The impact of charge regulation and ionic intranuclear environment on the nucleosome core particle DOI
Rikkert J. Nap, Paola Carrillo Gonzalez, A. E. Coraor

et al.

The Journal of Chemical Physics, Journal Year: 2024, Volume and Issue: 161(23)

Published: Dec. 20, 2024

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

Language: Английский

The shifting paradigm of chromatin structure: from the 30-nm chromatin fiber to liquid-like organization DOI Creative Commons
Kazuhiro Maeshima

Proceedings of the Japan Academy Series B, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

The organization and dynamics of chromatin are critical for genome functions such as transcription DNA replication/repair. Historically, was assumed to fold into the 30-nm fiber progressively arrange larger helical structures, described in textbook model. However, over past 15 years, extensive evidence including our studies has dramatically transformed view from a static, regular structure one that is more variable dynamic. In higher eukaryotic cells, forms condensed yet liquid-like domains, which appear be basic unit structure, replacing fiber. These domains maintain proper accessibility, ensuring regulation reaction processes. During mitosis, these assemble form gel-like mitotic chromosomes, further constrained by condensins other factors. Based on available evidence, I discuss physical properties live emphasizing its viscoelastic nature-balancing local fluidity with global stability support functions.

Language: Английский

Citations

0
Interpretable Protein-DNA Interactions Captured by Structure-based Optimization DOI Creative Commons

Yafan Zhang,

Irene Silvernail,

Zhuyang Lin

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 27, 2024

Abstract Sequence-specific DNA recognition underlies essential processes in gene regulation, yet methods for simultaneous prediction of genomic sites and their binding affinity remain lacking. Here, we present the Interpretable protein-DNA Energy Associative (IDEA) model, a residue-level, interpretable biophysical model capable predicting affinities DNA-binding proteins. By fusing structures sequences known complexes into an optimized energy IDEA enables direct interpretation physicochemical interactions among individual amino acids nucleotides. We demonstrate that this can accurately predict strengths across various protein families. Additionally, is integrated coarse-grained simulation framework quantitatively captures absolute free energies. Overall, provides computational platform alleviating experimental costs biases assessing be utilized mechanistic studies DNA-recognition processes.

Language: Английский

Citations

3
Toward decoding the mechanisms that shape sub-megabase-scale genome organization DOI
Joseph M. Paggi, Bin Zhang

Current Opinion in Structural Biology, Journal Year: 2025, Volume and Issue: 92, P. 103062 - 103062

Published: May 8, 2025

Language: Английский

Citations

0
The Impact of Charge Regulation and Ionic Intranuclear Environment on the Nucleosome Core Particle DOI Creative Commons
Rikkert J. Nap, Paola Carrillo Gonzalez, A. E. Coraor

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 12, 2024

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

Language: Английский

Citations

0
The impact of charge regulation and ionic intranuclear environment on the nucleosome core particle DOI
Rikkert J. Nap, Paola Carrillo Gonzalez, A. E. Coraor

et al.

The Journal of Chemical Physics, Journal Year: 2024, Volume and Issue: 161(23)

Published: Dec. 20, 2024

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

Language: Английский

Citations

0