51
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Xiang S, le Paige UB, Horn V, Houben K, Baldus M, van Ingen H. Site-Specific Studies of Nucleosome Interactions by Solid-State NMR Spectroscopy. Angew Chem Int Ed Engl 2018; 57:4571-4575. [PMID: 29465771 PMCID: PMC5947581 DOI: 10.1002/anie.201713158] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 02/08/2018] [Indexed: 01/01/2023]
Abstract
Chromatin function depends on a dense network of interactions between nucleosomes and a wide range of proteins. A detailed description of these protein-nucleosome interactions is required to reach a full molecular understanding of chromatin function in both genetics and epigenetics. Herein, we show that the structure, dynamics, and interactions of nucleosomes can be interrogated in a residue-specific manner by using state-of-the-art solid-state NMR spectroscopy. Using sedimented nucleosomes, high-resolution spectra were obtained for both flexible histone tails and the non-mobile histone core. Through co-sedimentation of a nucleosome-binding peptide, we demonstrate that protein-binding sites on the nucleosome surface can be determined. We believe that this approach holds great promise as it is generally applicable, extendable to include the structure and dynamics of the bound proteins, and scalable to interactions of proteins with higher-order chromatin structures, including isolated and cellular chromatin.
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Affiliation(s)
- ShengQi Xiang
- NMR Spectroscopy Research GroupBijvoet Center for Biomolecular ResearchUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| | - Ulric B. le Paige
- Macromolecular BiochemistryLeiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
- Current address: NMR Spectroscopy Research GroupBijvoet Center for Biomolecular ResearchUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| | - Velten Horn
- Macromolecular BiochemistryLeiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
- Current address: NMR Spectroscopy Research GroupBijvoet Center for Biomolecular ResearchUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| | - Klaartje Houben
- NMR Spectroscopy Research GroupBijvoet Center for Biomolecular ResearchUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
- Current address: DSM Food SpecialtiesDSM Biotechnology CenterAlexander Flemminglaan 12613 AXDelftThe Netherlands
| | - Marc Baldus
- NMR Spectroscopy Research GroupBijvoet Center for Biomolecular ResearchUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| | - Hugo van Ingen
- Macromolecular BiochemistryLeiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
- Current address: NMR Spectroscopy Research GroupBijvoet Center for Biomolecular ResearchUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
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52
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Morrison EA, Bowerman S, Sylvers KL, Wereszczynski J, Musselman CA. The conformation of the histone H3 tail inhibits association of the BPTF PHD finger with the nucleosome. eLife 2018; 7:31481. [PMID: 29648537 PMCID: PMC5953545 DOI: 10.7554/elife.31481] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 04/11/2018] [Indexed: 01/08/2023] Open
Abstract
Histone tails harbor a plethora of post-translational modifications that direct the function of chromatin regulators, which recognize them through effector domains. Effector domain/histone interactions have been broadly studied, but largely using peptide fragments of histone tails. Here, we extend these studies into the nucleosome context and find that the conformation adopted by the histone H3 tails is inhibitory to BPTF PHD finger binding. Using NMR spectroscopy and MD simulations, we show that the H3 tails interact robustly but dynamically with nucleosomal DNA, substantially reducing PHD finger association. Altering the electrostatics of the H3 tail via modification or mutation increases accessibility to the PHD finger, indicating that PTM crosstalk can regulate effector domain binding by altering nucleosome conformation. Together, our results demonstrate that the nucleosome context has a dramatic impact on signaling events at the histone tails, and highlights the importance of studying histone binding in the context of the nucleosome.
