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[U. of Ottawa NMR Facility Blog] Information-Rich 13C Satellites
Jun 20, 2018 - 8:56 PM - by nmrlearner
nmrlearner's Avatar Information-Rich 13C Satellites

Seemingly simple NMR spectra often contain much more information than one might think. For example, the 1H NMR spectrum of 1,4-dioxane is primarily a singlet from which one obtains only an isotropic 1H chemical shift value. There is however much more information available in the spectrum which is often not recognized or used. The 1H NMR spectrum of a naturally occurring sample of 1,4-dioxane is the weighted sum of the 1H spectra of all possible isotopomers. It is the dominant tetra-12C isotopomer that gives rise to the singlet but since 13C (spin I = 1/2) is 1.1% naturally abundant, one expects to observe also the mono-13C isotopomer. The di-, tri- and tetra-13C isotopomers are very rare and can be neglected. The symmetry in the mono-13C isotopomer is lost compared to the tetra-12C isotopomer and one obtains a complex second-order spectrum, part of which can be represented by an AA'BB'X spin system. The spectrum of the AA'BB'X spin system depends on many more parameters than just the isotropic 1H chemical shift. This is illustrated in the figure below.
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[NMR paper] Automated assignment of NMR spectra of macroscopically oriented proteins using simulated annealing.
Jun 20, 2018 - 8:56 PM - by nmrlearner
nmrlearner's Avatar Automated assignment of NMR spectra of macroscopically oriented proteins using simulated annealing.

Related Articles Automated assignment of NMR spectra of macroscopically oriented proteins using simulated annealing.

J Magn Reson. 2018 Jun 16;293:104-114

Authors: Lapin J, Nevzorov AA

Abstract
An automated technique for the sequential assignment of NMR backbone resonances of oriented protein samples has been developed and tested based on 15N-15N homonuclear exchange and spin-exchanged separated local-field spectra. By treating the experimental spectral intensity as a pseudopotential, the Monte-Carlo Simulated Annealing algorithm has been employed to seek lowest-energy assignment solutions over a large sampling space where direct enumeration would be unfeasible. The determined sequential assignments have been scored based on the positions of the crosspeaks resulting from the possible orders for the main peaks. This approach is versatile in terms of the parameters that can be specified to achieve the best-fit result. At a minimum the algorithm requires a continuous segment of the main-peak chemical shifts obtained from a uniformly labeled sample and a spin-exchanged experimental spectrum represented as a 2D matrix array. With selective labeling experiments, groups of chemical shifts corresponding to specific locations in the protein backbone can be fixed, thereby decreasing the sampling space.... [Read More]
0 Replies | 7 Views
[NMR paper] Protein-Protein Interfaces Probed by Methyl-Labeling and Proton-Detected Solid-State NMR Spectroscopy.
Jun 20, 2018 - 8:56 PM - by nmrlearner
nmrlearner's Avatar Protein-Protein Interfaces Probed by Methyl-Labeling and Proton-Detected Solid-State NMR Spectroscopy.

Related Articles Protein-Protein Interfaces Probed by Methyl-Labeling and Proton-Detected Solid-State NMR Spectroscopy.

Chemphyschem. 2018 Jun 19;:

Authors: Zinke M, Fricke P, Lange S, Zinn-Justin S, Lange A

Abstract
Proton detection and fast magic-angle spinning have advanced biological solid-state NMR, allowing for the backbone assignment of complex protein assemblies with high sensitivity and resolution. However, so far no method has been proposed to detect intermolecular interfaces in these assemblies by proton detection. Here, we introduce a concept based on methyl-labeling that allows for the assignment of these moieties and for the study of protein-protein interfaces at atomic resolution.


PMID: 29917302 [PubMed - as supplied by publisher]



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[NMR paper] Binding of a small molecule water channel inhibitor to aquaporin Z examined by solid-state MAS NMR.
Jun 20, 2018 - 8:56 PM - by nmrlearner
nmrlearner's Avatar Binding of a small molecule water channel inhibitor to aquaporin Z examined by solid-state MAS NMR.

Related Articles Binding of a small molecule water channel inhibitor to aquaporin Z examined by solid-state MAS NMR.

J Biomol NMR. 2018 Jun 18;:

Authors: Phillips M, To J, Yamazaki T, Nagashima T, Torres J, Pervushin K

Abstract
Aquaporins are integral membrane proteins that facilitate water flow across biological membranes. Their involvement in multiple physiological functions and disease states has prompted intense research to discover water channel activity modulators. However, inhibitors found so far are weak and/or lack specificity. For organic compounds, which lack of*high electron-dense atoms, the identification of binding sites is even more difficult. Nuclear magnetic resonance spectroscopy (NMR) requires large amounts of the protein, and expression and purification of mammalian aquaporins in large quantities is a difficult task. However, since aquaporin Z (AqpZ) can be purified and expressed in good quantities and has a high similarity to human AQP1 (~ 40% identity), it can be used as a model for studying the structure and function of human aquaporins. In the present study, we have used solid-state MAS NMR to investigate the binding of a lead compound [1-(4-methylphenyl)1H-pyrrole-2,5-dione] to AqpZ, through mapping of chemical shift perturbations in the presence of the compound.
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[NMR paper] Average orientation of a fluoroaromatic molecule in lipid bilayers from DFT-informed NMR measurements of 1H-19F dipolar couplings.
Jun 20, 2018 - 8:56 PM - by nmrlearner
nmrlearner's Avatar Average orientation of a fluoroaromatic molecule in lipid bilayers from DFT-informed NMR measurements of 1H-19F dipolar couplings.

