Mapping the electrostatic potential of the nucleosome acidic patch

Heyi Zhang,Hugo Van Ingen,Velten Horn,Raymond Schellevis,Jelmer Eerland

doi:10.1038/s41598-021-02436-3

Heyi Zhang, Hugo Van Ingen + Show 3 more

Open Access

https://doi.org/10.1038/s41598-021-02436-3

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Journal: Scientific Reports	Publication Date: Nov 26, 2021
Citations: 5	License type: open-access

Affiliation: Leiden University, Utrecht University

Abstract

The nucleosome surface contains an area with negative electrostatic potential known as the acidic patch, which functions as a binding platform for various proteins to regulate chromatin biology. The dense clustering of acidic residues may impact their effective pKa and thus the electronegativity of the acidic patch, which in turn could influence nucleosome-protein interactions. We here set out to determine the pKa values of residues in and around the acidic patch in the free H2A-H2B dimer using NMR spectroscopy. We present a refined solution structure of the H2A-H2B dimer based on intermolecular distance restraints, displaying a well-defined histone-fold core. We show that the conserved histidines H2B H46 and H106 that line the acidic patch have pKa of 5.9 and 6.5, respectively, and that most acidic patch carboxyl groups have pKa values well below 5.0. For H2A D89 we find strong evidence for an elevated pKa of 5.3. Our data establish that the acidic patch is highly negatively charged at physiological pH, while protonation of H2B H106 and H2B H46 at slightly acidic pH will reduce electronegativity. These results will be valuable to understand the impact of pH changes on nucleosome-protein interactions in vitro, in silico or in vivo.

Highlights

6.5, indicating a key role in modulating the effective acidic patch electrostatic potential and hydrogen bonding capacity upon protein binding or changes in local nuclear pH
Since the H2B αC helix carries two of the acidic patch residues, rearrangement of this helix could change the electrostatic potential of the acidic patch and invalidate the use of the H2AH2B dimer as a model system for the nucleosome acidic patch
Since the addition of distance restraints can greatly improve the definition of a structure in the CS-Rosetta approach[29], we collected intermolecular distance restraints to supplement the backbone chemical shifts and subsequently calculate a refined solution structure of the Drosophila melanogaster (Dm.) H2A-H2B heterodimer

Summary

Introduction

6.5, indicating a key role in modulating the effective acidic patch electrostatic potential and hydrogen bonding capacity upon protein binding or changes in local nuclear pH. Using a NOESY experiment recorded on dimers refolded from unlabeled H2A and perdeuterated and 15N-labeled H2B, intermolecular NOEs between H2B amide protons and H2A backbone or side chain protons were identified for most H2B residues in the histone-fold core (Y34-K122) (Fig. 1b).

Results

Conclusion