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Affiliation(s)
- Emma A Morrison
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, United States
| | - Samuel Bowerman
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois.,Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, Illinois
| | - Kelli L Sylvers
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, United States
| | - Jeff Wereszczynski
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois.,Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, Illinois
| | - Catherine A Musselman
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, United States
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53
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Xiang S, le Paige UB, Horn V, Houben K, Baldus M, van Ingen H. Site‐Specific Studies of Nucleosome Interactions by Solid‐State NMR Spectroscopy. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201713158] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- ShengQi Xiang
- NMR Spectroscopy Research Group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Ulric B. le Paige
- Macromolecular Biochemistry Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
- Current address: NMR Spectroscopy Research Group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Velten Horn
- Macromolecular Biochemistry Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
- Current address: NMR Spectroscopy Research Group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Klaartje Houben
- NMR Spectroscopy Research Group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
- Current address: DSM Food Specialties DSM Biotechnology Center Alexander Flemminglaan 1 2613 AX Delft The Netherlands
| | - Marc Baldus
- NMR Spectroscopy Research Group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Hugo van Ingen
- Macromolecular Biochemistry Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
- Current address: NMR Spectroscopy Research Group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
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54
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Kono H, Sakuraba S, Ishida H. Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA. PLoS Comput Biol 2018; 14:e1006024. [PMID: 29505570 PMCID: PMC5854429 DOI: 10.1371/journal.pcbi.1006024] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 03/15/2018] [Accepted: 02/01/2018] [Indexed: 11/19/2022] Open
Abstract
The eukaryotic genome is packaged into a nucleus in the form of chromatin. The fundamental structural unit of chromatin is a protein-DNA complex, the nucleosome, where 146 or 147 base pairs of DNA wrap 1.75 times around a histone core. To function in cellular processes, however, nucleosomal DNA must be unwrapped. Although this unwrapping has been experimentally investigated, details of the process at an atomic level are not yet well understood. Here, we used molecular dynamics simulation with an enhanced sampling method to calculate the free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA. A free energy change of about 11.5 kcal/mol for the unwrapping agrees well with values obtained in single molecule experiments. This simulation revealed a variety of conformational states, indicating there are many potential paths to outer superhelicdal turn unwrapping, but the dominant path is likely asymmetric. At one end of the DNA, the first five bps unwrap, after which a second five bps unwrap at the same end with no increase in free energy. The unwrapping then starts at the other end of the DNA, where 10 bps are unwrapped. During further unwrapping of 15 bps, the unwrapping advances at one of the ends, after which the other end of the DNA unwraps to complete the unwrapping of the outer superhelical turn. These results provide insight into the construction, disruption, and repositioning of nucleosomes, which are continuously ongoing during cellular processes.
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Affiliation(s)
- Hidetoshi Kono
- Molecular Modeling and Simulation Group, Department of Quantum Beam Life Science, National Institutes for Quantum and Radiological Science and Technology, Umemidai, Kizugawa, Kyoto, Japan
- * E-mail:
| | - Shun Sakuraba
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, Kashiwa, Chiba, Japan
| | - Hisashi Ishida
- Molecular Modeling and Simulation Group, Department of Quantum Beam Life Science, National Institutes for Quantum and Radiological Science and Technology, Umemidai, Kizugawa, Kyoto, Japan
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55
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Abstract
Various recent developments in solid-state nuclear magnetic resonance (ssNMR) spectroscopy have enabled an array of new insights regarding the structure, dynamics, and interactions of biomolecules. In the ever more integrated world of structural biology, ssNMR studies provide structural and dynamic information that is complementary to the data accessible by other means. ssNMR enables the study of samples lacking a crystalline lattice, featuring static as well as dynamic disorder, and does so independent of higher-order symmetry. The present study surveys recent applications of biomolecular ssNMR and examines how this technique is increasingly integrated with other structural biology techniques, such as (cryo) electron microscopy, solution-state NMR, and X-ray crystallography. Traditional ssNMR targets include lipid bilayer membranes and membrane proteins in a lipid bilayer environment. Another classic application has been in the area of protein misfolding and aggregation disorders, where ssNMR has provided essential structural data on oligomers and amyloid fibril aggregates. More recently, the application of ssNMR has expanded to a growing array of biological assemblies, ranging from non-amyloid protein aggregates, protein–protein complexes, viral capsids, and many others. Across these areas, multidimensional magic angle spinning (MAS) ssNMR has, in the last decade, revealed three-dimensional structures, including many that had been inaccessible by other structural biology techniques. Equally important insights in structural and molecular biology derive from the ability of MAS ssNMR to probe information beyond comprehensive protein structures, such as dynamics, solvent exposure, protein–protein interfaces, and substrate–enzyme interactions.