Related Articles Average orientation of a fluoroaromatic molecule in lipid bilayers from DFT-informed NMR measurements of 1H-19F dipolar couplings.

Phys Chem Chem Phys. 2018 Jun 19;:

Authors: Hughes E, Griffin JM, Coogan MP, Middleton DA

Abstract
Fluorine is often incorporated into the aromatic moieties of synthetic bioactive molecules such as pharmaceuticals and disease diagnostics in order to alter their physicochemical properties. Fluorine substitution may increase a molecule's lipophilicity, thereby enabling its diffusion across cell membranes to enhance bioavailability or to exert a direct physiological effect from within the lipid bilayer. Understanding the structure, dynamics and orientation of fluoroaromatic molecules in lipid bilayers can provide useful insight into the effect of fluorine on their mode of action, and their interactions with membrane-embedded targets or efflux proteins. Here we demonstrate that NMR measurements of 19F chemical shift anisotropy combined with 1H-19F dipolar coupling measurements together report on the average orientation of a lipophilic fluoroaromatic molecule, 4-(6-fluorobenzo[d]thiazol-2-yl)aniline (FBTA), rapidly rotating within a lipid bilayer. The 19F chemical shift tensor orientation in the molecular frame was... [Read More]
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[NMR paper] Macrodiscs Comprising SMALPs for Oriented Sample Solid-State NMR Spectroscopy of Membrane Proteins.
Jun 20, 2018 - 8:56 PM - by nmrlearner
nmrlearner's Avatar Macrodiscs Comprising SMALPs for Oriented Sample Solid-State NMR Spectroscopy of Membrane Proteins.

Related Articles Macrodiscs Comprising SMALPs for Oriented Sample Solid-State NMR Spectroscopy of Membrane Proteins.

Biophys J. 2018 Jun 15;:

Authors: Radoicic J, Park SH, Opella SJ

Abstract
Macrodiscs, which are magnetically alignable lipid bilayer discs with diameters of >30*nm, were obtained by solubilizing protein-containing liposomes with styrene-maleic acid copolymers. Macrodiscs provide a detergent-free phospholipid bilayer environment for biophysical and functional studies of membrane proteins under physiological conditions. The narrow resonance linewidths observed from membrane proteins in styrene-maleic acid macrodiscs advance structure determination by oriented sample solid-state NMR spectroscopy.


PMID: 29914645 [PubMed - as supplied by publisher]



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[NMR paper] Roles of structural plasticity in chaperone HdeA activity are revealed by 19F NMR.
Jun 20, 2018 - 8:56 PM - by nmrlearner
nmrlearner's Avatar Roles of structural plasticity in chaperone HdeA activity are revealed by 19F NMR.

Related Articles Roles of structural plasticity in chaperone HdeA activity are revealed by 19F NMR.

Chem Sci. 2016 Mar 01;7(3):2222-2228

Authors: Zhai Z, Wu Q, Zheng W, Liu M, Pielak GJ, Li C

Abstract
HdeA, a minimal ATP-independent acid chaperone, is crucial for the survival of enteric pathogens as they transit the acidic (pH 1-3) environment of the stomach. Although protein disorder (unfolding) and structural plasticity have been elegantly linked to HdeA function, the details of the linkage are lacking. Here, we apply 19F NMR to reveal the structural transition associated with activation. We find that unfolding is necessary but not sufficient for activation. Multiple conformations are present in the functional state at low pH, but the partially folded conformation is essential for HdeA chaperone activity, and HdeA's intrinsic disulfide bond is required to maintain the partially folded conformation. The results show that both disorder and order are key to function. The ability of 19F NMR to reveal and quantify multiple conformational states makes it a powerful tool for studying other chaperones.


PMID: 29910910 [PubMed]



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A table-top PXI based low-field spectrometer for solution dynamic nuclear polarization #DNPNMR #ODNP
Jun 20, 2018 - 8:56 PM - by nmrlearner
nmrlearner's Avatar From The DNP-NMR Blog:

A table-top PXI based low-field spectrometer for solution dynamic nuclear polarization #DNPNMR #ODNP

Biller, Joshua R., Karl F. Stupic, and J. Moreland. “A Table-Top PXI Based Low-Field Spectrometer for Solution Dynamic Nuclear Polarization.” Magnetic Resonance in Chemistry 56, no. 3 (2017): 153–63.


https://doi.org/10.1002/mrc.4672.


We present the development of a portable dynamic nuclear polarization (DNP) instrument based on the PCI eXtensions for Instrumentation platform. The main purpose of the instrument is for study of 1H polarization enhancements in solution through the Overhauser mechanism at low magnetic fields. A DNP probe set was constructed for use at 6.7 mT, using a modified Alderman–Grant resonator at 241 MHz for saturation of the electron transition. The solenoid for detection of the enhanced 1H signal at 288 kHz was constructed with Litz wire. The largest observed 1H enhancements (?) at 6.7 mT for 14N-CTPO radical in air saturated aqueous solution was ? 65. A concentration dependence of the enhancement is observed, with maximum ? at 5.5 mM. A low resonator efficiency for saturation of the electron paramagnetic resonance transition results in a decrease in ? for the 10.3 mM sample. At high incident powers (42 W) and long pump times, capacitor heating effects can also decrease the enhancement. The core unit and program described here could be easily adopted for multi-frequency DNP work, depending on available main magnets and selection of the “plug and play” arbitrary waveform... [Read More]
0 Replies | 7 Views
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