scholarly journals Spectroscopic Study of the Interaction of DNA with the Linker Histone H1 from Starfish Sperm Reveals Mechanisms of the Formation of Supercondensed Sperm Chromatin

2012 ◽  
Vol 27 ◽  
pp. 433-440 ◽  
Author(s):  
Elena Chikhirzhina ◽  
Tatyana Starkova ◽  
Elena Kostyleva ◽  
Alexander Polyanichko
Keyword(s):  
Protein Interactions ◽  
Histone H1 ◽  
Linker Histone ◽  
Sperm Chromatin ◽  
Dna Melting ◽  
Protein Protein Interactions ◽  
Asterias Amurensis ◽  
Linker Histones ◽  
Physiological Conditions ◽  
Two Peaks

The interaction of the linker histone H1Z from the sperm chromatin of starfishAsterias amurensiswith DNA was studied by spectroscopic and thermodynamic approaches. It has been shown that at the physiological conditions the interaction of the H1Z with DNA results in more compact structures compared to complexes of DNA with somatic histone H1. The typical profile of the DNA melting curves reveals two peaks attributed to the bound and unbound DNA. It has been shown that H1Z from starfish sperm stabilizes DNA to a greater extent compared to the somatic H1. It is possible that the presence of the additionalα—helical segments within the C-terminal part of the H1Z typical for the linker histones from echinoderm sperm facilitates the protein-protein interactions which in turn stimulate cooperative binding of the histones to DNA, resulting in the formation of the supercompact sperm chromatin.

Molecular interactions between multihaem cytochromes: probing the protein–protein interactions between pentahaem cytochromes of a nitrite reductase complex

2011 ◽  
Vol 39 (1) ◽  
pp. 263-268 ◽  
Author(s):  
Colin Lockwood ◽  
Julea N. Butt ◽  
Thomas A. Clarke ◽  
David J. Richardson
Keyword(s):  
Protein Interactions ◽  
Nitrite Reductase ◽  
Analytical Ultracentrifugation ◽  
Gel Filtration ◽  
Protein Protein Interactions ◽  
Physiological Conditions ◽  
Sulfate Reducing ◽  
Redox Partner ◽  
Electron Reduction ◽  
Reducing Bacteria

The cytochrome c nitrite reductase NrfA is a 53 kDa pentahaem enzyme that crystallizes as a decahaem homodimer. NrfA catalyses the reduction of NO2− to NH4+ through a six electron reduction pathway that is of major physiological significance to the anaerobic metabolism of enteric and sulfate reducing bacteria. NrfA receives electrons from the 21 kDa pentahaem NrfB donor protein. This requires that redox complexes form between the NrfA and NrfB pentahaem cytochromes. The formation of these complexes can be monitored using a range of methodologies for studying protein–protein interactions, including dynamic light scattering, gel filtration, analytical ultracentrifugation and visible spectroscopy. These methods have been used to show that oxidized NrfA exists in dynamic monomer–dimer equilibrium with a Kd (dissociation constant) of 4 μM. Significantly, the monomeric and dimeric forms of NrfA are equally active for either the six electron reduction of NO2− or HSO3−. When mixed together, NrfA and NrfB exist in equilibrium with NrfAB, which is described by a Kd of 50 nM. Thus, since NrfA and NrfB are present in micromolar concentrations in the periplasmic compartment, it is likely that NrfB remains tightly associated with its NrfA redox partner under physiological conditions.

scholarly journals The interactome of site-specifically acetylated linker histone H1

2021 ◽  
Author(s):  
Eva Hoellmueller ◽  
Katharina Greiner ◽  
Simon M Kienle ◽  
Martin Scheffner ◽  
Andreas Marx ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Posttranslational Modifications ◽  
Affinity Purification ◽  
Histone H1 ◽  
Linker Histone ◽  
Translational Initiation ◽  
Site Specific ◽  
Linker Histone H1 ◽  
Initiation Factors ◽  
Genetic Code Expansion

Linker histone H1 plays a key role in chromatin organization and maintenance, yet our knowledge of the regulation of H1 functions by posttranslational modifications (PTMs) is rather limited. In this study, we report on the generation of site-specifically mono- and di-acetylated linker histone H1.2 by genetic code expansion. We used these modified histones to identify and characterize the acetylation-dependent cellular interactome of H1.2 by affinity purification-mass spectrometry (AP-MS) and show that site-specific acetylation results in overlapping, but distinct groups of interacting partners. Among these, we find multiple translational initiation factors and transcriptional regulators such as the NAD+-dependent deacetylase SIRT1, which we demonstrate to act on acetylated H1.2. Taken together our data suggests that site-specific acetylation of H1.2 plays a role in modulating protein-protein interactions.

scholarly journals An Arsenite Relay between PSMD14 and AIRAP Enables Revival of Proteasomal DUB Activity

