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Related Concept Videos

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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.
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Each human somatic cell contains 6 billion base-pairs of DNA. Each base-pair is 0.34 nm long, which means that each diploid cell contains a staggering 2 meters of DNA. How is such a long DNA strand packed inside a nucleus measuring only 10 - 20 microns in diameter? 
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Mapping the electrostatic potential of the nucleosome acidic patch.

Heyi Zhang1,2, Jelmer Eerland1, Velten Horn1

  • 1Department of Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300, RA, Leiden, The Netherlands.

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The nucleosome's acidic patch, crucial for chromatin regulation, has key residues with altered acidity. Understanding these pKa values helps predict how pH affects protein binding to nucleosomes.

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Area of Science:

  • Biochemistry and Molecular Biology
  • Structural Biology
  • Epigenetics and Chromatin Dynamics

Background:

  • The nucleosome acidic patch is a key regulatory site for chromatin biology.
  • Dense acidic residue clustering may alter pKa values, influencing the patch's electronegativity and protein interactions.

Purpose of the Study:

  • To determine the pKa values of residues within the H2A-H2B dimer's acidic patch.
  • To investigate how residue pKa affects the acidic patch's charge and nucleosome-protein interactions.

Main Methods:

  • Nuclear Magnetic Resonance (NMR) spectroscopy was used to measure pKa values.
  • A refined solution structure of the H2A-H2B dimer was determined using intermolecular distance restraints.

Main Results:

  • Histidines H2B H46 and H106 have pKa values of 5.9 and 6.5, respectively.
  • Most acidic patch carboxyl groups exhibit pKa values below 5.0.
  • H2A D89 shows an elevated pKa of 5.3.

Conclusions:

  • The acidic patch is highly negatively charged at physiological pH.
  • Protonation of specific histidines at slightly acidic pH reduces the patch's electronegativity.
  • These findings aid in understanding pH-dependent nucleosome-protein interactions.