Multiscale modeling reveals the ion-mediated phase separation of nucleosome core particles

High-performance sodium-ion batteries using Na5PV2Mo10O40 modified reduced graphene oxide (rGO) composite materials induced by imidazole ionic liquids

Sodium-ion batteries (SIBs) have gained increasing attention as a promising alternative to lithium-ion batteries, owing to the abundance and low cost of sodium. However, despite these advantages, the performance of SIBs is hindered by the larger ionic radius of sodium, which not only reduces ion migration rates but also significantly decreases the specific capacity. To address this challenge, the present study explores the synthesis of Na5PV2Mo10O40 (PV2Mo10)-modified reduced graphene oxide (rGO) composites by employing imidazole ionic liquid (IL) as electrostatic attraction agent, this approach not only prevents the aggregation of polyoxometalates (POMs) but also increases the interlayer distance of rGO, improving the battery's specific capacity and enhancing the diffusion rate of Na+ ions. Experimental results indicate that the PV2Mo10-rGO-IL hybrid material exhibits exceptional electrochemical properties, characterized by significantly improved conductivity and an impressive specific capacity of 290mAh g-1 while achieving nearly 100 % Coulombic efficiency over 900 cycles. Furthermore, theoretical calculations reveal that the incorporation of POMs effectively reduces the electrode impedance of rGO and enhances the structural stability of POMs during cycling. This study opens up new avenues for the design of high-performance sodium ion batteries based on POMs.

CG modeling of nucleosome arrays reveals the salt-dependent chromatin fiber conformational variability

Eukaryotic DNA is packaged in the cell nucleus into chromatin, composed of arrays of DNA-histone protein octamer complexes, the nucleosomes. Over the past decade, it has become clear that chromatin structure in vivo is not a hierarchy of well-organized folded nucleosome fibers but displays considerable conformational variability and heterogeneity. In vitro and in vivo studies, as well as computational modeling, have revealed that attractive nucleosome-nucleosome interaction with an essential role of nucleosome stacking defines chromatin compaction. The internal structure of compacted nucleosome arrays is regulated by the flexible and dynamic histone N-terminal tails. Since DNA is a highly negatively charged polyelectrolyte, electrostatic forces make a decisive contribution to chromatin formation and require the histones, particularly histone tails, to carry a significant positive charge. This also results in an essential role of mobile cations of the cytoplasm (K+, Na+, Mg2+) in regulating electrostatic interactions. Building on a previously successfully established bottom-up coarse-grained (CG) nucleosome model, we have developed a CG nucleosome array (chromatin fiber) model with the explicit presence of mobile ions and studied its conformational variability as a function of Na+ and Mg2+ ion concentration. With progressively elevated ion concentrations, we identified four main conformational states of nucleosome arrays characterized as extended, flexible, nucleosome-clutched, and globular fibers.

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

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.

The Impact of Charge Regulation and Ionic Intranuclear Environment on the Nucleosome Core Particle

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, conformations, charges, and chemical states 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.

Liquid-liquid phase separation (LLPS) in DNA and chromatin systems from the perspective of colloid physical chemistry

DNA is a highly charged polyelectrolyte and is prone to associative phase separation driven by the presence of multivalent cations, charged surfactants, proteins, polymers and colloids. The process of DNA phase separation induced by positively charged species is often called DNA condensation. Generally, it refers to either intramolecular DNA compaction (coil-globule transition) or intermolecular DNA aggregation with macroscopic phase separation, but the formation of a DNA liquid crystalline system is also displayed. This has traditionally been described by polyelectrolyte theory and qualitative (Flory-Huggins-based) polymer theory approaches. DNA in the cell nucleus is packed into chromatin wound around the histone octamer (a protein complex comprising two copies each of the four histone proteins H2A, H2B, H3 and H4) to form nucleosomes separated by linker DNA. During the last decade, the phenomenon of the formation of biomolecular condensates (dynamic droplets) by liquid-liquid phase separation (LLPS) has emerged as a generally important mechanism for the formation of membraneless organelles from proteins, nucleic acids and their complexes. DNA and chromatin droplet formation through LLPS has recently received much attention by in vitro as well as in vivo studies that established the importance of this for compartmentalisation in the cell nucleus. Here, we review DNA and chromatin LLPS from a general colloid physical chemistry perspective. We start with a general discussion of colloidal phase separation in aqueous solutions and review the original (pre-LLPS era) work on DNA (macroscopic) phase separation for simpler systems with DNA in the presence of multivalent cations and well-defined surfactants and colloids. Following that, we discuss and illustrate the similarities of such macroscopic phase separation with the general behaviour of LLPS droplet formation by associative phase separation for DNA-protein systems, including chromatin; we also note cases of segregative association. The review ends with a discussion of chromatin LLPS in vivo and its physiological significance.