Na<sup>+</sup> and K<sup>+</sup> Ions Differently Affect Nucleosome Structure, Stability, and Interactions with Proteins

Андреева, Т. В.; Sivkina, Anastasiia; Chertkov, O. V.; Валиева, М. Е.; Kotova, Elena; Kirpichnikov, Mikhaǐl P.; Studitsky, Vasily M.; Feofanov, Аlexey V.

doi:10.1017/s1431927621013751

Cited by 5 publications

(1 citation statement)

References 38 publications

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“…Andreeva et al further compared the effects of Na + and K + ions on nucleosome structure, stability, and interactions with proteins. The stabilizing effect of K + was noticeably higher than that of Na + and was accompanied by a maximal stabilizing effect on nucleosomes at a concentration of 80–150 mM, while Na + supported a more efficient reorganization of the nucleosome structure by poly(ADP-ribose) polymerase 1 and ATP-independent uncoiling by FACT when compared to K + [ 131 ]. Another modeling study also demonstrated that ions could accumulate at the site between the nucleosomal DNA gyres, which would prevent nucleosome breathing [ 132 ].…”

Section: Multiple Regulatory Factors and Associated Mechanismmentioning

confidence: 99%

Studies of the Mechanism of Nucleosome Dynamics: A Review on Multifactorial Regulation from Computational and Experimental Cases

2023

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The nucleosome, which organizes the long coil of genomic DNA in a highly condensed, polymeric way, is thought to be the basic unit of chromosomal structure. As the most important protein–DNA complex, its structural and dynamic features have been successively revealed in recent years. However, its regulatory mechanism, which is modulated by multiple factors, still requires systemic discussion. This study summarizes the regulatory factors of the nucleosome’s dynamic features from the perspective of histone modification, DNA methylation, and the nucleosome-interacting factors (transcription factors and nucleosome-remodeling proteins and cations) and focuses on the research exploring the molecular mechanism through both computational and experimental approaches. The regulatory factors that affect the dynamic features of nucleosomes are also discussed in detail, such as unwrapping, wrapping, sliding, and stacking. Due to the complexity of the high-order topological structures of nucleosomes and the comprehensive effects of regulatory factors, the research on the functional modulation mechanism of nucleosomes has encountered great challenges. The integration of computational and experimental approaches, the construction of physical modes for nucleosomes, and the application of deep learning techniques will provide promising opportunities for further exploration.

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Section: Multiple Regulatory Factors and Associated Mechanismmentioning

confidence: 99%

Studies of the Mechanism of Nucleosome Dynamics: A Review on Multifactorial Regulation from Computational and Experimental Cases

2023

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Geometric variations in nucleosomal DNA dictate higher-order chromatin structure and enhancer–promoter communication

Todolli,

Nizovtseva,

Clauvelin

et al. 2024

The Journal of Chemical Physics

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The dynamic organization of chromatin plays an essential role in the regulation of genetic activity, interconverting between open and compact forms at the global level. The mechanisms underlying these large-scale changes remain a topic of widespread interest. The simulations of nucleosome-decorated DNA reported herein reveal profound effects of the nucleosome itself on overall chromatin properties. Models that capture the long-range communication between proteins on nucleosome-decorated DNA chains incorporate DNA pathways different from those that were previously proposed based on ultracentrifugation and chemical cross-linking data. New quantitative biochemical assays measuring the rates of communication between interacting proteins bound to a promoter and an enhancer at the ends of saturated, precisely positioned, nucleosome-decorated DNA chains reveal a chromatin architecture with a three-nucleosome repeat, a model inconsistent with the two-start configurations deduced from earlier physical studies. Accompanying computations uncover small differences in the twisting of successive base pairs that seemingly give rise to the observed global properties. These data suggest that the novel state of chromatin determined under physiological conditions differs from that deduced under standard physical conditions, likely reflecting the different salt conditions used in the two types of experiments. This novel chromatin state may be important for a number of DNA transactions that occur in the cell nucleus.

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The impact of charge regulation and ionic intranuclear environment on the nucleosome core particle

Nap,

Carillo Gonzalez,

Coraor

et al. 2024

The Journal of Chemical Physics

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We theoretically investigate how the intranuclear environment influences the charge of a nucleosome core particle (NCP)—the fundamental unit of chromatin consisting of DNA wrapped around a core of histone proteins. The molecular-based theory explicitly considers the size, shape, conformation, charge, and chemical state of all molecular species—thereby linking the structural state with the chemical/charged state of the system. We investigate how variations in monovalent and divalent salt concentrations, as well as pH, affect the charge distribution across different regions of an NCP and quantify the impact of charge regulation. The effective charge of an NCP emerges from a delicate and complex balance involving the chemical dissociation equilibrium of the amino acids and the DNA-phosphates, the electrostatic interaction between them, and the translational entropy of the mobile solution ions, i.e., counter ion release and ion condensation. From our results, we note the significant effect of divalent magnesium ions on the charge and electrostatic energy as well as the counterion cloud that surrounds an NCP. As a function of magnesium concentration, charge neutralization, and even charge inversion is predicted—in line with experimental observation of NCPs. The strong Mg-dependence of the nucleosome charge state arises from ion bridges between two DNA-phosphates and one Mg2+ ion. We demonstrate that to describe and predict the charged state of an NCP properly, it is essential to consider molecular details, such as DNA-phosphate ion condensation and the acid–base equilibrium of the amino acids that comprise the core histone proteins.

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Na⁺ and K⁺ Ions Differently Affect Nucleosome Structure, Stability, and Interactions with Proteins

Cited by 5 publications

References 38 publications

Studies of the Mechanism of Nucleosome Dynamics: A Review on Multifactorial Regulation from Computational and Experimental Cases

Studies of the Mechanism of Nucleosome Dynamics: A Review on Multifactorial Regulation from Computational and Experimental Cases

Geometric variations in nucleosomal DNA dictate higher-order chromatin structure and enhancer–promoter communication

The impact of charge regulation and ionic intranuclear environment on the nucleosome core particle

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Na+ and K+ Ions Differently Affect Nucleosome Structure, Stability, and Interactions with Proteins

Cited by 5 publications

References 38 publications

Studies of the Mechanism of Nucleosome Dynamics: A Review on Multifactorial Regulation from Computational and Experimental Cases

Studies of the Mechanism of Nucleosome Dynamics: A Review on Multifactorial Regulation from Computational and Experimental Cases

Geometric variations in nucleosomal DNA dictate higher-order chromatin structure and enhancer–promoter communication

The impact of charge regulation and ionic intranuclear environment on the nucleosome core particle

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Na⁺ and K⁺ Ions Differently Affect Nucleosome Structure, Stability, and Interactions with Proteins