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Title: Structural Flexibility of the Nucleosome Core Particle at Atomic Resolution studied by Molecular Dynamics Simulation.

Abstract

The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. Comparative explicit solvent molecular dynamics (MD) simulations have been performed on a complete nucleosome core particle with and without N-terminal histone tails for more than 20 ns. Main purpose of the simulations was to study the dynamics of mobile elements such as histone N-terminal tails and how packing and DNA-bending influences the fine structure and dynamics of DNA. Except for the tails, histone and DNA molecules stayed on average close to the crystallographic start structure supporting the quality of the current force field approach. Despite the packing strain, no increase of transitions to noncanonical nucleic acid backbone conformations compared to regular B-DNA was observed. The pattern of kinks and bends along the DNA remained close to the experiment overall. In addition to the local dynamics, the simulations allowed the analysis of the superhelical mobility indicating a limited relative mobility of DNA segments separated by one superhelical turn (mean relative displacement of approximately 60.2 nm, mainly along the superhelical axis). Anmore » even higher rigidity was found for relative motions (distance fluctuations) of segments separated by half a superhelical turn (approximately 60.1 nm). The N-terminal tails underwent dramatic conformational rearrangements on the nanosecond time scale toward partially and transiently wrapped states around the DNA. Many of the histone tail changes corresponded to coupled association and folding events from fully solvent-exposed states toward complexes with the major and minor grooves of DNA. The simulations indicate that the rapid conformational changes of the tails can modulate the DNA accessibility within a few nanoseconds. # 2007 Wiley Periodicals, Inc. Biopolymers 85: 407–421, 2007. Keywords: nucleic acid flexibility; nucleosome dynamics; DNA packing; DNA structure and dynamics; histone– DNA interaction; histone tail motion flexibility« less

Authors:
; ;
Publication Date:
Research Org.:
Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
Sponsoring Org.:
USDOE
OSTI Identifier:
921401
DOE Contract Number:
AC05-76RL01830
Resource Type:
Journal Article
Resource Relation:
Journal Name: Biopolymers, 85(5):407-421; Journal Volume: 85; Journal Issue: 5
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; CONFORMATIONAL CHANGES; DNA; FINE STRUCTURE; FLEXIBILITY; FLUCTUATIONS; HISTONES; NUCLEIC ACIDS; NUCLEOSOMES; RESOLUTION; SIMULATION; SOLVENTS; Environmental Molecular Sciences Laboratory

Citation Formats

Roccatano, Danilo, Barthel, Andre, and Zacharias, Martin W. Structural Flexibility of the Nucleosome Core Particle at Atomic Resolution studied by Molecular Dynamics Simulation.. United States: N. p., 2007. Web. doi:10.1002/bip.20690.
Roccatano, Danilo, Barthel, Andre, & Zacharias, Martin W. Structural Flexibility of the Nucleosome Core Particle at Atomic Resolution studied by Molecular Dynamics Simulation.. United States. doi:10.1002/bip.20690.
Roccatano, Danilo, Barthel, Andre, and Zacharias, Martin W. Wed . "Structural Flexibility of the Nucleosome Core Particle at Atomic Resolution studied by Molecular Dynamics Simulation.". United States. doi:10.1002/bip.20690.
@article{osti_921401,
title = {Structural Flexibility of the Nucleosome Core Particle at Atomic Resolution studied by Molecular Dynamics Simulation.},
author = {Roccatano, Danilo and Barthel, Andre and Zacharias, Martin W.},
abstractNote = {The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. Comparative explicit solvent molecular dynamics (MD) simulations have been performed on a complete nucleosome core particle with and without N-terminal histone tails for more than 20 ns. Main purpose of the simulations was to study the dynamics of mobile elements such as histone N-terminal tails and how packing and DNA-bending influences the fine structure and dynamics of DNA. Except for the tails, histone and DNA molecules stayed on average close to the crystallographic start structure supporting the quality of the current force field approach. Despite the packing strain, no increase of transitions to noncanonical nucleic acid backbone conformations compared to regular B-DNA was observed. The pattern of kinks and bends along the DNA remained close to the experiment overall. In addition to the local dynamics, the simulations allowed the analysis of the superhelical mobility indicating a limited relative mobility of DNA segments separated by one superhelical turn (mean relative displacement of approximately 60.2 nm, mainly along the superhelical axis). An even higher rigidity was found for relative motions (distance fluctuations) of segments separated by half a superhelical turn (approximately 60.1 nm). The N-terminal tails underwent dramatic conformational rearrangements on the nanosecond time scale toward partially and transiently wrapped states around the DNA. Many of the histone tail changes corresponded to coupled association and folding events from fully solvent-exposed states toward complexes with the major and minor grooves of DNA. The simulations indicate that the rapid conformational changes of the tails can modulate the DNA accessibility within a few nanoseconds. # 2007 Wiley Periodicals, Inc. Biopolymers 85: 407–421, 2007. Keywords: nucleic acid flexibility; nucleosome dynamics; DNA packing; DNA structure and dynamics; histone– DNA interaction; histone tail motion flexibility},
doi = {10.1002/bip.20690},
journal = {Biopolymers, 85(5):407-421},
number = 5,
volume = 85,
place = {United States},
year = {Wed Jan 24 00:00:00 EST 2007},
month = {Wed Jan 24 00:00:00 EST 2007}
}