• Title/Summary/Keyword: }NMR$

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Real-time Acquisition of Three Dimensional NMR Spectra by Non-uniform Sampling and Maximum Entropy Processing

  • Jee, Jun-Goo
    • Bulletin of the Korean Chemical Society
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    • v.29 no.10
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    • pp.2017-2022
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    • 2008
  • Of the experiments to shorten NMR measuring time by sparse sampling, non-uniform sampling (NUS) is advantageous. NUS miminizes systematic errors which arise due to the lack of samplings by randomization. In this study, I report the real-time acquisition of 3D NMR data using NUS and maximum-entropy (MaxEnt) data processing. The real-time acquisition combined with NUS can reduce NMR measuring time much more. Compared with multidimensional decomposition (MDD) method, which was originally suggested by Jaravine and Orekhov (JACS 2006, 13421-13426), MaxEnt is faster at least several times and more suitable for the realtime acquisition. The designed sampling schedule of current study makes all the spectra during acquisition have the comparable resulting resolutions by MaxEnt. Therefore, one can judge the quality of spectra easily by examining the intensities of peaks. I report two cases of 3D experiments as examples with the simulated subdataset from experimental data. In both cases, the spectra having good qualitie for data analysis could be obtained only with 3% of original data. Its corresponding NMR measuring time was 8 minutes for 3D HNCO of ubiquitin.

A NMR Study on the Micellization of Sodium Dodecyl Sulfate in ω-Phenylalkylammonium Salt Solution (1H NMR을 이용한 ω-Phenylalkylammonium Salt의 수용액에서 Sodium Dodecyl Sulfate의 미셀에 관한 연구)

  • Oh, Jung Hee
    • Applied Chemistry for Engineering
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    • v.10 no.4
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    • pp.628-634
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    • 1999
  • The orientational binding of ${\omega}$-phenylakylammonium ions to the sodium dodecyl (SDS) micellar interface has been studied from $^{1}H\;NMR$ chemical shift data. The NMR resonaces of the methylene protons of SDS and aromatic protons embedded into the micellar interior have shown the upfield shift. The aromatic induced chemical shifts of the alkyl chain methylene protons of SDS demonstrate the deep penetration into the palisade layer by these organic salts. Alkylammonium groups have been considered to be oriented toward outside of the micellar interface. Aromatic rings have been thought to be oriented toward the micellar core. The depth of penetration by organic salts has been observed to increase with the length of alkyl chain.

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Purification and Spectroscopic Characterization of the Human Protein Tyrosine Kinase-6 SH3 Domain

  • Koo, Bon-Kyung;Kim, Min-Hyung;Lee, Seung-Taek;Lee, Weon-Tae
    • BMB Reports
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    • v.35 no.3
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    • pp.343-347
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    • 2002
  • The human protein tyrosine kinase-6 (PTK6) polypeptide that is deduced from the cDNA sequence contains a Src homology (SH) 3 domain, SH2 domain, and catalytic domain of tyrosine kinase. We initiated biochemical and NMR characterization of PTK6 SH3 domain in order to correlate the structural role of the PTK6 using circular dichroism and heteronuclear NMR techniques. The circular dichroism data suggested that the secondary structural elements of the SH3 domain are mainly composed of $\beta$-sheet conformations. It is most stable when the pH is neutral based on the pH titration data. In addition, a number of cross peaks at the low-field area of the proton chemical shift of the NMR spectra indicated that the PTK6 SH3 domain retains a unique and folded conformation at the neutral pH condition. For other pH conditions, the SH3 domain became unstable and aggregated during NMR measurements, indicating that the structural stability is very sensitive to pH environments. Both the NMR and circular dichroism data indicate that the PTK6 SH3 domain experiences a conformational instability, even in an aqueous solution.

