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[NMR paper] STD-NMR experiments identify a structural motif with novel second-site activity against West Nile virus NS2B-NS3 protease.
Sep 21, 2017 - 7:24 PM - by nmrlearner
nmrlearner's Avatar STD-NMR experiments identify a structural motif with novel second-site activity against West Nile virus NS2B-NS3 protease.

Related Articles STD-NMR experiments identify a structural motif with novel second-site activity against West Nile virus NS2B-NS3 protease.

Antiviral Res. 2017 Sep 16;:

Authors: Schöne T, Grimm LL, Sakai N, Zhang L, Hilgenfeld R, Peters T

Abstract
West Nile virus (WNV) belongs to the genus Flavivirus of the family Flaviviridae. This mosquito-borne virus that is highly pathogenic to humans has been evolving into a global threat during the past two decades. Despite many efforts, neither antiviral drugs nor vaccines are available. The viral protease NS2B-NS3(pro) is essential for viral replication, and therefore it is considered a prime drug target. However, success in the development of specific NS2B-NS3(pro) inhibitors had been moderate so far. In the search for new structural motifs with binding affinity for NS2B-NS3(pro), we have screened a fragment library, the Maybridge Ro5 library, employing saturation transfer difference (STD) NMR experiments as readout. About 30% of 429 fragments showed binding to NS2B-NS3(pro). Subsequent STD-NMR competition experiments using the known active site fragment A as reporter ligand yielded 14 competitively binding fragments, and 22 fragments not competing with A. In a fluorophore-based protease assay, all of these fragments showed... [Read More]
0 Replies | 1 Views
[NMR paper] Measurement of amide proton chemical shift anisotropy in perdeuterated proteins using CSA amplification
Sep 21, 2017 - 2:38 AM - by nmrlearner
nmrlearner's Avatar Measurement of amide proton chemical shift anisotropy in perdeuterated proteins using CSA amplification

Publication date: Available online 19 September 2017
Source:Journal of Magnetic Resonance

Author(s): Yuwei Ge, Ivan Hung, Xiaoli Liu, Maili Liu, Zhehong Gan, Conggang Li

Measuring 1H chemical shift anisotropy (CSA) is useful for probing proton environments and dynamics but remains a challenge due to strong homonuclear interaction and relatively small shift anisotropy, especially in proteins with multiple proton sites. Here the extended chemical shift anisotropy amplification (xCSA) method is applied for amide proton CSA measurement in uniformly 2H enriched proteins under fast magic angle spinning. The xCSA method is capable of distinguishing the sign of the CSA asymmetry parameter, complimenting other multiple-pulse recoupling methods. A three-dimensional xCSA experiment is demonstrated for measuring the proton CSA of amide sites in a GB1 protein sample and the possible correlation of amide proton CSA with protein secondary structure is discussed.
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0 Replies | 7 Views
[NMR paper] A Discrete-State Kinetics Model for NMR-Based Analysis of Protein Translocation on DNA at Equilibrium.
Sep 21, 2017 - 2:38 AM - by nmrlearner
nmrlearner's Avatar A Discrete-State Kinetics Model for NMR-Based Analysis of Protein Translocation on DNA at Equilibrium.

Related Articles A Discrete-State Kinetics Model for NMR-Based Analysis of Protein Translocation on DNA at Equilibrium.

J Phys Chem B. 2017 Sep 19;:

Authors: Sahu D, Iwahara J

Abstract
In the target DNA search process, sequence-specific DNA-binding proteins first nonspecifically bind to DNA and stochastically move from one site to another before reaching their targets. To rigorously assess how the translocation process influences NMR signals from proteins interacting with nonspecific DNA, we incorporated a discrete-state kinetic model for protein translocation on DNA into the McConnell equation. Using this equation, we simulated line shapes of NMR signals from proteins undergoing translocations on DNA through sliding, dissociation / reassociation, and intersegment transfer. Through this analysis, we validated an existing NMR approach for kinetic investigations of protein translocation on DNA, which utilizes NMR line shapes of two nonspecific DNA-protein complexes and their mixture. We found that, despite its use of simplistic two-state approximation neglecting the presence of many microscopic states, the previously proposed NMR approach provides accurate kinetic information on the intermolecular translocations of proteins between two DNA molecules. Interestingly, our results suggest that... [Read More]
0 Replies | 9 Views
[NMR paper] Time-resolved in situ MAS NMR monitoring of the nucleation and growth of zeolite BEA catalysts under hydrothermal conditions
Sep 21, 2017 - 2:38 AM - by nmrlearner
nmrlearner's Avatar Time-resolved in situ MAS NMR monitoring of the nucleation and growth of zeolite BEA catalysts under hydrothermal conditions


