Strategies for Generating Modified Nucleosomes: Applications within Structural Biology Studies

Musselman, Catherine A.; Kutateladze, Tatiana G.

doi:10.1021/acschembio.8b01049

Cited by 9 publications

(8 citation statements)

References 85 publications

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“…Our results, showing that γ-thialysine is a very good lysine mimic for KMT catalysis, suggest that γ-thialysine could find an important application in studies of methylation processes on intact histones and the more complex nucleosome and chromatin forms, an area of current epigenetic interest. 35,36 More generally, our work shows that despite differences in the angle, bond length and basicity, lysine and γ-thialysine exhibit comparable structural and chemical properties that may justify a use of stable γ-thialysine for future biocatalytic, biomolecular and bioconjugation-based studies of peptides and proteins.…”

Section: Resultsmentioning

confidence: 69%

γ-Thialysine versus Lysine: An Insight into the Epigenetic Methylation of Histones

Temimi¹,

Bruijne²,

Proietti

et al. 2019

Bioconjugate Chem.

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Biomedicinally important histone lysine methyltransferases (KMTs) transfer a methyl group from S-adenosylmethionine to lysine residues in histones and other proteins. Here, we report comparative studies on epigenetic methylation of lysine and γ-thialysine, the simplest cysteinederived lysine analog, which can be introduced to histone peptides and histone proteins via site-specific bioconjugation-based cysteine alkylation. Enzyme assays and computational studies demonstrate that human KMTs catalyze an efficient methylation of histones that possess γ-thialysine. This work provides a molecular basis for the application of γ-thialysine for biomolecular studies of intact histones and the nucleosome assembly.

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Section: Resultsmentioning

confidence: 69%

γ-Thialysine versus Lysine: An Insight into the Epigenetic Methylation of Histones

Temimi¹,

Bruijne²,

Proietti

et al. 2019

Bioconjugate Chem.

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“…Furthermore, with the high structural similarity of Kbz with 2,5-2F-Kbz, the fluorinated benzoyllysines could directly be exploited as surrogates for probing benzoylation, offering diverse signals such as 19 F NMR spectra and fluorescence signals under a biological environment. Therefore, these genetically encoded benzoyllysines offer a versatile and highly valuable chemical tool for interrogating histone lysine benzoylations or non-histone lysine benzoylation, , enabling a new and direct avenue to interrogate histone benzoylation and interactions, which will afford broad utilities in chemical biology, protein science, medicinal chemistry, and biology research . Our future studies will aim at exploring site-specific histone benzoylation and PTM-related binding partner (e.g., histone readers and erasers) interactions in living systems with this chemical tool to gain insights into biological functions and epigenetic roles of histone benzoylation at specific modification sites for a better understanding of histone epigenetics …”

Section: Discussionmentioning

confidence: 99%

Genetically Encoded Benzoyllysines Serve as Versatile Probes for Interrogating Histone Benzoylation and Interactions in Living Cells

et al. 2021

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Histone posttranslational modifications (PTMs) are vital epigenetic regulators in many fundamental cell signaling pathways and diverse biological processes. Histone lysine benzoylation is a recently identified epigenetic mark associated with active transcription; however, it remains to be explored. Herein, we first report the genetic encoding of benzoyllysine and fluorinated benzoyllysines into full-length histone proteins in a site-specific manner in live cells, based on our rationally designed synthetase and fine-integrated fluorine element into benzoyllysines. The incorporated unnatural amino acids integrating unique features were demonstrated as versatile probes for investigating histone benzoylation under biological environments, conferring multiplex signals such as 19F NMR spectra with chemical clarity and fluorescence signals for benzoylation. Moreover, the site specifically incorporated lysine benzoylation within native full-length histone proteins revealed distinct dynamics of debenzoylation in the presence of debenzoylase sirtuin 2 (SIRT2). Our developed strategy for genetic encoding of benzoyllysines offers a general and novel approach to gain insights into interactions of site-specific histone benzoylation modifications with interactomes and molecular mechanisms in physiological settings, which could not be accessible with fragment histone peptides. This versatile chemical tool enables a direct and new avenue to explore benzoylation, interactions, and histone epigenetics, which will provide broad utilities in chemical biology, protein science, and basic biology research.

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“…Characterizing the conformational ensemble and dynamics of the histone tails in the nucleosomal context has been challenging as they exchange between a broad range of conformations. Furthermore, reconstitution of nucleosomes in large quantities can be challenging, especially if specific post-translational modifications (PTMs) are desired [100]. Outlined here are methods that have been especially useful for studying histone tails conformation and dynamics.…”

Section: Box 1 Structural and Biophysical Methods For Studying Histomentioning

confidence: 99%

Histone Tail Conformations: A Fuzzy Affair with DNA

Ghoneim

Fuchs

Musselman

2021

Trends in Biochemical Sciences

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The core histone tails are critical in chromatin structure and signaling. Studies over the past several decades have provided a wealth of information on the histone tails and their interaction with chromatin factors. However, the conformation of the histone tails in a chromatin relevant context has remained elusive. Only recently has enough evidence emerged to start to build a structural model of the tails in the context of nucleosomes and nucleosome arrays. Here, we review these studies and propose that the histone tails adopt a high-affinity fuzzy complex with DNA, characterized by robust but dynamic association. Furthermore, we discuss how these DNA-bound conformational ensembles promote distinct chromatin structure and signaling, and that their fuzzy nature is important in transitioning between functional states. Highlights Eukaryotic DNA is wrapped around histone proteins to form nucleosomes that fold into higher-order chromatin structures, and the local chromatin structure regulates all DNA-templated processes. All core histone proteins contain intrinsically disordered tail regions that protrude from the DNA-wrapped core and are known to be critical in chromatin regulation. Recent studies have revealed that the core histone tails adopt multiple conformations on the nucleosomal and linker DNA; these tail/DNA interactions are robust, but exchange quickly between multiple conformations consistent with a so-called fuzzy complex. Intra-versus inter-nucleosome contacts by the tails differentially contribute to the local chromatin state and thus regulation of DNA-templated processes. Histone post-translational modifications and chromatin-associated factors can modulate these fuzzy conformational ensembles and tail accessibility, indicating that the tail/DNA interactions are an important regulatory mechanism of chromatin.

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Strategies for Generating Modified Nucleosomes: Applications within Structural Biology Studies

Cited by 9 publications

References 85 publications

γ-Thialysine versus Lysine: An Insight into the Epigenetic Methylation of Histones

γ-Thialysine versus Lysine: An Insight into the Epigenetic Methylation of Histones

Genetically Encoded Benzoyllysines Serve as Versatile Probes for Interrogating Histone Benzoylation and Interactions in Living Cells

Histone Tail Conformations: A Fuzzy Affair with DNA

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