Structure, dynamics, and stability of the globular domain of human linker histone H1.0 and the role of positive charges

Abstract

Linker histone H1 (H1) is an abundant chromatin-binding protein that acts as an epigenetic regulator binding to nucleosomes and altering chromatin structures and dynamics. Nonetheless, the mechanistic details of its function remain poorly understood. Recent work suggest that the number and position of charged side chains on the globular domain (GD) of H1 influence chromatin structure and hence gene repression. Here, we solved the solution structure of the unbound GD of human H1.0, revealing that the structure is almost completely unperturbed by complex formation, except for a loop connecting two antiparallel β-strands. We further quantified the role of the many positive charges of the GD for its structure and conformational stability through the analysis of 11 charge variants. We find that modulating the number of charges has little effect on the structure, but the stability is affected, resulting in a difference in melting temperature of 26 K between GD of net charge +5 versus +13. This result suggests that the large number of positive charges on H1-GDs have evolved for function rather than structure and high stability. The stabilization of the GD upon binding to DNA can thus be expected to have a pronounced electrostatic component, a contribution that is amenable to modulation by posttranslational modifications, especially acetylation and phosphorylation.

Ultrafast molecular dynamics observed within a dense protein condensate

“…Initially, 12 ProTα and 10 H1 molecules were randomly placed in a 25-nm cubic box, and the energy of the system was minimized with the steepest-descent algorithm. Although the CG model itself is capable of capturing the structure of the small globular domain (GD) of H1, we performed a 1-ns NVT run at 300 K with PLUMED (74) restraints, using the list of native contacts based on the experimental structure (75) (PDB 6HQ1), to ensure that the structure of the GDs was sufficiently close to the experimental structure (needed for all-atom reconstruction, below). In the next step, the box edge was decreased to 13.35 nm in a 30-ps NPT run to obtain an average protein density close to that of the dense phase in experiment.…”

Location, Location, Location: Protein kinase nanoclustering for optimized signalling output

“…Src family kinases (SFKs) are aberrantly activated in cancer, particularly in solid tumours (94). SFKs have been shown to play important roles in the clustering and mobility of receptors such as nicotinic acetylcholine receptors, GPI-anchored receptors, B-cell receptors, and cytokine receptors (27,(95)(96)(97)(98).…”

Location, location, location: Protein kinase nanoclustering for optimised signalling output

“…SFKs are aberrantly activated in cancer, particularly in solid tumours ( Martinsen et al, 2022 ). SFKs have been shown to play important roles in the clustering and mobility of receptors, such as nicotinic acetylcholine receptors, GPI-anchored receptors, B-cell receptors, and cytokine receptors ( Chhabra et al, 2023 ; Flynn and Syed, 2020 ; Sohn et al, 2008 ; Suzuki et al, 2007 ; Stone et al, 2017 ).…”