Role of Histone Tails in Structural Stability of the Nucleosome
Abstract
Histone tails play an important role in nucleosome structure and dynamics. Here we investigate the effect of truncation of histone tails H3, H4, H2A and H2B on nucleosome structure with 100 ns all-atom molecular dynamics simulations. Tail domains of H3 and H2B show propensity of α-helics formation during the intact nucleosome simulation. On truncation of H4 or H2B tails no structural change occurs in histones. However, H3 or H2A tail truncation results in structural alterations in the histone core domain, and in both the cases the structural change occurs in the H2Aα3 domain. We also find that the contacts between the histone H2A C terminal docking domain and surrounding residues are destabilized upon H3 tail truncation. The relation between the present observations and corresponding experiments is discussed.
- Authors:
-
- Univ. of Heidelberg (Germany). Interdisciplinary Center for Scientific Computing (IWR). Computational Molecular Biophysics
- German Cancer Research Center (DKFZ), Heidelberg (Germany). Biophysics of Macromolecules
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Center for Molecular Biophysics
- German Cancer Research Center (DKFZ), Heidelberg (Germany). Biophysics of Macromolecules
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division; German Research Foundation (DFG)
- OSTI Identifier:
- 1627219
- Grant/Contract Number:
- AC05-00OR22725; SM 63/11-1
- Resource Type:
- Accepted Manuscript
- Journal Name:
- PLoS Computational Biology (Online)
- Additional Journal Information:
- Journal Name: PLoS Computational Biology (Online); Journal Volume: 7; Journal Issue: 12; Journal ID: ISSN 1553-7358
- Publisher:
- Public Library of Science
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 97 MATHEMATICS AND COMPUTING; Biochemistry & Molecular Biology; Mathematical & Computational Biology
Citation Formats
Biswas, Mithun, Voltz, Karine, Smith, Jeremy C., and Langowski, Jörg. Role of Histone Tails in Structural Stability of the Nucleosome. United States: N. p., 2011.
Web. doi:10.1371/journal.pcbi.1002279.
Biswas, Mithun, Voltz, Karine, Smith, Jeremy C., & Langowski, Jörg. Role of Histone Tails in Structural Stability of the Nucleosome. United States. https://doi.org/10.1371/journal.pcbi.1002279
Biswas, Mithun, Voltz, Karine, Smith, Jeremy C., and Langowski, Jörg. Thu .
"Role of Histone Tails in Structural Stability of the Nucleosome". United States. https://doi.org/10.1371/journal.pcbi.1002279. https://www.osti.gov/servlets/purl/1627219.
@article{osti_1627219,
title = {Role of Histone Tails in Structural Stability of the Nucleosome},
author = {Biswas, Mithun and Voltz, Karine and Smith, Jeremy C. and Langowski, Jörg},
abstractNote = {Histone tails play an important role in nucleosome structure and dynamics. Here we investigate the effect of truncation of histone tails H3, H4, H2A and H2B on nucleosome structure with 100 ns all-atom molecular dynamics simulations. Tail domains of H3 and H2B show propensity of α-helics formation during the intact nucleosome simulation. On truncation of H4 or H2B tails no structural change occurs in histones. However, H3 or H2A tail truncation results in structural alterations in the histone core domain, and in both the cases the structural change occurs in the H2Aα3 domain. We also find that the contacts between the histone H2A C terminal docking domain and surrounding residues are destabilized upon H3 tail truncation. The relation between the present observations and corresponding experiments is discussed.},
doi = {10.1371/journal.pcbi.1002279},
journal = {PLoS Computational Biology (Online)},
number = 12,
volume = 7,
place = {United States},
year = {Thu Dec 15 00:00:00 EST 2011},
month = {Thu Dec 15 00:00:00 EST 2011}
}
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Works referenced in this record:
Molecular Dynamics of DNA: Comparison of Force Fields and Terminal Nucleotide Definitions
journal, August 2010
- Ricci, Clarisse G.; de Andrade, Alex S. C.; Mottin, Melina
- The Journal of Physical Chemistry B, Vol. 114, Issue 30
CHARMM: the biomolecular simulation program
text, January 2009
- Brooks, B. R.; Brooks, C. L.; Mackerell, A. D.
- Wiley-Blackwell
MolSurfer: a macromolecular interface navigator
journal, July 2003
- Gabdoulline, R. R.
