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Correction to: NMR structure of the HIV-1 reverse transcriptase thumb subdomain
Dec 12, 2017 - 2:13 PM - by nmrlearner
nmrlearner's Avatar Correction to: NMR structure of the HIV-1 reverse transcriptase thumb subdomain

Abstract

In the original publication of the article, the given name and family name of the author P. Andrew Karplus was published incorrectly. The name should read as "P. Andrew" ?? Given name and "Karplus" ?? Family name.



Source: Journal of Biomolecular NMR
0 Replies | 20 Views
[U. of Ottawa NMR Facility Blog] NMR of Cranberries. Why Are They So Sour?
Dec 12, 2017 - 2:12 AM - by nmrlearner
nmrlearner's Avatar NMR of Cranberries. Why Are They So Sour?

Arguably, one of the highlights of the Christmas season is a delicious turkey dinner. The most common condiment for the turkey is a tart, mouth watering cranberry sauce. Have you ever wondered why cranberries are so sour? The sour taste comes from organic acids. These can easily be detected in the 1H and 13C NMR spectra of cranberries. The figure below shows the 1H and 13C NMR spectra of a D2O extract of crushed fresh cranberries.
Malic acid, citric acid, quinic acid and benzoic acid can easily be identified in the spectra. These account for the sour taste. Glucose, fructose and sucrose can also be identified however, the taste is dominated by the acids. There are of course many other compounds present in cranberries at much lower concentrations than the acids and sugars. Many of these account for the brilliant red color and antioxidant properties of this delicious healthy berry. Enjoy your Christmas turkey accompanied by tasty, tart, cranberries! ... [Read More]
0 Replies | 12 Views
[NMR paper] A bioresistant nitroxide spin label for in-cell EPR spectroscopy: in vitro and in oocytes protein structural dynamics studies.
Dec 12, 2017 - 2:12 AM - by nmrlearner
nmrlearner's Avatar A bioresistant nitroxide spin label for in-cell EPR spectroscopy: in vitro and in oocytes protein structural dynamics studies.


Approaching proteins structural dynamics and protein-protein interactions in the cellular environment is a fundamental challenge. Due to its absolute sensitivity and to its selectivity to paramagnetic species, Site-Directed Spin Labeling (SDSL) combined with Electron Paramagnetic Resonance (EPR) has the potential to evolve into an efficient method to follow conformational changes in proteins directly inside cells. Until now, the use of nitroxyde-based spin labels for in-cell studies has represented a major hurdle because of their short persistence in the cellular context. In this work we present the design and synthesis of the first maleimido-proxyl-based spin label (M-TETPO) resistant towards reduction and being efficient to probe protein dynamics by continuous wave and pulsed EPR. In particular, the extended lifetime of M-TETPO enabled the study of structural features of a chaperone in the absence and presence of its binding partner at endogenous concentration directly inside cells.

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0 Replies | 40 Views
Real-Time Analysis of Folding upon Binding of a Disordered Protein by Using Dissolution DNP NMR Spectroscopy #DNPNMR
Dec 12, 2017 - 2:12 AM - by nmrlearner
nmrlearner's Avatar From The DNP-NMR Blog:

Real-Time Analysis of Folding upon Binding of a Disordered Protein by Using Dissolution DNP NMR Spectroscopy #DNPNMR

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Ragavan, M., et al., Real-Time Analysis of Folding upon Binding of a Disordered Protein by Using Dissolution DNP NMR Spectroscopy. Angew Chem Int Ed Engl, 2017. 56(25): p. 7070-7073.


https://www.ncbi.nlm.nih.gov/pubmed/28508552


The kinase inhibitory domain of the cell cycle regulatory protein p27(Kip1) (p27) was nuclear spin hyperpolarized using dissolution dynamic nuclear polarization (D-DNP). While intrinsically disordered in isolation, p27 adopts secondary structural motifs, including an alpha-helical structure, upon binding to cyclin-dependent kinase 2 (Cdk2)/cyclin A. The sensitivity gains obtained with hyperpolarization enable the real-time observation of (13) C NMR signals during p27 folding upon binding to Cdk2/cyclin A on a time scale of several seconds. Time-dependent intensity changes are dependent on the extent of folding and binding, as manifested in differential spin relaxation. The analysis of signal decay rates suggests the existence of a partially folded p27 intermediate during the timescale of the D-DNP NMR experiment.
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[NMR paper] Stable and rigid DTPA-like paramagnetic tags suitable for in vitro and in situ protein NMR analysis.
Dec 11, 2017 - 12:45 PM - by nmrlearner
nmrlearner's Avatar Stable and rigid DTPA-like paramagnetic tags suitable for in vitro and in situ protein NMR analysis.

Stable and rigid DTPA-like paramagnetic tags suitable for in vitro and in situ protein NMR analysis.

