Global analysis of the ground-state wrapping conformation of a charged polymer on an oppositely charged nano-sphere

Boroudjerdi, Hoda; Naji, Ali; Netz, Roland R.

doi:10.1140/epje/i2014-14021-6

Cited by 11 publications

(11 citation statements)

References 113 publications

(271 reference statements)

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“…The histone core charges stems mainly from the basic Arg and Lys protein residues [21]. A number of theoretical and computational models of DNA wrapping in the NCP have been proposed in recent years [22][23][24][25][26][27]. However, the description of experimental data overviewed in [13], vital for rationalizing the properties of higher-order DNA compaction in chromatin, remained without proper theoretical attention.…”

Section: The Model Of Es-motivated Dna Wrappingmentioning

confidence: 99%

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

Cherstvy¹,

Teif²

2014

Phys. Biol.

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Within a simple biophysical model we describe the effect of electrostatic binding of H1 histone proteins on the nucleosome repeat length in chromatin. The length of wrapped DNA optimizes its binding energy to the histone core and the elastic energy penalty of DNA wrapping. The magnitude of the effect predicted from our model is in agreement with the systematic experimental data on the linear variation of nucleosome repeat lengths with H1/nucleosome ratio (Woodcock C L et al 2006 Chromos. Res. 14 17-25). We compare our model to the data for different cell types and organisms, with a widely varying ratio of bound H1 histones per nucleosome. We underline the importance of this non-specific histone-DNA charge-balance mechanism in regulating the positioning of nucleosomes and the degree of compaction of chromatin fibers in eukaryotic cells.

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Section: The Model Of Es-motivated Dna Wrappingmentioning

confidence: 99%

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

Cherstvy¹,

Teif²

2014

Phys. Biol.

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“…9We note also that in the high-charge and low-salt limit—owing to strong ES PE–PE repulsion (along the sphere surface and across its interior)—the PE configurations in the adsorbed states observed in the simulations are not azimuthally random. The PE chains are rather adsorbed in somewhat ordered patterns in order to stay away from the neighbouring adsorbed PEs (see also [40,59,89,95,96]). Adsorbed PE chains can thereby form peculiar geometric structures similar to a Wigner crystal [97] (see figure 1 and the video files at low salt in the electronic supplementary material).…”

Section: Endnotesmentioning

confidence: 99%

Critical adsorption of multiple polyelectrolytes onto a nanosphere: splitting the adsorption–desorption transition boundary

Caetano

Carvalho

Metzler

et al. 2020

J. R. Soc. Interface.

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Employing extensive Monte Carlo computer simulations, we investigate in detail the properties of multichain adsorption of charged flexible polyelectrolytes (PEs) onto oppositely charged spherical nanoparticles (SNPs). We quantify the conditions of critical adsorption—the phase-separation curve between the adsorbed and desorbed states of the PEs—as a function of the SNP surface-charge density and the concentration of added salt. We study the degree of fluctuations of the PE–SNP electrostatic binding energy, which we use to quantify the emergence of the phase subtransitions, including a series of partially adsorbed PE configurations. We demonstrate how the phase-separation adsorption–desorption boundary shifts and splits into multiple subtransitions at low-salt conditions, thereby generalizing and extending the results for critical adsorption of a single PE onto the SNP. The current findings are relevant for finite concentrations of PEs around the attracting SNP, such as the conditions for PE adsorption onto globular proteins carrying opposite electric charges.

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“…There are a number of theoretical studies addressing the conditions in which the polyelectrolytes-surface intera e-mail: sidneyjc@ibilce.unesp.br action is strong enough to get adsorption as well as the conformational states of the adsorbed chain [10,[29][30][31][32][33][34][35][36][37][38][39][40][41][42]. In particular, the adsorption of a single random polyampholyte chain on a flat charged surface was addressed theoretically by Dobrynin and co-authors [43].…”

Section: Introductionmentioning

confidence: 99%

Conformational properties of block-polyampholytes adsorbed on charged cylindrical surfaces

Caetano

Carvalho

2017

Eur. Phys. J. E

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Polyampholytes are polymers that have positive and negative monomers along their chain. The adsorption of polyampholytes on charged surfaces has been the subject of a large number of theoretical, computational and experimental studies due to its importance in a variety of bio and nanothechnological systems. However, computational studies focusing on interaction between polyampholytes and cylindrical charged surfaces are rather scarce. This study, therefore, aims to investigate the conformational properties of block-polyampholytes in the presence of a negatively charged cylinder by means of Metropolis Monte Carlo simulations. Adopting a simplified model in which the electrolyte solution is treated at the Debye-Hückel level, the effects of the ionic strength, the linear charge density of the cylinder and the block length on monomers distributions have been investigated. It was found that increasing the salt concentration promotes a transition from a conformation characterized by large loops to a necklace-like conformation parallel to the surface. It was also shown that, at low cylinder charge density, the increase in salt concentration and the length of the blocks lead to a change in the orientation of the adsorbed chain.

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Global analysis of the ground-state wrapping conformation of a charged polymer on an oppositely charged nano-sphere

Cited by 11 publications

References 113 publications

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

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

Critical adsorption of multiple polyelectrolytes onto a nanosphere: splitting the adsorption–desorption transition boundary

Conformational properties of block-polyampholytes adsorbed on charged cylindrical surfaces

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