- Nucleic Acids Research, Vol. 31, Issue 13
Chromatin Modifications and Their Function
journal, February 2007
- Kouzarides, Tony
- Cell, Vol. 128, Issue 4
Sin mutations alter inherent nucleosome mobility
journal, January 2004
- Flaus, Andrew; Rencurel, Chantal; Ferreira, Helder
- The EMBO Journal, Vol. 23, Issue 2
Scalable molecular dynamics with NAMD
journal, January 2005
- Phillips, James C.; Braun, Rosemary; Wang, Wei
- Journal of Computational Chemistry, Vol. 26, Issue 16, p. 1781-1802
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
journal, February 2008
- Hess, Berk; Kutzner, Carsten; van der Spoel, David
- Journal of Chemical Theory and Computation, Vol. 4, Issue 3
Mechanisms of ATP dependent chromatin remodeling
journal, May 2007
- Gangaraju, Vamsi K.; Bartholomew, Blaine
- Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, Vol. 618, Issue 1-2
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
journal, March 1977
- Ryckaert, Jean-Paul; Ciccotti, Giovanni; Berendsen, Herman J. C.
- Journal of Computational Physics, Vol. 23, Issue 3
Histone H2A C-Terminus Regulates Chromatin Dynamics, Remodeling, and Histone H1 Binding
journal, December 2010
- Vogler, Christine; Huber, Claudia; Waldmann, Tanja
- PLoS Genetics, Vol. 6, Issue 12
Methylation at arginine 17 of histone H3 is linked to gene activation
journal, January 2002
- Bauer, Uta‐Maria; Daujat, Sylvain; Nielsen, Søren J.
- EMBO reports, Vol. 3, Issue 1
Structural Equilibrium of DNA Represented with Different Force Fields
journal, July 1998
- Feig, Michael; Pettitt, B. Montgomery
- Biophysical Journal, Vol. 75, Issue 1
A new class of histone H2A mutations in Saccharomyces cerevisiae causes specific transcriptional defects in vivo.
journal, April 1995
- Hirschhorn, J. N.; Bortvin, A. L.; Ricupero-Hovasse, S. L.
- Molecular and Cellular Biology, Vol. 15, Issue 4
Histone octamer function in vivo : mutations in the dimer-tetramer interfaces disrupt both gene activation and repression
journal, May 1997
- Santisteban, Maria Soledad; Arents, Gina; Moudrianakis, Evangelos N.
- The EMBO Journal, Vol. 16, Issue 9
DNA and its counterions: a molecular dynamics study
journal, August 2004
- Varnai, P.
- Nucleic Acids Research, Vol. 32, Issue 14
The complex language of chromatin regulation during transcription
journal, May 2007
- Berger, Shelley L.
- Nature, Vol. 447, Issue 7143
Histone and chromatin cross-talk
journal, April 2003
- Fischle, Wolfgang; Wang, Yanming; Allis, C. David
- Current Opinion in Cell Biology, Vol. 15, Issue 2
Constant pressure molecular dynamics simulation: The Langevin piston method
journal, September 1995
- Feller, Scott E.; Zhang, Yuhong; Pastor, Richard W.
- The Journal of Chemical Physics, Vol. 103, Issue 11
CHARMM: The biomolecular simulation program
journal, July 2009
- Brooks, B. R.; Brooks, C. L.; Mackerell, A. D.
- Journal of Computational Chemistry, Vol. 30, Issue 10
Ion motions in molecular dynamics simulations on DNA
journal, October 2004
- Ponomarev, S. Y.; Thayer, K. M.; Beveridge, D. L.
- Proceedings of the National Academy of Sciences, Vol. 101, Issue 41
Two distinct modes of protein-induced bending in DNA 1 1Edited by J. Karn
journal, September 1998
- El Hassan, M. A.; Calladine, C. R.
- Journal of Molecular Biology, Vol. 282, Issue 2
The docking domain of histone H2A is required for H1 binding and RSC-mediated nucleosome remodeling
journal, December 2010
- Shukla, Manu Shubhdarshan; Syed, Sajad Hussain; Goutte-Gattat, Damien
- Nucleic Acids Research, Vol. 39, Issue 7
The folding and unfolding of eukaryotic chromatin
journal, April 2009
- Bassett, Andrew; Cooper, Sarah; Wu, Chenyi
- Current Opinion in Genetics & Development, Vol. 19, Issue 2
Structural flexibility of the nucleosome core particle at atomic resolution studied by molecular dynamics simulation
journal, April 2007
- Roccatano, Danilo; Barthel, Andre; Zacharias, Martin
- Biopolymers, Vol. 85, Issue 5-6
New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning
journal, February 1998
- Lowary, P. T.; Widom, J.
