A software framework for analysing solid-state MAS NMR data

Stevens, Tim J.; Fogh, Rasmus H.; Boucher, Wayne; Higman, Victoria Ann; Eisenmenger, Frank; Bardiaux, Benjamin; Rossum, Barth‐Jan van; Oschkinat, Hartmut; Laue, Ernest D.

doi:10.1007/s10858-011-9569-2

Cited by 141 publications

(115 citation statements)

References 46 publications

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“…The chemical shift referencing of all spectra was done with respect to the DSS proton chemical shift as an internal reference. All of the spectra were processed with TOPSPIN and analyzed using CcpNMR (50). A complete list of ssNMR experiments and the corresponding experimental parameters is provided in SI Appendix, Table S1.…”

Section: Methodsmentioning

confidence: 99%

β-Helical architecture of cytoskeletal bactofilin filaments revealed by solid-state NMR

Vasa¹,

Lin

Shi

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Bactofilins are a widespread class of bacterial filament-forming proteins, which serve as cytoskeletal scaffolds in various cellular pathways. They are characterized by a conserved architecture, featuring a central conserved domain (DUF583) that is flanked by variable terminal regions. Here, we present a detailed investigation of bactofilin filaments from Caulobacter crescentus by highresolution solid-state NMR spectroscopy. De novo sequential resonance assignments were obtained for residues Ala39 to Phe137, spanning the conserved DUF583 domain. Analysis of the secondary chemical shifts shows that this core region adopts predominantly β-sheet secondary structure. Mutational studies of conserved hydrophobic residues located in the identified β-strand segments suggest that bactofilin folding and polymerization is mediated by an extensive and redundant network of hydrophobic interactions, consistent with the high intrinsic stability of bactofilin polymers. Transmission electron microscopy revealed a propensity of bactofilin to form filament bundles as well as sheet-like, 2D crystalline assemblies, which may represent the supramolecular arrangement of bactofilin in the native context. Based on the diffraction pattern of these 2D crystalline assemblies, scanning transmission electron microscopy measurements of the mass per length of BacA filaments, and the distribution of β-strand segments identified by solid-state NMR, we propose that the DUF583 domain adopts a β-helical architecture, in which 18 β-strand segments are arranged in six consecutive windings of a β-helix.solid-state NMR | cytoskeleton | protein structure | filaments

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Section: Methodsmentioning

confidence: 99%

β-Helical architecture of cytoskeletal bactofilin filaments revealed by solid-state NMR

Vasa¹,

Lin

Shi

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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“…The spectra were processed in Topspin and analyzed in CCPNmr (Stevens et al 2011) and MATLAB (MATLAB 2011R, The MathWorks Inc., Natick, MA, 2011. Figure 1a shows that the proton coherence life times, T 2 0 , increase linearly with MAS frequencies in the range from 30 to 90 kHz, as measured on the amide proton signals (integral over amide region) from ubiquitin as function of the MAS frequency.…”

Section: Nmr Spectroscopymentioning

confidence: 99%

Protein resonance assignment at MAS frequencies approaching 100 kHz: a quantitative comparison of J-coupling and dipolar-coupling-based transfer methods

et al. 2015

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We discuss the optimum experimental conditions to obtain assignment spectra for solid proteins at magic-angle spinning (MAS) frequencies around 100 kHz. We present a systematic examination of the MAS dependence of the amide proton T 2' times and a site-specific comparison of T 2' at 93 kHz versus 60 kHz MAS frequency. A quantitative analysis of transfer efficiencies of building blocks, as they are used for typical 3D experiments, was performed. To do this, we compared dipolar-coupling and J-coupling based transfer steps. The building blocks were then combined into 3D experiments for sequential resonance assignment, where we evaluated signal-to-noise ratio and information content of the different 3D spectra in order to identify the best assignment strategy. Based on this comparison, six experiments were selected to optimally assign the model protein ubiquitin, solely using spectra acquired at 93 kHz MAS. Within 3 days of instrument time, the required spectra were recorded from which the backbone resonances have been assigned to over 96%.

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“…Exponential line broadening of 5 Hz was applied to all spectra acquired on the 600 MHz spectromter. Peak picking, peak intensity measurements, and plotting were done using CcpNmr Analysis program from the Collaborative Computation Project for the NMR community (CcpNmr) (38,39).…”

Section: Mas Ssnmr Spectroscopymentioning

confidence: 99%

MAS 1 H NMR Probes Freezing Point Depression of Water and Liquid-Gel Phase Transitions in Liposomes

Mandal

Wel

2016

Biophysical Journal

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The lipid bilayer typical of hydrated biological membranes is characterized by a liquid-crystalline, highly dynamic state. Upon cooling or dehydration, these membranes undergo a cooperative transition to a rigidified, more-ordered, gel phase. This characteristic phase transition is of significant biological and biophysical interest, for instance in studies of freezing-tolerant organisms. Magic-angle-spinning (MAS) solid-state NMR (ssNMR) spectroscopy allows for the detection and characterization of the phase transitions over a wide temperature range. In this study we employ MAS 1 H NMR to probe the phase transitions of both solvent molecules and different hydrated phospholipids, including tetraoleoyl cardiolipin (TOCL) and several phosphatidylcholine lipid species. The employed MAS NMR sample conditions cause a previously noted substantial reduction in the freezing point of the solvent phase. The effect on the solvent is caused by confinement of the aqueous solvent in the small and densely packed MAS NMR samples. In this study we report and examine how the freezing point depression also impacts the lipid phase transition, causing a ssNMR-observed reduction in the lipids' melting temperature (T m ). The molecular underpinnings of this phenomenon are discussed and compared with previous studies of membrane-associated water phases and the impact of membrane-protective cryoprotectants.

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A software framework for analysing solid-state MAS NMR data

Cited by 141 publications

References 46 publications

β-Helical architecture of cytoskeletal bactofilin filaments revealed by solid-state NMR

β-Helical architecture of cytoskeletal bactofilin filaments revealed by solid-state NMR

Protein resonance assignment at MAS frequencies approaching 100 kHz: a quantitative comparison of J-coupling and dipolar-coupling-based transfer methods

MAS 1 H NMR Probes Freezing Point Depression of Water and Liquid-Gel Phase Transitions in Liposomes

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