Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization DOI Creative Commons
Xingcheng Lin, Bin Zhang

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: May 18, 2023

Abstract Molecular mechanisms that dictate chromatin organization in vivo are under active investigation, and the extent to which intrinsic interactions contribute this process remains debatable. A central quantity for evaluating their contribution is strength of nucleosome-nucleosome binding, previous experiments have estimated range from 2 14 k B T . We introduce an explicit ion model dramatically enhance accuracy residue-level coarse-grained modeling approaches across a wide ionic concentrations. This allows de novo predictions computationally efficient, enabling large-scale conformational sampling free energy calculations. It reproduces energetics protein-DNA binding unwinding single nucleosomal DNA, resolves differential impact mono divalent ions on conformations. Moreover, we showed can reconcile various quantifying interactions, providing explanation large discrepancy between existing estimations. predict interaction at physiological conditions be 9 , value nonetheless sensitive DNA linker length presence histones. Our study strongly supports physicochemical phase behavior aggregates inside nucleus.

Language: Английский

Chromatin structure and dynamics: one nucleosome at a time DOI
Diego M. Presman,

Belén Benítez,

Agustina L. Lafuente

et al.

Histochemistry and Cell Biology, Journal Year: 2024, Volume and Issue: 162(1-2), P. 79 - 90

Published: April 12, 2024

Language: Английский

Citations

8
Explicit ion modeling predicts physicochemical interactions for chromatin organization DOI Creative Commons
Xingcheng Lin, Bin Zhang

eLife, Journal Year: 2023, Volume and Issue: 12

Published: Aug. 21, 2023

Molecular mechanisms that dictate chromatin organization in vivo are under active investigation, and the extent to which intrinsic interactions contribute this process remains debatable. A central quantity for evaluating their contribution is strength of nucleosome-nucleosome binding, previous experiments have estimated range from 2 14 k B T . We introduce an explicit ion model dramatically enhance accuracy residue-level coarse-grained modeling approaches across a wide ionic concentrations. This allows de novo predictions computationally efficient, enabling large-scale conformational sampling free energy calculations. It reproduces energetics protein-DNA binding unwinding single nucleosomal DNA, resolves differential impact mono- divalent ions on conformations. Moreover, we showed can reconcile various quantifying interactions, providing explanation large discrepancy between existing estimations. predict interaction at physiological conditions be 9 , value nonetheless sensitive DNA linker length presence histones. Our study strongly supports physicochemical phase behavior aggregates inside nucleus.

Language: Английский

Citations

16
Effect of local active fluctuations on structure and dynamics of flexible biopolymers DOI
Sayantan Dutta, Ashesh Ghosh, Andrew J. Spakowitz

et al.

Soft Matter, Journal Year: 2024, Volume and Issue: 20(8), P. 1694 - 1701

Published: Jan. 1, 2024

Active fluctuations play a significant role in the structure and dynamics of biopolymers (

Language: Английский

Citations

6
Explicit ion modeling predicts physicochemical interactions for chromatin organization DOI Creative Commons
Xingcheng Lin, Bin Zhang

eLife, Journal Year: 2024, Volume and Issue: 12

Published: Jan. 30, 2024

Molecular mechanisms that dictate chromatin organization in vivo are under active investigation, and the extent to which intrinsic interactions contribute this process remains debatable. A central quantity for evaluating their contribution is strength of nucleosome-nucleosome binding, previous experiments have estimated range from 2 14 k B T . We introduce an explicit ion model dramatically enhance accuracy residue-level coarse-grained modeling approaches across a wide ionic concentrations. This allows de novo predictions computationally efficient, enabling large-scale conformational sampling free energy calculations. It reproduces energetics protein-DNA binding unwinding single nucleosomal DNA, resolves differential impact mono- divalent ions on conformations. Moreover, we showed can reconcile various quantifying interactions, providing explanation large discrepancy between existing estimations. predict interaction at physiological conditions be 9 , value nonetheless sensitive DNA linker length presence histones. Our study strongly supports physicochemical phase behavior aggregates inside nucleus.

Language: Английский

Citations

5
Motorized chain models of the ideal chromosome DOI Creative Commons
Zhiyu Cao, Peter G. Wolynes

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(28)

Published: July 2, 2024

An array of motor proteins consumes chemical energy in setting up the architectures chromosomes. Here, we explore how structure ideal polymer chains is influenced by two classes motors. The first class which call "swimming motors" acts to propel chromatin fiber through three-dimensional space. They represent a caricature motors such as RNA polymerases. Previously, they have often been described adding persistent flow onto Brownian diffusion chain. second motors, "grappling caricatures loop extrusion processes segments fibers some distance apart are brought together. We analyze these models using self-consistent variational phonon approximation many-body Master equation incorporating activities. show that whether swimming lead contraction or expansion depends on susceptibility is, their activity forces must exert. Grappling contrast long-ranged correlations resemble those suggested for fractal globules and consistent with effective interactions inferred landscape analyses Hi-C data interphase chromosome.

Language: Английский

Citations

3
Model chromatin flows: numerical analysis of linear and nonlinear hydrodynamics inside a sphere DOI
Iraj Eshghi, Alexandra Zidovska, Alexander Y. Grosberg

et al.

The European Physical Journal E, Journal Year: 2023, Volume and Issue: 46(8)

Published: Aug. 1, 2023

Language: Английский

Citations

4
Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization DOI Creative Commons
Xingcheng Lin, Bin Zhang

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: May 18, 2023

Abstract Molecular mechanisms that dictate chromatin organization in vivo are under active investigation, and the extent to which intrinsic interactions contribute this process remains debatable. A central quantity for evaluating their contribution is strength of nucleosome-nucleosome binding, previous experiments have estimated range from 2 14 k B T . We introduce an explicit ion model dramatically enhance accuracy residue-level coarse-grained modeling approaches across a wide ionic concentrations. This allows de novo predictions computationally efficient, enabling large-scale conformational sampling free energy calculations. It reproduces energetics protein-DNA binding unwinding single nucleosomal DNA, resolves differential impact mono divalent ions on conformations. Moreover, we showed can reconcile various quantifying interactions, providing explanation large discrepancy between existing estimations. predict interaction at physiological conditions be 9 , value nonetheless sensitive DNA linker length presence histones. Our study strongly supports physicochemical phase behavior aggregates inside nucleus.

Language: Английский

Citations

1