors MarA and Rob Drives DNA Recognition. J Phys Chem B 2021; 125:6791-6806. [PMID: 34137249 PMCID: PMC8279559 DOI: 10.1021/acs.jpcb.1c00771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
DNA-binding proteins
play an important role in gene regulation
and cellular function. The transcription factors MarA and Rob are
two homologous members of the AraC/XylS family that regulate multidrug
resistance. They share a common DNA-binding domain, and Rob possesses
an additional C-terminal domain that permits binding of low-molecular
weight effectors. Both proteins possess two helix-turn-helix (HTH)
motifs capable of binding DNA; however, while MarA interacts with
its promoter through both HTH-motifs, prior studies indicate that
Rob binding to DNA via a single HTH-motif is sufficient for tight
binding. In the present work, we perform microsecond time scale all-atom
simulations of the binding of both transcription factors to different
DNA sequences to understand the determinants of DNA recognition and
binding. Our simulations characterize sequence-dependent changes in
dynamical behavior upon DNA binding, showcasing the role of Arg40
of the N-terminal HTH-motif in allowing for specific tight binding.
Finally, our simulations demonstrate that an acidic C-terminal loop
of Rob can control the DNA binding mode, facilitating interconversion
between the distinct DNA binding modes observed in MarA and Rob. In
doing so, we provide detailed molecular insight into DNA binding and
recognition by these proteins, which in turn is an important step
toward the efficient design of antivirulence agents that target these
proteins.
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Affiliation(s)
- Marina Corbella
- Science for Life Laboratory, Department of Chemistry-BMC, Uppsala University, Uppsala, S-751 23, Sweden
| | - Qinghua Liao
- Science for Life Laboratory, Department of Chemistry-BMC, Uppsala University, Uppsala, S-751 23, Sweden
| | - Cátia Moreira
- Science for Life Laboratory, Department of Chemistry-BMC, Uppsala University, Uppsala, S-751 23, Sweden
| | - Antonietta Parracino
- Science for Life Laboratory, Department of Chemistry-BMC, Uppsala University, Uppsala, S-751 23, Sweden
| | - Peter M Kasson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, S-65124, Sweden.,Departments of Molecular Physiology and Biomedical Engineering, University of Virginia, Charlottesville, Virginia 22908, United States
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13
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Revealing atomic-scale molecular diffusion of a plant-transcription factor WRKY domain protein along DNA. Proc Natl Acad Sci U S A 2021; 118:2102621118. [PMID: 34074787 PMCID: PMC8201915 DOI: 10.1073/pnas.2102621118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In transcription factors’ search for target genes, one-dimensional diffusion of the protein along DNA is essential. Experimentally, it remains challenging to resolve the individual diffusional steps of protein on DNA. Here, we report mainly all-atom equilibrium simulations of a WRKY domain protein in association with and diffusion along DNA. We demonstrate a complete stepping cycle of the protein for one base pair on DNA within microseconds, along with stochastic motions. Processive protein diffusions on DNA have been further sampled in a coarse-grained model. We have also found preferential DNA-strand association of the domain protein, which becomes most prominent at specific DNA binding, and it can be common for small-domain proteins to balance movements on the DNA with the sequence recognition. Transcription factor (TF) target search on genome is highly essential for gene expression and regulation. High-resolution determination of TF diffusion along DNA remains technically challenging. Here, we constructed a TF model system using the plant WRKY domain protein in complex with DNA from crystallography and demonstrated microsecond diffusion dynamics of WRKY on DNA by employing all-atom molecular-dynamics (MD) simulations. Notably, we found that WRKY preferentially binds to one strand of DNA with significant energetic bias compared with the other, or nonpreferred strand. The preferential DNA-strand binding becomes most prominent in the static process, from nonspecific to specific DNA binding, but less distinct during diffusive movements of the domain protein on the DNA. Remarkably, without employing acceleration forces or bias, we captured a complete one-base-pair stepping cycle of the protein tracking along major groove of DNA with a homogeneous poly-adenosine sequence, as individual hydrogen bonds break and reform at the protein–DNA binding interface. Further DNA-groove tracking motions of the protein forward or backward, with occasional sliding as well as strand crossing to minor groove of DNA, were also captured. The processive diffusion of WRKY along DNA has been further sampled via coarse-grained MD simulations. The study thus provides structural dynamics details on diffusion of a small TF domain protein, suggests how the protein approaches a specific recognition site on DNA, and supports further high-precision experimental detection. The stochastic movements revealed in the TF diffusion also provide general clues about how other protein walkers step and slide along DNA.
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14
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Bigman LS, Greenblatt HM, Levy Y. What Are the Molecular Requirements for Protein Sliding along DNA? J Phys Chem B 2021; 125:3119-3131. [PMID: 33754737 PMCID: PMC8041311 DOI: 10.1021/acs.jpcb.1c00757] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
![]()
DNA-binding proteins rely on linear
diffusion along the longitudinal
DNA axis, supported by their nonspecific electrostatic affinity for
DNA, to search for their target recognition sites. One may therefore
expect that the ability to engage in linear diffusion along DNA is
universal to all DNA-binding proteins, with the detailed biophysical
characteristics of that diffusion differing between proteins depending
on their structures and functions. One key question is whether the
linear diffusion mechanism is defined by translation coupled with
rotation, a mechanism that is often termed sliding. We conduct coarse-grained
and atomistic molecular dynamics simulations to investigate the minimal
requirements for protein sliding along DNA. We show that coupling,
while widespread, is not universal. DNA-binding proteins that slide
along DNA transition to uncoupled translation–rotation (i.e.,
hopping) at higher salt concentrations. Furthermore, and consistently
with experimental reports, we find that the sliding mechanism is the
less dominant mechanism for some DNA-binding proteins, even at low
salt concentrations. In particular, the toroidal PCNA protein is shown
to follow the hopping rather than the sliding mechanism.
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Affiliation(s)
- Lavi S Bigman
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Harry M Greenblatt
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yaakov Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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15
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Tian J, Wang L, Da LT. Atomic resolution of short-range sliding dynamics of thymine DNA glycosylase along DNA minor-groove for lesion recognition. Nucleic Acids Res 2021; 49:1278-1293. [PMID: 33469643 PMCID: PMC7897493 DOI: 10.1093/nar/gkaa1252] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 12/10/2020] [Accepted: 12/15/2020] [Indexed: 02/06/2023] Open
Abstract
Thymine DNA glycosylase (TDG), as a repair enzyme, plays essential roles in maintaining the genome integrity by correcting several mismatched/damaged nucleobases. TDG acquires an efficient strategy to search for the lesions among a vast number of cognate base pairs. Currently, atomic-level details of how TDG translocates along DNA as it approaches the lesion site and the molecular mechanisms of the interplay between TDG and DNA are still elusive. Here, by constructing the Markov state model based on hundreds of molecular dynamics simulations with an integrated simulation time of ∼25 μs, we reveal the rotation-coupled sliding dynamics of TDG along a 9 bp DNA segment containing one G·T mispair. We find that TDG translocates along DNA at a relatively faster rate when distant from the lesion site, but slows down as it approaches the target, accompanied by deeply penetrating into the minor-groove, opening up the mismatched base pair and significantly sculpturing the DNA shape. Moreover, the electrostatic interactions between TDG and DNA are found to be critical for mediating the TDG translocation. Notably, several uncharacterized TDG residues are identified to take part in regulating the conformational switches of TDG occurred in the site-transfer process, which warrants further experimental validations.
