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Solid-state NMR spectroscopic trends for supramolecular assemblies and protein aggregates
Aug 25, 2017 - 4:11 AM - by nmrlearner
nmrlearner's Avatar Solid-state NMR spectroscopic trends for supramolecular assemblies and protein aggregates

Publication date: Available online 24 August 2017
Source:Solid State Nuclear Magnetic Resonance

Author(s): Rasmus Linser

Solid-state NMR is able to generate structural data on sample preparations that are explicitly non-crystalline. In particular, for amyloid fibril samples, which can comprise significant degrees of sample disorder, solid-state NMR has been used very successfully. But also solid-state NMR studies of other supramolecular assemblies that have resisted assessment by more standard methods are being performed with increasing ease and biological impact, many of which are briefly reviewed here. New technical trends with respect to structure calculation, protein dynamics and smaller sample amounts have reshaped the field of solid-state NMR recently. In particular, proton-detected approaches based on fast Magic-Angle Spinning (MAS) were demonstrated for crystalline systems initially. Currently, such approaches are being expanded to the above-mentioned non-crystalline targets, the characterization of which can now be pursued with sample amounts on the order of a milligram. In this Trends article, I am giving a brief overview about achievements of the last years as well as the directions that the field has been heading into and delineate some satisfactory perspectives for solid-state NMR's future striving.
Graphical abstract

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[NMR paper] Analytical description of NMR relaxation highlights correlated dynamics in intrinsically disordered proteins.
Aug 25, 2017 - 4:11 AM - by nmrlearner
nmrlearner's Avatar Analytical description of NMR relaxation highlights correlated dynamics in intrinsically disordered proteins.

Related Articles Analytical description of NMR relaxation highlights correlated dynamics in intrinsically disordered proteins.

Angew Chem Int Ed Engl. 2017 Aug 22;:

Authors: Blackledge M, Salvi N, Abyzov A

Abstract
The dynamic fluctuations of intrinsically disordered proteins (IDPs) define their function. Although experimental nuclear magnetic resonance (NMR) relaxation reveals the motional complexity of these highly flexible proteins, the absence of physical models describing IDP dynamics hinders their mechanistic interpretation. Combining molecular dynamics simulation and NMR, we introduce a framework in which distinct motions are attributed to local libration, backbone dihedral angle dynamics and longer-range tumbling of one or more peptide planes. This model provides unique insight into segmental organization of dynamics in IDPs and allows us to investigate the presence and extent of the correlated motions that are essential for function.


PMID: 28834051 [PubMed - as supplied by publisher]



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0 Replies | 30 Views
[NMR paper] Conformational heterogeneity in the Hsp70 chaperone-substrate ensemble: identified from analysis of NMR-detected titration data.
Aug 25, 2017 - 4:11 AM - by nmrlearner
nmrlearner's Avatar Conformational heterogeneity in the Hsp70 chaperone-substrate ensemble: identified from analysis of NMR-detected titration data.

Related Articles Conformational heterogeneity in the Hsp70 chaperone-substrate ensemble: identified from analysis of NMR-detected titration data.

Protein Sci. 2017 Aug 19;:

Authors: Sekhar A, Nagesh J, Rosenzweig R, Kay LE

Abstract
The Hsp70 chaperone system plays a critical role in cellular homeostasis by binding to client protein molecules. We have recently shown by methyl-TROSY NMR methods that the Escherichia coli Hsp70, DnaK, can form multiple bound complexes with a small client protein, hTRF1. In an effort to characterize the interactions further we report here the results of an NMR-based titration study of hTRF1 and DnaK, where both molecular components are monitored simultaneously, leading to a binding model. A central finding is the formation of a previously undetected 3:1 hTRF1-DnaK complex, suggesting that under heat shock conditions, DnaK might be able to protect cytosolic proteins whose net concentrations would exceed that of the chaperone. Moreover, these results provide new insight into the heterogeneous ensemble of complexes formed by DnaK chaperones and further emphasize the unique role of NMR spectroscopy in obtaining information about individual events in a complex binding scheme by exploiting a large number of probes that report uniquely on distinct binding processes. This article is protected by copyright. All... [Read More]
0 Replies | 22 Views
[NMR paper] A novel approach based on low-field NMR for the detection of the pathological components of sputum in cystic fibrosis patients.
Aug 25, 2017 - 4:11 AM - by nmrlearner
nmrlearner's Avatar A novel approach based on low-field NMR for the detection of the pathological components of sputum in cystic fibrosis patients.

Related Articles A novel approach based on low-field NMR for the detection of the pathological components of sputum in cystic fibrosis patients.