J Biomol NMR. 2017 Dec 09;:

Authors: Chen JL, Zhao Y, Gong YJ, Pan BB, Wang X, Su XC

Abstract
Organic synthesis of a ligand with high binding affinities for paramagnetic lanthanide ions is an effective way of generating paramagnetic effects on proteins. These paramagnetic effects manifested in high-resolution NMR spectroscopy are valuable dynamic and structural restraints of proteins and protein-ligand complexes. A paramagnetic tag generally contains a metal chelating moiety and a reactive group for protein modification. Herein we report two new DTPA-like tags, 4PS-PyDTTA and 4PS-6M-PyDTTA that can be site-specifically attached to a protein with a stable thioether bond. Both protein-tag adducts form stable lanthanide complexes, of which the binding affinities and paramagnetic tensors are tunable with respect to the 6-methyl group in pyridine. Paramagnetic relaxation enhancement (PRE) effects of Gd(III) complex on protein-tag adducts were evaluated in comparison with pseudocontact shift (PCS), and the results indicated that both 4PS-PyDTTA and 4PS-6M-PyDTTA tags are rigid and present high-quality PREs that are crucially important in elucidation of the dynamics and interactions of proteins and protein-ligand complexes. We also show that these two tags are suitable for in-situ protein NMR analysis.


PMID: 29224182 [PubMed - as supplied by publisher]



... [Read More]
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[NMR paper] Progress in proton-detected solid-state NMR (SSNMR): Super-fast 2D SSNMR collection for nano-mole-scale proteins.
Dec 11, 2017 - 12:45 PM - by nmrlearner
nmrlearner's Avatar Progress in proton-detected solid-state NMR (SSNMR): Super-fast 2D SSNMR collection for nano-mole-scale proteins.

Progress in proton-detected solid-state NMR (SSNMR): Super-fast 2D SSNMR collection for nano-mole-scale proteins.

J Magn Reson. 2017 Nov 28;286:99-109

Authors: Ishii Y, Wickramasinghe A, Matsuda I, Endo Y, Ishii Y, Nishiyama Y, Nemoto T, Kamihara T

Abstract
Proton-detected solid-state NMR (SSNMR) spectroscopy has attracted much attention due to its excellent sensitivity and effectiveness in the analysis of trace amounts of amyloid proteins and other important biological systems. In this perspective article, we present the recent sensitivity limit of 1H-detected SSNMR using "ultra-fast" magic-angle spinning (MAS) at a spinning rate (?R) of 80-100 kHz. It was demonstrated that the high sensitivity of 1H-detected SSNMR at ?R of 100 kHz and fast recycling using the paramagnetic-assisted condensed data collection (PACC) approach permitted "super-fast" collection of 1H-detected 2D protein SSNMR. A 1H-detected 2D 1H-15N correlation SSNMR spectrum for ~27 nmol of a uniformly 13C- and 15N-labeled GB1 protein sample in microcrystalline form was acquired in only 9 s with 50% non-uniform sampling and short recycle delays of 100 ms. Additional data suggests that it is now feasible to detect as little as 1 nmol of the protein in 5.9 h by 1H-detected 2D 1H-15N SSNMR at a nominal signal-to-noise ratio of five. The demonstrated sensitivity is comparable to that of modern solution protein NMR. Moreover, this article summarizes the influence of ultra-fast MAS and 1H-detection on the spectral resolution and sensitivity of protein SSNMR. Recent... [Read More]
0 Replies | 24 Views
[NMR paper] New insights into the influence of Monofluorination on Dimyristoylphosphatidylcholine membrane properties: A solid-state NMR study.
Dec 11, 2017 - 12:45 PM - by nmrlearner
nmrlearner's Avatar New insights into the influence of Monofluorination on Dimyristoylphosphatidylcholine membrane properties: A solid-state NMR study.

New insights into the influence of Monofluorination on Dimyristoylphosphatidylcholine membrane properties: A solid-state NMR study.

Biochim Biophys Acta. 2017 Dec 06;:

Authors: Gagnon MC, Strandberg E, Ulrich AS, Paquin JF, Auger M

Abstract
Solid-state 19F NMR spectroscopy is a method of choice to study the interactions between lipid membranes and other molecules such as peptides, proteins or drugs. Numerous fluorine-labeled NMR probes have been developed over the last few years, especially fluorine-labeled peptides. In order to develop a new kind of NMR reporter molecule and a complementary approach to fluorine-labeling of peptides, we synthesized six monofluorinated derivatives of the lipid dimyristoylphosphatidylcholine (F-DMPC), with the fluorine atom located along the acyl chain linked to the central glycerol position. To better understand the behavior of these fluorine-labeled lipids, we report here the investigation of F-DMPC membrane properties using solid-state 2H-, 15N-, 19F and 31P NMR spectroscopy. This study was carried out on pure F-DMPC bilayers as well as F-DMPC/DMPC mixtures at various ratios. Slight perturbations were observed for pure F-DMPC multilamellar vesicles (MLVs), most noticeable for lipids with the fluorine atom located at the extremities of the acyl chain. On the other hand, no significant perturbations were observed for F-DMPC/DMPC MLVs containing up to 25% F-DMPC, nor for any fluorine-labeled bilayers that were prepared as macroscopically oriented samples. To test the interaction... [Read More]
0 Replies | 29 Views
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