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Affiliation(s)
- Jiaqi Tian
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Lingyan Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Lin-Tai Da
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
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16
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Pantatosaki E, Papadopoulos GK. Binding Dynamics of siRNA with Selected Lipopeptides: A Computer-Aided Study of the Effect of Lipopeptides' Functional Groups and Stereoisomerism. J Chem Theory Comput 2020; 16:3842-3855. [PMID: 32324997 DOI: 10.1021/acs.jctc.9b01261] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The engineering issues pertaining to nanoparticle systems toward targeted gene therapies have not been fully probed. Recent experiments have identified specific structural characteristics of a novel class of lipopeptides (LP) that may lead to potent nanocarriers intended as RNAi therapeutics, albeit the molecular mechanism that underlies their performance remains unexplored. We conducted molecular dynamics simulations in atomistic detail coupled with free energy computations to study the dynamics and thermodynamics of an acrylate- and an epoxide-derived LP, members of the aforesaid class, upon their binding to siRNA in aqueous solution aiming at examining structure-potency relations. We found that the entropic part of the free energy of binding predominates; moreover, the first LP class tends to disrupt the Watson-Crick base pairing of siRNA, whereas the latter leaves the double helix intact. Moreover, the identified tug-of-war effect between LP-water and LP-siRNA hydrogen bonding in the supramolecular complex can underpin synthesis routes toward tuning the association dynamics. Our simulations on two diastereomers of the epoxide-derived LP showed significant structural and energetics differences upon binding, as a result of steric effects imposed by the different absolute configurations at their chiral centers. These findings may serve as crucial design parameters toward modulating the interplay between complex stability and ease of releasing the nucleic acid drug into the cell.
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Affiliation(s)
- Evangelia Pantatosaki
- School of Chemical Engineering, National Technical University of Athens, 15780 Athens, Greece
| | - George K Papadopoulos
- School of Chemical Engineering, National Technical University of Athens, 15780 Athens, Greece.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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17
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Chen Y, Zhao G, Zahumensky J, Honey S, Futcher B. Differential Scaling of Gene Expression with Cell Size May Explain Size Control in Budding Yeast. Mol Cell 2020; 78:359-370.e6. [PMID: 32246903 DOI: 10.1016/j.molcel.2020.03.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 12/14/2019] [Accepted: 03/10/2020] [Indexed: 01/25/2023]
Abstract
Yeast cells must grow to a critical size before committing to division. It is unknown how size is measured. We find that as cells grow, mRNAs for some cell-cycle activators scale faster than size, increasing in concentration, while mRNAs for some inhibitors scale slower than size, decreasing in concentration. Size-scaled gene expression could cause an increasing ratio of activators to inhibitors with size, triggering cell-cycle entry. Consistent with this, expression of the CLN2 activator from the promoter of the WHI5 inhibitor, or vice versa, interfered with cell size homeostasis, yielding a broader distribution of cell sizes. We suggest that size homeostasis comes from differential scaling of gene expression with size. Differential regulation of gene expression as a function of cell size could affect many cellular processes.
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Affiliation(s)
- Yuping Chen
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY 11794-5222, USA
| | - Gang Zhao
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY 11794-5222, USA
| | - Jakub Zahumensky
- Department of Functional Organization of Biomembranes, Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, Prague 142 20, Czech Republic
| | - Sangeet Honey
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY 11794-5222, USA
| | - Bruce Futcher
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY 11794-5222, USA.
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18
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Mishra G, Bigman LS, Levy Y. ssDNA diffuses along replication protein A via a reptation mechanism. Nucleic Acids Res 2020; 48:1701-1714. [PMID: 31919510 PMCID: PMC7038930 DOI: 10.1093/nar/gkz1202] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 11/23/2019] [Accepted: 01/08/2020] [Indexed: 01/30/2023] Open
Abstract
Replication protein A (RPA) plays a critical role in all eukaryotic DNA processing involving single-stranded DNA (ssDNA). Contrary to the notion that RPA provides solely inert protection to transiently formed ssDNA, the RPA-ssDNA complex acts as a dynamic DNA processing unit. Here, we studied the diffusion of RPA along 60 nt ssDNA using a coarse-grained model in which the ssDNA-RPA interface was modeled by both aromatic and electrostatic interactions. Our study provides direct evidence of bulge formation during the diffusion of ssDNA along RPA. Bulges can form at a few sites along the interface and store 1-7 nt of ssDNA whose release, upon bulge dissolution, leads to propagation of ssDNA diffusion. These findings thus support the reptation mechanism, which involves bulge formation linked to the aromatic interactions, whose short range nature reduces cooperativity in ssDNA diffusion. Greater cooperativity and a larger diffusion coefficient for ssDNA diffusion along RPA are observed for RPA variants with weaker aromatic interactions and for interfaces homogenously stabilized by electrostatic interactions. ssDNA propagation in the latter instance is characterized by lower probabilities of bulge formation; thus, it may fit the sliding-without-bulge model better than the reptation model. Thus, the reptation mechanism allows ssDNA mobility despite the extensive and high affinity interface of RPA with ssDNA. The short-range aromatic interactions support bulge formation while the long-range electrostatic interactions support the release of the stored excess ssDNA in the bulge and thus the overall diffusion.
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Affiliation(s)
- Garima Mishra
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel.,Department of Physics, Indian Institute of Technology Kanpur, Kanpur, 208016, India
| | - Lavi S Bigman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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19
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Felipe C, Shin J, Loginova Y, Kolomeisky AB. The effect of obstacles in multi-site protein target search with DNA looping. J Chem Phys 2020; 152:025101. [PMID: 31941320 DOI: 10.1063/1.5135917] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Many fundamental biological processes are regulated by protein-DNA complexes called synaptosomes, which possess multiple interaction sites. Despite the critical importance of synaptosomes, the mechanisms of their formation are not well understood. Because of the multisite nature of participating proteins, it is widely believed that their search for specific sites on DNA involves the formation and breaking of DNA loops and sliding in the looped configurations. In reality, DNA in live cells is densely covered by other biological molecules that might interfere with the formation of synaptosomes. In this work, we developed a theoretical approach to evaluate the role of obstacles in the target search of multisite proteins when the formation of DNA loops and the sliding in looped configurations are possible. Our theoretical method is based on analysis of a discrete-state stochastic model that uses a master equations approach and extensive computer simulations. It is found that the obstacle slows down the search dynamics in the system when DNA loops are long-lived, but the effect is minimal for short-lived DNA loops. In addition, the relative positions of the target and the obstacle strongly influence the target search kinetics. Furthermore, the presence of the obstacle might increase the noise in the system. These observations are discussed using physical-chemical arguments. Our theoretical approach clarifies the molecular mechanisms of formation of protein-DNA complexes with multiple interactions sites.