- Journal of Molecular Biology, Vol. 276, Issue 1
All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data
journal, January 2000
- Foloppe, Nicolas; MacKerell, Jr., Alexander D.
- Journal of Computational Chemistry, Vol. 21, Issue 2
Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems
journal, June 1993
- Darden, Tom; York, Darrin; Pedersen, Lee
- The Journal of Chemical Physics, Vol. 98, Issue 12
3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
journal, September 2003
- Lu, X. -J.
- Nucleic Acids Research, Vol. 31, Issue 17
All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution
journal, January 2000
- MacKerell, Alexander D.; Banavali, Nilesh K.
- Journal of Computational Chemistry, Vol. 21, Issue 2
Phylogenomics of the nucleosome
journal, October 2003
- Malik, Harmit S.; Henikoff, Steven
- Nature Structural & Molecular Biology, Vol. 10, Issue 11
Chromatin Dynamics: Nucleosomes go Mobile through Twist Defects
journal, October 2003
- Kulić, I. M.; Schiessel, H.
- Physical Review Letters, Vol. 91, Issue 14
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
journal, December 1983
- Kabsch, Wolfgang; Sander, Christian
- Biopolymers, Vol. 22, Issue 12
Histone Tails and the H3 αN Helix Regulate Nucleosome Mobility and Stability
journal, March 2007
- Ferreira, Helder; Somers, Joanna; Webster, Ryan
- Molecular and Cellular Biology, Vol. 27, Issue 11
Regulated nucleosome mobility and the histone code
journal, November 2004
- Cosgrove, Michael S.; Boeke, Jef D.; Wolberger, Cynthia
- Nature Structural & Molecular Biology, Vol. 11, Issue 11
Histone H3 N-terminus regulates higher order structure of yeast heterochromatin
journal, August 2009
- Sperling, A. S.; Grunstein, M.
- Proceedings of the National Academy of Sciences, Vol. 106, Issue 32
Spheroid Chromatin Units (ngr Bodies)
journal, January 1974
- Olins, A. L.; Olins, D. E.
- Science, Vol. 183, Issue 4122
Functions of Site-Specific Histone Acetylation and Deacetylation
journal, June 2007
- Shahbazian, Mona D.; Grunstein, Michael
- Annual Review of Biochemistry, Vol. 76, Issue 1
Regions of variant histone His2AvD required for Drosophila development
journal, June 1999
- Clarkson, Michael John; Wells, Julian R. E.; Gibson, Frank
- Nature, Vol. 399, Issue 6737
Nucleosome eviction and activated transcription require p300 acetylation of histone H3 lysine 14
journal, October 2010
- Luebben, W. R.; Sharma, N.; Nyborg, J. K.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 45
The Biology of Chromatin Remodeling Complexes
journal, June 2009
- Clapier, Cedric R.; Cairns, Bradley R.
- Annual Review of Biochemistry, Vol. 78, Issue 1
Constant pressure molecular dynamics algorithms
journal, September 1994
- Martyna, Glenn J.; Tobias, Douglas J.; Klein, Michael L.
- The Journal of Chemical Physics, Vol. 101, Issue 5
The language of covalent histone modifications
journal, January 2000
- Strahl, Brian D.; Allis, C. David
- Nature, Vol. 403, Issue 6765
Improving the specificity of organophosphorus hydrolase to acephate by mutagenesis at its binding site: a computational study
journal, May 2021
- Badakhshan, Reza; Mohammadi, Mozafar; Farnoosh, Gholamreza
- Journal of Molecular Modeling, Vol. 27, Issue 6
VMD: Visual molecular dynamics
journal, February 1996
- Humphrey, William; Dalke, Andrew; Schulten, Klaus
- Journal of Molecular Graphics, Vol. 14, Issue 1
Chromatin Compaction at the Mononucleosome Level
journal, February 2006
- Tóth, Katalin; Brun, Nathalie; Langowski, Jörg
- Biochemistry, Vol. 45, Issue 6
H2a-specific proteolysis as a unique probe in the analysis of the histone octamer.
journal, December 1988
- Eickbush, T. H.; Godfrey, J. E.; Elia, M. C.
