scholarly journals Emerging Contributions of Solid-State NMR Spectroscopy to Chromatin Structural Biology

2021 ◽  
Vol 8 ◽  
Author(s):  
Bryce E. Ackermann ◽  
Galia T. Debelouchina
Keyword(s):  
Gene Expression ◽  
Solid State ◽  
Structural Biology ◽  
Chromatin Structure ◽  
Histone Variants ◽  
Mas Nmr ◽  
Resonance Spectroscopy ◽  
Magic Angle ◽  
Nmr Studies ◽  
Chromatin Structural

The eukaryotic genome is packaged into chromatin, a polymer of DNA and histone proteins that regulates gene expression and the spatial organization of nuclear content. The repetitive character of chromatin is diversified into rich layers of complexity that encompass DNA sequence, histone variants and post-translational modifications. Subtle molecular changes in these variables can often lead to global chromatin rearrangements that dictate entire gene programs with far reaching implications for development and disease. Decades of structural biology advances have revealed the complex relationship between chromatin structure, dynamics, interactions, and gene expression. Here, we focus on the emerging contributions of magic-angle spinning solid-state nuclear magnetic resonance spectroscopy (MAS NMR), a relative newcomer on the chromatin structural biology stage. Unique among structural biology techniques, MAS NMR is ideally suited to provide atomic level information regarding both the rigid and dynamic components of this complex and heterogenous biological polymer. In this review, we highlight the advantages MAS NMR can offer to chromatin structural biologists, discuss sample preparation strategies for structural analysis, summarize recent MAS NMR studies of chromatin structure and dynamics, and close by discussing how MAS NMR can be combined with state-of-the-art chemical biology tools to reconstitute and dissect complex chromatin environments.

scholarly journals A novel multinuclear solid-state NMR approach for the characterization of kidney stones

2021 ◽  
Vol 2 (2) ◽  
pp. 653-671
Author(s):  
César Leroy ◽  
Laure Bonhomme-Coury ◽  
Christel Gervais ◽  
Frederik Tielens ◽  
Florence Babonneau ◽  
...  
Keyword(s):  
Solid State ◽  
Kidney Stones ◽  
Solid State Nmr ◽  
Magic Angle Spinning ◽  
Mas Nmr ◽  
Magic Angle ◽  
Nmr Studies ◽  
Stone Composition ◽  
Analytical Technique ◽  
Nmr Data

Abstract. The spectroscopic study of pathological calcifications (including kidney stones) is extremely rich and helps to improve the understanding of the physical and chemical processes associated with their formation. While Fourier transform infrared (FTIR) imaging and optical/electron microscopies are routine techniques in hospitals, there has been a dearth of solid-state NMR studies introduced into this area of medical research, probably due to the scarcity of this analytical technique in hospital facilities. This work introduces effective multinuclear and multidimensional solid-state NMR methodologies to study the complex chemical and structural properties characterizing kidney stone composition. As a basis for comparison, three hydrates (n=1, 2 and 3) of calcium oxalate are examined along with nine representative kidney stones. The multinuclear magic angle spinning (MAS) NMR approach adopted investigates the 1H, 13C, 31P and 31P nuclei, with the 1H and 13C MAS NMR data able to be readily deconvoluted into the constituent elements associated with the different oxalates and organics present. For the first time, the full interpretation of highly resolved 1H NMR spectra is presented for the three hydrates, based on the structure and local dynamics. The corresponding 31P MAS NMR data indicates the presence of low-level inorganic phosphate species; however, the complexity of these data make the precise identification of the phases difficult to assign. This work provides physicians, urologists and nephrologists with additional avenues of spectroscopic investigation to interrogate this complex medical dilemma that requires real, multitechnique approaches to generate effective outcomes.

Phosphorus-31 and vanadium-51 solid-state nuclear magnetic resonance spectroscopy of β-vanadyl phosphate — Effects of homo- and heteronuclear spin-spin, electrostatic, and paramagnetic interactions

2011 ◽  
Vol 89 (7) ◽  
pp. 870-884 ◽  
Author(s):  
Klaus Eichele ◽  
Arnd-Rüdiger Grimmer
Keyword(s):  
Solid State ◽  
Chemical Shift ◽  
Chemical Shift Anisotropy ◽  
Lattice Relaxation ◽  
Nuclear Quadrupole Interaction ◽  
Magic Angle Spinning ◽  
Spin Lattice Relaxation ◽  
Resonance Spectroscopy ◽  
Magic Angle ◽  
Nmr Studies

Field-dependent 31P solid-state NMR studies demonstrate that the line shape in spectra of β-VOPO4 depends on 51V–31P direct and indirect spin-spin interactions (M2 (51V, 31P) = 101(23) × 106 rad2 s–2, 2Jiso (51V, 31P) = 48(5) Hz) and, to a lesser extent, on 31P chemical shift anisotropy (δiso = –10.4(2), Ω = δ11 – δ33 = 22(2) ppm) and 31P–31P interactions (M2 (31P, 31P) = 6.7(1) × 106 rad2 s–2). In contrast, homonuclear dipolar interactions play an important role for the field and spinning rate dependent 31P spin-lattice relaxation via paramagnetic impurities (T1 = 20–60 s). Vanadium-51 magic-angle spinning NMR spectra indicate a sizeable chemical shift anisotropy (δiso = –754(1), δ11 = –336(10), δ22 = –344(6), δ33 = –1581(8) ppm) and nuclear quadrupole interaction (χ = 1.5(1) MHz, η = 0.35(5)); the principal axis systems of both interactions are clearly not coincident, with an angle of 35(5)° between the greatest component of the electric field gradient tensor and δ33.