Magn Reson Med. 2017 Aug 22;:

Authors: Abrami M, Ascenzioni F, Di Domenico EG, Maschio M, Ventura A, Confalonieri M, Di Gioia S, Conese M, Dapas B, Grassi G, Grassi M

Abstract
PURPOSE: Development of a reliable, simple method to monitor lung condition in cystic fibrosis (CF) patients. Lung functionality assessment in CF patients is relevant, as most of them still die of respiratory failure. In lung mucus (sputum) of CF patients, components such as proteins, biopolymers, DNA, bacteria, and mucin are pathologically increased. As lung functionality is related to the amount of the pathological components in the sputum, their determination can help clinicians in monitoring lung condition and planning therapy.
METHODS: Low-field NMR was used to evaluate the variation of the relaxation time (T2m ) of the water hydrogens present in CF sputum in relation to the amounts of the pathological components. Low-field NMR was tested in artificial samples (mucin or alginates), then in conditional sputum (saliva from healthy volunteers, added by different amounts of the pathological components), and finally in 12 patients' sputums, in which T2m was correlated to a commonly used lung monitoring test... [Read More]
0 Replies | 22 Views
[NMR paper] Solution NMR Spectroscopy in Target-Based Drug Discovery.
Aug 25, 2017 - 4:11 AM - by nmrlearner
nmrlearner's Avatar Solution NMR Spectroscopy in Target-Based Drug Discovery.

Related Articles Solution NMR Spectroscopy in Target-Based Drug Discovery.

Molecules. 2017 Aug 23;22(9):

Authors: Li Y, Kang C

Abstract
Solution NMR spectroscopy is a powerful tool to study protein structures and dynamics under physiological conditions. This technique is particularly useful in target-based drug discovery projects as it provides protein-ligand binding information in solution. Accumulated studies have shown that NMR will play more and more important roles in multiple steps of the drug discovery process. In a fragment-based drug discovery process, ligand-observed and protein-observed NMR spectroscopy can be applied to screen fragments with low binding affinities. The screened fragments can be further optimized into drug-like molecules. In combination with other biophysical techniques, NMR will guide structure-based drug discovery. In this review, we describe the possible roles of NMR spectroscopy in drug discovery. We also illustrate the challenges encountered in the drug discovery process. We include several examples demonstrating the roles of NMR in target-based drug discoveries such as hit identification, ranking ligand binding affinities, and mapping the ligand binding site. We also speculate the possible roles of NMR in target engagement based on recent processes in in-cell NMR spectroscopy.


PMID: 28832542 [PubMed - in process]



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0 Replies | 30 Views
[NMR paper] Self-assembled Oligopeptide as a Versatile NMR Alignment Medium for the Measurements of Residual Dipolar Couplings in Methanol
Aug 23, 2017 - 5:25 PM - by nmrlearner
nmrlearner's Avatar Self-assembled Oligopeptide as a Versatile NMR Alignment Medium for the Measurements of Residual Dipolar Couplings in Methanol


Residual dipolar coupling (RDC) constitutes a powerful structural parameter for the determination of constitution, conformation and configuration of organic molecules. Here, we report the first liquid crystalline based orientating medium that is compatible with MeOH, thus enabling RDC acquisitions of a wide range of intermediate to polar organic molecules. The liquid crystals were produced by the self-assembled oligopeptide nanotubes (AAKLVFF), which are stable at very low concentration. The presented alignment medium is highly homogeneous and the size of RDCs can be scaled with the concentration of the peptide. To assess the accuracy of the RDC measurement by employing this newly introduced medium, seven bioactive natural products from different classes were chosen and analyzed. The straightforward preparation of the anisotropic alignment sample will offer a versatile and robust protocol for the routine RDC measurement of natural products.

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0 Replies | 42 Views
Depolarization of nuclear spin polarized 129Xe gas by dark rubidium during spin-exchange optical pumping
Aug 23, 2017 - 5:25 PM - by nmrlearner
nmrlearner's Avatar From The DNP-NMR Blog:

Depolarization of nuclear spin polarized 129Xe gas by dark rubidium during spin-exchange optical pumping

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Antonacci, M.A., et al., Depolarization of nuclear spin polarized 129Xe gas by dark rubidium during spin-exchange optical pumping. J Magn Reson, 2017. 279: p. 60-67.


https://www.ncbi.nlm.nih.gov/pubmed/28475947


Continuous-flow spin-exchange optical pumping (SEOP) continues to serve as the most widespread method of polarizing 129Xe for magnetic resonance experiments. Unfortunately, continuous-flow SEOP still suffers from as-yet unidentified inefficiencies that prevent the production of large volumes of xenon with a nuclear spin polarization close to theoretically calculated values. In this work we use a combination of ultra-low field nuclear magnetic resonance spectroscopy and atomic absorption spectroscopy (AAS) measurements to study the effects of dark Rb vapor on hyperpolarized 129Xe in situ during continuous-flow SEOP. We find that dark Rb vapor in the optical cell outlet has negligible impact on the final 129Xe polarization at typical experimental conditions, but can become significant at higher oven temperatures and lower flow rates. Additionally, in the AAS spectra we also look for a signature of paramagnetic Rb clusters, previously identified as a source of xenon depolarization and a cause for SEOP inefficiency, for which we are able to set an upper limit of 8.3x1015 Rb dimers... [Read More]
0 Replies | 74 Views
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