Biomolecules ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 1317
Author(s):  
Sigalit Sukenik ◽  
Ilana Braunstein ◽  
Ariel Stanhill
Keyword(s):  
Protein Interactions ◽  
Ubiquitin Proteasome System ◽  
Cellular Mechanism ◽  
26S Proteasome ◽  
Zinc Binding ◽  
Protein Protein Interactions ◽  
Associate Protein ◽  
Physiological Conditions ◽  
Ubiquitin Proteasome ◽  
Fundamental Requirement

Maintaining 26S proteasome activity under diverse physiological conditions is a fundamental requirement in order to maintain cellular proteostasis. Several quantitative and qualitative mechanisms have evolved to ensure that ubiquitin–proteasome system (UPS) substrates do not accumulate and lead to promiscuous protein–protein interactions that, in turn, lead to cellular malfunction. In this report, we demonstrate that Arsenite Inducible Regulatory Particle-Associate Protein (AIRAP), previously reported as a proteasomal adaptor required for maintaining proteasomal flux during arsenite exposure, can directly bind arsenite molecules. We further show that arsenite inhibits Psmd14/Rpn11 metalloprotease deubiquitination activity by substituting zinc binding to the MPN/JAMM domain. The proteasomal adaptor AIRAP is able to directly relieve PSMD14/Rpn11 inhibition. A possible metal relay between arsenylated PSMD14/Rpn11 and AIRAP may serve as a cellular mechanism that senses proteasomal inhibition to restore Psmd14/Rpn11 activity.

scholarly journals Converting histidine-induced 3D protein arrays in crystals into their 3D analogues in solution by metal coordination cross-linking

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Xiaoyi Tan ◽  
Hai Chen ◽  
Chunkai Gu ◽  
Jiachen Zang ◽  
Tuo Zhang ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Structural Information ◽  
Building Blocks ◽  
Metal Coordination ◽  
Protein Protein Interactions ◽  
Protonation State ◽  
Physiological Conditions ◽  
Simple Cubic ◽  
Stacking Pattern ◽  
Crystal Structural

Abstract Histidine (His) residues represent versatile motifs for designing protein-protein interactions because the protonation state of the imidazole group of His is the only moiety in protein to be significantly pH dependent under physiological conditions. Here we show that, by the designed His motifs nearby the C4 axes, ferritin nanocages arrange in crystals with a simple cubic stacking pattern. The X-ray crystal structures obtained at pH 4.0, 7.0, and 9.0 in conjunction with thermostability analyses reveal the strength of the π–π interactions between two adjacent protein nanocages can be fine-tuned by pH. By using the crystal structural information as a guide, we constructed 3D protein frameworks in solution by a combination of the relatively weak His–His interaction and Ni2+-participated metal coordination with Glu residues from two adjacent protein nanocages. These findings open up a new way of organizing protein building blocks into 3D protein crystalline frameworks.

scholarly journals Multifunctionality of the linker histones: an emerging role for protein-protein interactions

Cell Research ◽  
2010 ◽  
Vol 20 (5) ◽  
pp. 519-528 ◽  
Author(s):  
Steven J McBryant ◽  
Xu Lu ◽  
Jeffrey C Hansen
Keyword(s):  
Protein Interactions ◽  
Protein Protein Interactions ◽  
Linker Histones

Somatic linker histone H1 is present throughout mouse embryogenesis and is not replaced by variant H1 degrees

2000 ◽  
Vol 113 (16) ◽  
pp. 2897-2907
Author(s):  
P.G. Adenot ◽  
E. Campion ◽  
E. Legouy ◽  
C.D. Allis ◽  
S. Dimitrov ◽  
...  
Keyword(s):  
Nuclear Envelope ◽  
High Mobility ◽  
Histone H1 ◽  
Linker Histone ◽  
Mouse Development ◽  
Cell Stage ◽  
Linker Histones ◽  
Donor Nucleus ◽  
Significant Difference ◽  
Early Mouse

A striking feature of early embryogenesis in a number of organisms is the use of embryonic linker histones or high mobility group proteins in place of somatic histone H1. The transition in chromatin composition towards somatic H1 appears to be correlated with a major increase in transcription at the activation of the zygotic genome. Previous studies have supported the idea that the mouse embryo essentially follows this pattern, with the significant difference that the substitute linker histone might be the differentiation variant H1 degrees, rather than an embryonic variant. We show that histone H1 degrees is not a major linker histone during early mouse development. Instead, somatic H1 was present throughout this period. Though present in mature oocytes, somatic H1 was not found on maternal metaphase II chromatin. Upon formation of pronuclear envelopes, somatic H1 was rapidly incorporated onto maternal and paternal chromatin, and the amount of somatic H1 steadily increased on embryonic chromatin through to the 8-cell stage. Microinjection of somatic H1 into oocytes, and nuclear transfer experiments, demonstrated that factors in the oocyte cytoplasm and the nuclear envelope, played central roles in regulating the loading of H1 onto chromatin. Exchange of H1 from transferred nuclei onto maternal chromatin required breakdown of the nuclear envelope and the extent of exchange was inversely correlated with the developmental advancement of the donor nucleus.