scholarly journals Preparation of Li3PS4–Li3PO4 Solid Electrolytes by Liquid-Phase Shaking for All-Solid-State Batteries

2021 ◽  
Vol 2 (1) ◽  
pp. 39-48
Author(s):  
Nguyen H. H. Phuc ◽  
Takaki Maeda ◽  
Tokoharu Yamamoto ◽  
Hiroyuki Muto ◽  
Atsunori Matsuda
Keyword(s):  
Solid Solution ◽  
Solid State ◽  
Liquid Phase ◽  
Room Temperature ◽  
Reaction Medium ◽  
Magic Angle Spinning ◽  
Resonance Spectroscopy ◽  
Synthesis Methods ◽  
Magic Angle ◽  
Angle Spinning

A solid solution of a 100Li3PS4·xLi3PO4 solid electrolyte was easily prepared by liquid-phase synthesis. Instead of the conventional solid-state synthesis methods, ethyl propionate was used as the reaction medium. The initial stage of the reaction among Li2S, P2S5 and Li3PO4 was proved by ultraviolet-visible spectroscopy. The powder X-ray diffraction (XRD) results showed that the solid solution was formed up to x = 6. At x = 20, XRD peaks of Li3PO4 were detected in the prepared sample after heat treatment at 170 °C. However, the samples obtained at room temperature showed no evidence of Li3PO4 remaining for x = 20. Solid phosphorus-31 magic angle spinning nuclear magnetic resonance spectroscopy results proved the formation of a POS33− unit in the sample with x = 6. Improvements of ionic conductivity at room temperature and activation energy were obtained with the formation of the solid solution. The sample with x = 6 exhibited a better stability against Li metal than that with x = 0. The all-solid-state half-cell employing the sample with x = 6 at the positive electrode exhibited a better charge–discharge capacity than that employing the sample with x = 0.

scholarly journals Combination of solid state NMR and DFT calculation to elucidate the state of sodium in hard carbon electrodes

2016 ◽  
Vol 4 (34) ◽  
pp. 13183-13193 ◽  
Author(s):  
Ryohei Morita ◽  
Kazuma Gotoh ◽  
Mika Fukunishi ◽  
Kei Kubota ◽  
Shinichi Komaba ◽  
...  
Keyword(s):  
Solid State ◽  
Solid State Nmr ◽  
Dft Calculation ◽  
Magic Angle Spinning ◽  
The State ◽  
Mas Nmr ◽  
Magic Angle ◽  
Multiple Quantum ◽  
Hard Carbon ◽  
Angle Spinning

We examined the state of sodium electrochemically inserted in HC prepared at 700–2000 °C using solid state Na magic angle spinning (MAS) NMR and multiple quantum (MQ) MAS NMR.

Solid-State MAS NMR Studies of Sulfonic Acid-Functionalized SBA-15

2007 ◽  
Vol 32 (4) ◽  
pp. 513-526 ◽  
Author(s):  
R. Kanthasamy ◽  
I. K. Mbaraka ◽  
B. H. Shanks ◽  
S. C. Larsen
Keyword(s):  
Solid State ◽  
Sulfonic Acid ◽  
Mas Nmr ◽  
Nmr Studies

scholarly journals Characterization of nucleosome sediments for protein interaction studies by solid-state NMR spectroscopy

2021 ◽  
Author(s):  
Ulric B. le Paige ◽  
ShengQi Xiang ◽  
Marco M. R. M. Hendrix ◽  
Yi Zhang ◽  
Markus Weingarth ◽  
...  
Keyword(s):  
Solid State ◽  
Nmr Spectroscopy ◽  
Solid State Nmr ◽  
Magic Angle Spinning ◽  
Magic Angle ◽  
Dense Phase ◽  
Binding Studies ◽  
Nmr Studies ◽  
Solid State Nmr Spectroscopy ◽  
Wide Range

Abstract. Regulation of DNA-templated processes such as gene transcription and DNA repair depend on the interaction of a wide range of proteins to the nucleosome, the fundamental building block of chromatin. Both solution and solid-state NMR spectroscopy have become an attractive approach to study the dynamics and interactions of nucleosomes, despite their high molecular weight of ~200 kDa. For solid-state NMR (ssNMR) studies, dilute solutions of nucleosomes are converted to a dense phase by sedimentation or precipitation. Since nucleosomes are known to self-associate, these dense phases may induce extensive interactions between nucleosomes, which could interfere with protein binding studies. Here, we characterized the packing of nucleosomes in the dense phase created by sedimentation using NMR and small-angle x-ray scattering (SAXS) experiments. We found that nucleosome sediments are gels with variable degrees of solidity, have nucleosome concentration close to that found in crystals, and are stable for weeks under high-speed magic angle spinning (MAS). Furthermore, SAXS data recorded on recovered sediments indicate that there is no pronounced long-range ordering of nucleosomes in the sediment. Finally, we show that the sedimentation approach can also be used to study low affinity protein interactions with the nucleosome. Together, our results give new insights into the sample characteristics of nucleosome sediments for ssNMR studies and illustrate the broad applicability of sedimentation-based NMR studies.

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