Atomic-resolution structure of cytoskeletal bactofilin by solid-state NMR

Bactofilins are a recently discovered class of cytoskeletal proteins of which no atomic-resolution structure has been reported thus far. The bacterial cytoskeleton plays an essential role in a wide range of processes, including morphogenesis, cell division, and motility. Among the cytoskeletal proteins, the bactofilins are bacteria-specific and do not have a eukaryotic counterpart. The bactofilin BacA of the speciesCaulobacter crescentusis not amenable to study by x-ray crystallography or solution nuclear magnetic resonance (NMR) because of its inherent noncrystallinity and insolubility. We present the atomic structure of BacA calculated from solid-state NMR–derived distance restraints. We show that the core domain of BacA forms a right-handed β helix with six windings and a triangular hydrophobic core. The BacA structure was determined to 1.0 Å precision (heavy-atom root mean square deviation) on the basis of unambiguous restraints derived from four-dimensional (4D) HN-HN and 2D C-C NMR spectra.

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Dipole tensor-based atomic-resolution structure determination of a nanocrystalline protein by solid-state NMR

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.0712393105 ◽

2008 ◽

Vol 105 (12) ◽

pp. 4621-4626 ◽

Cited By ~ 118

Author(s):

W. T. Franks ◽

B. J. Wylie ◽

H. L. F. Schmidt ◽

A. J. Nieuwkoop ◽

R.-M. Mayrhofer ◽

...

Keyword(s):

Solid State ◽

Structure Determination ◽

Solid State Nmr ◽

Atomic Resolution ◽

Resolution Structure

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Simultaneous use of solution, solid-state NMR and X-ray crystallography to study the conformational landscape of the Crh protein during oligomerization and crystallization

Advances and Applications in Bioinformatics and Chemistry ◽

10.2147/aabc.s8715 ◽

2010 ◽

pp. 25

Author(s):

Malliavin

Keyword(s):

Solid State ◽

Solid State Nmr ◽

X Ray ◽

X Ray Crystallography ◽

Conformational Landscape ◽

Simultaneous Use

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

10.5194/mr-2021-21 ◽

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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FEI Titan 80-300 TEM

Journal of large-scale research facilities JLSRF ◽

10.17815/jlsrf-2-66 ◽

2016 ◽

Vol 2 ◽

Cited By ~ 36

Author(s):

Andreas Thust ◽

Juri Barthel ◽

Karsten Tillmann

Keyword(s):

Electron Microscope ◽

Solid State ◽

Spherical Aberration ◽

Atomic Scale ◽

Atomic Resolution ◽

Lens System ◽

Stage Design ◽

Precise Positioning ◽

Transmission Electron ◽

Wide Range

The FEI Titan 80-300 TEM is a high-resolution transmission electron microscope equipped with a field emission gun and a corrector for the spherical aberration (CS) of the imaging lens system. The instrument is designed for the investigation of a wide range of solid state phenomena taking place on the atomic scale, which requires true atomic resolution capabilities. Under optimum optical settings of the image CS-corrector (CEOS CETCOR) the point-resolution is extended up to the information limit of well below 100 pm with 200 keV and 300 keV electrons. A special piezo-stage design allows ultra-precise positioning of the specimen in all 3 dimensions. Digital images are acquired with a Gatan 2k x 2k slow-scan charged coupled device camera.

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Solid State NMR as A Probe of Inorganic Materials:Examples From Glasses and Sol-Gels

MRS Proceedings ◽

10.1557/proc-984-0984-mm12-01 ◽

2006 ◽

Vol 984 ◽

Cited By ~ 1

Author(s):

Paul Guerry ◽

Donna L Carroll ◽

Phillips N Gunawidjaja ◽

Prodipta Bhattacharya ◽

Daniela Carta ◽

...

