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 [NMR paper] NMR resonance assignments for a ProQ homolog from Legionella pneumophila. |
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Jun 25, 2018 - 5:58 AM - by nmrlearner
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NMR resonance assignments for a ProQ homolog from Legionella pneumophila.
 Related Articles NMR resonance assignments for a ProQ homolog from Legionella pneumophila.
Biomol NMR Assign. 2018 Jun 22;:
Authors: Immer C, Hacker C, Wöhnert J
Abstract
Regulation of gene expression on a post-transcriptional level by small non-coding regulatory RNAs (sRNAs) is very common in bacteria. sRNAs base pair with sequences in their target messenger RNAs (mRNAs) and thereby regulate translation initiation or mRNA stability. Specialized RNA-binding proteins (RBPs) facilitate these regulatory sRNA/mRNA interactions by acting as RNA chaperones. A well-known example for such an RNA chaperone which is widespread in bacteria is the Hfq protein. Recently, the ProQ/FinO protein family was identified as a new class of RNA chaperones involved in sRNA based regulation. Only a few members of this protein family have been structurally characterized so far. In particular, the structural basis for RNA-binding and recognition has not yet been established for this class of proteins. Here, we report the 1H, 13C and 15N NMR resonance assignments for a ProQ homolog (Lpp 1663) from the... [Read More]
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0 Replies | 1 Views
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[NMR paper] Perspective: next generation isotope-aided methods for protein NMR spectroscopy. |
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Jun 25, 2018 - 5:58 AM - by nmrlearner
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Perspective: next generation isotope-aided methods for protein NMR spectroscopy.
Related Articles Perspective: next generation isotope-aided methods for protein NMR spectroscopy.
J Biomol NMR. 2018 Jun 22;:
Authors: Kainosho M, Miyanoiri Y, Terauchi T, Takeda M
Abstract
In this perspective, we describe our efforts to innovate the current isotope-aided NMR methodology to investigate biologically important large proteins and protein complexes, for which only limited structural information could be obtained by conventional NMR approaches. At the present time, it is widely believed that only backbone amide and methyl signals are amenable for investigating such difficult targets. Therefore, our primary mission is to disseminate our novel knowledge within the biological NMR community; specifically, that any type of NMR signals other than methyl and amide groups can be obtained, even for quite large proteins, by optimizing the transverse relaxation properties by isotope labeling methods. The idea of "TROSY by isotope labeling" has been cultivated through our endeavors aiming to improve the original stereo-array isotope labeling (SAIL) method (Kainosho et al.,... [Read More]
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0 Replies | 1 Views
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[NMR paper] Collagen Structure-Function Relationships from Solid-State NMR Spectroscopy. |
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Jun 23, 2018 - 2:31 PM - by nmrlearner
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Collagen Structure-Function Relationships from Solid-State NMR Spectroscopy.
Related Articles Collagen Structure-Function Relationships from Solid-State NMR Spectroscopy.
Acc Chem Res. 2018 Jun 22;:
Authors: Goldberga I, Li R, Duer MJ
Abstract
The extracellular matrix of a tissue is as important to life as the cells within it. Its detailed molecular structure defines the environment of a tissue's cells and thus their properties, including differentiation and metabolic status. Collagen proteins are the major component of extracellular matrices. Self-assembled collagen fibrils provide both specific mechanical properties to handle external stresses on tissues and, at the molecular level, well-defined protein binding sites to interact with cells. How the cell-matrix interactions are maintained against the stresses on the tissue is an important and as yet unanswered question. Similarly, how collagen molecular and fibrillar structures change in aging and disease is a crucial open question. Solid-state NMR spectroscopy offers insight into collagen molecular conformation in intact in vivo and in vitro tissues, and in this Account we review how NMR spectroscopy is beginning to provide answers to these questions. In vivo 13C,15N labeling of the extracellular matrix has given insight into collagen molecular dynamics and generated multidimensional NMR "fingerprints" of collagen molecular structure that... [Read More]
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0 Replies | 21 Views
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Perspective: next generation isotope-aided methods for protein NMR spectroscopy |
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Jun 23, 2018 - 12:47 AM - by nmrlearner
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Perspective: next generation isotope-aided methods for protein NMR spectroscopy
Abstract
In this perspective, we describe our efforts to innovate the current isotope-aided NMR methodology to investigate biologically important large proteins and protein complexes, for which only limited structural information could be obtained by conventional NMR approaches. At the present time, it is widely believed that only backbone amide and methyl signals are amenable for investigating such difficult targets. Therefore, our primary mission is to disseminate our novel knowledge within the biological NMR community; specifically, that any type of NMR signals other than methyl and amide groups can be obtained, even for quite large proteins, by optimizing the transverse relaxation properties by isotope labeling methods. The idea of â??TROSY by isotope labelingâ?? has been cultivated through our endeavors aiming to improve the original stereo-array isotope labeling (SAIL) method (Kainosho et al., Nature 440:52â??57, 2006). The SAIL TROSY methods subsequently culminated in the successful observations of individual NMR signals for the side-chain aliphatic and aromatic 13CH groups in large proteins, as exemplified by the 82Â*kDa single domain protein, malate synthase G. Meanwhile, the expected role of NMR spectroscopy in the emerging integrative structural biology has been rapidly shifting, from structure determination to the acquisition of biologically relevant structural dynamics, which are poorly accessible by X-ray crystallography or cryo-electron microscopy. Therefore, the newly accessible NMR probes, in addition to the methyl and amide signals, will open up a new horizon for investigating difficult protein targets, such as membrane proteins and... [Read More]
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0 Replies | 29 Views
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Electron spin resonance studies on deuterated nitroxyl spin probes used in Overhauser-enhanced magnetic resonance imaging #DNPNMR #ODNP |
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Jun 23, 2018 - 12:47 AM - by nmrlearner
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From The DNP-NMR Blog:
Electron spin resonance studies on deuterated nitroxyl spin probes used in Overhauser-enhanced magnetic resonance imaging #DNPNMR #ODNP
Jebaraj, D. David, Hideo Utsumi, and A. Milton Franklin Benial. “Electron Spin Resonance Studies on Deuterated Nitroxyl Spin Probes Used in Overhauser-Enhanced Magnetic Resonance Imaging.” Magnetic Resonance in Chemistry 55, no. 8 (2017): 700–705.
https://doi.org/10.1002/mrc.4576.
