scholarly journals Binding of regulatory proteins to nucleosomes is modulated by dynamic histone tails

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yunhui Peng ◽  
Shuxiang Li ◽  
Alexey Onufriev ◽  
David Landsman ◽  
Anna R. Panchenko
Keyword(s):  
Regulatory Proteins ◽  
Binding Modes ◽  
Dna Interactions ◽  
Histone Tail ◽  
Histone Tails ◽  
Post Translational Modifications ◽  
Conformational Ensembles ◽  
Dna Accessibility ◽  
Nucleosomal Dna ◽  
Dynamics Simulations

AbstractLittle is known about the roles of histone tails in modulating nucleosomal DNA accessibility and its recognition by other macromolecules. Here we generate extensive atomic level conformational ensembles of histone tails in the context of the full nucleosome, totaling 65 microseconds of molecular dynamics simulations. We observe rapid conformational transitions between tail bound and unbound states, and characterize kinetic and thermodynamic properties of histone tail-DNA interactions. Different histone types exhibit distinct binding modes to specific DNA regions. Using a comprehensive set of experimental nucleosome complexes, we find that the majority of them target mutually exclusive regions with histone tails on nucleosomal/linker DNA around the super-helical locations ± 1, ± 2, and ± 7, and histone tails H3 and H4 contribute most to this process. These findings are explained within competitive binding and tail displacement models. Finally, we demonstrate the crosstalk between different histone tail post-translational modifications and mutations; those which change charge, suppress tail-DNA interactions and enhance histone tail dynamics and DNA accessibility.

scholarly journals Binding of regulatory proteins to nucleosomes is modulated by dynamic histone tails

2020 ◽  
Author(s):  
Yunhui Peng ◽  
Shuxiang Li ◽  
Alexey Onufriev ◽  
David Landsman ◽  
Anna R. Panchenko
Keyword(s):  
Solvent Accessibility ◽  
Binding Modes ◽  
Dna Interactions ◽  
Histone Tail ◽  
Histone Tails ◽  
Post Translational Modifications ◽  
Conformational Ensembles ◽  
Nucleosomal Dna ◽  
Dynamics Simulations ◽  
Nucleosome Binding

AbstractDespite histone tails’ critical roles in epigenetic regulation, little is known about mechanisms of how histone tails modulate the nucleosomal DNA solvent accessibility and recognition of nucleosomes by other macromolecules. Here we generate extensive atomic level conformational ensembles of histone tails in the context of the full human nucleosome, totaling 26 microseconds of molecular dynamics simulations. We explore the histone tail binding with the nucleosomal and linker DNA and observe rapid conformational transitions between bound and unbound states allowing us to estimate kinetic and thermodynamic properties of the histone tail-DNA interactions. Different histone types exhibit distinct, although conformationally heterogeneous, binding modes and each histone type occludes specific DNA regions from the solvent. Using a comprehensive set of experimental data on nucleosome structural complexes, we find that majority of the studied nucleosome-binding proteins and histone tails target mutually exclusive regions on nucleosomal or linker DNA around the super-helical locations ±1, ±2, and ±7. This finding is explained within the generalized competitive binding and tail displacement models of partners recruitment to nucleosomes. Finally, we demonstrate the crosstalk between different histone post-translational modifications, where charge-altering modifications and mutations typically suppress tail-DNA interactions and enhance histone tail dynamics.

scholarly journals Persistent Interactions of Core Histone Tails with Nucleosomal DNA following Acetylation and Transcription Factor Binding

1998 ◽  
Vol 18 (11) ◽  
pp. 6293-6304 ◽  
Author(s):  
Vesco Mutskov ◽  
Delphine Gerber ◽  
Dimitri Angelov ◽  
Juan Ausio ◽  
Jerry Workman ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Molecular Biology ◽  
Binding Sites ◽  
Cross Linking ◽  
Uv Laser ◽  
Histone Tail ◽  
Histone Tails ◽  
Nucleosomal Dna ◽  
Core Histones