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Affiliation(s)
- Cayke Felipe
- Department of Physics, Rice University, Houston, Texas 77005, USA
| | - Jaeoh Shin
- Department of Chemistry, Rice University, Houston, Texas 77005, USA
| | - Yulia Loginova
- Department of Chemistry, Moscow State University, Moscow, Russia
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20
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Pal S, Hoinka J, Przytycka TM. Co-SELECT reveals sequence non-specific contribution of DNA shape to transcription factor binding in vitro. Nucleic Acids Res 2020; 47:6632-6641. [PMID: 31226207 DOI: 10.1093/nar/gkz540] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 05/31/2019] [Accepted: 06/06/2019] [Indexed: 12/22/2022] Open
Abstract
Understanding the principles of DNA binding by transcription factors (TFs) is of primary importance for studying gene regulation. Recently, several lines of evidence suggested that both DNA sequence and shape contribute to TF binding. However, the following compelling question is yet to be considered: in the absence of any sequence similarity to the binding motif, can DNA shape still increase binding probability? To address this challenge, we developed Co-SELECT, a computational approach to analyze the results of in vitro HT-SELEX experiments for TF-DNA binding. Specifically, Co-SELECT leverages the presence of motif-free sequences in late HT-SELEX rounds and their enrichment in weak binders allows Co-SELECT to detect an evidence for the role of DNA shape features in TF binding. Our approach revealed that, even in the absence of the sequence motif, TFs have propensity to bind to DNA molecules of the shape consistent with the motif specific binding. This provides the first direct evidence that shape features that accompany the preferred sequence motifs also bestow an advantage for weak, sequence non-specific binding.
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Affiliation(s)
- Soumitra Pal
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Jan Hoinka
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Teresa M Przytycka
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
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21
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Liu Y, Ren X, He L. A DFT study of energetic and structural properties of a full turn of A-form DNA under relaxed and stretching conditions. J Chem Phys 2019; 151:215102. [DOI: 10.1063/1.5129716] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Yue Liu
- CAS Key Laboratory of Quantum Information, University of Science and Technology of China, Hefei 230026, Anhui, China
- CAS Center for Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, Anhui, China
| | - Xinguo Ren
- CAS Key Laboratory of Quantum Information, University of Science and Technology of China, Hefei 230026, Anhui, China
- CAS Center for Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, Anhui, China
| | - Lixin He
- CAS Key Laboratory of Quantum Information, University of Science and Technology of China, Hefei 230026, Anhui, China
- CAS Center for Excellence in Quantum Information and Quantum Physics, University of Science and Technology of China, Hefei 230026, Anhui, China
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22
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Daitchman D, Greenblatt HM, Levy Y. Diffusion of ring-shaped proteins along DNA: case study of sliding clamps. Nucleic Acids Res 2019; 46:5935-5949. [PMID: 29860305 PMCID: PMC6158715 DOI: 10.1093/nar/gky436] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 05/08/2018] [Indexed: 12/13/2022] Open
Abstract
Several DNA-binding proteins, such as topoisomerases, helicases and sliding clamps, have a toroidal (i.e. ring) shape that topologically traps DNA, with this quality being essential to their function. Many DNA-binding proteins that function, for example, as transcription factors or enzymes were shown to be able to diffuse linearly (i.e. slide) along DNA during the search for their target binding sites. The protein's sliding properties and ability to search DNA, which often also involves hopping and dissociation, are expected to be different when it encircles the DNA. In this study, we explored the linear diffusion of four ring-shaped proteins of very similar structure: three sliding clamps (PCNA, β-clamp, and the gp45) and the 9-1-1 protein, with a particular focus on PCNA. Coarse-grained molecular dynamics simulations were performed to decipher the sliding mechanism adopted by these ring-shaped proteins and to determine how the molecular properties of the inner and outer ring govern its search speed. We designed in silico variants to dissect the contributions of ring geometry and electrostatics to the sliding speed of ring-shaped proteins along DNA. We found that the toroidal proteins diffuse when they are tilted relative to the DNA axis and able to rotate during translocation, but that coupling between rotation and translocation is quite weak. Their diffusion speed is affected by the shape of the inner ring and, to a lesser extent, by its electrostatic properties. However, breaking the symmetry of the electrostatic potential can result in deviation of the DNA from the center of the ring and cause slower linear diffusion. The findings are discussed in light of earlier computational and experimental studies on the sliding of clamps.
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Affiliation(s)
- Dina Daitchman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Harry M Greenblatt
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
- To whom correspondence should be addressed. Tel: +972 8 9344587;
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23
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Shin J, Kolomeisky AB. Facilitation of DNA loop formation by protein-DNA non-specific interactions. SOFT MATTER 2019; 15:5255-5263. [PMID: 31204761 DOI: 10.1039/c9sm00671k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Complex DNA topological structures, including polymer loops, are frequently observed in biological processes when protein molecules simultaneously bind to several distant sites on DNA. However, the molecular mechanisms of formation of these systems remain not well understood. Existing theoretical studies focus only on specific interactions between protein and DNA molecules at target sequences. However, the electrostatic origin of primary protein-DNA interactions suggests that interactions of proteins with all DNA segments should be considered. Here we theoretically investigate the role of non-specific interactions between protein and DNA molecules on the dynamics of loop formation. Our approach is based on analyzing a discrete-state stochastic model via a method of first-passage probabilities supplemented by Monte Carlo computer simulations. It is found that depending on a protein sliding length during the non-specific binding event three different dynamic regimes of the DNA loop formation might be observed. In addition, the loop formation time might be optimized by varying the protein sliding length, the size of the DNA molecule, and the position of the specific target sequences on DNA. Our results demonstrate the importance of non-specific protein-DNA interactions in the dynamics of DNA loop formations.
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Affiliation(s)
- Jaeoh Shin
- Department of Chemistry, Rice University, Houston, Texas 77005, USA.
| | - Anatoly B Kolomeisky
- Department of Chemistry, Rice University, Houston, Texas 77005, USA. and Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA and Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
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24
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Kongsema M, Wongkhieo S, Khongkow M, Lam EWF, Boonnoy P, Vongsangnak W, Wong-Ekkabut J. Molecular mechanism of Forkhead box M1 inhibition by thiostrepton in breast cancer cells. Oncol Rep 2019; 42:953-962. [PMID: 31322278 PMCID: PMC6667886 DOI: 10.3892/or.2019.7225] [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: 01/15/2019] [Accepted: 07/03/2019] [Indexed: 12/16/2022] Open
Abstract
Breast cancer is the most common type of malignancies in women worldwide, and genotoxic chemotherapeutic drugs are effective by causing DNA damage in cancer cells. However, >90% of patients with metastatic cancer are resistant to chemotherapy. The Forkhead box M1 (FOXM1) transcription factor plays a pivotal role in the resistance of breast cancer cells to chemotherapy by promoting DNA damage repair following genotoxic drug treatment. The aim of the present study was to investigate the inhibition of the FOXM1 protein by thiostrepton, a natural antibiotic produced by the Streptomyces species. Experimental studies were designed to examine the effectiveness of thiostrepton in downregulating FOXM1 mRNA expression and activity, leading to senescence and apoptosis of breast cancer cells. The cytotoxicity of thiostrepton in breast cancer was determined using cell viability assay. Additionally, thiostrepton treatment decreased the mRNA expression of cyclin B1 (CCNB1), a downstream target of FOXM1. The present results indicated that thiostrepton inhibited FOXM1 mRNA expression and its effect on CCNB1. Molecular dynamic simulations were performed to study the interactions between FOXM1-DNA and thiostrepton after molecular docking. The results revealed that the possible mechanism underlying the inhibitory effect of thiostrepton on FOXM1 function was by forming a tight complex with the DNA and FOXM1 via its binding domain. Collectively, these results indicated that thiostrepton is a specific and direct inhibitor of the FOXM1 protein in breast cancer. The findings of the present study may lead to the development of novel therapeutic strategies for breast cancer and help overcome resistance to conventional chemotherapeutic drugs.
