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[NMR paper] Chemical Synthesis of the Highly Hydrophobic Antiviral Membrane Associated Protein IFITM3 and Modified Variants
Aug 21, 2017 - 2:23 PM - by nmrlearner
nmrlearner's Avatar Chemical Synthesis of the Highly Hydrophobic Antiviral Membrane Associated Protein IFITM3 and Modified Variants


Interferon-induced transmembrane protein 3 (IFITM3) is an antiviral transmembrane protein thought to serve as the primary factor for inhibiting replication of a large number of viruses, including the West Nile virus, the Dengue virus, the Ebola virus, and the Zika virus. Production of this 14.5 kDa, 133-residue, transmembrane protein, especially with essential posttranslational modifications by recombinant expression is challenging. In this report, we document the chemical synthesis of IFTIM3 in multimilligram quantities (>15 mg) and the preparation of phosphorylated and fluorescent variants. The synthesis was accomplished by KAHA ligations, which operate under acidic aqueous/organic mixtures that excel at solubilizing even the exceptionally hydrophobic C-terminal region of IFITM3. The synthetic material readily incorporates in model vesicles and forms the basis for using synthetic, homogenous IFITM3 and its derivatives for further studying its structure and biological mode of action.

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Dynamic nuclear polarisation by thermal mixing: quantum theory and macroscopic simulations #DNPNMR
Aug 21, 2017 - 2:23 PM - by nmrlearner
nmrlearner's Avatar From The DNP-NMR Blog:

Dynamic nuclear polarisation by thermal mixing: quantum theory and macroscopic simulations #DNPNMR

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Karabanov, A., et al., Dynamic nuclear polarisation by thermal mixing: quantum theory and macroscopic simulations. Phys. Chem. Chem. Phys., 2016. 18(43): p. 30093-30104.


https://www.ncbi.nlm.nih.gov/pubmed/27775111


A theory of dynamic nuclear polarisation (DNP) by thermal mixing is suggested based on purely quantum considerations. A minimal 6-level microscopic model is developed to test the theory and link it to the well-known thermodynamic model. Optimal conditions for the nuclear polarization enhancement and effects of inhomogeneous broadening of the electron resonance are discussed. Macroscopic simulations of nuclear polarization spectra displaying good agreement with experiments, involving BDPA and trityl free radicals, are presented.
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Go to The DNP-NMR Blog for more info.
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EMSL has expanded far beyond original focus 20 years ago - Tri-City Herald
Aug 21, 2017 - 2:11 AM - by nmrlearner
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Tri-City Herald


EMSL has expanded far beyond original focus 20 years ago
Tri-City Herald
For example, EMSL collaborators have used nuclear magnetic resonance spectrometers to reveal novel structures in more than 100 proteins, from microorganisms to plants and humans. This research is part of the Worldwide Protein Data Bank accessed by ...



EMSL has expanded far beyond original focus 20 years ago - Tri-City Herald
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Structure of superlong, ice-binding protein reported - Chemical & Engineering News
Aug 19, 2017 - 6:43 PM - by nmrlearner
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Chemical & Engineering News


Structure of superlong, ice-binding protein reported
Chemical & Engineering News
They have now used X-ray crystallography, nuclear magnetic resonance, and small-angle X-ray scattering to analyze RI, RIII, and RV, enabling them to assemble the entire structure (Sci. Adv. 2017, DOI: 10.1126/sciadv.1701440). â??The dissect-and-conquer ...



Structure of superlong, ice-binding protein reported - Chemical & Engineering News
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[NMR paper] Extended Physicochemical Characterization of the Synthetic Anticoagulant Pentasaccharide Fondaparinux Sodium by Quantitative NMR and Single Crystal X-ray Analysis.
Aug 18, 2017 - 4:59 PM - by nmrlearner
nmrlearner's Avatar Extended Physicochemical Characterization of the Synthetic Anticoagulant Pentasaccharide Fondaparinux Sodium by Quantitative NMR and Single Crystal X-ray Analysis.

Extended Physicochemical Characterization of the Synthetic Anticoagulant Pentasaccharide Fondaparinux Sodium by Quantitative NMR and Single Crystal X-ray Analysis.

Molecules. 2017 Aug 17;22(8):

Authors: Wildt W, Kooijman H, Funke C, Üstün B, Leika A, Lunenburg M, Kaspersen F, Kellenbach E

Abstract
Fondaparinux sodium is a synthetic pentasaccharide representing the high affinity antithrombin III binding site in heparin. It is the active pharmaceutical ingredient of the anticoagulant drug Arixtra(®). The single crystal X-ray structure of Fondaparinux sodium is reported, unequivocally confirming both structure and absolute configuration. The iduronic acid adopts a somewhat distorted chair conformation. Due to the presence of many sulfur atoms in the highly sulfated pentasaccharide, anomalous dispersion could be applied to determine the absolute configuration. A comparison with the conformation of Fondaparinux in solution, as well as complexed with proteins is presented. The content of the solution reference standard was determined by quantitative NMR using an internal standard both in 1999 and in 2016. A comparison of the results allows the conclusion that this method shows remarkable precision over time, instrumentation and analysts.