ABSTRACT In this study, we examined the effect of acetylation of the NH2 tails of core histones on their binding to nucleosomal DNA in the absence or presence of bound transcription factors. To do this, we used a novel UV laser-induced protein-DNA cross-linking technique, combined with immunochemical and molecular biology approaches. Nucleosomes containing one or five GAL4 binding sites were reconstituted with hypoacetylated or hyperacetylated core histones. Within these reconstituted particles, UV laser-induced histone-DNA cross-linking was found to occur only via the nonstructured histone tails and thus presented a unique tool for studying histone tail interactions with nucleosomal DNA. Importantly, these studies demonstrated that the NH2 tails were not released from nucleosomal DNA upon histone acetylation, although some weakening of their interactions was observed at elevated ionic strengths. Moreover, the binding of up to five GAL4-AH dimers to nucleosomes occupying the central 90 bp occurred without displacement of the histone NH2 tails from DNA. GAL4-AH binding perturbed the interaction of each histone tail with nucleosomal DNA to different degrees. However, in all cases, greater than 50% of the interactions between the histone tails and DNA was retained upon GAL4-AH binding, even if the tails were highly acetylated. These data illustrate an interaction of acetylated or nonacetylated histone tails with DNA that persists in the presence of simultaneously bound transcription factors.

scholarly journals Dynamic and Structural Modeling of the Specificity in Protein-DNA Interactions Guided by Binding Assay and Structure Data

2018 ◽  
Author(s):  
Cheng Tan ◽  
Shoji Takada
Keyword(s):  
Structure Data ◽  
Dna Sequences ◽  
Complex Structure ◽  
Specific Protein ◽  
Coarse Grained ◽  
Binding Modes ◽  
Binding Assays ◽  
Dna Interactions ◽  
Protein Dna Interactions ◽  
Dynamics Simulations

ABSTRACTHow transcription factors (TFs) recognize their DNA sequences is often investigated complementarily by high-throughput protein binding assays and by structural biology experiments. The former quantifies the specificity of TF binding sites for numerous DNA sequences, often represented as the position-weight-matrix (PWM). The latter provides mechanistic insights into the interactions via the protein-DNA complex structures. However, these two types of data are not readily integrated. Here, we propose and test a new modeling method that incorporates the PWM with complex structure data. Based on pre-tuned coarse-grained models for proteins and DNAs, we model the specific protein-DNA interactions, PWMcos, in terms of an orientation-dependent potential function, which enables us to perform molecular dynamics simulations at unprecedentedly large scales. We show that the PWMcos model reproduces subtle specificity in the protein-DNA recognition. During the target search in genomic sequences, TF moves on highly rugged landscapes and occasionally flips on DNA depending on the sequence. The TATA-binding protein exhibits two remarkably distinct binding modes, of which frequencies differ between TATA-containing and TATA-less promoters. The PWMcos is general and can be applied to any protein-DNA interactions given their PWMs and complex structure data are available.

scholarly journals p53 and TDG are dominant in regulating the activity of the human de novo DNA methyltransferase DNMT3A on nucleosomes

2020 ◽  
pp. jbc.RA120.016125
Author(s):  
Jonathan E. Sandoval ◽  
Norbert O. Reich
Keyword(s):  
Dna Methylation ◽  
Dna Methyltransferase ◽  
De Novo ◽  
Functional Characterization ◽  
Regulatory Proteins ◽  
Relative Role ◽  
Histone Tails ◽  
Nucleosomal Dna ◽  
Wide Range ◽  
Histone Modifiers