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Affiliation(s)
- Mesayamas Kongsema
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Sudtirak Wongkhieo
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Mattaka Khongkow
- National Nanotechnology Centre (NANOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Eric W-F Lam
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Phansiri Boonnoy
- Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Jirasak Wong-Ekkabut
- Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
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25
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Schutt TC, Shukla MK. Predicting the Impact of Aqueous Ions on Fate and Transport of Munition Compounds in the Environment. J Phys Chem A 2019; 123:4973-4979. [PMID: 31070365 DOI: 10.1021/acs.jpca.9b01742] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A model framework for natural water has been developed using computational chemistry techniques to elucidate the interactions between solvated munition compounds and eight common ions in naturally occurring water sources. The interaction energies, residence times, coordination statistics, and surface preferences of nine munition-related compounds with each ion were evaluated. The propensity of these interactions to increase degradation of the munition compound was predicted using accelerated replica QM/MM simulations. The degradation prediction data qualitatively align with previous quantum mechanical studies. The results suggest that primary ions of interest for fate and transport modeling of munition compounds in natural waters may follow the relative importance of SO42-, Cl- ≫ HCO3-, Na+, Mg2+ > Ca2+, K+, and NH4+.
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Affiliation(s)
- Timothy C Schutt
- U.S. Army Engineer Research and Development Center , Environmental Laboratory , 3909 Halls Ferry Road , Vicksburg , Mississippi 39180 , United States
| | - Manoj K Shukla
- U.S. Army Engineer Research and Development Center , Environmental Laboratory , 3909 Halls Ferry Road , Vicksburg , Mississippi 39180 , United States
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26
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Liao Q, Lüking M, Krüger DM, Deindl S, Elf J, Kasson PM, Lynn Kamerlin SC. Long Time-Scale Atomistic Simulations of the Structure and Dynamics of Transcription Factor-DNA Recognition. J Phys Chem B 2019; 123:3576-3590. [PMID: 30952192 DOI: 10.1021/acs.jpcb.8b12363] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Recent years have witnessed an explosion of interest in computational studies of DNA binding proteins, including both coarse-grained and atomistic simulations of transcription factor-DNA recognition, to understand how these transcription factors recognize their binding sites on the DNA with such exquisite specificity. The present study performs microsecond time scale all-atom simulations of the dimeric form of the lactose repressor (LacI), both in the absence of any DNA and in the presence of both specific and nonspecific complexes, considering three different DNA sequences. We examine, specifically, the conformational differences between specific and nonspecific protein-DNA interactions, as well as the behavior of the helix-turn-helix motif of LacI when interacting with the DNA. Our simulations suggest that stable LacI binding occurs primarily to bent A-form DNA, with a loss of LacI conformational entropy and optimization of correlated conformational equilibria across the protein. In addition, binding to the specific operator sequence involves a slightly larger number of stabilizing DNA-protein hydrogen bonds (in comparison to nonspecific complexes), which may account for the experimentally observed specificity for this operator. In doing so, our simulations provide a detailed atomistic description of potential structural drivers for LacI selectivity.
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Affiliation(s)
- Qinghua Liao
- Science for Life Laboratory, Department of Chemistry-BMC , Uppsala University , BMC Box 576, S-751 24 Uppsala , Sweden
| | - Malin Lüking
- Science for Life Laboratory, Department of Chemistry-BMC , Uppsala University , BMC Box 576, S-751 24 Uppsala , Sweden
| | - Dennis M Krüger
- Science for Life Laboratory, Department of Cell and Molecular Biology , Uppsala University , BMC Box 596, S-751 23 Uppsala , Sweden.,Department for Epigenetics and Systems Medicine in Neurodegenerative Diseases, Bioinformatics Unit , German Center for Neurodegenerative Diseases, Göttingen , von Siebold Strasse 3A , 37075 Göttingen , Germany
| | - Sebastian Deindl
- Science for Life Laboratory, Department of Cell and Molecular Biology , Uppsala University , BMC Box 596, S-751 23 Uppsala , Sweden
| | - Johan Elf
- Science for Life Laboratory, Department of Cell and Molecular Biology , Uppsala University , BMC Box 596, S-751 23 Uppsala , Sweden
| | - Peter M Kasson
- Science for Life Laboratory, Department of Cell and Molecular Biology , Uppsala University , BMC Box 596, S-751 23 Uppsala , Sweden
| | - Shina Caroline Lynn Kamerlin
- Science for Life Laboratory, Department of Chemistry-BMC , Uppsala University , BMC Box 576, S-751 24 Uppsala , Sweden
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27
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Gomez D, Gavrilov Y, Levy Y. Sliding Mechanism at a Coiled-Coil Interface. Biophys J 2019; 116:1228-1238. [PMID: 30904175 DOI: 10.1016/j.bpj.2019.02.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/16/2019] [Accepted: 02/26/2019] [Indexed: 12/15/2022] Open
Abstract
The α-helical coiled coil (CC) is a common protein motif that because of the simplicity of its sequence/structure relationship, it has been studied extensively to address fundamental questions in protein science as well as to develop strategies for designing protein with novel architectures. Nevertheless, a complete understanding of CC structures and their dynamics is still far from achieved. Particularly, spontaneous sliding at interfaces of CC proteins was observed for some systems, but its mechanism and usage as an intrinsic conformational change at CCs in protein-protein interfaces is unclear. Using coarse-grained and atomistic simulations, we study various sequences of homodimeric CC, in both parallel and antiparallel configurations. Both the strength of the hydrophobic core and the existence of salt bridges at the periphery of the interface affect sliding dynamics at the CC interface. Although the energy landscape for sliding along a CC interface is different for parallel and antiparallel configurations, both are characterized by a free energy of 1-1.5 kcal/mol, depending on the residues that constitute the CC interface. These barrier heights suggest that sliding kinetics is relatively slow in CC systems and are not expected to be of long length scale, yet they can be involved in functional motions. Our study explains the sliding that has been experimentally observed for the antiparallel CC of the dynein stalk region and the nuclear pore complex and suggests that this one-dimensional motion is an intrinsic feature in CC systems that can be involved in other CC systems.