- Journal of Biological Chemistry, Vol. 263, Issue 35
Structural flexibility of the nucleosome core particle at atomic resolution studied by molecular dynamics simulation
journal, April 2007
- Roccatano, Danilo; Barthel, Andre; Zacharias, Martin
- Biopolymers, Vol. 85, Issue 5-6
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
journal, December 1983
- Kabsch, Wolfgang; Sander, Christian
- Biopolymers, Vol. 22, Issue 12
CHARMM: The biomolecular simulation program
journal, July 2009
- Brooks, B. R.; Brooks, C. L.; Mackerell, A. D.
- Journal of Computational Chemistry, Vol. 30, Issue 10
Chromatin Modifications and Their Function
journal, February 2007
- Kouzarides, Tony
- Cell, Vol. 128, Issue 4
The folding and unfolding of eukaryotic chromatin
journal, April 2009
- Bassett, Andrew; Cooper, Sarah; Wu, Chenyi
- Current Opinion in Genetics & Development, Vol. 19, Issue 2
Mechanisms of ATP dependent chromatin remodeling
journal, May 2007
- Gangaraju, Vamsi K.; Bartholomew, Blaine
- Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, Vol. 618, Issue 1-2
Solvent Mediated Interactions in the Structure of the Nucleosome Core Particle at 1.9Å Resolution
journal, June 2002
- Davey, Curt A.; Sargent, David F.; Luger, Karolin
- Journal of Molecular Biology, Vol. 319, Issue 5
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
journal, February 2008
- Hess, Berk; Kutzner, Carsten; van der Spoel, David
- Journal of Chemical Theory and Computation, Vol. 4, Issue 3
Molecular Dynamics of DNA: Comparison of Force Fields and Terminal Nucleotide Definitions
journal, August 2010
- Ricci, Clarisse G.; de Andrade, Alex S. C.; Mottin, Melina
- The Journal of Physical Chemistry B, Vol. 114, Issue 30
Regions of variant histone His2AvD required for Drosophila development
journal, June 1999
- Clarkson, Michael John; Wells, Julian R. E.; Gibson, Frank
- Nature, Vol. 399, Issue 6737
The language of covalent histone modifications
journal, January 2000
- Strahl, Brian D.; Allis, C. David
- Nature, Vol. 403, Issue 6765
The complex language of chromatin regulation during transcription
journal, May 2007
- Berger, Shelley L.
- Nature, Vol. 447, Issue 7143
Phylogenomics of the nucleosome
journal, October 2003
- Malik, Harmit S.; Henikoff, Steven
- Nature Structural & Molecular Biology, Vol. 10, Issue 11
Sin mutations alter inherent nucleosome mobility
journal, January 2004
- Flaus, Andrew; Rencurel, Chantal; Ferreira, Helder
- The EMBO Journal, Vol. 23, Issue 2
Constant pressure molecular dynamics algorithms
journal, September 1994
- Martyna, Glenn J.; Tobias, Douglas J.; Klein, Michael L.
- The Journal of Chemical Physics, Vol. 101, Issue 5
Ion motions in molecular dynamics simulations on DNA
journal, October 2004
- Ponomarev, S. Y.; Thayer, K. M.; Beveridge, D. L.
- Proceedings of the National Academy of Sciences, Vol. 101, Issue 41
Histone H3 N-terminus regulates higher order structure of yeast heterochromatin
journal, August 2009
- Sperling, A. S.; Grunstein, M.
- Proceedings of the National Academy of Sciences, Vol. 106, Issue 32
Nucleosome eviction and activated transcription require p300 acetylation of histone H3 lysine 14
journal, October 2010
- Luebben, W. R.; Sharma, N.; Nyborg, J. K.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 45
Methylation at arginine 17 of histone H3 is linked to gene activation
journal, January 2002
- Bauer, Uta‐Maria; Daujat, Sylvain; Nielsen, Søren J.
- EMBO reports, Vol. 3, Issue 1
Histone octamer function in vivo : mutations in the dimer-tetramer interfaces disrupt both gene activation and repression
journal, May 1997
- Santisteban, Maria Soledad; Arents, Gina; Moudrianakis, Evangelos N.
- The EMBO Journal, Vol. 16, Issue 9
MolSurfer: a macromolecular interface navigator
journal, July 2003
- Gabdoulline, R. R.