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56
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Elbahnsi A, Retureau R, Baaden M, Hartmann B, Oguey C. Holding the Nucleosome Together: A Quantitative Description of the DNA–Histone Interface in Solution. J Chem Theory Comput 2018; 14:1045-1058. [DOI: 10.1021/acs.jctc.7b00936] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Ahmad Elbahnsi
- LBPA,
UMR 8113, ENS Paris-Saclay - CNRS, 61 avenue du Président Wilson, 94235 cedex Cachan, France
- LPTM,
UMR 8089, CNRS, Université de Cergy-Pontoise, 2 avenue Adolphe Chauvin, 95302 Cergy-Pontoise, France
| | - Romain Retureau
- LBPA,
UMR 8113, ENS Paris-Saclay - CNRS, 61 avenue du Président Wilson, 94235 cedex Cachan, France
| | - Marc Baaden
- Laboratoire
de Biochimie Théorique, CNRS, UPR9080, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Brigitte Hartmann
- LBPA,
UMR 8113, ENS Paris-Saclay - CNRS, 61 avenue du Président Wilson, 94235 cedex Cachan, France
| | - Christophe Oguey
- LPTM,
UMR 8089, CNRS, Université de Cergy-Pontoise, 2 avenue Adolphe Chauvin, 95302 Cergy-Pontoise, France
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57
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The 10-nm chromatin fiber and its relationship to interphase chromosome organization. Biochem Soc Trans 2017; 46:67-76. [PMID: 29263138 PMCID: PMC5818668 DOI: 10.1042/bst20170101] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 10/25/2017] [Accepted: 10/27/2017] [Indexed: 01/09/2023]
Abstract
A chromosome is a single long DNA molecule assembled along its length with nucleosomes and proteins. During interphase, a mammalian chromosome exists as a highly organized supramolecular globule in the nucleus. Here, we discuss new insights into how genomic DNA is packaged and organized within interphase chromosomes. Our emphasis is on the structural principles that underlie chromosome organization, with a particular focus on the intrinsic contributions of the 10-nm chromatin fiber, but not the regular 30-nm fiber. We hypothesize that the hierarchical globular organization of an interphase chromosome is fundamentally established by the self-interacting properties of a 10-nm zig-zag array of nucleosomes, while histone post-translational modifications, histone variants, and chromatin-associated proteins serve to mold generic chromatin domains into specific structural and functional entities.
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58
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Kashefi M, Thompson LK. Signaling-Related Mobility Changes in Bacterial Chemotaxis Receptors Revealed by Solid-State NMR. J Phys Chem B 2017; 121:8693-8705. [PMID: 28816463 PMCID: PMC5613836 DOI: 10.1021/acs.jpcb.7b06475] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
![]()
Bacteria employ remarkable
membrane-bound nanoarrays to sense their
environment and direct their swimming. Arrays consist of chemotaxis
receptor trimers of dimers that are bridged at their membrane-distal
tips by rings of two cytoplasmic proteins, a kinase CheA and a coupling
protein CheW. It is not clear how ligand binding to the periplasmic
domain of the receptor deactivates the CheA kinase bound to the cytoplasmic
tip ∼300 Å away, but the mechanism is thought to involve
changes in dynamics within the cytoplasmic domain. To test these proposals,
we applied solid-state NMR mobility-filtered experiments to functional
complexes of the receptor cytoplasmic fragment (U–13C,15N-CF), CheA, and CheW. Assembly of these proteins
into native-like, homogeneous arrays is mediated by either vesicle
binding or molecular crowding agents, and paramagnetic relaxation
enhancement is used to overcome sensitivity challenges in these large
complexes. INEPT spectra reveal that a significant fraction of the
receptor is dynamic on the nanosecond or shorter time scale, and these
dynamics change with signaling state. The mobile regions are identified
through a combination of biochemical and NMR approaches (protein truncations
and unique chemical shifts). The INEPT spectra are consistent with
an asymmetric mobility in the methylation region (N-helix mobility
≫ C-helix mobility) and reveal an increase in the mobility
of the N-helix in the kinase-off state. This finding identifies functionally
relevant dynamics in the receptor, and suggests that this N-helix
segment plays a key role in propagating the signal.