Keyword(s):

Solid State ◽

Phosphate Glass ◽

Solid State Nmr ◽

Short Range ◽

Sol Gel ◽

The Other ◽

Disordered Materials ◽

Structural Sensitivity ◽

Nmr Data ◽

Wide Range

AbstractTo understand amorphous and structurally disordered materials requires the application of a wide-range of advanced physical probe techniques and herein a combined methodology is outlined. The relatively short-range structural sensitivity of solid state NMR means that it is a core probe technique for characterizing such materials. The aspects of the solid state NMR contribution are emphasized here with examples given from a number of systems, with especial emphasis on the information available from 17O NMR in oxygen-containing materials. 17O NMR data for crystallization of pure sol-gel prepared oxides is compared, with new data presented from In2O3 and Sc2O3. Sol-gel formed oxide mixtures containing silica have been widely studied, but again the role and effect of the other added oxide varies widely. In a ternary ZrO2-TiO2-SiO2 silicate sol-gel the level of Q4 formation is dependent not only on the composition, as expected, but also the nature of the second added oxide. Sol-gel formed phosphates have been much less widely studied than silicates and some 31P NMR data from xerogel, sonogel and melt-quench glasses of the same composition are compared. The effect of small amounts of added antibacterial copper on phosphate glass networks is also explored.

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Probing solid iminobis(diorganophosphine chalcogenide) systems with multinuclear magnetic resonance

Canadian Journal of Chemistry ◽

10.1139/v08-150 ◽

2009 ◽

Vol 87 (1) ◽

pp. 348-360 ◽

Cited By ~ 1

Author(s):

Bryan A Demko ◽

Roderick E Wasylishen

Keyword(s):

Solid State ◽

Chemical Shift ◽

Solid State Nmr ◽

Magnetic Shielding ◽

Chemical Shift Tensors ◽

X Ray ◽

X Ray Crystallography ◽

Shielding Tensor ◽

Nuclear Magnetic Shielding Tensors ◽

Nuclear Magnetic

A 31P and 77Se solid-state NMR investigation of the iminobis(diorganophosphine chalcogenide) HN(R2PE)2 (R = Ph,iPr; E = O, S, Se) systems is presented. The NMR results are discussed in terms of the known HN(R2PE)2 structures available from X-ray crystallography. The phosphorus chemical shift tensors are found to be sensitive to the nature of the alkyl and chalcogen substituents. The nature of the R group also influences the selenium chemical shift tensors of HN(R2PSe)2 (R = Ph, iPr), which are shown to be sensitive to hydrogen bonding in the dimer structure of HN(Ph2PSe)2 and to the presence of disorder in the case of HN(iPr2PSe)2. Scalar relativistic ZORA DFT nuclear magnetic shielding tensor calculations were performed yielding the orientations of the corresponding chemical shift tensors. A theoretical investigation into the effect of the E-P···P-E “torsion” angle on the phosphorus and selenium chemical shift tensors of a truncated HN(Me2PSe)2 system indicates that the electronic effect of the alkyl group on the respective nuclear magnetic shielding tensors are more important than the steric effect of the E-P···P-E torsion angle.Key words: iminobis(diorganophosphine chalcogenide), solid-state NMR, 31P NMR, 77Se NMR, ZORA DFT.

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Solid-State NMR Techniques for the Structural Characterization of Cyclic Aggregates Based on Borane–Phosphane Frustrated Lewis Pairs

Molecules ◽

10.3390/molecules25061400 ◽

2020 ◽

Vol 25 (6) ◽

pp. 1400 ◽

Cited By ~ 1

Author(s):

Robert Knitsch ◽

Melanie Brinkkötter ◽

Thomas Wiegand ◽

Gerald Kehr ◽

Gerhard Erker ◽

...

Keyword(s):

Solid State ◽

Structural Characterization ◽

Solid State Nmr ◽

Magic Angle ◽

Frustrated Lewis Pairs ◽

Wide Range ◽

Nmr Techniques ◽

Nmr Methods ◽

Lewis Pairs

Modern solid-state NMR techniques offer a wide range of opportunities for the structural characterization of frustrated Lewis pairs (FLPs), their aggregates, and the products of cooperative addition reactions at their two Lewis centers. This information is extremely valuable for materials that elude structural characterization by X-ray diffraction because of their nanocrystalline or amorphous character, (pseudo-)polymorphism, or other types of disordering phenomena inherent in the solid state. Aside from simple chemical shift measurements using single-pulse or cross-polarization/magic-angle spinning NMR detection techniques, the availability of advanced multidimensional and double-resonance NMR methods greatly deepened the informational content of these experiments. In particular, methods quantifying the magnetic dipole–dipole interaction strengths and indirect spin–spin interactions prove useful for the measurement of intermolecular association, connectivity, assessment of FLP–ligand distributions, and the stereochemistry of adducts. The present review illustrates several important solid-state NMR methods with some insightful applications to open questions in FLP chemistry, with a particular focus on supramolecular associates.

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