- Nucleic Acids Research, Vol. 31, Issue 13
3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
journal, September 2003
- Lu, X. -J.
- Nucleic Acids Research, Vol. 31, Issue 17
DNA and its counterions: a molecular dynamics study
journal, August 2004
- Varnai, P.
- Nucleic Acids Research, Vol. 32, Issue 14
The docking domain of histone H2A is required for H1 binding and RSC-mediated nucleosome remodeling
journal, December 2010
- Shukla, Manu Shubhdarshan; Syed, Sajad Hussain; Goutte-Gattat, Damien
- Nucleic Acids Research, Vol. 39, Issue 7
Polymer Reptation and Nucleosome Repositioning
journal, May 2001
- Schiessel, H.; Widom, J.; Bruinsma, R. F.
- Physical Review Letters, Vol. 86, Issue 19
Role of Histone N-Terminal Tails and Their Acetylation in Nucleosome Dynamics
journal, October 2000
- Morales, Violette; Richard-Foy, Hélène
- Molecular and Cellular Biology, Vol. 20, Issue 19
Functions of Site-Specific Histone Acetylation and Deacetylation
journal, June 2007
- Shahbazian, Mona D.; Grunstein, Michael
- Annual Review of Biochemistry, Vol. 76, Issue 1
The Biology of Chromatin Remodeling Complexes
journal, June 2009
- Clapier, Cedric R.; Cairns, Bradley R.
- Annual Review of Biochemistry, Vol. 78, Issue 1
Chromatin dynamics: Nucleosomes go mobile through twist defects
text, January 2003
- Kulic, I. M.; Schiessel, H.
- arXiv
Works referencing / citing this record:
High precision FRET studies reveal reversible transitions in nucleosomes between microseconds and minutes
journal, November 2018
- Gansen, Alexander; Felekyan, Suren; Kühnemuth, Ralf
- Nature Communications, Vol. 9, Issue 1
Epigenetic Modulation of Stem Cells in Neurodevelopment: The Role of Methylation and Acetylation
journal, February 2017
- Podobinska, Martyna; Szablowska-Gadomska, Ilona; Augustyniak, Justyna
- Frontiers in Cellular Neuroscience, Vol. 11
DNA accessibility of chromatosomes quantified by automated image analysis of AFM data
journal, September 2019
- Würtz, Martin; Aumiller, Dennis; Gundelwein, Lina
- Scientific Reports, Vol. 9, Issue 1
Dynamics of the nucleosomal histone H3 N-terminal tail revealed by high precision single-molecule FRET
journal, January 2020
- Lehmann, Kathrin; Felekyan, Suren; Kühnemuth, Ralf
- Nucleic Acids Research, Vol. 48, Issue 3
Jörg Langowski: his scientific legacy and the future it promises
journal, July 2018
- Chirico, Giuseppe; Gansen, Alexander; Leuba, Sanford H.
- BMC Biophysics, Vol. 11, Issue 1
Distinct Roles of Histone H3 and H2A Tails in Nucleosome Stability
journal, August 2016
- Li, Zhenhai; Kono, Hidetoshi
- Scientific Reports, Vol. 6, Issue 1
Molecular mechanism of histone variant H2A.B on stability and assembly of nucleosome and chromatin structures
journal, July 2020
- Peng, Junhui; Yuan, Chuang; Hua, Xinfan
- Epigenetics & Chromatin, Vol. 13, Issue 1
Histone Tail Dynamics in Partially Disassembled Nucleosomes During Chromatin Remodeling
journal, November 2019
- Kameda, Takeru; Awazu, Akinori; Togashi, Yuichi
- Frontiers in Molecular Biosciences, Vol. 6
CENP-C unwraps the CENP-A nucleosome through the H2A C-terminal tail
posted_content, January 2019
- Ali-Ahmad, Ahmad; Bilokapić, Silvija; Schäfer, Ingmar B.
- BioRxiv
Regulation of the DNA damage response by ubiquitin conjugation
journal, March 2015
- Brinkmann, Kerstin; Schell, Michael; Hoppe, Thorsten
- Frontiers in Genetics, Vol. 6
Chasing Tails: Cathepsin-L Improves Structural Analysis of Histones by HX-MS*[S]
journal, October 2019
- Papanastasiou, Malvina; Mullahoo, James; DeRuff, Katherine C.
