# Histone Variant H2A.Z Enhances Histone and Nucleosome Dynamics

## TL;DR

This study shows that replacing histone H2A with variant H2A.Z increases the flexibility of histone complexes, which may explain how these structurally similar proteins perform different functions in the cell.

## Contribution

The study reveals that subtle amino acid changes in H2A.Z enhance histone dynamics, providing a mechanistic explanation for functional differences between histone variants.

## Key findings

- Replacing H2A with H2A.Z increases the dynamics of H2B in histone heterodimers.
- Molecular dynamics simulations show fewer hydrogen bonds in nucleosomes containing H2A.Z.
- Dynamics differences are more pronounced in human H2A.Z-H2B than in frog homologs.

## Abstract

Interchanging canonical histone H2A with variant H2A.Z in chromatin complexes is vital for the proper regulation of transcription, DNA damage repair, and centromere maintenance. However, the physical mechanisms underlying functional differences between H2A and H2A.Z complexes are unclear. Human H2A and H2A.Z exhibit high sequence and structural conservation, with subtle differences in the H2A DNA-binding loops. In this study, we employ hydrogen-deuterium exchange coupled with mass spectrometry and molecular dynamics simulation to investigate the differences in solution behavior between human H2A-H2B and H2A.Z-H2B. We demonstrate that replacing H2A with H2A.Z enhances the dynamics of the refolded histone heterodimer, whether it is in nucleosomes, in complex with H3-H4, or alone in solution. In all situations, enhanced dynamics are observed for H2B, suggesting altered interaction with H2A.Z and DNA. Parallel comparisons of H2A-H2B orthologs between humans and frogs reveal fewer differences in dynamics. Our findings provide mechanistic insights into the function of histone variants and reveal how differences in dynamics may underlie functional differences between structurally similar proteins.

•Histone sequences and structures are highly conserved among variants and homologs.•We use modified HDX-MS to compare histone homologs distinguished by stable isotopes.•Replacing H2A with H2A.Z in histone complexes enhances the dynamics of H2B.•MD simulations show fewer H-bonds in nucleosomes with H2A.Z in place of H2A.

Histone sequences and structures are highly conserved among variants and homologs.

We use modified HDX-MS to compare histone homologs distinguished by stable isotopes.

Replacing H2A with H2A.Z in histone complexes enhances the dynamics of H2B.

MD simulations show fewer H-bonds in nucleosomes with H2A.Z in place of H2A.

The sequence and structure of the histone H2A-H2B heterodimer are highly conserved among eukaryotic homologs, such as frogs and humans, as well as functionally distinct variants, such as H2A.Z-H2B. Using hydrogen-deuterium exchange mass spectrometry and molecular dynamics simulations, we show that amino acid substitutions, even those seemingly conservative, can alter the solution dynamics of the histone heterodimer when it is alone and, in some cases, when it is bound to the histone (H3-H4)2 tetramer or in the nucleosome.