SIMPSON: A general simulation program for solid-state NMR spectroscopy

Bak, Mads; Rasmussen, Jan T.; Nielsen, Niels Chr.

doi:10.1016/j.jmr.2011.09.008

Cited by 1,357 publications

(317 citation statements)

References 43 publications

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“…Spectrometer settings, as well as acquisition and processing parameters specific for each 2D and 3D spectrum, are discussed in Supporting Information and summarized in Tables S4 and S5. Simulations of the isotropic 13 C-13 C mixing were performed using the software package SIMPSON (70) and are reported in Fig. S5.…”

Section: Methodsmentioning

confidence: 99%

Structure of fully protonated proteins by proton-detected magic-angle spinning NMR

Andreas

Jaudzems

Staněk

et al. 2016

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

230

288

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Protein structure determination by proton-detected magic-angle spinning (MAS) NMR has focused on highly deuterated samples, in which only a small number of protons are introduced and observation of signals from side chains is extremely limited. Here, we show in two fully protonated proteins that, at 100-kHz MAS and above, spectral resolution is high enough to detect resolved correlations from amide and side-chain protons of all residue types, and to reliably measure a dense network of 1 H-1 H proximities that define a protein structure. The high data quality allowed the correct identification of internuclear distance restraints encoded in 3D spectra with automated data analysis, resulting in accurate, unbiased, and fast structure determination. Additionally, we find that narrower proton resonance lines, longer coherence lifetimes, and improved magnetization transfer offset the reduced sample size at 100-kHz spinning and above. Less than 2 weeks of experiment time and a single 0.5-mg sample was sufficient for the acquisition of all data necessary for backbone and side-chain resonance assignment and unsupervised structure determination. We expect the technique to pave the way for atomic-resolution structure analysis applicable to a wide range of proteins.NMR spectroscopy | magic-angle spinning | protein structures | proton detection | viral nucleocapsids D espite tremendous progress in the analysis of biomolecular samples over the last two decades (1-7), routine application of magic-angle spinning (MAS) NMR in biology is still limited by the inherently low sensitivity. The direct detection of proton resonances is a straightforward way to counter this problem, but entails a trade-off with resolution due to the strong homonuclear dipolar interactions among proton nuclei. High-resolution proton-detected methods were first demonstrated with modest spinning frequencies by today's standards (∼10 kHz) and relied on a reduction of 1 H-1 H couplings by high levels of dilution with deuterium, typically perdeuteration, and complete (8, 9) or partial (10-12) protonation at exchangeable sites. The need for narrow proton resonances without such extreme levels of deuteration has motivated a continuous technological development, resulting in a dramatic increase in the available spinning frequency (13)(14)(15)(16)(17)(18)(19)(20).At MAS frequencies of 40-60 kHz, deuteration and 100% reprotonation at exchangeable sites, primarily amide protons, result in resolved and sensitive spectra, similar in quality to the case of higher dilution levels and lower spinning frequencies (21-23). This opens the way to rapid sequential assignment of backbone resonances (24-27), as well as to the unambiguous measurement of detailed structural and dynamical parameters (28-32). A further increase in the MAS frequency to 100 kHz allows resonance assignment (20), a structure determination of a model protein (16), and interaction studies (15) with as little as 0.5 mg of sample. However, a high deuteration level severely limits observation of side-chain s...

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Section: Methodsmentioning

confidence: 99%

Structure of fully protonated proteins by proton-detected magic-angle spinning NMR

Andreas

Jaudzems

Staněk

et al. 2016

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

230

288

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“…For magic angle spinning spectroscopy, the spinning frequency was set to 10 kHz, and the temperature for all NMR measurements was controlled with a 270 K cooling N 2 flow (corresponding to the ϳ280 K sample temperature estimated from the 1 H chemical shift of H 2 O). The REDOR curves were fit to a model 13 C, 31 P two-spin system using a SIMPSON simulation package and the best fit internuclear distances were reported (39).…”

Section: Methodsmentioning

confidence: 99%

Distinct Membrane Disruption Pathways Are Induced by 40-Residue β-Amyloid Peptides

Delgado

Doherty

Cheng

et al. 2016

Journal of Biological Chemistry

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Cellular membrane disruption induced by ␤-amyloid (A␤) peptides has been considered one of the major pathological mechanisms for Alzheimer disease. Mechanistic studies of the membrane disruption process at a high-resolution level, on the other hand, are hindered by the co-existence of multiple possible pathways, even in simplified model systems such as the phospholipid liposome. Therefore, separation of these pathways is crucial to achieve an in-depth understanding of the A␤-induced membrane disruption process. This study, which utilized a combination of multiple biophysical techniques, shows that the peptide-to-lipid (P:L) molar ratio is an important factor that regulates the selection of dominant membrane disruption pathways in the presence of 40-residue A␤ peptides in liposomes. Three distinct pathways (fibrillation with membrane content leakage, vesicle fusion, and lipid uptake through a temporarily stable ionic channel) become dominant in model liposome systems under specific conditions. These individual systems are characterized by both the initial states of A␤ peptides and the P:L molar ratio. Our results demonstrated the possibility to generate simplified A␤-membrane model systems with a homogeneous membrane disruption pathway, which will benefit high-resolution mechanistic studies in the future. Fundamentally, the possibility of pathway selection controlled by P:L suggests that the driving forces for A␤ aggregation and A␤-membrane interactions may be similar at the molecular level.

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“…MAS rates of between 58.6 and 62.5 kHz were selected, so that the The anisotropy and asymmetry parameters for the chemical shift are defined according to ζ = δzz -δiso and η = (δyy -δxx)/ζ, respectively, with the principal components ordered according to |δzz -δiso | ≥ | δxx -δiso | ≥ | δyy -δiso |. Numerical simulations of the recoupled 1 H CSA lineshapes were performed using SIMPSON [20]. Powder averaging was achieved using 615 (α,β) orientations chosen according to the scheme of Zaremba [21] and 40 uniformly distributed values of γ. B1 inhomogeneity was included by summing 17 simulations carried out using rf amplitudes weighted according to the experimentally determined B1 distribution.…”

Section: Methodsmentioning

confidence: 99%

Measuring proton shift tensors with ultrafast MAS NMR

Miah

Bennett

Iuga

et al. 2013

Journal of Magnetic Resonance

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A new proton anisotropic-isotropic shift correlation experiment is described which operates with ultrafast MAS, resulting in good resolution of isotropic proton shifts in the detection dimension. The new experiment makes use of a recoupling sequence designed using symmetry principles which reintroduces the proton chemical shift anisotropy in the indirect dimension. The experiment has been used to measure the proton shift tensor parameters for the OH hydrogen-bonded protons in tyrosine.HCl and citric acid at Larmor frequencies of up to 850 MHz.

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SIMPSON: A general simulation program for solid-state NMR spectroscopy

Cited by 1,357 publications

References 43 publications

Structure of fully protonated proteins by proton-detected magic-angle spinning NMR

Structure of fully protonated proteins by proton-detected magic-angle spinning NMR

Distinct Membrane Disruption Pathways Are Induced by 40-Residue β-Amyloid Peptides

Measuring proton shift tensors with ultrafast MAS NMR

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