- Molecular & Cellular Proteomics, Vol. 18, Issue 10
Contribution of histone N-terminal tails to the structure and stability of nucleosomes
journal, January 2013
- Iwasaki, Wakana; Miya, Yuta; Horikoshi, Naoki
- FEBS Open Bio, Vol. 3, Issue 1
Shearing of the CENP-A dimerization interface mediates plasticity in the octameric centromeric nucleosome
journal, November 2015
- Winogradoff, David; Zhao, Haiqing; Dalal, Yamini
- Scientific Reports, Vol. 5, Issue 1
CENP ‐C unwraps the human CENP ‐A nucleosome through the H2A C‐terminal tail
journal, September 2019
- Ali‐Ahmad, Ahmad; Bilokapić, Silvija; Schäfer, Ingmar B.
- EMBO reports, Vol. 20, Issue 10
Histone H3 Lysine 56 Acetylation Is Required for Formation of Normal Levels of Meiotic DNA Breaks in S. cerevisiae
journal, January 2020
- Karányi, Zsolt; Hornyák, Lilla; Székvölgyi, Lóránt
- Frontiers in Cell and Developmental Biology, Vol. 7
Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA
journal, March 2018
- Kono, Hidetoshi; Sakuraba, Shun; Ishida, Hisashi
- PLOS Computational Biology, Vol. 14, Issue 3
An Advanced Coarse-Grained Nucleosome Core Particle Model for Computer Simulations of Nucleosome-Nucleosome Interactions under Varying Ionic Conditions
journal, February 2013
- Fan, Yanping; Korolev, Nikolay; Lyubartsev, Alexander P.
- PLoS ONE, Vol. 8, Issue 2
Histone Tail Dynamics in Partially Disassembled Nucleosomes During Chromatin Remodeling
journal, January 2019
- Kameda, T.; Awazu, A.; Togashi, Y.
- Frontiers in Molecular Biosciences
A Comprehensive View of the Epigenetic Landscape. Part II: Histone Post-translational Modification, Nucleosome Level, and Chromatin Regulation by ncRNAs
journal, December 2014
- Sadakierska-Chudy, Anna; Filip, Małgorzata
- Neurotoxicity Research, Vol. 27, Issue 2
Structure and dynamics of DNA loops on nucleosomes studied with atomistic, microsecond-scale molecular dynamics
journal, April 2016
- Pasi, Marco; Lavery, Richard
- Nucleic Acids Research, Vol. 44, Issue 11
Causes and consequences of epigenetic regulation in wound healing: Epigenetic alteration in wound healing
journal, May 2014
- Ti, Dongdong; Li, Meirong; Fu, Xiaobing
- Wound Repair and Regeneration, Vol. 22, Issue 3
New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions
journal, January 2018
- Yoo, Jejoong; Aksimentiev, Aleksei
- Physical Chemistry Chemical Physics, Vol. 20, Issue 13
Modulation of nucleosomal DNA accessibility via charge-altering post-translational modifications in histone core
journal, March 2018
- Fenley, Andrew T.; Anandakrishnan, Ramu; Kidane, Yared H.
- Epigenetics & Chromatin, Vol. 11, Issue 1
Histone H2A variants in nucleosomes and chromatin: more or less stable?
journal, September 2012
- Bonisch, C.; Hake, S. B.
- Nucleic Acids Research, Vol. 40, Issue 21
The effect of epigenetic modifications on the secondary structures and possible binding positions of the N-terminal tail of histone H3 in the nucleosome: a computational study
journal, March 2017
- du Preez, Louis L.; Patterton, Hugh-G
- Journal of Molecular Modeling, Vol. 23, Issue 4
A Comprehensive View of the Epigenetic Landscape. Part II: Histone Post-translational Modification, Nucleosome Level, and Chromatin Regulation by ncRNAs
journal, December 2014
- Sadakierska-Chudy, Anna; Filip, Małgorzata
- Neurotoxicity Research, Vol. 27, Issue 2
The Role of Histone Tails in the Nucleosome: A Computational Study
journal, December 2014
- Erler, Jochen; Zhang, Ruihan; Petridis, Loukas
- Biophysical Journal, Vol. 107, Issue 12
Speed of Conformational Change: Comparing Explicit and Implicit Solvent Molecular Dynamics Simulations
journal, March 2015
- Anandakrishnan, Ramu; Drozdetski, Aleksander; Walker, Ross C.