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Affiliation(s)
- Maryam Kashefi
- Department of Chemistry, ‡Program in Molecular and Cellular Biology, University of Massachusetts Amherst , Amherst, Massachusetts 01003, United States
| | - Lynmarie K Thompson
- Department of Chemistry, ‡Program in Molecular and Cellular Biology, University of Massachusetts Amherst , Amherst, Massachusetts 01003, United States
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59
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Gibson MD, Brehove M, Luo Y, North J, Poirier MG. Methods for Investigating DNA Accessibility with Single Nucleosomes. Methods Enzymol 2017; 581:379-415. [PMID: 27793287 DOI: 10.1016/bs.mie.2016.08.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nucleosomes are the fundamental organizing unit of all eukaryotic genomes. Understanding how proteins gain access to DNA-binding sites located within nucleosomes is important for understanding DNA processing including transcription, replication, and repair. Single-molecule total internal reflection fluorescence (smTIRF) microscopy measurements can provide key insight into how proteins gain and maintain access to DNA sites within nucleosomes. Here, we describe methods for smTIRF experiments including the preparation of fluorophore-labeled nucleosomes, the smTIRF system, data acquisition, analysis, and controls. These methods are presented for investigating transcription factor binding within nucleosomes. However, they are applicable for investigating the binding of any site-specific DNA-binding protein within nucleosomes.
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Affiliation(s)
- M D Gibson
- The Ohio State University, Columbus, OH, United States
| | - M Brehove
- The Ohio State University, Columbus, OH, United States
| | - Y Luo
- The Ohio State University, Columbus, OH, United States
| | - J North
- The Ohio State University, Columbus, OH, United States
| | - M G Poirier
- The Ohio State University, Columbus, OH, United States.
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60
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Chakraborty K, Loverde SM. Asymmetric breathing motions of nucleosomal DNA and the role of histone tails. J Chem Phys 2017; 147:065101. [DOI: 10.1063/1.4997573] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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61
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Gopinath T, Nelson SED, Soller KJ, Veglia G. Probing the Conformationally Excited States of Membrane Proteins via 1H-Detected MAS Solid-State NMR Spectroscopy. J Phys Chem B 2017; 121:4456-4465. [DOI: 10.1021/acs.jpcb.7b03268] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- T. Gopinath
- Department of Chemistry and ‡Department of Biochemistry, Molecular Biology, and
Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Sarah E. D. Nelson
- Department of Chemistry and ‡Department of Biochemistry, Molecular Biology, and
Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Kailey J. Soller
- Department of Chemistry and ‡Department of Biochemistry, Molecular Biology, and
Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Gianluigi Veglia
- Department of Chemistry and ‡Department of Biochemistry, Molecular Biology, and
Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
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62
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Nuzzio KM, Watt ED, Boettcher JM, Gajsiewicz JM, Morrissey JH, Rienstra CM. High-Resolution NMR Studies of Human Tissue Factor. PLoS One 2016; 11:e0163206. [PMID: 27657719 PMCID: PMC5033421 DOI: 10.1371/journal.pone.0163206] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 09/06/2016] [Indexed: 11/20/2022] Open
Abstract
In normal hemostasis, the blood clotting cascade is initiated when factor VIIa (fVIIa, other clotting factors are named similarly) binds to the integral membrane protein, human tissue factor (TF). The TF/fVIIa complex in turn activates fX and fIX, eventually concluding with clot formation. Several X-ray crystal structures of the soluble extracellular domain of TF (sTF) exist; however, these structures are missing electron density in functionally relevant regions of the protein. In this context, NMR can provide complementary structural information as well as dynamic insights into enzyme activity. The resolution and sensitivity for NMR studies are greatly enhanced by the ability to prepare multiple milligrams of protein with various isotopic labeling patterns. Here, we demonstrate high-yield production of several isotopically labeled forms of recombinant sTF, allowing for high-resolution NMR studies both in the solid and solution state. We also report solution NMR spectra at sub-mM concentrations of sTF, ensuring the presence of dispersed monomer, as well as the first solid-state NMR spectra of sTF. Our improved sample preparation and precipitation conditions have enabled the acquisition of multidimensional NMR data sets for TF chemical shift assignment and provide a benchmark for TF structure elucidation.