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Affiliation(s)
- David Gomez
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yulian Gavrilov
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
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28
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Raccaud M, Friman ET, Alber AB, Agarwal H, Deluz C, Kuhn T, Gebhardt JCM, Suter DM. Mitotic chromosome binding predicts transcription factor properties in interphase. Nat Commun 2019; 10:487. [PMID: 30700703 PMCID: PMC6353955 DOI: 10.1038/s41467-019-08417-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 01/08/2019] [Indexed: 12/31/2022] Open
Abstract
Mammalian transcription factors (TFs) differ broadly in their nuclear mobility and sequence-specific/non-specific DNA binding. How these properties affect their ability to occupy specific genomic sites and modify the epigenetic landscape is unclear. The association of TFs with mitotic chromosomes observed by fluorescence microscopy is largely mediated by non-specific DNA interactions and differs broadly between TFs. Here we combine quantitative measurements of mitotic chromosome binding (MCB) of 501 TFs, TF mobility measurements by fluorescence recovery after photobleaching, single molecule imaging of DNA binding, and mapping of TF binding and chromatin accessibility. TFs associating to mitotic chromosomes are enriched in DNA-rich compartments in interphase and display slower mobility in interphase and mitosis. Remarkably, MCB correlates with relative TF on-rates and genome-wide specific site occupancy, but not with TF residence times. This suggests that non-specific DNA binding properties of TFs regulate their search efficiency and occupancy of specific genomic sites.
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Affiliation(s)
- Mahé Raccaud
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Elias T Friman
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Andrea B Alber
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Harsha Agarwal
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Cédric Deluz
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Timo Kuhn
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - J Christof M Gebhardt
- Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - David M Suter
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland.
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29
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Seckfort D, Montgomery Pettitt B. Price of disorder in the lac repressor hinge helix. Biopolymers 2019; 110:e23239. [PMID: 30485404 PMCID: PMC6335174 DOI: 10.1002/bip.23239] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 09/12/2018] [Accepted: 10/04/2018] [Indexed: 12/26/2022]
Abstract
The Lac system of genes has been pivotal in understanding gene regulation. When the lac repressor protein binds to the correct DNA sequence, the hinge region of the protein goes through a disorder to order transition. The structure of this region of the protein is well understood when it is in this bound conformation, but less so when it is not. Structural studies show that this region is flexible. Our simulations show this region is extremely flexible in solution; however, a high concentration of salt can help kinetically trap the hinge helix. Thermodynamically, disorder is more favorable without the DNA present.
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Affiliation(s)
- Danielle Seckfort
- Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas
| | - B Montgomery Pettitt
- Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, Texas
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30
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Abstract
In the past decades, advances in microscopy have made it possible to study the dynamics of individual biomolecules in vitro and resolve intramolecular kinetics that would otherwise be hidden in ensemble averages. More recently, single-molecule methods have been used to image, localize, and track individually labeled macromolecules in the cytoplasm of living cells, allowing investigations of intermolecular kinetics under physiologically relevant conditions. In this review, we illuminate the particular advantages of single-molecule techniques when studying kinetics in living cells and discuss solutions to specific challenges associated with these methods.
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Affiliation(s)
- Johan Elf
- Department of Cell and Molecular Biology, Uppsala University, 75124 Uppsala, Sweden;
| | - Irmeli Barkefors
- Department of Cell and Molecular Biology, Uppsala University, 75124 Uppsala, Sweden;
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31
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Eisold A, Labudde D. Detailed Analysis of 17β-Estradiol-Aptamer Interactions: A Molecular Dynamics Simulation Study. Molecules 2018; 23:molecules23071690. [PMID: 29997341 PMCID: PMC6100600 DOI: 10.3390/molecules23071690] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/06/2018] [Accepted: 07/09/2018] [Indexed: 12/16/2022] Open
Abstract
Micro-pollutants such as 17β-Estradiol (E2) have been detected in different water resources and their negative effects on the environment and organisms have been observed. Aptamers are established as a possible detection tool, but the underlying ligand binding is largely unexplored. In this study, a previously described 35-mer E2-specific aptamer was used to analyse the binding characteristics between E2 and the aptamer with a MD simulation in an aqueous medium. Because there is no 3D structure information available for this aptamer, it was modeled using coarse-grained modeling method. The E2 ligand was positioned inside a potential binding area of the predicted aptamer structure, the complex was used for an 25 ns MD simulation, and the interactions were examined for each time step. We identified E2-specific bases within the interior loop of the aptamer and also demonstrated the influence of frequently underestimated water-mediated hydrogen bonds. The study contributes to the understanding of the behavior of ligands binding with aptamer structure in an aqueous solution. The developed workflow allows generating and examining further appealing ligand-aptamer complexes.
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Affiliation(s)
- Alexander Eisold
- Faculty of Applied Computer and Biosciences, University of Applied Sciences Mittweida, Technikumplatz 17, 09648 Mittweida, Germany.
- Institute for Organic Chemistry, Technische Universität Bergakademie Freiberg, Leipziger Straße 29, 09599 Freiberg, Germany.
| | - Dirk Labudde
- Faculty of Applied Computer and Biosciences, University of Applied Sciences Mittweida, Technikumplatz 17, 09648 Mittweida, Germany.
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32
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Sequence-dependent catalytic regulation of the SpoIIIE motor activity ensures directionality of DNA translocation. Sci Rep 2018; 8:5254. [PMID: 29588476 PMCID: PMC5869595 DOI: 10.1038/s41598-018-23400-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 03/09/2018] [Indexed: 12/02/2022] Open
Abstract
Transport of cellular cargo by molecular motors requires directionality to ensure proper biological functioning. During sporulation in Bacillus subtilis, directionality of chromosome transport is mediated by the interaction between the membrane-bound DNA translocase SpoIIIE and specific octameric sequences (SRS). Whether SRS regulate directionality by recruiting and orienting SpoIIIE or by simply catalyzing its translocation activity is still unclear. By using atomic force microscopy and single-round fast kinetics translocation assays we determined the localization and dynamics of diffusing and translocating SpoIIIE complexes on DNA with or without SRS. Our findings combined with mathematical modelling revealed that SpoIIIE directionality is not regulated by protein recruitment to SRS but rather by a fine-tuned balance among the rates governing SpoIIIE-DNA interactions and the probability of starting translocation modulated by SRS. Additionally, we found that SpoIIIE can start translocation from non-specific DNA, providing an alternative active search mechanism for SRS located beyond the exploratory length defined by 1D diffusion. These findings are relevant in vivo in the context of chromosome transport through an open channel, where SpoIIIE can rapidly explore DNA while directionality is modulated by the probability of translocation initiation upon interaction with SRS versus non-specific DNA.
