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Journal Highlight: Molecular dynamics and composition of crude oil by low-field nuclear magnetic resonance
Aug 29, 2016 - 12:50 PM - by nmrlearner
nmrlearner's Avatar Journal Highlight: Molecular dynamics and composition of crude oil by low-field nuclear magnetic resonance

Low-field NMR relaxation measurements have been used to reveal the composition of crude oil, offering a low-cost method that can be used under poor working conditions in the field and in the wellbore.

Read the rest at Spectroscopynow.com
0 Replies | 5 Views
[NMR paper] Comprehensive structural and dynamical view of an unfolded protein from the combination of single-molecule FRET, NMR, and SAXS.
Aug 28, 2016 - 11:03 AM - by nmrlearner
nmrlearner's Avatar Comprehensive structural and dynamical view of an unfolded protein from the combination of single-molecule FRET, NMR, and SAXS.

Comprehensive structural and dynamical view of an unfolded protein from the combination of single-molecule FRET, NMR, and SAXS.

Proc Natl Acad Sci U S A. 2016 Aug 26;

Authors: Aznauryan M, Delgado L, Soranno A, Nettels D, Huang JR, Labhardt AM, Grzesiek S, Schuler B

Abstract
The properties of unfolded proteins are essential both for the mechanisms of protein folding and for the function of the large group of intrinsically disordered proteins. However, the detailed structural and dynamical characterization of these highly dynamic and conformationally heterogeneous ensembles has remained challenging. Here we combine and compare three of the leading techniques for the investigation of unfolded proteins, NMR spectroscopy (NMR), small-angle X-ray scattering (SAXS), and single-molecule Förster resonance energy transfer (FRET), with the goal of quantitatively testing their consistency and complementarity and for obtaining a comprehensive view of the unfolded-state ensemble. Using unfolded ubiquitin as a test case, we find that its average dimensions derived from FRET and from structural ensembles calculated using the program X-PLOR-NIH based on NMR and SAXS restraints agree remarkably well; even the shapes of the underlying intramolecular distance distributions are in good agreement, attesting to the reliability of the approaches. The NMR-based results provide a highly sensitive way of quantifying residual structure in the unfolded state. FRET-based nanosecond fluorescence correlation spectroscopy allows long-range distances... [Read More]
0 Replies | 49 Views
[NMR paper] (13)C-NMR studies on disulfide bond isomerization in bovine pancreatic trypsin inhibitor (BPTI).
Aug 28, 2016 - 11:03 AM - by nmrlearner
nmrlearner's Avatar (13)C-NMR studies on disulfide bond isomerization in bovine pancreatic trypsin inhibitor (BPTI).

(13)C-NMR studies on disulfide bond isomerization in bovine pancreatic trypsin inhibitor (BPTI).

J Biomol NMR. 2016 Aug 26;

Authors: Takeda M, Miyanoiri Y, Terauchi T, Kainosho M

Abstract
Conformational isomerization of disulfide bonds is associated with the dynamics and thus the functional aspects of proteins. However, our understanding of the isomerization is limited by experimental difficulties in probing it. We explored the disulfide conformational isomerization of the Cys14-Cys38 disulfide bond in bovine pancreatic trypsin inhibitor (BPTI), by performing an NMR line-shape analysis of its Cys carbon peaks. In this approach, 1D (13)C spectra were recorded at small temperature intervals for BPTI samples selectively labeled with site-specifically (13)C-enriched Cys, and the recorded peaks were displayed in the order of the temperature after the spectral scales were normalized to a carbon peak. Over the profile of the line-shape, exchange broadening that altered with temperature was manifested for the carbon peaks of Cys14 and Cys38. The Cys14-Cys38 disulfide bond reportedly exists in equilibrium between a high-populated (M) and two low-populated states (m c14 and m c38). Consistent with the three-site exchange model, biphasic exchange broadening arising from the two processes was observed for the peak of the Cys14 ?-carbon. As the exchange broadening is maximized when the exchange rate equals the chemical shift difference in Hz between equilibrating sites, semi-quantitative information that was useful for establishing conditions for (13)C... [Read More]
0 Replies | 31 Views
13 C-NMR studies on disulfide bond isomerization in bovine pancreatic trypsin inhibitor (BPTI)
Aug 26, 2016 - 6:56 PM - by nmrlearner
nmrlearner's Avatar 13 C-NMR studies on disulfide bond isomerization in bovine pancreatic trypsin inhibitor (BPTI)