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Affiliation(s)
- Kristin M. Nuzzio
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Eric D. Watt
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - John M. Boettcher
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Joshua M. Gajsiewicz
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - James H. Morrissey
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Chad M. Rienstra
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail:
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63
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Erler J, Zhang R, Petridis L, Cheng X, Smith JC, Langowski J. The role of histone tails in the nucleosome: a computational study. Biophys J 2016; 107:2911-2922. [PMID: 25517156 DOI: 10.1016/j.bpj.2014.10.065] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 10/13/2014] [Accepted: 10/15/2014] [Indexed: 11/29/2022] Open
Abstract
Histone tails play an important role in gene transcription and expression. We present here a systematic computational study of the role of histone tails in the nucleosome, using replica exchange molecular dynamics simulations with an implicit solvent model and different well-established force fields. We performed simulations for all four histone tails, H4, H3, H2A, and H2B, isolated and with inclusion of the nucleosome. The results confirm predictions of previous theoretical studies for the secondary structure of the isolated tails but show a strong dependence on the force field used. In the presence of the entire nucleosome for all force fields, the secondary structure of the histone tails is destabilized. Specific contacts are found between charged lysine and arginine residues and DNA phosphate groups and other binding sites in the minor and major DNA grooves. Using cluster analysis, we found a single dominant configuration of binding to DNA for the H4 and H2A histone tails, whereas H3 and H2B show multiple binding configurations with an equal probability. The leading stabilizing contribution for those binding configurations is the attractive interaction between the positively charged lysine and arginine residues and the negatively charged phosphate groups, and thus the resulting charge neutralization. Finally, we present results of molecular dynamics simulations in explicit solvent to confirm our conclusions. Results from both implicit and explicit solvent models show that large portions of the histone tails are not bound to DNA, supporting the complex role of these tails in gene transcription and expression and making them possible candidates for binding sites of transcription factors, enzymes, and other proteins.
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Affiliation(s)
- Jochen Erler
- Division of Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany
| | - Ruihan Zhang
- Division of Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany
| | - Loukas Petridis
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Xiaolin Cheng
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Jörg Langowski
- Division of Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany.
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64
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H3 Histone Tail Conformation within the Nucleosome and the Impact of K14 Acetylation Studied Using Enhanced Sampling Simulation. PLoS Comput Biol 2016; 12:e1004788. [PMID: 26967163 PMCID: PMC4788430 DOI: 10.1371/journal.pcbi.1004788] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 02/03/2016] [Indexed: 11/19/2022] Open
Abstract
Acetylation of lysine residues in histone tails is associated with gene transcription. Because histone tails are structurally flexible and intrinsically disordered, it is difficult to experimentally determine the tail conformations and the impact of acetylation. In this work, we performed simulations to sample H3 tail conformations with and without acetylation. The results show that irrespective of the presence or absence of the acetylation, the H3 tail remains in contact with the DNA and assumes an α-helix structure in some regions. Acetylation slightly weakened the interaction between the tail and DNA and enhanced α-helix formation, resulting in a more compact tail conformation. We inferred that this compaction induces unwrapping and exposure of the linker DNA, enabling DNA-binding proteins (e.g., transcription factors) to bind to their target sequences. In addition, our simulation also showed that acetylated lysine was more often exposed to the solvent, which is consistent with the fact that acetylation functions as a post-translational modification recognition site marker. Post-translational modification (PTM) of histone tails is an important component of epigenetics. Acetylation of histone tails generally functions to activate gene expression, though the molecular mechanism is not well understood. We used enhanced sampling simulation to examine the impact of acetylation on the structure of the histone H3 tail within the nucleosome. The results suggest acetylation makes the H3 tail conformation more compact and enhances dissociation of nucleosomal DNA from the histone core. Further, the acetylated lysine was more exposed to the solvent, which is consistent with its role as a PTM recognition site marker. These findings increase our understanding of the impact of PTM on nucleosome stability and dynamics and on the higher order structure of chromatin.