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33
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Role of Macromolecular Crowding on the Intracellular Diffusion of DNA Binding Proteins. Sci Rep 2018; 8:844. [PMID: 29339733 PMCID: PMC5770392 DOI: 10.1038/s41598-017-18933-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 12/20/2017] [Indexed: 11/08/2022] Open
Abstract
Recent experiments suggest that cellular crowding facilitates the target search dynamics of proteins on DNA, the mechanism of which is not yet known. By using large scale computer simulations, we show that two competing factors, namely the width of the depletion layer that separates the crowder cloud from the DNA molecule and the degree of protein-crowder crosstalk, act in harmony to affect the target search dynamics of proteins. The impacts vary from nonspecific to specific target search regime. During a nonspecific search, dynamics of a protein is only minimally affected, whereas, a significantly different behaviour is observed when the protein starts forming a specific protein-DNA complex. We also find that the severity of impacts largely depends upon physiological crowder concentration and deviation from it leads to attenuation in the binding kinetics. Based on extensive kinetic study and binding energy landscape analysis, we further present a comprehensive molecular description of the search process that allows us to interpret the experimental findings.
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34
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Bai Y, Gao M, Wen L, He C, Chen Y, Liu C, Fu X, Huang S. Applications of Microfluidics in Quantitative Biology. Biotechnol J 2017; 13:e1700170. [PMID: 28976637 DOI: 10.1002/biot.201700170] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 09/03/2017] [Indexed: 01/15/2023]
Abstract
Quantitative biology is dedicated to taking advantage of quantitative reasoning and advanced engineering technologies to make biology more predictable. Microfluidics, as an emerging technique, provides new approaches to precisely control fluidic conditions on small scales and collect data in high-throughput and quantitative manners. In this review, the authors present the relevant applications of microfluidics to quantitative biology based on two major categories (channel-based microfluidics and droplet-based microfluidics), and their typical features. We also envision some other microfluidic techniques that may not be employed in quantitative biology right now, but have great potential in the near future.
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Affiliation(s)
- Yang Bai
- Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Meng Gao
- Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Lingling Wen
- Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Caiyun He
- Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Yuan Chen
- Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Chenli Liu
- Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Xiongfei Fu
- Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Shuqiang Huang
- Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
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35
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Tavakoli M, Taylor JN, Li CB, Komatsuzaki T, Pressé S. Single Molecule Data Analysis: An Introduction. ADVANCES IN CHEMICAL PHYSICS 2017. [DOI: 10.1002/9781119324560.ch4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Meysam Tavakoli
- Physics Department; Indiana University-Purdue University Indianapolis; Indianapolis IN 46202 USA
| | - J. Nicholas Taylor
- Research Institute for Electronic Science; Hokkaido University; Kita 20 Nishi 10 Kita-Ku Sapporo 001-0020 Japan
| | - Chun-Biu Li
- Research Institute for Electronic Science; Hokkaido University; Kita 20 Nishi 10 Kita-Ku Sapporo 001-0020 Japan
- Department of Mathematics; Stockholm University; 106 91 Stockholm Sweden
| | - Tamiki Komatsuzaki
- Research Institute for Electronic Science; Hokkaido University; Kita 20 Nishi 10 Kita-Ku Sapporo 001-0020 Japan
| | - Steve Pressé
- Physics Department; Indiana University-Purdue University Indianapolis; Indianapolis IN 46202 USA
- Department of Chemistry and Chemical Biology; Indiana University-Purdue University Indianapolis; Indianapolis IN 46202 USA
- Department of Cell and Integrative Physiology; Indiana University School of Medicine; Indianapolis IN 46202 USA
- Department of Physics and School of Molecular Sciences; Arizona State University; Tempe AZ 85287 USA
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36
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Pan H, Bilinovich SM, Kaur P, Riehn R, Wang H, Williams DC. CpG and methylation-dependent DNA binding and dynamics of the methylcytosine binding domain 2 protein at the single-molecule level. Nucleic Acids Res 2017. [PMID: 28637186 PMCID: PMC5587734 DOI: 10.1093/nar/gkx548] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The methylcytosine-binding domain 2 (MBD2) protein recruits the nucleosome remodeling and deacetylase complex (NuRD) to methylated DNA to modify chromatin and regulate transcription. Importantly, MBD2 functions within CpG islands that contain 100s to 1000s of potential binding sites. Since NuRD physically rearranges nucleosomes, the dynamic mobility of this complex is directly related to function. In these studies, we use NMR and single-molecule atomic force microscopy and fluorescence imaging to study DNA binding dynamics of MBD2. Single-molecule fluorescence tracking on DNA tightropes containing regions with CpG-rich and CpG-free regions reveals that MBD2 carries out unbiased 1D diffusion on CpG-rich DNA but subdiffusion on CpG-free DNA. In contrast, the protein stably and statically binds to methylated CpG (mCpG) regions. The intrinsically disordered region (IDR) on MBD2 both reduces exchange between mCpG sites along the DNA as well as the dissociation from DNA, acting like an anchor that restricts the dynamic mobility of the MBD domain. Unexpectedly, MBD2 binding to methylated CpGs induces DNA bending that is augmented by the IDR region of the protein. These results suggest that MBD2 targets NuRD to unmethylated or methylated CpG islands where its distinct dynamic binding modes help maintain open or closed chromatin, respectively.
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Affiliation(s)
- Hai Pan
- Department of Physics, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - Stephanie M Bilinovich
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Parminder Kaur
- Department of Physics, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - Robert Riehn
- Department of Physics, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - Hong Wang
- Department of Physics, North Carolina State University, Raleigh, North Carolina, NC 27695, USA.,Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina, NC 27695, USA
| | - David C Williams
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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37
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Wieczór M, Czub J. How proteins bind to DNA: target discrimination and dynamic sequence search by the telomeric protein TRF1. Nucleic Acids Res 2017. [PMID: 28633355 PMCID: PMC5737604 DOI: 10.1093/nar/gkx534] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Target search as performed by DNA-binding proteins is a complex process, in which multiple factors contribute to both thermodynamic discrimination of the target sequence from overwhelmingly abundant off-target sites and kinetic acceleration of dynamic sequence interrogation. TRF1, the protein that binds to telomeric tandem repeats, faces an intriguing variant of the search problem where target sites are clustered within short fragments of chromosomal DNA. In this study, we use extensive (>0.5 ms in total) MD simulations to study the dynamical aspects of sequence-specific binding of TRF1 at both telomeric and non-cognate DNA. For the first time, we describe the spontaneous formation of a sequence-specific native protein-DNA complex in atomistic detail, and study the mechanism by which proteins avoid off-target binding while retaining high affinity for target sites. Our calculated free energy landscapes reproduce the thermodynamics of sequence-specific binding, while statistical approaches allow for a comprehensive description of intermediate stages of complex formation.