The electron spin resonance studies were carried out for 2 mm concentration of 14N-labeled and 15N-labeled 3-carbamoyl-2,2,5,5-tetramethyl-pyrrolidine-1-oxyl, 3-carboxy-2,2,5,5-tetramethyl-pyrrolidine-1-oxyl, 3-methoxycarbonyl-2,2,5,5-tetramethyl-pyrrolidine-1-oxyl and their deuterated nitroxyl radicals using X-band electron spin resonance spectrometer. The electron spin resonance line shape analysis was carried out. The electron spin resonance parameters such as linewidth, Lorentzian component, signal intensity ratio, rotational correlation time, hyperfine coupling constant and g-factor were estimated. The deuterated nitroxyl radicals have narrow linewidth and an increase in Lorentzian component, compared with undeuterated nitroxyl radicals. The dynamic nuclear polarization factor was observed for all nitroxyl radicals. Upon 2H labeling, about 70% and 40% increase in dynamic nuclear polarization factor were observed for 14N-labeled and 15N-labeled nitroxyl radicals, respectively. The signal intensity ratio and g-value indicate the isotropic nature of the nitroxyl radicals in pure water. Therefore, the deuterated nitroxyl radicals are suitable spin probes for... [Read More]
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0 Replies | 27 Views
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[NMR paper] Site-Specific Isotope-Labeling of Inosine Phosphoramidites and NMR Analysis of an Inosine-Containing RNA Duplex. |
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Jun 22, 2018 - 10:54 AM - by nmrlearner
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Site-Specific Isotope-Labeling of Inosine Phosphoramidites and NMR Analysis of an Inosine-Containing RNA Duplex.
Related Articles Site-Specific Isotope-Labeling of Inosine Phosphoramidites and NMR Analysis of an Inosine-Containing RNA Duplex.
Chemistry. 2016 Oct 17;22(43):15350-15359
Authors: Dallmann A, Beribisky AV, Gnerlich F, Rübbelke M, Schiesser S, Carell T, Sattler M
Abstract
Structural features and internal dynamics of inosine-containing RNAs are poorly understood. NMR studies of such RNAs require 13 C,15 N-labeling, which cannot be achieved using in vitro transcription as inosine and guanosine are not distinguished by RNA polymerase. Herein, we report the synthesis of an inosine phosphoramidite with selective 13 C8 and 15 N7-isotope incorporation in the base and uniform 13 C-labeling of the ribose. Chemical synthesis of an RNA duplex containing four consecutive IU base pairs with this optimized isotope-labeling scheme greatly simplifies NMR spectra and resolves signal overlap. The absence of detectable NMR signals of imino protons and unusual inter-residue NOE correlations in this RNA indicate deviations from standard A-form geometry, consistent with reduced stability of this duplex seen in UV melting studies compared to its nonedited RNA counterparts. These studies indicate that the introduction of IU base pairs distorts and destabilizes RNA helices significantly compared to... [Read More]
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0 Replies | 31 Views
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[U. of Ottawa NMR Facility Blog] Glycine as a 13C CPMAS Setup Sample |
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Jun 21, 2018 - 10:11 PM - by nmrlearner
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Glycine as a 13C CPMAS Setup Sample
Glycine is an excellent setup compound for 13C CPMAS NMR measurements. Its utility in this regard has been described in detail.1,2 It can easily be observed in one scan and has reasonably short 1H T1's, allowing it to be used for 1H 90° pulse calibration and to setup the Hartmann Hahn matching condition. The width of the methylene carbon signal can be conveniently used to evaluate the proton decoupling efficiency. The width and shape of the carbonyl signal are very sensitive to the angle at which the sample is spun and can be used to set the magic angle with a reasonably high degree of precision. In addition the carbonyl resonance is sharp and can be used as a secondary standard for chemical shift calibration. If used as a secondary chemical shift standard, one must be aware that glycine has three ... [Read More]
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0 Replies | 20 Views
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[NMR paper] Monitoring 15N Chemical Shifts During Protein Folding by Pressure-Jump NMR. |
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Jun 21, 2018 - 10:11 PM - by nmrlearner
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Monitoring 15N Chemical Shifts During Protein Folding by Pressure-Jump NMR.
 Related Articles Monitoring 15N Chemical Shifts During Protein Folding by Pressure-Jump NMR.
J Am Chem Soc. 2018 Jun 20;:
Authors: Charlier C, Courtney JM, Alderson TR, Anfinrud P, Bax A
Abstract
Novel pressure-jump NMR hardware permits direct observation of protein NMR spectra during a cyclically repeated protein folding process. While protein folding transpires, nuclei change their resonance frequencies from those of the fully disordered protein to those of the folded protein. For a two-state folding protein, the change in resonance frequency will occur nearly instantaneously when the protein clears the transition state barrier, and the ensemble average observed by NMR spectroscopy will reflect mono-exponential kinetics. However, protein folding pathways can be more complex and contain meta-stable intermediates. With a pseudo-3D NMR experiment that utilizes stroboscopic observation, we demonstrate that it is possible to measure the ensemble-averaged chemical shifts, including those of... [Read More]
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0 Replies | 25 Views
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