DNA methylation and histone tail modifications are interrelated mechanisms involved in a wide range of biological processes, and disruption of this crosstalk is linked to diseases like acute myeloid leukemia (AML).  In addition, DNMT3A activity is modulated by several regulatory proteins, including p53 and TDG.  However, the relative role of histone tails and regulatory proteins in the simultaneous coordination of DNMT3A activity remains obscure.  We observed that DNMT3A binds H3 tails and p53 or TDG at distinct allosteric sites to form DNMT3A-H3 tail-p53 or -TDG multiprotein complexes.  Functional characterization of DNMT3A-H3 tail-p53 or -TDG complexes on human-derived synthetic histone H3 tails, mono- or polynucleosomes shows p53 and TDG play dominant roles in the modulation of DNMT3A activity.  Intriguingly, this dominance occurs even when DNMT3A is actively methylating nucleosome substrates.  The activity of histone-modifiers is influenced by their ability to sense modifications on histone tails within the same nucleosome or histone tails on neighboring nucleosomes.  In contrast, we show here that DNMT3A acts on DNA within a single nucleosome, on nucleosomal DNA within adjacent nucleosomes, and DNA not associated with the DNMT3A-nucleosome complex.  Our findings have direct bearing on how the histone code drives changes in DNA methylation and highlight the complex interplay between histone tails, epigenetic enzymes and modulators of enzymatic activity. 

scholarly journals Generation of Remosomes by the SWI/SNF Chromatin Remodeler Family

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Manu Shubhdarshan Shukla ◽  
Sajad Hussain Syed ◽  
Ramachandran Boopathi ◽  
Elsa Ben Simon ◽  
Sunil Nahata ◽  
...  
Keyword(s):  
Dna Repair ◽  
High Resolution ◽  
Restriction Enzymes ◽  
Dna Interactions ◽  
Nucleosome Remodeling ◽  
Chromatin Remodelers ◽  
Dna Accessibility ◽  
Nucleosomal Dna ◽  
Dnase I Footprinting ◽  
High Resolution Microscopy

Abstract Chromatin remodelers are complexes able to both alter histone-DNA interactions and to mobilize nucleosomes. The mechanism of their action and the conformation of remodeled nucleosomes remain a matter of debates. In this work we compared the type and structure of the products of nucleosome remodeling by SWI/SNF and ACF complexes using high-resolution microscopy combined with novel biochemical approaches. We find that SWI/SNF generates a multitude of nucleosome-like metastable particles termed “remosomes”. Restriction enzyme accessibility assay, DNase I footprinting and AFM experiments reveal perturbed histone-DNA interactions within these particles. Electron cryo-microscopy shows that remosomes adopt a variety of different structures with variable irregular DNA path, similar to those described upon RSC remodeling. Remosome DNA accessibility to restriction enzymes is also markedly increased. We suggest that the generation of remosomes is a common feature of the SWI/SNF family remodelers. In contrast, the ACF remodeler, belonging to ISWI family, only produces repositioned nucleosomes and no evidence for particles associated with extra DNA, or perturbed DNA paths was found. The remosome generation by the SWI/SNF type of remodelers may represent a novel mechanism involved in processes where nucleosomal DNA accessibility is required, such as DNA repair or transcription regulation.

scholarly journals The conformation of the histone H3 tail inhibits association of the BPTF PHD finger with the nucleosome

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Emma A Morrison ◽  
Samuel Bowerman ◽  
Kelli L Sylvers ◽  
Jeff Wereszczynski ◽  
Catherine A Musselman
Keyword(s):  
Histone H3 ◽  
Md Simulations ◽  
Peptide Fragments ◽  
Histone Tails ◽  
Post Translational Modifications ◽  
Effector Domain ◽  
Phd Finger ◽  
Effector Domains ◽  
Chromatin Regulators ◽  
Nucleosomal Dna