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Affiliation(s)
- Milosz Wieczór
- Department of Physical Chemistry, Gdansk University of Technology, ul. Narutowicza 11/12, 80-233 Gdansk, Poland
| | - Jacek Czub
- Department of Physical Chemistry, Gdansk University of Technology, ul. Narutowicza 11/12, 80-233 Gdansk, Poland
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38
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Mondal A, Bhattacherjee A. Understanding the Role of DNA Topology in Target Search Dynamics of Proteins. J Phys Chem B 2017; 121:9372-9381. [DOI: 10.1021/acs.jpcb.7b08199] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anupam Mondal
- School of Computational and
Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Arnab Bhattacherjee
- School of Computational and
Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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39
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Zhdanov VP. Kinetics of lipid-nanoparticle-mediated intracellular mRNA delivery and function. Phys Rev E 2017; 96:042406. [PMID: 29347496 DOI: 10.1103/physreve.96.042406] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Indexed: 06/07/2023]
Abstract
mRNA delivery into cells forms the basis for one of the new and promising ways to treat various diseases. Among suitable carriers, lipid nanoparticles (LNPs) with a size of about 100 nm are now often employed. Despite high current interest in this area, the understanding of the basic details of LNP-mediated mRNA delivery and function is limited. To clarify the kinetics of mRNA release from LNPs, the author uses three generic models implying (i) exponential, (ii) diffusion-controlled, and (iii) detachment-controlled kinetic regimes, respectively. Despite the distinct differences in these kinetics, the associated transient kinetics of mRNA translation to the corresponding protein and its degradation are shown to be not too sensitive to the details of the mRNA delivery by LNPs (or other nanocarriers). In addition, the author illustrates how this protein may temporarily influence the expression of one gene or a few equivalent genes. The analysis includes positive or negative regulation of the gene transcription via the attachment of the protein without or with positive or negative feedback in the gene expression. Stable, bistable, and oscillatory schemes have been scrutinized in this context.
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Affiliation(s)
- Vladimir P Zhdanov
- Section of Biological Physics, Department of Physics, Chalmers University of Technology, Göteborg, Sweden and Boreskov Institute of Catalysis, Russian Academy of Sciences, Novosibirsk, Russia
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40
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Pohjolainen E, Malola S, Groenhof G, Häkkinen H. Exploring Strategies for Labeling Viruses with Gold Nanoclusters through Non-equilibrium Molecular Dynamics Simulations. Bioconjug Chem 2017; 28:2327-2339. [DOI: 10.1021/acs.bioconjchem.7b00367] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Emmi Pohjolainen
- Department of Physics and ‡Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland FI-40014
| | - Sami Malola
- Department of Physics and ‡Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland FI-40014
| | - Gerrit Groenhof
- Department of Physics and ‡Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland FI-40014
| | - Hannu Häkkinen
- Department of Physics and ‡Department of Chemistry, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland FI-40014
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41
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Garza de Leon F, Sellars L, Stracy M, Busby SJW, Kapanidis AN. Tracking Low-Copy Transcription Factors in Living Bacteria: The Case of the lac Repressor. Biophys J 2017; 112:1316-1327. [PMID: 28402875 PMCID: PMC5390046 DOI: 10.1016/j.bpj.2017.02.028] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 01/20/2017] [Accepted: 02/16/2017] [Indexed: 11/30/2022] Open
Abstract
Transcription factors control the expression of genes by binding to specific sites in DNA and repressing or activating transcription in response to stimuli. The lac repressor (LacI) is a well characterized transcription factor that regulates the ability of bacterial cells to uptake and metabolize lactose. Here, we study the intracellular mobility and spatial distribution of LacI in live bacteria using photoactivated localization microscopy combined with single-particle tracking. Since we track single LacI molecules in live cells by stochastically photoactivating and observing fluorescent proteins individually, there are no limitations on the copy number of the protein under study; as a result, we were able to study the behavior of LacI in bacterial strains containing the natural copy numbers (∼40 monomers), as well as in strains with much higher copy numbers due to LacI overexpression. Our results allowed us to determine the relative abundance of specific, near-specific, and non-specific DNA binding modes of LacI in vivo, showing that all these modes are operational inside living cells. Further, we examined the spatial distribution of LacI in live cells, confirming its specific binding to lac operator regions on the chromosome; we also showed that mobile LacI molecules explore the bacterial nucleoid in a way similar to exploration by other DNA-binding proteins. Our work also provides an example of applying tracking photoactivated localization microscopy to studies of low-copy-number proteins in living bacteria.
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Affiliation(s)
- Federico Garza de Leon
- Gene Machines Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, United Kingdom
| | - Laura Sellars
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Mathew Stracy
- Gene Machines Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, United Kingdom
| | - Stephen J W Busby
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Achillefs N Kapanidis
- Gene Machines Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, United Kingdom.
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42
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Zhdanov VP. Mathematical aspects of the regulation of gene transcription by promoters. Math Biosci 2017; 283:84-90. [DOI: 10.1016/j.mbs.2016.11.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Revised: 09/01/2016] [Accepted: 11/05/2016] [Indexed: 01/14/2023]
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43
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Gardini S, Furini S, Santucci A, Niccolai N. A structural bioinformatics investigation on protein–DNA complexes delineates their modes of interaction. MOLECULAR BIOSYSTEMS 2017; 13:1010-1017. [DOI: 10.1039/c7mb00071e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A non-redundant dataset of 629 protein–DNA complexes has been used to investigate on amino acid composition of protein-DNA interfaces. Structural proteins, transcription factors and DNA-related enzymes show specific patterns accounting for different modes of their interaction with DNA.
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Affiliation(s)
- Simone Gardini
- Department of Biotechnology
- Chemistry and Pharmacy
- University of Siena
- Italy
| | - Simone Furini
- Department of Medical Biotechnologies
- University of Siena
- Siena
- Italy
| | - Annalisa Santucci
- Department of Biotechnology
- Chemistry and Pharmacy
- University of Siena
- Italy
| | - Neri Niccolai
- Department of Biotechnology
- Chemistry and Pharmacy
- University of Siena
- Italy
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44
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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
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45
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Coarse-grained models for studying protein diffusion along DNA. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2016. [DOI: 10.1002/wcms.1262] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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46
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Maximova T, Moffatt R, Ma B, Nussinov R, Shehu A. Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics. PLoS Comput Biol 2016; 12:e1004619. [PMID: 27124275 PMCID: PMC4849799 DOI: 10.1371/journal.pcbi.1004619] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Investigation of macromolecular structure and dynamics is fundamental to understanding how macromolecules carry out their functions in the cell. Significant advances have been made toward this end in silico, with a growing number of computational methods proposed yearly to study and simulate various aspects of macromolecular structure and dynamics. This review aims to provide an overview of recent advances, focusing primarily on methods proposed for exploring the structure space of macromolecules in isolation and in assemblies for the purpose of characterizing equilibrium structure and dynamics. In addition to surveying recent applications that showcase current capabilities of computational methods, this review highlights state-of-the-art algorithmic techniques proposed to overcome challenges posed in silico by the disparate spatial and time scales accessed by dynamic macromolecules. This review is not meant to be exhaustive, as such an endeavor is impossible, but rather aims to balance breadth and depth of strategies for modeling macromolecular structure and dynamics for a broad audience of novices and experts.
