Investigating the Dynamics of Destabilized Nucleosomes Using Methyl-TROSY NMR

Kitevski-LeBlanc, Julianne L.; Kay, Lewis E.; Dyer, Pamela N.; Rudolph, Johannes; Luger, Karolin

doi:10.1021/jacs.8b00931

Cited by 43 publications

(37 citation statements)

References 28 publications

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“…This study determined the H2A secondary structure and confirmed the interface structure between the nucleosome and LANA previously determined by X‐ray crystallography . The inherent plasticity of the central HO enables the NCP serving as a structural scaffold in the nucleosome compaction and facilitating DNA‐templated processes . The dynamics of protein and DNA at multiple spatial and temporal scales play critical roles in regulation of chromatin functions .…”

Section: Figuresupporting

confidence: 79%

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: 79%

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

Shi

Prasanna

Nagashima³

et al. 2018

Angewandte Chemie

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“…Relevant to these observations, several prior studies have provided evidence for intrinsic dynamics within nucleosomes. These include spontaneous unpeeling of nucleosomal DNA (G. Li et al, 2005), the identification by EM of alternative configurations of histone helices within distorted nucleosomes (Bilokapic et al, 2018b) and the identification of histone mutants than increase the spontaneous dynamics (Kitevski-LeBlanc et al, 2018) of core histone resides. It has been further demonstrated that core histone dynamics enable spontaneous nucleosome sliding (Bilokapic et al, 2018a).…”

Section: Discussionmentioning

confidence: 99%

Electron cryo-microscopy structures of remodeler-nucleosome intermediates suggest allosteric control through the nucleosome

Armache¹,

Gamarra²,

Sl³

et al. 2019

Preprint

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18The SNF2h remodeler slides nucleosomes most efficiently as a dimer, yet how the two 19 protomers avoid a tug-of-war is unclear. Furthermore, SNF2h couples histone octamer 20 deformation to nucleosome sliding, but the underlying structural basis remains unknown. Here 21 we present cryo-EM structures of SNF2h-nucleosome complexes with ADP-BeFx that capture 22 two reaction intermediates. In one structure, histone residues near the dyad and in the H2A- 23H2B acidic patch, distal to the active SNF2h protomer, are disordered. The disordered acidic 24 patch is expected to inhibit the second SNF2h promoter, while disorder near the dyad is 25 expected to promote DNA translocation. The other structure doesn't show octamer deformation, 26but surprisingly shows a 2bp translocation. FRET studies indicate that ADP-BeFx predisposes 27 SNF2h-nucleosome complexes for an elemental translocation step. We propose a model for 28 allosteric control through the nucleosome, where one SNF2h protomer promotes asymmetric 29 octamer deformation to inhibit the second protomer, while stimulating directional DNA 30 translocation. 31 32 One sentence summary: Cryo-EM structures capture different conformational states of 33 chromatin remodeler-nucleosome complexes. 34 35 65 complex: a state with an unexpectedly translocated nucleosome (Figure 1, Figure 1-supplement 66 1-6), a state with two SNF2h protomers bound to a nucleosome (Figure 2A, Figure 2-67 supplement 1) and a state with one protomer bound to a nucleosome that shows increased 68 disorder within the histone core (Figure 2B). The locations of histone disorder strongly suggest a 69 4 role for octamer deformation in protomer coordination and directional DNA translocation. In 70 addition, we detect new ISWI-histone contacts that make significant contributions to 71 nucleosome sliding and help explain why ISWI may differ in mechanism from Swi2/Snf2 (Figure 72 3) (Liu et al., 2017).73 74 Overview of SNF2h-nucleosome structures 75 Like most ISWI remodelers, SNF2h slides mono-nucleosomes assembled on short stretches of 76 DNA towards the center of the DNA (Clapier and Cairns, 2009; Narlikar et al., 2013; Zhou et al., 77 2016). In previous studies we have found that while a monomer of SNF2h can slide 78 nucleosomes, SNF2h functions most optimally as a dimer (Leonard and Narlikar, 2015; Racki et 79 al., 2009). In these studies, we were able to visualize both singly bound and doubly bound 80 SNF2h using negative stain EM (Racki et al., 2009). Previous studies have further shown that 81 binding of the ATP analog, ADP-BeF x , promotes a restricted conformation of the ATPase active 82 site in a manner that is dependent on the H4 tail (Racki et al., 2014). The restricted 83 conformation is consistent with observations showing an activating role for the H4 tail (Clapier et 84 al., 2001; 2002; Hamiche et al., 2001). Further, binding of ADP-BeF x to SNF2h promotes 85 conformational flexibility of buried histone residues (Sinha et al., 2017). This conformational 86 flexibility is functionally important ...

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“…These measurements have been complemented with more sophisticated experiments and analyses to obtain also intermediate and slow time scale information from µs up to ms. This includes the 15 N CPMG-or 15 N R 1 based relaxation dispersion experiments 17,18 , CEST or DEST measurements 9,12 and alternatively 13 C methyl relaxation measurements covering protein side-chain dynamics 19,20 . Towards a more comprehensive picture of dynamics, residual-dipolar couplings 11,21,22 , cross-correlated relaxation 4,7,23 , paramagnetic relaxation enhancement (PRE) [24][25][26] and eNOE-based 6,27 data have been acquired and can be used in combination with molecular dynamics simulation 28,29 or ensemble averaging 5,11,27,30,31 and chemical-shift based structural ensemble prediction [32][33][34] .…”

Section: Introductionmentioning

confidence: 99%

15N transverse relaxation measurements for the characterization of µs–ms dynamics are deteriorated by the deuterium isotope effect on 15N resulting from solvent exchange

et al. 2018

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15 N R 2 relaxation measurements are key for the elucidation of the dynamics of both folded and intrinsically disordered proteins (IDPs). Here we show, on the example of the intrinsically disordered protein α-synuclein and the folded domain PDZ2, that at physiological pH and near physiological temperatures amide-water exchange can severely skew Hahn-echo based 15 N R 2 relaxation measurements as well as low frequency data points in CPMG relaxation dispersion experiments. The nature thereof is the solvent exchange with deuterium in the sample buffer, which modulates the 15 N chemical shift tensor via the deuterium isotope effect, adding to the apparent relaxation decay which leads to systematic errors in the relaxation data. This results in an artificial increase of the measured apparent 15 N R 2 rate constants  which should not be mistaken with protein inherent chemical exchange contributions, R ex , to 15 N R 2. For measurements of 15 N R 2 rate constants of IDPs and folded proteins at physiological temperatures and pH, we recommend therefore the use of a very low D 2 O molar fraction in the sample buffer, as low as 1%, or the use of an external D 2 O reference along with a modified 15 N R 2 Hahn-echo based experiment. This combination allows for the measurement of R ex contributions to 15 N R 2 originating from conformational exchange in a time window from µs to ms.

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Investigating the Dynamics of Destabilized Nucleosomes Using Methyl-TROSY NMR

Cited by 43 publications

References 28 publications

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

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

Electron cryo-microscopy structures of remodeler-nucleosome intermediates suggest allosteric control through the nucleosome

15N transverse relaxation measurements for the characterization of µs–ms dynamics are deteriorated by the deuterium isotope effect on 15N resulting from solvent exchange

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