An Investigation of the Sample Rotation Effects on Suppression of Convective Flows in PGSE Diffusion NMR Experiments

  • Kim, Minkyoung;Chung, Kee-Choo
    • Journal of the Korean Magnetic Resonance Society
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    • v.20 no.2
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    • pp.61-65
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    • 2016
  • Undesirable convective flow in an NMR tube inhibits the accurate measurement of diffusion coefficients by NMR spectroscopy. To minimize the convection effects, various methods have been suggested, and it has been known that the use of sample rotation can be useful. However, it has not been clearly examined that the convection suppressing effect of the sample rotation under the different spinning speeds. In this study, the relation between convective flow and the sample rotation was investigated using PGSE NMR diffusion experiments to reveal the feasibility for controlling the convective flow in an NMR tube by sample rotation itself. The viscosity effect was also examined using solvents with four different viscosities, acetone-$d_6$ chloroform-d, pyridine-$d_5$, and $D_2O$. The sample rotation showed apparent convection suppressing effects at all temperature range for the low viscosity solvents, acetone-$d_6$ and chloroform-d, even at the faster than 5 Hz spinning rate. The similar patterns were also observed for pyridine-$d_5$ and $D_2O$, which have higher viscosity. This effect was observed even at high temperatures where convective flow arises conspicuously.

A simple guide to the structural study on membrane proteins in detergents using solution NMR

  • Sim, Dae-Won;Lee, Yoo-sup;Seo, Min-Duk;Won, Hyung-Sik;Kim, Ji-hun
    • Journal of the Korean Magnetic Resonance Society
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    • v.19 no.3
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    • pp.137-142
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    • 2015
  • NMR-based structural studies on membrane proteins are appreciated quite challenging due to various reasons, generally including the narrow dispersion of NMR spectra, the severe peak broadening, and the lack of long range NOEs. In spite of the poor biophysical properties, structural studies on membrane proteins have got to go on, considering their functional importance in biological systems. In this review, we provide a simple overview of the techniques generally used in structural studies of membrane proteins by solution NMR, with experimental examples of a helical membrane protein, caveolin 3. Detergent screening is usually employed as the first step and the selection of appropriate detergent is the most important for successful approach to membrane proteins. Various tools can then be applied as specialized NMR techniques in solution that include sample deteuration, amino-acid selective isotope labeling, residual dipolar coupling, and paramagnetic relaxation enhancement.

Per-deuteration and NMR experiments for the backbone assignment of 62 kDa protein, Hsp31

  • Kim, Jihong;Choi, Dongwook;Park, Chankyu;Ryu, Kyoung-Seok
    • Journal of the Korean Magnetic Resonance Society
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    • v.19 no.3
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    • pp.112-118
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    • 2015
  • Hsp31 protein is one of the members of DJ-1 superfamily proteins and has a dimeric structure of which molecular weight (MW) is 62 kDa. The mutation of DJ-1 is closely related to early onset of Parkinson's disease. Hsp31 displays $Zn^{+2}$-binding activity and was first reported to be a holding chaperone in E. coli. Its additional glyoxalase III active has recently been characterized. Moreover, an incubation at $60^{\circ}C$ induces Hsp31 protein to form a high MW oligomer (HMW) in vitro, which accomplishes an elevated holding chaperone activity. The NMR technique is elegant method to probe any local or global structural change of a protein in responses to environmental stresses (heat, pH, and metal). Although the presence of the backbone chemical shifts (bbCSs) is a prerequisite for detailed NMR analyses of the structural changes, general HSQC-based triple resonance experiments could not be used for 62 kDa Hsp31 protein. Here, we prepared the per-deuterated Hsp31 and performed the TROSY-based triple resonance experiments for the bbCSs assignment. Here, detailed processes of per-deuteration and the NMR experiments are described for other similar NMR approaches.

Easy-to-execute 'One-pot' Synthesis of 1,2,4,5-Tetrazines Catalyzed by Activated Fly Ash (활성화된 비산회 촉매를 이용하여 간단히 수행된 1,2,4,5-Tetrazines의 One-pot 합성)

  • Gopalakrishnan, M.;Thanusu, J.;Kanagarajan, V.
    • Journal of the Korean Chemical Society
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    • v.51 no.6
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    • pp.520-525
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    • 2007
  • Three-component coupling of thiourea/urea, various structurally diverse aromatic aldehydes and ammonium acetate is catalyzed by activated fly ash in dry media under microwave irradiation to give 6-aryl-1,2,4,5-tetrazinan- 3-thiones/ones in good yields. The structure of 6-aryl-1,2,4,5-tetrazinan-3-thiones/ones have been elucidated on the basis of their melting points, elemental analysis, MS, IR, 1H NMR, D2O exchange, 13C NMR and two dimensional NMR spectral studies including Homonuclear Correlation (HOMOCOR) and Heteronuclear Single Quantum Correlation (HSQC) spectra.

