Site‐Specific Studies of Nucleosome Interactions by Solid‐State NMR Spectroscopy

Paige, Ulric B. le; Horn, Velten; Houben, Klaartje; Baldus, Marc; Ingen, Hugo van

doi:10.1002/anie.201713158

Cited by 43 publications

(53 citation statements)

References 50 publications

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“…Solid‐state NMR (SSNMR) has been emerging as a powerful technique for biomolecular structure and dynamics characterization and has been successfully employed for studying various systems . In a recent study, proton‐detected SSNMR experiments were performed on the NCP and NCP:LANA complex, which included 2 H, 13 C, 15 N‐labeled H2A . This study determined the H2A secondary structure and confirmed the interface structure between the nucleosome and LANA previously determined by X‐ray crystallography .…”

Section: Figuresupporting

confidence: 68%

Structure and Dynamics in the Nucleosome Revealed by Solid‐State NMR

Shi

Prasanna

Nagashima³

et al. 2018

Angewandte Chemie

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Eukaryotic chromatin structure and dynamics play key roles in genomic regulation. In the current study, the secondary structure and intramolecular dynamics of human histone H4 (hH4) in the nucleosome core particle (NCP) and in a nucleosome array are determined by solid‐state NMR (SSNMR). Secondary structure elements are successfully localized in the hH4 in the NCP precipitated with Mg2+. In particular, dynamics on nanosecond to microsecond and microsecond to millisecond timescales are elucidated, revealing diverse internal motions in the hH4 protein. Relatively higher flexibility is observed for residues participating in the regulation of chromatin mobility and DNA accessibility. Furthermore, our study reveals that hH4 in the nucleosome array adopts the same structure and show similar internal dynamics as that in the NCP assembly while exhibiting relatively restricted motions in several regions consisting of residues in the N‐terminus, Loop 1, and the α3 helix region.

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Section: Figuresupporting

confidence: 68%

Structure and Dynamics in the Nucleosome Revealed by Solid‐State NMR

Shi

Prasanna

Nagashima³

et al. 2018

Angewandte Chemie

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“…[7] In ar ecent study, proton-detected SSNMR experiments were performed on the NCP and NCP:LANAc omplex, which included 2 H, 13 C, 15 Nlabeled H2A. [8] This study determined the H2A secondary structure and confirmed the interface structure between the nucleosome and LANAp reviously determined by X-ray crystallography. [9] Thei nherent plasticity of the central HO enables the NCP serving as as tructural scaffold in the nucleosome compaction and facilitating DNA-templated processes.…”

mentioning

confidence: 76%

Structure and Dynamics in the Nucleosome Revealed by Solid‐State NMR

Shi

Prasanna

Nagashima³

et al. 2018

Angew Chem Int Ed

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Eukaryotic chromatin structure and dynamics play key roles in genomic regulation. In the current study, the secondary structure and intramolecular dynamics of human histone H4 (hH4) in the nucleosome core particle (NCP) and in a nucleosome array are determined by solid-state NMR (SSNMR). Secondary structure elements are successfully localized in the hH4 in the NCP precipitated with Mg . In particular, dynamics on nanosecond to microsecond and microsecond to millisecond timescales are elucidated, revealing diverse internal motions in the hH4 protein. Relatively higher flexibility is observed for residues participating in the regulation of chromatin mobility and DNA accessibility. Furthermore, our study reveals that hH4 in the nucleosome array adopts the same structure and show similar internal dynamics as that in the NCP assembly while exhibiting relatively restricted motions in several regions consisting of residues in the N-terminus, Loop 1, and the α3 helix region.

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“…This is for some of these systems probably a consequence of oligomerization that has been induced by the high protein concentrations (Bertini et al, 2013;Fragai et al, 2013). Protein-protein complexes were studied by co-sedimentation (Gardiennet et al, 2016;Xiang et al, 2018) and protein-ligand complexes by sedimentation with the respective ligand (e.g. nucleic acids) directly into the NMR rotor (Wiegand et al, 2016a;Kaur et al, 2018;Stöppler et al, 2018;Lacabanne et al, 2019b).…”

Section: Introductionmentioning

confidence: 99%

Sedimentation Yields Long-Term Stable Protein Samples as Shown by Solid-State NMR

Wiegand

Lacabanne

Torosyan

et al. 2020

Front. Mol. Biosci.

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Today, the sedimentation of proteins into a magic-angle spinning (MAS) rotor gives access to fast and reliable sample preparation for solid-state Nuclear Magnetic Resonance (NMR), and this has allowed for the investigation of a variety of noncrystalline protein samples. High protein concentrations on the order of 400 mg/mL can be achieved, meaning that around 50-60% of the NMR rotor content is protein; the rest is a buffer solution, which includes counter ions to compensate for the charge of the protein. We have demonstrated herein the long-term stability of four sedimented proteins and complexes thereof with nucleotides, comprising a bacterial DnaB helicase, an ABC transporter, an archaeal primase, and an RNA polymerase subunit. Solid-state NMR spectra recorded directly after sample filling and up to 5 years later indicated no spectral differences and no loss in signal intensity, allowing us to conclude that protein sediments in the rotor can be stable over many years. We have illustrated, using an example of an ABC transporter, that not only the structure is maintained, but that the protein is still functional after long-term storage in the sedimented state.

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Site‐Specific Studies of Nucleosome Interactions by Solid‐State NMR Spectroscopy

Cited by 43 publications

References 50 publications

Structure and Dynamics in the Nucleosome Revealed by Solid‐State NMR

Structure and Dynamics in the Nucleosome Revealed by Solid‐State NMR

Structure and Dynamics in the Nucleosome Revealed by Solid‐State NMR

Sedimentation Yields Long-Term Stable Protein Samples as Shown by Solid-State NMR

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