Effects of MacroH2A and H2A.Z on Nucleosome Dynamics as Elucidated by Molecular Dynamics Simulations

Biophysical Journal
Samuel Bowerman, Jeff Wereszczynski

Abstract

Eukaryotes tune the transcriptional activity of their genome by altering the nucleosome core particle through multiple chemical processes. In particular, replacement of the canonical H2A histone with the variants macroH2A and H2A.Z has been shown to affect DNA accessibility and nucleosome stability; however, the processes by which this occurs remain poorly understood. In this study, we elucidate the molecular mechanisms of these variants with an extensive molecular dynamics study of the canonical nucleosome along with three variant-containing structures: H2A.Z, macroH2A, and an H2A mutant with macroH2A-like L1 loops. Simulation results show that variant L1 loops play a pivotal role in stabilizing DNA binding to the octamer through direct interactions, core structural rearrangements, and altered allosteric networks in the nucleosome. All variants influence dynamics; however, macroH2A-like systems have the largest effect on energetics. In addition, we provide a comprehensive analysis of allosteric networks in the nucleosome and demonstrate that variants take advantage of stronger interactions between L1 loops to propagate dynamics throughout the complex. Furthermore, we show that posttranslational modifications are enriched at ke...Continue Reading

References

Sep 4, 1992·Science·J R Pehrson, V A Fried
Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
Jun 25, 2002·Journal of Molecular Biology·Curt A DaveyTimothy J Richmond
Jun 26, 2002·The Journal of Cell Biology·Brian P Chadwick, Huntington F Willard
Apr 22, 2005·Journal of Biomolecular Structure & Dynamics·Thomas C Bishop
Aug 19, 2005·Molecular and Cellular Biology·Srinivas ChakravarthyKarolin Luger
Aug 25, 2005·Cold Spring Harbor Symposia on Quantitative Biology·S ChakravarthyK Luger
Oct 14, 2005·Journal of Computational Chemistry·James C PhillipsKlaus Schulten
Dec 16, 2005·Proteins·Oliver F Lange, Helmut Grubmüller
Jan 18, 2006·Biophysical Journal·James Gumbart, Klaus Schulten
Jan 20, 2006·Human Molecular Genetics·Jung Ha ChooJoomyeong Kim
Mar 3, 2006·Acta Crystallographica. Section F, Structural Biology and Crystallization Communications·Christopher M WoodJohn P Baldwin
Jun 29, 2006·The Journal of Biological Chemistry·Srinivas Chakravarthy, Karolin Luger
Aug 17, 2006·Results and Problems in Cell Differentiation·Mary Ann OsleyCheng-Fu Kao
Jun 19, 2007·Genes & Development·Chunyuan Jin, Gary Felsenfeld
Sep 19, 2007·Proteins·Oliver F Lange, Helmut Grubmüller
Dec 3, 2008·The Journal of Chemical Physics·Michael R Shirts, John D Chodera
Sep 8, 2009·Nature Structural & Molecular Biology·Marcus BuschbeckLuciano Di Croce
Apr 7, 2010·Epigenetics : Official Journal of the DNA Methylation Society·Maud MarquesLuc Gaudreau
Dec 24, 2010·Nucleic Acids Research·Vera BöhmJörg Langowski
Apr 19, 2011·Journal of Computational Chemistry·Naveen Michaud-AgrawalOliver Beckstein
Dec 6, 2011·Nucleic Acids Research·Satyajeet P KhareSanjeev Galande
Dec 31, 2011·PLoS Computational Biology·Mithun BiswasJörg Langowski
Oct 1, 2007·Journal of Biomolecular Structure & Dynamics·M VijayalakshmiR Sowdhamini
Jun 23, 2012·Nature Reviews. Molecular Cell Biology·Karolin LugerDavid J Tremethick
Jul 4, 2012·Nucleic Acids Research·Srinivas ChakravarthyGregory D Bowman
Sep 25, 2012·Nucleic Acids Research·Clemens Bönisch, Sandra B Hake
Jan 15, 2013·Journal of Chemical Theory and Computation·Christopher L McClendonMatthew P Jacobson
May 8, 2014·Journal of Chemical Theory and Computation·Adam T Van WartRommie E Amaro
Aug 20, 2014·Proceedings of the National Academy of Sciences of the United States of America·Ana CuervoLaura Fumagalli
Nov 27, 2014·Chemical Reviews·Gregory D Bowman, Michael G Poirier
Mar 4, 2015·Current Opinion in Structural Biology·Alexey K ShaytanAnna R Panchenko
Jul 9, 2013·Journal of Chemical Theory and Computation·Daniel R Roe, Thomas E Cheatham
Feb 8, 2011·Journal of Chemical Theory and Computation·Mats H M OlssonJan H Jensen

❮ Previous
Next ❯

Citations

Aug 17, 2016·Scientific Reports·Zhenhai Li, Hidetoshi Kono
Aug 31, 2016·PLoS Pathogens·Rebecca L GibeaultLuis M Schang
Mar 31, 2017·Nature Communications·Zenita AdhireksanCurt A Davey
Sep 28, 2016·Journal of Computational Chemistry·Steven C HowellJoseph E Curtis
Aug 16, 2017·The Journal of Chemical Physics·Kaushik Chakraborty, Sharon M Loverde
Jun 27, 2018·Nucleic Acids Research·Akihisa OsakabeFrédéric Berger
Mar 20, 2019·Nature Reviews. Genetics·Paul B TalbertSteven Henikoff
Nov 8, 2020·Nature Communications·Kai NiKathrin Muegge
Dec 15, 2020·Journal of Molecular Biology·Jan Huertas, Vlad Cojocaru
Dec 14, 2019·Plant Communications·Bingkun Lei, Frédéric Berger
Nov 21, 2020·Cells·Imtiaz Nisar LoneHani Alotaibi
Feb 9, 2021·Trends in Biochemical Sciences·Mohamed GhoneimCatherine A Musselman
Feb 21, 2021·Biophysical Journal·Havva Kohestani, Jeff Wereszczynski
Apr 23, 2020·Biophysical Journal·Joshua Moller, Juan J de Pablo
Mar 16, 2017·Journal of Molecular Graphics & Modelling·Weihong ZhangJoseph E Curtis
Mar 6, 2021·Journal of Molecular Biology·Dustin C WoodsJeff Wereszczynski
Apr 21, 2021·Expert Opinion on Drug Discovery·Giulia PalermoAlessandra Magistrato
Jun 4, 2021·PLoS Computational Biology·Jan HuertasVlad Cojocaru
Jun 11, 2021·Current Opinion in Structural Biology·Amarjeet KumarHidetoshi Kono
Jun 25, 2021·The Journal of Physical Chemistry Letters·Emmanuelle BignonElise Dumont
Mar 30, 2019·The Journal of Physical Chemistry. B·María J Beltrán-LeivaRamiro Arratia-Pérez
Apr 26, 2019·ACS Chemical Biology·Chuxuan Li, Sarah Delaney
Nov 28, 2018·The Journal of Physical Chemistry. B·Kaushik ChakrabortySharon M Loverde
Dec 18, 2018·The Journal of Physical Chemistry. B·Samuel BowermanJeff Wereszczynski
Aug 19, 2020·Journal of Chemical Theory and Computation·Eva MatouškováFilip Lankaš

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Cell and Tissue Research
Burcu Biterge, Robert Schneider
Cold Spring Harbor Symposia on Quantitative Biology
E N Moudrianakis, G Arents
Trends in Biochemical Sciences
Michael S Kobor, Matthew C Lorincz
© 2022 Meta ULC. All rights reserved