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65
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Shaytan AK, Armeev GA, Goncearenco A, Zhurkin VB, Landsman D, Panchenko AR. Coupling between Histone Conformations and DNA Geometry in Nucleosomes on a Microsecond Timescale: Atomistic Insights into Nucleosome Functions. J Mol Biol 2015; 428:221-237. [PMID: 26699921 DOI: 10.1016/j.jmb.2015.12.004] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 12/04/2015] [Accepted: 12/07/2015] [Indexed: 12/16/2022]
Abstract
An octamer of histone proteins wraps about 200bp of DNA into two superhelical turns to form nucleosomes found in chromatin. Although the static structure of the nucleosomal core particle has been solved, details of the dynamic interactions between histones and DNA remain elusive. We performed extensively long unconstrained, all-atom microsecond molecular dynamics simulations of nucleosomes including linker DNA segments and full-length histones in explicit solvent. For the first time, we were able to identify and characterize the rearrangements in nucleosomes on a microsecond timescale including the coupling between the conformation of the histone tails and the DNA geometry. We found that certain histone tail conformations promoted DNA bulging near its entry/exit sites, resulting in the formation of twist defects within the DNA. This led to a reorganization of histone-DNA interactions, suggestive of the formation of initial nucleosome sliding intermediates. We characterized the dynamics of the histone tails upon their condensation on the core and linker DNA and showed that tails may adopt conformationally constrained positions due to the insertion of "anchoring" lysines and arginines into the DNA minor grooves. Potentially, these phenomena affect the accessibility of post-translationally modified histone residues that serve as important sites for epigenetic marks (e.g., at H3K9, H3K27, H4K16), suggesting that interactions of the histone tails with the core and linker DNA modulate the processes of histone tail modifications and binding of the effector proteins. We discuss the implications of the observed results on the nucleosome function and compare our results to different experimental studies.
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Affiliation(s)
- Alexey K Shaytan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Grigoriy A Armeev
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Alexander Goncearenco
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Victor B Zhurkin
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Landsman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Anna R Panchenko
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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66
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Ward ME, Ritz E, Ahmed MAM, Bamm VV, Harauz G, Brown LS, Ladizhansky V. Proton detection for signal enhancement in solid-state NMR experiments on mobile species in membrane proteins. JOURNAL OF BIOMOLECULAR NMR 2015; 63:375-388. [PMID: 26494649 DOI: 10.1007/s10858-015-9997-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 10/15/2015] [Indexed: 05/09/2023]
Abstract
Direct proton detection is becoming an increasingly popular method for enhancing sensitivity in solid-state nuclear magnetic resonance spectroscopy. Generally, these experiments require extensive deuteration of the protein, fast magic angle spinning (MAS), or a combination of both. Here, we implement direct proton detection to selectively observe the mobile entities in fully-protonated membrane proteins at moderate MAS frequencies. We demonstrate this method on two proteins that exhibit different motional regimes. Myelin basic protein is an intrinsically-disordered, peripherally membrane-associated protein that is highly flexible, whereas Anabaena sensory rhodopsin is composed of seven rigid transmembrane α-helices connected by mobile loop regions. In both cases, we observe narrow proton linewidths and, on average, a 10× increase in sensitivity in 2D insensitive nuclear enhancement of polarization transfer-based HSQC experiments when proton detection is compared to carbon detection. We further show that our proton-detected experiments can be easily extended to three dimensions and used to build complete amino acid systems, including sidechain protons, and obtain inter-residue correlations. Additionally, we detect signals which do not correspond to amino acids, but rather to lipids and/or carbohydrates which interact strongly with membrane proteins.