- Biophysical Journal, Vol. 108, Issue 5
Nucleosome Core Particle Disassembly and Assembly Kinetics Studied Using Single-Molecule Fluorescence
journal, October 2015
- Hazan, Noa Plavner; Tomov, Toma E.; Tsukanov, Roman
- Biophysical Journal, Vol. 109, Issue 8
High precision FRET studies reveal reversible transitions in nucleosomes between microseconds and minutes
journal, November 2018
- Gansen, Alexander; Felekyan, Suren; Kühnemuth, Ralf
- Nature Communications, Vol. 9, Issue 1
Shearing of the CENP-A dimerization interface mediates plasticity in the octameric centromeric nucleosome
journal, November 2015
- Winogradoff, David; Zhao, Haiqing; Dalal, Yamini
- Scientific Reports, Vol. 5, Issue 1
Distinct Roles of Histone H3 and H2A Tails in Nucleosome Stability
journal, August 2016
- Li, Zhenhai; Kono, Hidetoshi
- Scientific Reports, Vol. 6, Issue 1
Histone H2A variants in nucleosomes and chromatin: more or less stable?
journal, September 2012
- Bonisch, C.; Hake, S. B.
- Nucleic Acids Research, Vol. 40, Issue 21
Structure and dynamics of DNA loops on nucleosomes studied with atomistic, microsecond-scale molecular dynamics
journal, April 2016
- Pasi, Marco; Lavery, Richard
- Nucleic Acids Research, Vol. 44, Issue 11
Histone H2A variants confer specific properties to nucleosomes and impact on chromatin accessibility
journal, June 2018
- Osakabe, Akihisa; Lorković, Zdravko J.; Kobayashi, Wataru
- Nucleic Acids Research, Vol. 46, Issue 15
Mechanical evolution of DNA double-strand breaks in the nucleosome
journal, January 2018
- Cleri, Fabrizio; Landuzzi, Fabio; Blossey, Ralf
- PLOS Computational Biology
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journal, July 2018
- Chirico, Giuseppe; Gansen, Alexander; Leuba, Sanford H.
- BMC Biophysics, Vol. 11, Issue 1
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journal, March 2018
- Kono, Hidetoshi; Sakuraba, Shun; Ishida, Hisashi
- PLOS Computational Biology, Vol. 14, Issue 3
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journal, March 2015
- Kono, Hidetoshi; Shirayama, Kazuyoshi; Arimura, Yasuhiro
- PLOS ONE, Vol. 10, Issue 3
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journal, September 2019
- Ali‐Ahmad, Ahmad; Bilokapić, Silvija; Schäfer, Ingmar B.
- EMBO reports, Vol. 20, Issue 10
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text, January 2017
- Sharif, Ali; Akhtar, Muhammad Furqan; Akhtar, Bushra
- Technische Universität Dortmund
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journal, January 2019
- Kono, Hidetoshi; Sakuraba, Shun; Ishida, Hisashi
- Biophysics and Physicobiology, Vol. 16, Issue 0
Reading, writing, and repair: the role of ubiquitin and the ubiquitin-like proteins in DNA damage signaling and repair
journal, January 2013
- Pinder, Jordan B.; Attwood, Kathleen M.; Dellaire, Graham
- Frontiers in Genetics, Vol. 4
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- Brinkmann, Kerstin; Schell, Michael; Hoppe, Thorsten
- Frontiers in Genetics, Vol. 6
Histone Acetylation as a Regenerative Target in the Dentine-Pulp Complex
journal, February 2020
- Yamauchi, Yukako; Cooper, Paul Roy; Shimizu, Emi
- Frontiers in Genetics, Vol. 11
Histone Tail Dynamics in Partially Disassembled Nucleosomes During Chromatin Remodeling
journal, November 2019
- Kameda, Takeru; Awazu, Akinori; Togashi, Yuichi
- Frontiers in Molecular Biosciences, Vol. 6
Epigenetic Modulation of Stem Cells in Neurodevelopment: The Role of Methylation and Acetylation
journal, February 2017
- Podobinska, Martyna; Szablowska-Gadomska, Ilona; Augustyniak, Justyna
- Frontiers in Cellular Neuroscience, Vol. 11
Identification and Characterization of Switchgrass Histone H3 and CENH3 Genes
journal, July 2016
- Miao, Jiamin; Frazier, Taylor; Huang, Linkai
- Frontiers in Plant Science, Vol. 7