Electrostatic effect of H1-histone protein binding on nucleosome repeat length

Cherstvy, Andrey G.; Teif, Vladimir B.

doi:10.1088/1478-3975/11/4/044001

Cited by 27 publications

(25 citation statements)

References 62 publications

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“…Electrostatic interactions are modified with salts, allowing the prediction of small electrostatic contribution under physiological conditions in the case of DNA cyclization. 37 Adsorption processes on nanoparticles or surfaces involving DNA-like chains are commonly studied by computer simulations. 33 Interesting trends related to the formation of complexes between chains and nanoparticles, or more generally surfaces, have been investigated.…”

Section: Introductionmentioning

confidence: 99%

Modelling the interaction processes between nanoparticles and biomacromolecules of variable hydrophobicity: Monte Carlo simulations

Carnal

Clavier

Stoll

2015

Environ. Sci.: Nano

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The conformational properties and formation of a complex between a weak flexible biomacromolecule chain of variable hydrophobicity and one negatively charged nanoparticle in the presence of explicit counterions are investigated here using Monte Carlo simulations. The influence of the charge distribution and hydrophobicity, monomer distribution of the chain as well as the pH of the solution are systematically investigated. It is shown that the isolated chain conformations, built with random and block distribution of carboxylic, amino and hydrophobic groups, are the result of the subtle competition between intrachain attractive and repulsive electrostatic interactions as well as intrachain attractive short-range interactions due to hydrophobic properties. Extended conformations are found at low and high pH and folded conformations at physiological pH when hydrophilic and block polymer chains are considered. On the other hand, hydrophobic chain conformations do not show pH dependency and remain folded. The intrachain attractive electrostatic interactions clearly promote the deprotonation of carboxylic groups at low pH and the protonation of amino groups at high pH with higher efficiency for hydrophilic chains. The additional set of electrostatic interactions due to the presence of one negatively charged nanoparticle limits the deprotonation of carboxylic groups at low pH. Moreover, the attractive interactions between the biomacromolecule and the nanoparticle allow to observe the formation of a complex considering intermediate and hydrophilic chains even close to the chain isoelectric point due to the charge inhomogeneity distribution. Hydrophobic chain segments are not affected by the presence of the nanoparticle and remain desorbed. In all cases, the presence of one nanoparticle influences the biomacromolecule structures and acid/base properties, leading to more stretched conformations

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Section: Introductionmentioning

confidence: 99%

Modelling the interaction processes between nanoparticles and biomacromolecules of variable hydrophobicity: Monte Carlo simulations

Carnal

Clavier

Stoll

2015

Environ. Sci.: Nano

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“…Researchers have suggested that the electrostatic interactions between H1 and DNA/nucleosome are a major determinant of the stoichiometry of direct binding of H1 to the nucleosome based on a theoretical study. 49 They estimated the parameters of their electrostatic model for direct binding of H1 to DNA with experimental data showing a linear dependence of NRL on H1 stoichiometry. 50 It is widely accepted that NRL is very much heterogeneous and polydisperse.…”

Section: Discussionmentioning

confidence: 99%

Single-Molecule Studies of the Linker Histone H1 Binding to DNA and the Nucleosome

Yue

Wei

et al. 2016

Biochemistry

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Linker histone H1 regulates chromatin structure and gene expression. Investigating the dynamics and stoichiometry of binding of H1 to DNA and the nucleosome is crucial to elucidating its functions. Because of the abundant positive charges and the strong self-affinity of H1, quantitative in vitro studies of its binding to DNA and the nucleosome have generated results that vary widely and, therefore, should be interpreted in a system specific manner. We sought to overcome this limitation by developing a specially passivated microscope slide surface to monitor binding of H1 to DNA and the nucleosome at a single-molecule level. According to our measurements, the stoichiometry of binding of H1 to DNA and the nucleosome is very heterogeneous with a wide distribution whose averages are in reasonable agreement with previously published values. Our study also revealed that H1 does not dissociate from DNA or the nucleosome on a time scale of tens of minutes. We found that histone chaperone Nap1 readily dissociates H1 from DNA and superstoichiometrically bound H1 from the nucleosome, supporting a hypothesis whereby histone chaperones contribute to the regulation of the H1 profile in chromatin.

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“…They exert this effect by modulating local chromatin structure and thereby changing the accessibility of TFs. As a matter of fact, some other factors can also shape chromatin and then control gene activity, such as the electrostatic effect and concentration of H1 histone, DNA sequence, and long-range internucleosome interactions, which influence DNA compaction by regulating the distance between two neighboring nucleosomes, namely nucleosome repeat length (NRL) (Beshnova et al, 2014;Cherstvy and Teif, 2014), and the similarities in the structure of chromatin fibers (structural homology), which affect their pairing by electrostatic and protein-mediated bridging interactions (Cherstvy and Teif, 2013). Because of the close relationship between these factors and DNA structure, it is possible to construct a model predicting gene transcription level by them, too.…”

Section: Discussionmentioning

confidence: 99%

Identification of peculiar and common effects of histone modifications on transcription

Liu

Yang

2015

Journal of Theoretical Biology

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Electrostatic effect of H1-histone protein binding on nucleosome repeat length

Cited by 27 publications

References 62 publications

Modelling the interaction processes between nanoparticles and biomacromolecules of variable hydrophobicity: Monte Carlo simulations

Modelling the interaction processes between nanoparticles and biomacromolecules of variable hydrophobicity: Monte Carlo simulations

Single-Molecule Studies of the Linker Histone H1 Binding to DNA and the Nucleosome

Identification of peculiar and common effects of histone modifications on transcription

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