Abstract

Conformational isomerization of disulfide bonds is associated with the dynamics and thus the functional aspects of proteins. However, our understanding of the isomerization is limited by experimental difficulties in probing it. We explored the disulfide conformational isomerization of the Cys14â??Cys38 disulfide bond in bovine pancreatic trypsin inhibitor (BPTI), by performing an NMR line-shape analysis of its Cys carbon peaks. In this approach, 1D 13C spectra were recorded at small temperature intervals for BPTI samples selectively labeled with site-specifically 13C-enriched Cys, and the recorded peaks were displayed in the order of the temperature after the spectral scales were normalized to a carbon peak. Over the profile of the line-shape, exchange broadening that altered with temperature was manifested for the carbon peaks of Cys14 and Cys38. The Cys14â??Cys38 disulfide bond reportedly exists in equilibrium between a high-populated (M) and two low-populated states (m c14 and m c38). Consistent with the three-site exchange model, biphasic exchange broadening arising from the two processes was observed for the peak of the Cys14 α-carbon. As the exchange broadening is maximized when the exchange rate equals the chemical shift difference in Hz between equilibrating sites, semi-quantitative information that was useful for establishing conditions for 13C relaxation dispersion experiments was obtained through the carbon line-shape profile. With respect to the m c38 isomerization, the 1H-13C signals at... [Read More]
0 Replies | 36 Views
On The Potential of Dynamic Nuclear Polarization Enhanced Diamonds in Solid-State and Dissolution 13 C NMR Spectroscopy #DNPNMR
Aug 26, 2016 - 6:56 PM - by nmrlearner
nmrlearner's Avatar From The DNP-NMR Blog:

On The Potential of Dynamic Nuclear Polarization Enhanced Diamonds in Solid-State and Dissolution 13 C NMR Spectroscopy #DNPNMR


Bretschneider, C.O., et al., On The Potential of Dynamic Nuclear Polarization Enhanced Diamonds in Solid-State and Dissolution 13 C NMR Spectroscopy. ChemPhysChem, 2016: p. n/a-n/a.


http://www.ncbi.nlm.nih.gov/pubmed/27416769


Dynamic nuclear polarization (DNP) is a versatile option to improve the sensitivity of NMR and MRI. This versatility has elicited interest for overcoming potential limitations of these techniques, including the achievement of solid-state polarization enhancement at ambient conditions, and the maximization of 13 C signal lifetimes for performing in vivo MRI scans. This study explores whether diamond's 13 C behavior in nano- and micro-particles could be used to achieve these ends. The characteristics of diamond's DNP enhancement were analyzed for different magnetic fields, grain sizes, and sample environments ranging from cryogenic to ambient temperatures, in both solution and solid-state experiments. It was found that 13 C NMR signals could be boosted by orders of magnitude in either low- or room-temperature solid-state DNP experiments by utilizing naturally occurring paramagnetic P1 substitutional nitrogen defects. We attribute this behavior to the unusually long electronic/nuclear spin-lattice relaxation times characteristic of diamond, coupled with a time-independent cross-effect-like polarization transfer mechanism... [Read More]
0 Replies | 45 Views
[NMR paper] The C-terminal domain of human Cdc37 studied by solution NMR.
Aug 25, 2016 - 6:10 PM - by nmrlearner
nmrlearner's Avatar The C-terminal domain of human Cdc37 studied by solution NMR.

Related Articles The C-terminal domain of human Cdc37 studied by solution NMR.

J Biomol NMR. 2015 Nov;63(3):315-21

Authors: Zhang Z, Keramisanou D, Dudhat A, Paré M, Gelis I

PMID: 26400850 [PubMed - indexed for MEDLINE]



More...
0 Replies | 32 Views
[NMR paper] Molecular dynamics simulations on PGLa using NMR orientational constraints.
Aug 25, 2016 - 6:10 PM - by nmrlearner
nmrlearner's Avatar Molecular dynamics simulations on PGLa using NMR orientational constraints.

Related Articles Molecular dynamics simulations on PGLa using NMR orientational constraints.

J Biomol NMR. 2015 Nov;63(3):265-74

Authors: Sternberg U, Witter R

Abstract
NMR data obtained by solid state NMR from anisotropic samples are used as orientational constraints in molecular dynamics simulations for determining the structure and dynamics of the PGLa peptide within a membrane environment. For the simulation the recently developed molecular dynamics with orientational constraints technique (MDOC) is used. This method introduces orientation dependent pseudo-forces into the COSMOS-NMR force field. Acting during a molecular dynamics simulation these forces drive molecular rotations, re-orientations and folding in such a way that the motional time-averages of the tensorial NMR properties are consistent with the experimentally measured NMR parameters. This MDOC strategy does not depend on the initial choice of atomic coordinates, and is in principle suitable for any flexible... [Read More]
0 Replies | 42 Views
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