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Affiliation(s)
- Meaghan E Ward
- Department of Physics, University of Guelph, Guelph, ON, Canada
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada
| | - Emily Ritz
- Department of Physics, University of Guelph, Guelph, ON, Canada
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada
| | - Mumdooh A M Ahmed
- Department of Physics, University of Guelph, Guelph, ON, Canada
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
- The Department of Physics, Faculty of Science, Suez University, Suez, 43533, Egypt
| | - Vladimir V Bamm
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - George Harauz
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Leonid S Brown
- Department of Physics, University of Guelph, Guelph, ON, Canada
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada
| | - Vladimir Ladizhansky
- Department of Physics, University of Guelph, Guelph, ON, Canada.
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada.
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67
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Kim J, Lee J, Lee TH. Lysine Acetylation Facilitates Spontaneous DNA Dynamics in the Nucleosome. J Phys Chem B 2015; 119:15001-5. [PMID: 26575591 DOI: 10.1021/acs.jpcb.5b09734] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The nucleosome, comprising a histone protein core wrapped around by DNA, is the fundamental packing unit of DNA in cells. Lysine acetylation at the histone core elevates DNA accessibility in the nucleosome, the mechanism of which remains largely unknown. By employing our recently developed hybrid single molecule approach, here we report how the structural dynamics of DNA in the nucleosome is altered upon acetylation at histone H3 lysine 56 (H3K56) that is critical for elevated DNA accessibility. Our results indicate that H3K56 acetylation facilitates the structural dynamics of the DNA at the nucleosome termini that spontaneously and repeatedly open and close on a ms time scale. The results support a molecular mechanism of histone acetylation in catalyzing DNA unpacking whose efficiency is ultimately limited by the spontaneous DNA dynamics at the nucleosome temini. This study provides the first and unique experimental evidence revealing a role of protein chemical modification in directly regulating the kinetic stability of the DNA packing unit.
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Affiliation(s)
- Jongseong Kim
- Department of Chemistry, Eberly College of Science, The Pennsylvania State University , University Park, Pennsylvania, 16802, United States
| | - Jaehyoun Lee
- Department of Chemistry, Eberly College of Science, The Pennsylvania State University , University Park, Pennsylvania, 16802, United States
| | - Tae-Hee Lee
- Department of Chemistry, Eberly College of Science, The Pennsylvania State University , University Park, Pennsylvania, 16802, United States
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68
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Mishima Y, Jayasinghe CD, Lu K, Otani J, Shirakawa M, Kawakami T, Kimura H, Hojo H, Carlton P, Tajima S, Suetake I. Nucleosome compaction facilitates HP1γ binding to methylated H3K9. Nucleic Acids Res 2015; 43:10200-12. [PMID: 26319017 PMCID: PMC4666388 DOI: 10.1093/nar/gkv841] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 08/07/2015] [Indexed: 12/15/2022] Open
Abstract
The α, β and γ isoforms of mammalian heterochromatin protein 1 (HP1) selectively bind to methylated lysine 9 of histone H3 via their chromodomains. Although the phenotypes of HP1-knockout mice are distinct for each isoform, the molecular mechanisms underlying HP1 isoform-specific function remain elusive. In the present study, we found that in contrast to HP1α, HP1γ could not bind tri-methylated H3 lysine 9 in a reconstituted tetra-nucleosomes when the nucleosomes were in an uncompacted state. The hinge region connecting HP1's chromodomain and chromoshadow domain contributed to the distinct recognition of the nucleosomes by HP1α and HP1γ. HP1γ, but not HP1α, was strongly enhanced in selective binding to tri-methylated lysine 9 in histone H3 by the addition of Mg(2+) or linker histone H1, which are known to induce compaction of nucleosomes. We propose that this novel property of HP1γ recognition of lysine 9 in the histone H3 tail in different nucleosome structures plays a role in reading the histone code.
