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Related Concept Videos

Histone Modification02:32

Histone Modification

The histone proteins have a flexible N-terminal tail extending out from the nucleosome. These histone tails are often subjected to post-translational modifications such as acetylation, methylation, phosphorylation, and ubiquitination. Particular combinations of these modifications form “histone codes” that influence the chromatin folding and tissue-specific gene expression.
Acetylation
The enzyme histone acetyltransferase adds acetyl group to the histones. Another enzyme, histone deacetylase,...
Histone Modification02:32

Histone Modification

The histone proteins have a flexible N-terminal tail extending out from the nucleosome. These histone tails are often subjected to post-translational modifications such as acetylation, methylation, phosphorylation, and ubiquitination. Particular combinations of these modifications form “histone codes” that influence the chromatin folding and tissue-specific gene expression.
Acetylation
The enzyme histone acetyltransferase adds acetyl group to the histones. Another enzyme, histone deacetylase,...
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...
Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

The histone proteins in the nucleosomes are post-translationally modified (PTM) to increase or decrease access to DNA. The commonly observed PTMs are methylation, acetylation, phosphorylation, and ubiquitination of lysine amino acids in the histone H3 tail region. These histone modifications have specific meaning for the cell. Hence, they are called "histone code". The protein complex involved in histone modification is termed as "reader-writer" complex.
Writers
The writer is an enzyme that can...
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...
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...

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Sequential Salt Extractions for the Analysis of Bulk Chromatin Binding Properties of Chromatin Modifying Complexes
07:41

Sequential Salt Extractions for the Analysis of Bulk Chromatin Binding Properties of Chromatin Modifying Complexes

Published on: October 2, 2017

Does bromodomain flexibility influence histone recognition?

Sandra Steiner1, Andrea Magno, Danzhi Huang

  • 1Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.

FEBS Letters
|May 29, 2013
PubMed
Summary
This summary is machine-generated.

Bromodomains, which bind acetylated lysines on histones, exhibit flexible binding sites. Simulations reveal that this flexibility and self-occluded states affect histone tail recognition.

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Last Updated: May 11, 2026

Sequential Salt Extractions for the Analysis of Bulk Chromatin Binding Properties of Chromatin Modifying Complexes
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Published on: October 2, 2017

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Epigenetics

Background:

  • Bromodomains are protein modules recognizing acetylated lysine residues on histone proteins.
  • This recognition is crucial for epigenetic regulation and gene expression.
  • Understanding bromodomain binding site dynamics is key to deciphering their function.

Purpose of the Study:

  • To investigate the flexibility and dynamics of the binding sites of 20 human bromodomains.
  • To explore the structural variations and accessibility of the bromodomain binding pockets.
  • To understand how binding site dynamics influence the recognition of acetylated histones.

Main Methods:

  • Multiple molecular dynamics simulations were performed on 20 human bromodomain constructs.
  • Analysis focused on side chain orientations and binding site accessibility.
  • Specific attention was given to conserved residues involved in ligand binding.

Main Results:

  • Simulations revealed significant flexibility in the binding sites of several bromodomains.
  • Alternative side chain conformations were observed for conserved residues.
  • Binding site occlusion, involving displacement of aromatic residues, was noted in BAZ2B and CREBBP bromodomains.
  • A high degree of variability in binding site accessibility was observed, contrasting with static structural data.

Conclusions:

  • The bromodomain binding site is highly flexible, with significant conformational variability.
  • Metastable, self-occluded states of the binding site can occur.
  • Binding site flexibility and the presence of these occluded states are critical factors influencing the recognition of acetylated lysine on histone tails.