Time-resolved 13C, 23Na, 27Al and 29Si MAS NMR has been applied in situ for monitoring the hydrothermal synthesis of zeolite BEA. Isotopic labelling with 29Si and 13C isotopes has been used to follow the fate of silicious species and structure directing agent ((13CH3-CH2)4NOH). Two mechanistic pathways, namely, solution mediated and solid-solid hydrogel rearrangement have been distinguished for two synthesis procedures studied. The mechanisms of structure directing behavior of TEA+ cations in two reaction pathways have been elucidated. The results show that multinuclear MAS NMR can serve as a superior tool for monitoring hydrothermal synthesis of various solids including zeolites, zeotypes, mesoporous materials, metal organic frameworks and etc. and for the design of novel outstanding materials for different applications.

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0 Replies | 9 Views
Measuring Nano- to Microstructures from Relayed Dynamic Nuclear Polarization NMR #DNPNMR
Sep 21, 2017 - 2:38 AM - by nmrlearner
nmrlearner's Avatar From The DNP-NMR Blog:

Measuring Nano- to Microstructures from Relayed Dynamic Nuclear Polarization NMR #DNPNMR

p.p1 {margin: 0.0px 0.0px 0.0px 36.0px; text-indent: -36.0px; font: 12.0px Helvetica}
Pinon, A.C., et al., Measuring Nano- to Microstructures from Relayed Dynamic Nuclear Polarization NMR. The Journal of Physical Chemistry C, 2017. 121(29): p. 15993-16005.


http://dx.doi.org/10.1021/acs.jpcc.7b04438


We show how dynamic nuclear polarization (DNP) NMR can be used in combination with models for polarization dynamics to determine the domain sizes in complex materials. By selectively doping a source component with radicals and leaving the target undoped, we can measure experimental polarization buildup curves which can be compared with simulations based on heterogeneous distributions of polarization within the sample. The variation of the integrated DNP enhancement as a function of the polarization time is found to be characteristic of the geometry. We demonstrate the method experimentally on four different systems where we successfully determine domain sizes between 200 and 20 000 nm, specifically in powdered histidine hydrochloride monohydrate, pore lengths of mesoporous silica materials, and two domain sizes in two-component polymer film coatings. Additionally, we find that even in the apparently homogeneous frozen solutions used as polarization sources in most DNP experiments, polarization is relayed from protons near the radicals to the bulk of the solution by spin diffusion, which... [Read More]
0 Replies | 7 Views
[NMR paper] Quantitative determination and validation of octreotide acetate using (1) H-NMR spectroscopy with internal standard method.
Sep 19, 2017 - 4:40 PM - by nmrlearner
nmrlearner's Avatar Quantitative determination and validation of octreotide acetate using (1) H-NMR spectroscopy with internal standard method.

Related Articles Quantitative determination and validation of octreotide acetate using (1) H-NMR spectroscopy with internal standard method.

Magn Reson Chem. 2017 Sep 15;:

Authors: Yu C, Zhang Q, Xu PY, Bai Y, Shen WB, Di B, Su MX

Abstract
Quantitative nuclear magnetic resonance (qNMR) is a well-established technique in quantitative analysis. We presented a validated (1) H quantitative nuclear magnetic resonance ((1) H-qNMR) method for assay of octreotide acetate (OCT-Ac), a kind of cyclic octopeptide. Deuterium oxide was used to remove the undesired exchangeable peaks, which was referred to as proton exchange, in order to make the quantitative signals isolated in the crowded spectrum of the peptide and ensure precise quantitative analysis. Gemcitabine hydrochloride was chosen as the suitable internal standard (IS). Experimental conditions, including relaxation delay time,the numbers of scans and pulse angle were optimized first. Then method validation was carried out in terms of selectivity, stability, linearity, precision and robustness. The assay result was compared with that by means of high performance liquid chromatography (HPLC), which is provided by Chinese Pharmacopoeia. The statistical F test, student t test and nonparametric test at 95% confidence level... [Read More]
0 Replies | 12 Views
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