PMID: 28817073 [PubMed - in process]



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[NMR paper] Signaling-Related Mobility Changes in Bacterial Chemotaxis Receptors Revealed by Solid-State NMR.
Aug 18, 2017 - 4:59 PM - by nmrlearner
nmrlearner's Avatar Signaling-Related Mobility Changes in Bacterial Chemotaxis Receptors Revealed by Solid-State NMR.

Signaling-Related Mobility Changes in Bacterial Chemotaxis Receptors Revealed by Solid-State NMR.

J Phys Chem B. 2017 Aug 17;:

Authors: Kashefi M, Thompson LK

Abstract
Bacteria employ remarkable membrane-bound nanoarrays to sense their environment and direct their swimming. Arrays consist of chemotaxis receptor trimers of dimers that are bridged at their membrane-distal tips by rings of two cytoplasmic proteins, a kinase CheA and a coupling protein CheW. It is not clear how ligand binding to the periplasmic domain of the receptor deactivates the CheA kinase bound to the cytoplasmic tip ~300 Å away, but the mechanism is thought to involve changes in dynamics within the cytoplasmic domain. To test these proposals, we applied solid-state NMR mobility-filtered experiments to functional complexes of the receptor cytoplasmic fragment (U-(13)C,(15)N-CF), CheA, and CheW. Assembly of these proteins into native-like, homogeneous arrays is mediated by either vesicle binding or molecular crowding agents, and paramagnetic relaxation enhancement is used to overcome sensitivity challenges in these large complexes. INEPT spectra reveal that a significant fraction of the receptor is dynamic on the ns or shorter timescale, and these dynamics change with signaling state. The mobile regions are identified through a combination of biochemical and NMR approaches (protein truncations and unique chemical shifts). The INEPT spectra are consistent with an asymmetric mobility in the methylation region (N-helix mobility >> C-helix mobility) and reveal an increase in the mobility of the N-helix in the kinase-off... [Read More]
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[NMR paper] NOAH: NMR Supersequences for Small Molecule Analysis and Structure Elucidation
Aug 18, 2017 - 4:59 PM - by nmrlearner
nmrlearner's Avatar NOAH: NMR Supersequences for Small Molecule Analysis and Structure Elucidation


Nested NMR experiments combining up to five conventional NMR pulse sequences into one supersequence are introduced. The core 2D NMR techniques routinely employed in small molecule NMR spectroscopy, such as HSQC, HMQC, HMBC, COSY, NOESY, TOCSY, and similar, can be recorded in a single measurement. In this way the data collection time may be dramatically reduced and sample throughput increased for basic NMR applications, such as structure elucidation and verification in synthetic, medicinal, and natural product chemistry.NOAH's Ark: The nesting of up to five conventional NMR pulse sequences into one “NOAH supersequence”, employing only a single recovery delay, saves a significant amount of time during data collection for the analysis of small molecules. These experiments do not require specialist spectrometer hardware.

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Free Radical Imaging Using In Vivo Dynamic Nuclear Polarization-MRI #DNPNMR #ODNP
Aug 18, 2017 - 4:59 PM - by nmrlearner
nmrlearner's Avatar From The DNP-NMR Blog:

Free Radical Imaging Using In Vivo Dynamic Nuclear Polarization-MRI #DNPNMR #ODNP

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Utsumi, H. and F. Hyodo, Free Radical Imaging Using In Vivo Dynamic Nuclear Polarization-MRI. Methods Enzymol, 2015. 564: p. 553-71.


https://www.ncbi.nlm.nih.gov/pubmed/26477265


Redox reactions that generate free radical intermediates are essential to metabolic processes, and their intermediates can produce reactive oxygen species, which may promote diseases related to oxidative stress. The development of an in vivo electron spin resonance (ESR) spectrometer and its imaging enables us noninvasive and direct measurement of in vivo free radical reactions in living organisms. The dynamic nuclear polarization magnetic resonance imaging (DNP-MRI), also called PEDRI or OMRI, is also a new imaging method for observing free radical species in vivo. The spatiotemporal resolution of free radical imaging with DNP-MRI is comparable with that in MRI, and each of the radical species can be distinguished in the spectroscopic images by changing the frequency or magnetic field of ESR irradiation. Several kinds of stable nitroxyl radicals were used as spin probes to detect in vivo redox reactions. The signal decay of nitroxyl probes, which is determined with in vivo DNP-MRI, reflects the redox status under oxidative stress, and the signal decay is suppressed by prior administration of antioxidants. In addition, DNP-MRI can also visualize various intermediate free radicals from the intrinsic redox... [Read More]
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