On the stability and layered organization of protein-DNA condensates

Latham, A. J. H.; Zhang, Bin

doi:10.1101/2021.08.22.457249

Cited by 3 publications

(3 citation statements)

References 86 publications

(80 reference statements)

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“…These results are in qualitative agreement with the trends seen in ref for polyelectrolyte coacervation. Though the authors of that work only studied a maximum of B = 8 consecutive positive residues, we see that the general trend of increasing phase separability extends to the maximum blockiness possible for this system, B = 43.…”

Section: Resultssupporting

confidence: 92%

“…Figure A shows the CH1 in complex with 20 base pair double-stranded DNA (20-bp dsDNA) in both atomistic (left) and CG (right) representations. We note here that recent efforts have been made to probe phase separation between full-length H1 and DNA with a 1-site-per-nucleotide CG DNA model, , but a single isotropic CG site cannot accurately account for the excluded volume of a nucleotide; therefore, we have chosen to use three sites per nucleotide in this work.…”

Section: Methodsmentioning

confidence: 99%

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Tuning Formation of Protein–DNA Coacervates by Sequence and Environment

Lebold

Best

2022

J. Phys. Chem. B

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The high concentration of nucleic acids and positively charged proteins in the cell nucleus provides many possibilities for complex coacervation. We consider a prototypical mixture of nucleic acids together with the polycationic C-terminus of histone H1 (CH1). Using a minimal coarse-grained model that captures the shape, flexibility, and charge distributions of the molecules, we find that coacervates are readily formed at physiological ionic strengths, in agreement with experiment, with a progressive increase in local ordering at low ionic strength. Variation of the positions of charged residues in the protein tunes phase separation: for well-mixed or only moderately blocky distributions of charge, there is a modest increase of local ordering with increasing blockiness that is also associated with an increased propensity to phase separate. This ordering is also associated with a slowdown of rotational and translational diffusion in the dense phase. However, for more extreme blockiness (and consequently higher local charge density), we see a qualitative change in the condensed phase to become a segregated structure with a dramatically increased ordering of the DNA. Naturally occurring proteins with these sequence properties, such as protamines in sperm cells, are found to be associated with very dense packing of nucleic acids.

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Section: Resultssupporting

confidence: 92%

Section: Methodsmentioning

confidence: 99%

Tuning Formation of Protein–DNA Coacervates by Sequence and Environment

Lebold

Best

2022

J. Phys. Chem. B

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“…27,32 There are ongoing efforts to develop and evaluate a nucleic acid (DNA/RNA) CG model to study protein-nucleic acid interactions and the role DNA plays in LLPS. [57][58][59][60] Here, we use a model that separates the nucleotide into two beads; one bead represents the sugar-phosphate backbone, carrying an overall -1 charge, and the other represents the base but differentiates between bases ADE, THY, CYT, and GUA in their respective stacking and hydrogen bonding interactions. Using our CG nucleic acid model, we studied the effects of DNA addition on the LLPS of HP1α by conducting CG coexistence simulations of HP1α homodimers containing a small mole fraction of 205 bp dsDNA, 0.02 and 0.038, at 320 K. This system can be reasonably compared to an experimental system containing 50µM/100 µM of HP1α with 1.5µM of the same 205 bp dsDNA.…”

Section: Computational Studies Of Hp1α Llps In the Presence Of Dnamentioning

confidence: 99%

Molecular interactions underlying the phase separation of HP1α: Role of phosphorylation, ligand and nucleic acid binding

Her

Phan

Jovic

et al. 2022

Preprint

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Heterochromatin protein 1α (HP1α) is a crucial component for the proper maintenance of chromatin structure and function. It has been proposed that HP1α functions through liquid-liquid phase separation (LLPS), which allows it to sequester and compact chromatin into transcriptionally repressed heterochromatin regions. In vitro, HP1α can form phase separated liquid droplets upon phosphorylation of its N-terminus extension (NTE) and/or through interactions with DNA and chromatin. While it is known that LLPS requires homodimerization of HP1α and that it involves interactions between the positively charged hinge region of HP1α and the negatively charged phosphorylated NTE or nucleic acid, the precise molecular details of this process and its regulation are still unclear. Here, we combine computational modeling and experimental approaches to elucidate the phase separation properties of HP1α under phosphorylation-driven and DNA-driven LLPS conditions. We also tune these properties using peptides from four HP1α binding partners (Sgo1, CAF-1, LBR, and H3). In phosphorylation-driven LLPS, HP1α can exchange intradimer hinge-NTE interactions with interdimer contacts, which also leads to a structural change from a compacted to an extended HP1α dimer conformation. This process can be enhanced by the presence of positively charged peptide ligands such as Sgo1 and H3 and disrupted by the addition of negatively charged or neutral peptides such as LBR and CAF-1. In DNA-driven LLPS, both positively and negatively charged peptide ligands can perturb phase separation. Our findings demonstrate the importance of electrostatic interactions in the LLPS of HP1α where binding partners can modulate the overall charge of the droplets and screen or enhance hinge region interactions through specific and non-specific effects. Our study illuminates the complex molecular framework that can fine tune the properties of HP1α and that can contribute to heterochromatin regulation and function.

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Uncovering the molecular interactions underlying MBD2 and MBD3 phase separation

Maurici,

Phan,

Henty-Ridilla

et al. 2024

Preprint

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Chromatin organization controls DNA's accessibility to regulatory factors to influence gene expression. Heterochromatin, or transcriptionally silent chromatin enriched in methylated DNA and methylated histone tails, self-assembles through multivalent interactions with its associated proteins into a condensed, but dynamic state. Liquid-liquid phase separation (LLPS) of key heterochromatin regulators, such as heterochromatin protein 1 (HP1), plays an essential role in heterochromatin assembly and function. Methyl-CpG-binding protein 2 (MeCP2), the most studied member of the methyl-CpG-binding domain (MBD) family of proteins, has been recently shown to undergo LLPS in the absence and presence of methylated DNA. These studies provide a new mechanistic framework for understanding the role of methylated DNA and its readers in heterochromatin formation. However, the details of the molecular interactions by which other MBD family members undergo LLPS to mediate genome organization and transcriptional regulation are not fully understood. Here, we focus on two MBD proteins, MBD2 and MBD3, that have distinct but interdependent roles in gene regulation. Using an integrated computational and experimental approach, we uncover the homotypic and heterotypic interactions governing MBD2 and MBD3 phase separation and DNA's influence on this process. We show that despite sharing the highest sequence identity and structural homology among all the MBD protein family members, MBD2 and MBD3 exhibit differing residue patterns resulting in distinct phase separation mechanisms. Understanding the molecular underpinnings of MBD protein condensation offers insights into the higher-order, LLPS-mediated organization of heterochromatin.

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On the stability and layered organization of protein-DNA condensates

Cited by 3 publications

References 86 publications

Tuning Formation of Protein–DNA Coacervates by Sequence and Environment

Tuning Formation of Protein–DNA Coacervates by Sequence and Environment

Molecular interactions underlying the phase separation of HP1α: Role of phosphorylation, ligand and nucleic acid binding

Uncovering the molecular interactions underlying MBD2 and MBD3 phase separation

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