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Affiliation(s)
- Tatiana Maximova
- Department of Computer Science, George Mason University, Fairfax, Virginia, United States of America
| | - Ryan Moffatt
- Department of Computer Science, George Mason University, Fairfax, Virginia, United States of America
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland, United States of America
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland, United States of America
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Amarda Shehu
- Department of Computer Science, George Mason University, Fairfax, Virginia, United States of America
- Department of Biongineering, George Mason University, Fairfax, Virginia, United States of America
- School of Systems Biology, George Mason University, Manassas, Virginia, United States of America
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47
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Sun L, Tabaka M, Hou S, Li L, Burdzy K, Aksimentiev A, Maffeo C, Zhang X, Holyst R. The Hinge Region Strengthens the Nonspecific Interaction between Lac-Repressor and DNA: A Computer Simulation Study. PLoS One 2016; 11:e0152002. [PMID: 27008630 PMCID: PMC4805274 DOI: 10.1371/journal.pone.0152002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/06/2016] [Indexed: 11/30/2022] Open
Abstract
LacI is commonly used as a model to study the protein-DNA interaction and gene regulation. The headpiece of the lac-repressor (LacI) protein is an ideal system for investigation of nonspecific binding of the whole LacI protein to DNA. The hinge region of the headpiece has been known to play a key role in the specific binding of LacI to DNA, whereas its role in nonspecific binding process has not been elucidated. Here, we report the results of explicit solvent molecular dynamics simulation and continuum electrostatic calculations suggesting that the hinge region strengthens the nonspecific interaction, accounting for up to 50% of the micro-dissociation free energy of LacI from DNA. Consequently, the rate of microscopic dissociation of LacI from DNA is reduced by 2~3 orders of magnitude in the absence of the hinge region. We find the hinge region makes an important contribution to the electrostatic energy, the salt dependence of electrostatic energy, and the number of salt ions excluded from binding of the LacI-DNA complex.
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Affiliation(s)
- Lili Sun
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01–224, Warsaw, Poland
| | - Marcin Tabaka
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01–224, Warsaw, Poland
| | - Sen Hou
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01–224, Warsaw, Poland
| | - Lin Li
- Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, South Carolina, 29634, United States of America
| | - Krzysztof Burdzy
- Department of Mathematics, University of Washington, Seattle, Washington, 98195–4350, United States of America
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois, Urbana, Illinois, 61801, United States of America
| | - Christopher Maffeo
- Department of Physics, University of Illinois, Urbana, Illinois, 61801, United States of America
| | - Xuzhu Zhang
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01–224, Warsaw, Poland
| | - Robert Holyst
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01–224, Warsaw, Poland
- * E-mail:
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Sun L, Tabaka M, Hou S, Li L, Burdzy K, Aksimentiev A, Maffeo C, Zhang X, Holyst R. The Hinge Region Strengthens the Nonspecific Interaction between Lac-Repressor and DNA: A Computer Simulation Study. PLoS One 2016; 11:e0152002. [PMID: 27008630 DOI: 10.1371/joumal.pone.0152002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/06/2016] [Indexed: 05/27/2023] Open
Abstract
LacI is commonly used as a model to study the protein-DNA interaction and gene regulation. The headpiece of the lac-repressor (LacI) protein is an ideal system for investigation of nonspecific binding of the whole LacI protein to DNA. The hinge region of the headpiece has been known to play a key role in the specific binding of LacI to DNA, whereas its role in nonspecific binding process has not been elucidated. Here, we report the results of explicit solvent molecular dynamics simulation and continuum electrostatic calculations suggesting that the hinge region strengthens the nonspecific interaction, accounting for up to 50% of the micro-dissociation free energy of LacI from DNA. Consequently, the rate of microscopic dissociation of LacI from DNA is reduced by 2~3 orders of magnitude in the absence of the hinge region. We find the hinge region makes an important contribution to the electrostatic energy, the salt dependence of electrostatic energy, and the number of salt ions excluded from binding of the LacI-DNA complex.
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Affiliation(s)
- Lili Sun
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Marcin Tabaka
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Sen Hou
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Lin Li
- Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, South Carolina, 29634, United States of America
| | - Krzysztof Burdzy
- Department of Mathematics, University of Washington, Seattle, Washington, 98195-4350, United States of America
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois, Urbana, Illinois, 61801, United States of America
| | - Christopher Maffeo
- Department of Physics, University of Illinois, Urbana, Illinois, 61801, United States of America
| | - Xuzhu Zhang
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Robert Holyst
- Institute of Physical Chemistry PAS, Kasprzaka 44/52, 01-224, Warsaw, Poland
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Beuerle MG, Dufton NP, Randi AM, Gould IR. Molecular dynamics studies on the DNA-binding process of ERG. MOLECULAR BIOSYSTEMS 2016; 12:3600-3610. [DOI: 10.1039/c6mb00506c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Molecular dynamics study elucidating the mechanistic background of the DNA-binding process and the sequence specificity of the transcription factor ERG. Along with the biological findings the capabilities of unbiased DNA-binding simulations in combination with various means of analysis in the field of protein DNA-interactions are shown.
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Affiliation(s)
- Matthias G. Beuerle
- Department of Chemistry and Institute of Chemical Biology
- Imperial College London
- South Kensington SW7 2AZ
- UK
| | - Neil P. Dufton
- National Heart and Lung Institute (NHLI) Vascular Sciences
- Hammersmith Hospital
- Imperial College London
- London W12 0NN
- UK
| | - Anna M. Randi
- National Heart and Lung Institute (NHLI) Vascular Sciences
- Hammersmith Hospital
- Imperial College London
- London W12 0NN
- UK
| | - Ian R. Gould
- Department of Chemistry and Institute of Chemical Biology
- Imperial College London
- South Kensington SW7 2AZ
- UK
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50
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Hauser K, Essuman B, He Y, Coutsias E, Garcia-Diaz M, Simmerling C. A human transcription factor in search mode. Nucleic Acids Res 2015; 44:63-74. [PMID: 26673724 PMCID: PMC4705650 DOI: 10.1093/nar/gkv1091] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 10/07/2015] [Indexed: 12/14/2022] Open
Abstract
Transcription factors (TF) can change shape to bind and recognize DNA, shifting the energy landscape from a weak binding, rapid search mode to a higher affinity recognition mode. However, the mechanism(s) driving this conformational change remains unresolved and in most cases high-resolution structures of the non-specific complexes are unavailable. Here, we investigate the conformational switch of the human mitochondrial transcription termination factor MTERF1, which has a modular, superhelical topology complementary to DNA. Our goal was to characterize the details of the non-specific search mode to complement the crystal structure of the specific binding complex, providing a basis for understanding the recognition mechanism. In the specific complex, MTERF1 binds a significantly distorted and unwound DNA structure, exhibiting a protein conformation incompatible with binding to B-form DNA. In contrast, our simulations of apo MTERF1 revealed significant flexibility, sampling structures with superhelical pitch and radius complementary to the major groove of B-DNA. Docking these structures to B-DNA followed by unrestrained MD simulations led to a stable complex in which MTERF1 was observed to undergo spontaneous diffusion on the DNA. Overall, the data support an MTERF1-DNA binding and recognition mechanism driven by intrinsic dynamics of the MTERF1 superhelical topology.
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Affiliation(s)
- Kevin Hauser
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA
| | | | - Yiqing He
- Great Neck South High School, Great Neck, NY 11023, USA
| | - Evangelos Coutsias
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Miguel Garcia-Diaz
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Carlos Simmerling
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA
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