Theoretical and Experimental 31P NMR and ESI-MS Study of Hg2+ Binding to Fenitrothion

  • Koo, In-Sun;Ali, Dildar;Yang, Ki-Yull;vanLoon, Gary W.;Buncel, Erwin
    • Bulletin of the Korean Chemical Society
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    • v.30 no.6
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    • pp.1257-1261
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    • 2009
  • We present the theoretical and experimental results of $^{31}P$ NMR and low energy CID MS/MS study of $Hg^{2+}$ binding to fenitrothion (FN). The calculated $^{31}P$ NMR chemical shifts order for FN with $Hg^{2+}$ complex is in good agreement with experimental $^{31}P$ NMR chemical shifts order. The experimental and theoretical $^{31}P$ NMR study of organophosphorus pesticide with $Hg^{2+}$ gives to important information for organophosphorus pesticide metal complexes. ESI-MS and low energy CID MS/MS experiments of $Hg^{2+}$-FN complexes combined with accurate mass measurements give insight into the metal localization and allow unambiguous identification of fragments and hydrolysis products.

27Al Solid-state NMR Structural Studies of Hydrotalcite Compounds Calcined at Different Temperatures

  • Park, Tae-Joon;Choi, Sung-Sub;Kim, Yong-Ae
    • Bulletin of the Korean Chemical Society
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    • v.30 no.1
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    • pp.149-152
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    • 2009
  • Hydrotalcites are anionic clays that are quite prevalent in nature and their importance is growing more and more because of their very wide range of potential applications and uses. Understanding the structural and compositional changes that occur on the molecular scale during the thermal decomposition of hydrotalcite compounds is essential for the basic prediction and comprehensive understanding of the behavior and technical application of these materials. In this study, several hydrotalcite compounds calcined at different temperatures for applications in a chlorine resistant textile were prepared and 27-Aluminm solid-state nuclear magnetic resonance (NMR) spectroscopy was used as a tool to study their local structure and behavior. The changes in the Al coordination of the hydrotalcite compounds were investigated with one dimensional (1D) solid-state magic angle spinning (MAS) NMR spectroscopy. The two broad resonances arising from the structurally different Al coordinations of these compounds were clearly resolved by two dimensional (2D) triple quantum magic angle spinning (3QMAS) NMR spectroscopy.

Pattern Recognition Using NMR Spectral Data for Metabonomic Analysis of Urine Samples from Experimental Animals (실험동물 뇨시료의 대사체학적 분석을 위한 핵자기공명스펙트럼 패턴인식)

  • Joo Hyun Jin;Cho JungHwan
    • YAKHAK HOEJI
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    • v.49 no.1
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    • pp.74-79
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    • 2005
  • Metabonomic analysis has been recognized as a powerful approach for characterizing metabolic changes in biofluids due to toxicity, disease process or environmental influences. To investigate the possibility of relating metabolic changes with $^{1}H-NMR$ spectra, urine samples from Sprague-Dawley rats treated with various dietary restrictions or toxic substances (nicotine) were analysed using $^{1}H-NMR$ spectroscopy and pattern recognition techniques. Dietary restrictions-given to male rats were normal diet and high fat diet and fasting. The nicotine urine samples were collected from SD rats administered with nicotine (25 mg/kg) at the various time intervals. $^{1}H-NMR$ spectra of all urine samples were acquired at 400 MHz on a VARIAN spectrometer. To establish the presence of any intrinsic class-related patterns or clusters in each NMR data, methods of PCA (principal component analysis) and soft independent modeling of class analogy (SIMCA) analysis were used, and the results from these analyses were compared to each other. In all cases of dietary conditions and nicotine treatment, SIMCA analysis gave better results for the discrimination of NMR spectra of urine samples than PCA.