scholarly journals On the stability and layered organization of protein-DNA condensates

2021 ◽  
Author(s):  
Andrew P Latham ◽  
Bin Zhang
Keyword(s):  
Protein Interactions ◽  
Spatial Organization ◽  
Strong Dependence ◽  
Histone H1 ◽  
Protein Protein Interactions ◽  
Chromatin Regulators ◽  
Atomistic Models ◽  
The Stability ◽  
Experimental Findings ◽  
Component Phase

Multi-component phase separation is emerging as a key mechanism for the formation of biological condensates that play essential roles in signal sensing and transcriptional regulation. The molecular factors that dictate these condensates' stability and spatial organization are not fully understood, and it remains challenging to predict their microstructures. Using a near-atomistic, chemically accurate force field, we studied the phase behavior of chromatin regulators that are crucial for heterochromatin organization and their interactions with DNA. Our computed phase diagrams recapitulated previous experimental findings on different proteins. They revealed a strong dependence of condensate stability on the protein-DNA mixing ratio as a result of balancing protein-protein interactions and charge neutralization. Notably, a layered organization was observed in condensates formed by mixing HP1, histone H1, and DNA. This layered organization may be of biological relevance as it enables cooperative DNA packaging between the two chromatin regulators: histone H1 softens the DNA to facilitate the compaction induced by HP1 droplets. Our study supports near atomistic models as a valuable tool for characterizing the structure and stability of biological condensates.

scholarly journals Complete depletion of Arabidopsis linker histones impairs the correlations among chromatin compartmentalization, DNA methylation and gene expression

2021 ◽  
Author(s):  
Zhenfei Sun ◽  
Min Li ◽  
Hui Zhnag ◽  
Yu Zhang ◽  
Min Ma ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Three Dimensional ◽  
Histone H1 ◽  
Linker Histone ◽  
Functional Link ◽  
Chromosome Conformation ◽  
Linker Histones ◽  
Linker Histone H1 ◽  
Nucleosome Density ◽  
Genome Bisulfite Sequencing

In eukaryotic cells, linker histone H1 anchors in and out ends of nucleosome DNA to promote chromatin to fold into the 30 nm fiber. However, if H1 plays a role in coordinating the three-dimensional (3D) chromatin architecture, DNA methylation, and transcriptional regulation is not clear. We engineered H1 knockout mutants in Arabidopsis thaliana which shows pleiotropic phenotypes. Using High-throughput Chromosome Conformation Capture (Hi-C), we found that H1 complete depletion dampens inter- and intra-chromosomal interactions, as well as intra- and inter-chromosomal arm interactions. MNase accessibility assays followed by sequencing (MNase-seq) showed that the nucleosome density decreases in centromeric regions and increases in chromosome arms. In contrast, DNA methylation level in CHG and CHH contexts increases in centromeric regions and decreases in chromosome arms as revealed by whole genome bisulfite sequencing (WGBS) in h1 mutant. Importantly, the functional link between DNA methylation and gene transcription is defected, and the extensive switches between chromatin compartment A and B are uncoupled from genome-wide DNA methylation and most of gene transcriptions upon H1 depletion. These results suggested that linker histone H1 works as linkers among chromatin compartmentalization, DNA methylation and transcription.

Actinin-1 binds to the C-terminus of A2B adenosine receptor (A2BAR) and enhances A2BAR cell-surface expression

2016 ◽  
Vol 473 (14) ◽  
pp. 2179-2186 ◽  
Author(s):  
Ying Sun ◽  
Wenbao Hu ◽  
Xiaojie Yu ◽  
Zhengzhao Liu ◽  
Robert Tarran ◽  
...  
Keyword(s):  
Cell Surface ◽  
Protein Interactions ◽  
Adenosine Receptor ◽  
Point Mutations ◽  
Surface Expression ◽  
Cell Surface Expression ◽  
Protein Protein Interactions ◽  
Physiological Conditions ◽  
A2b Adenosine Receptor ◽  
C Terminus

A2BAR (A2B adenosine receptor) has been implicated in several physiological conditions, such as allergic or inflammatory disorders, vasodilation, cell growth and epithelial electrolyte secretion. For mediating the protein–protein interactions of A2BAR, the receptor's C-terminus is recognized to be crucial. In the present study, we unexpectedly found that two point mutations in the A2BAR C-terminus (F297A and R298A) drastically impaired the expression of A2BAR protein by accelerating its degradation. Thus we tested the hypothesis that these two point mutations disrupt A2BAR's interaction with a protein essential for A2BAR stability. Our results show that both mutations disrupted the interaction of A2BAR with actinin-1, an actin-associated protein. Furthermore, actinin-1 binding stabilized the global and cell-surface expression of A2BAR. By contrast, actinin-4, another non-muscle actinin isoform, did not bind to A2BAR. Thus our findings reveal a previously unidentified regulatory mechanism of A2BAR abundance.

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