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Related Concept Videos

The Nucleosome Core Particle02:10

The Nucleosome Core Particle

Nucleosomes are the DNA-histone complex, where the DNA strand is wound around the histone core. The histone core is an octamer containing two copies of H2A, H2B, H3, and H4 histone proteins.
The paradox
Nucleosomes, paradoxically, perform two opposite functions simultaneously. On the one hand, their main responsibility is to protect the delicate DNA strands from physical damage and help achieve a higher compaction ratio. While on the other hand, they must allow polymerase enzymes to access DNA...
The Nucleosome Core Particle01:12

The Nucleosome Core Particle

Nucleosomes are the DNA-histone complex, where the DNA strand is wound around the histone core. The histone core is an octamer containing two copies of H2A, H2B, H3, and H4 histone proteins.
Nucleosomes, paradoxically, perform two opposite functions simultaneously. On the one hand, their primary aim is to protect the delicate DNA strands from physical damage and help achieve a higher compaction ratio. On the other hand, they must allow polymerase enzymes to access histone-bound DNA during...
Nucleosome Remodeling02:54

Nucleosome Remodeling

Nucleosomes are the basic units of chromatin compaction. Each nucleosome consists of the DNA bound tightly around a histone core, which makes the DNA inaccessible to DNA binding proteins such as DNA polymerase and RNA polymerase. Hence, the fundamental problem is to ensure access to DNA when appropriate, despite the compact and protective chromatin structure.
Nucleosome remodeling complex
Eukaryotic cells have specialized enzymes called ATP-dependent nucleosome remodeling enzymes. These enzymes...
The Nucleosome02:33

The Nucleosome

DNA in a human cell is almost 2m long and it is packed inside a tiny nucleus that is only a few microns in diameter. The level of compaction of DNA inside the nucleus is astonishing. It is organized into several sequentially higher levels of compaction to fit into such a tiny space. The most compact form of DNA is a chromosome that can be seen under a microscope in a dividing cell.
DNA is wound twice around a protein complex called histone core, that consist of 8 histone proteins. This complex...
The Nucleosome01:19

The Nucleosome

Human DNA is almost two meters long. However, it is compressed inside a tiny nucleus measuring only a few microns in diameter. To make this degree of compaction possible, DNA is organized into several sequential levels so that it can fit into such a tiny space. The most compact form of DNA is a chromosome that can be seen under a microscope in a dividing cell.
In a chromosome, DNA is wound twice around a protein complex called a histone octamer core, which consists of 8 histone proteins. This...
The Nucleosome02:33

The Nucleosome

DNA in a human cell is almost 2m long and it is packed inside a tiny nucleus that is only a few microns in diameter. The level of compaction of DNA inside the nucleus is astonishing. It is organized into several sequentially higher levels of compaction to fit into such a tiny space. The most compact form of DNA is a chromosome that can be seen under a microscope in a dividing cell.
DNA is wound twice around a protein complex called histone core, that consist of 8 histone proteins. This complex...

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Related Experiment Video

Updated: Jul 7, 2026

Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging
09:52

Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging

Published on: January 31, 2019

Coarse-grained force field for the nucleosome from self-consistent multiscaling.

Karine Voltz1, Joanna Trylska, Valentina Tozzini

  • 1Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany.

Journal of Computational Chemistry
|February 14, 2008
PubMed
Summary
This summary is machine-generated.

A new coarse-grained simulation model for the nucleosome was developed. This model accurately reproduces structural properties and accelerates simulations by 1000-fold, enabling longer timescale studies.

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In Situ Nucleosome Assembly for Single-Molecule Correlative Force and Fluorescence Microscopy
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In Situ Nucleosome Assembly for Single-Molecule Correlative Force and Fluorescence Microscopy

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Assembly of Nucleosomal Arrays from Recombinant Core Histones and Nucleosome Positioning DNA
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Assembly of Nucleosomal Arrays from Recombinant Core Histones and Nucleosome Positioning DNA

Published on: September 10, 2013

Related Experiment Videos

Last Updated: Jul 7, 2026

Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging
09:52

Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging

Published on: January 31, 2019

In Situ Nucleosome Assembly for Single-Molecule Correlative Force and Fluorescence Microscopy
05:58

In Situ Nucleosome Assembly for Single-Molecule Correlative Force and Fluorescence Microscopy

Published on: September 6, 2024

Assembly of Nucleosomal Arrays from Recombinant Core Histones and Nucleosome Positioning DNA
10:40

Assembly of Nucleosomal Arrays from Recombinant Core Histones and Nucleosome Positioning DNA

Published on: September 10, 2013

Area of Science:

  • Computational Biology
  • Structural Biology
  • Biophysics

Background:

  • Nucleosomes are fundamental units of DNA packaging in eukaryotes.
  • Understanding nucleosome dynamics is crucial for gene regulation and chromatin structure.
  • All-atom molecular dynamics (MD) simulations provide detailed insights but are computationally expensive.

Purpose of the Study:

  • To develop a coarse-grained simulation model for the nucleosome.
  • To enable efficient and accurate simulations of nucleosome dynamics.
  • To facilitate the study of biologically relevant phenomena on microsecond timescales and beyond.

Main Methods:

  • A coarse-grained model representing protein residues and DNA nucleotides as beads.
  • Utilized harmonic and Morse potentials for interactions.
  • Estimated force-field parameters via Boltzmann inversion of radial distribution functions from all-atom MD simulations.
  • Refined parameters for agreement with all-atom MD simulations.

Main Results:

  • Developed a self-consistent multiscale coarse-grained model for the nucleosome.
  • The model accurately reproduces equilibrium structural properties from 50-ns all-atom MD simulations.
  • Achieved a 1000-fold speedup in simulation time compared to all-atom methods.

Conclusions:

  • The developed coarse-grained model is a powerful tool for studying nucleosome structure and dynamics.
  • Enables efficient exploration of longer timescales relevant to biological processes.
  • Facilitates research into nucleosome behavior in gene regulation and chromatin dynamics.