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Affiliation(s)
- Yuichi Mishima
- Laboratory of Epigenetics, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Chanika D Jayasinghe
- Laboratory of Epigenetics, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kai Lu
- Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Junji Otani
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Masahiro Shirakawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan
| | - Toru Kawakami
- Laboratory of Organic Chemistry, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Hironobu Kimura
- Laboratory of Epigenetics, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hironobu Hojo
- Laboratory of Organic Chemistry, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Peter Carlton
- Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Shoji Tajima
- Laboratory of Epigenetics, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Isao Suetake
- Laboratory of Epigenetics, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan
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69
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Collepardo-Guevara R, Portella G, Vendruscolo M, Frenkel D, Schlick T, Orozco M. Chromatin Unfolding by Epigenetic Modifications Explained by Dramatic Impairment of Internucleosome Interactions: A Multiscale Computational Study. J Am Chem Soc 2015; 137:10205-15. [PMID: 26192632 PMCID: PMC6251407 DOI: 10.1021/jacs.5b04086] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Histone tails and their epigenetic modifications play crucial roles in gene expression regulation by altering the architecture of chromatin. However, the structural mechanisms by which histone tails influence the interconversion between active and inactive chromatin remain unknown. Given the technical challenges in obtaining detailed experimental characterizations of the structure of chromatin, multiscale computations offer a promising alternative to model the effect of histone tails on chromatin folding. Here we combine multimicrosecond atomistic molecular dynamics simulations of dinucleosomes and histone tails in explicit solvent and ions, performed with three different state-of-the-art force fields and validated by experimental NMR measurements, with coarse-grained Monte Carlo simulations of 24-nucleosome arrays to describe the conformational landscape of histone tails, their roles in chromatin compaction, and the impact of lysine acetylation, a widespread epigenetic change, on both. We find that while the wild-type tails are highly flexible and disordered, the dramatic increase of secondary-structure order by lysine acetylation unfolds chromatin by decreasing tail availability for crucial fiber-compacting internucleosome interactions. This molecular level description of the effect of histone tails and their charge modifications on chromatin folding explains the sequence sensitivity and underscores the delicate connection between local and global structural and functional effects. Our approach also opens new avenues for multiscale processes of biomolecular complexes.
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Affiliation(s)
- Rosana Collepardo-Guevara
- Chemistry Department, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
- Joint BSC-CRG-IRB Pro-gramme on Computational Biology. Institute for Research in Biomedicine. Baldiri i Reixac 19. 08028, Barcelona, Spain
| | - Guillem Portella
- Chemistry Department, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
- Joint BSC-CRG-IRB Pro-gramme on Computational Biology. Institute for Research in Biomedicine. Baldiri i Reixac 19. 08028, Barcelona, Spain
| | - Michele Vendruscolo
- Chemistry Department, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Daan Frenkel
- Chemistry Department, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Tamar Schlick
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY 10003, USA
- Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY 10012, USA
| | - Modesto Orozco
- Joint BSC-CRG-IRB Pro-gramme on Computational Biology. Institute for Research in Biomedicine. Baldiri i Reixac 19. 08028, Barcelona, Spain
- Departament de Bioquímica i Biologia Molecular. Facultat de Biologia. Universitat de Barcelona. Avgda Diagonal 643, 08028, Barcelona, Spain
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70
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Affiliation(s)
- Manuel M. Müller
- Department of Chemistry, Princeton University,
Frick Laboratory, Princeton, New Jersey 08544, United States
| | - Tom W. Muir
- Department of Chemistry, Princeton University,
Frick Laboratory, Princeton, New Jersey 08544, United States
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71
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Bowman GD, Poirier MG. Post-translational modifications of histones that influence nucleosome dynamics. Chem Rev 2015; 115:2274-95. [PMID: 25424540 PMCID: PMC4375056 DOI: 10.1021/cr500350x] [Citation(s) in RCA: 319] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Indexed: 12/12/2022]
Affiliation(s)
- Gregory D. Bowman
- T.
C. Jenkins Department of Biophysics, Johns
Hopkins University, Baltimore, Maryland 21218, United States
| | - Michael G. Poirier
- Department of Physics, and Department of
Chemistry and Biochemistry, The Ohio State
University, Columbus, Ohio 43210, United
States
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