Histone tails harbor a plethora of post-translational modifications that direct the function of chromatin regulators, which recognize them through effector domains. Effector domain/histone interactions have been broadly studied, but largely using peptide fragments of histone tails. Here, we extend these studies into the nucleosome context and find that the conformation adopted by the histone H3 tails is inhibitory to BPTF PHD finger binding. Using NMR spectroscopy and MD simulations, we show that the H3 tails interact robustly but dynamically with nucleosomal DNA, substantially reducing PHD finger association. Altering the electrostatics of the H3 tail via modification or mutation increases accessibility to the PHD finger, indicating that PTM crosstalk can regulate effector domain binding by altering nucleosome conformation. Together, our results demonstrate that the nucleosome context has a dramatic impact on signaling events at the histone tails, and highlights the importance of studying histone binding in the context of the nucleosome.

scholarly journals Torsional stress can regulate the unwrapping of two outer half superhelical turns of nucleosomal DNA

2021 ◽  
Vol 118 (7) ◽  
pp. e2020452118
Author(s):  
Hisashi Ishida ◽  
Hidetoshi Kono
Keyword(s):  
Large Scale ◽  
Stable State ◽  
Regulatory Proteins ◽  
Torsional Stress ◽  
Major Groove ◽  
Free Energies ◽  
Nucleosomal Dna ◽  
Inherent Nature ◽  
The Stability ◽  
Dynamics Simulations

Torsional stress has a significant impact on the structure and stability of the nucleosome. RNA polymerase imposes torsional stress on the DNA in chromatin and unwraps the DNA from the nucleosome to access the genetic information encoded in the DNA. To understand how the torsional stress affects the stability of the nucleosome, we examined the unwrapping of two half superhelical turns of nucleosomal DNA from either end of the DNA under torsional stress with all-atom molecular dynamics simulations. The free energies for unwrapping the DNA indicate that positive stress that overtwists DNA facilitates a large-scale asymmetric unwrapping of the DNA without a large extension of the DNA. During the unwrapping, one end of the DNA was dissociated from H3 and H2A-H2B, while the other end of the DNA stably remained wrapped. The detailed analysis indicates that this asymmetric dissociation is facilitated by the geometry and bendability of the DNA under positive stress. The geometry stabilized the interaction between the major groove of the twisted DNA and the H3 αN-helix, and the straightened DNA destabilized the interaction with H2A-H2B. Under negative stress, the DNA became more bendable and flexible, which facilitated the binding of the unwrapped DNA to the octamer in a stable state. Consequently, we conclude that the torsional stress has a significant impact on the affinity of the DNA and the octamer through the inherent nature of the DNA and can change the accessibility of regulatory proteins.

scholarly journals A Metadynamics-Based Protocol for the Determination of GPCR-Ligand Binding Modes

2019 ◽  
Vol 20 (8) ◽  
pp. 1970 ◽  
Author(s):  
Christian A. Söldner ◽  
Anselm H. C. Horn ◽  
Heinrich Sticht
Keyword(s):  
Ligand Binding ◽  
Pharmaceutical Research ◽  
Binding Mode ◽  
Model Systems ◽  
Binding Modes ◽  
Enhanced Sampling ◽  
Conformational Ensembles ◽  
Precise Knowledge ◽  
Preferential Binding ◽  
Dynamics Simulations

G protein-coupled receptors (GPCRs) are a main drug target and therefore a hot topic in pharmaceutical research. One important prerequisite to understand how a certain ligand affects a GPCR is precise knowledge about its binding mode and the specific underlying interactions. If no crystal structure of the respective complex is available, computational methods can be used to deduce the binding site. One of them are metadynamics simulations which have the advantage of an enhanced sampling compared to conventional molecular dynamics simulations. However, the enhanced sampling of higher-energy states hampers identification of the preferred binding mode. Here, we present a novel protocol based on clustering of multiple walker metadynamics simulations which allows identifying the preferential binding mode from such conformational ensembles. We tested this strategy for three different model systems namely the histamine H1 receptor in combination with its physiological ligand histamine, as well as the β 2 adrenoceptor with its agonist adrenaline and its antagonist alprenolol. For all three systems, the proposed protocol was able to reproduce the correct binding mode known from the literature suggesting that the approach can more generally be applied to the prediction of GPCR ligand binding in future.

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