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High-Pressure NMR for Studying Protein Structure and Dynamics
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LI Hua, Yuji O. KAMATARI, Ryo KITAHARA, Kazuyuki AKASAKA
Chinese Journal of Magnetic Resonance, 2016, 33(1): 1-26.
DOI: 10.11938/cjmr20160101
Proteins are thermodynamic entities that exist in general as an equilibrium mixture of the basic folded states, denatured states and various intermediate states with varying populations at certain temperature and pressure. When using pressure as a perturbation, the population will be scanned from the states with larger partial molar volumes to the states with smaller ones. Therefore, high-pressure NMR is applicable to study protein structure and dynamics at wider conformational space at the atomic level. Furthermore, under physiological conditions, the difficulty of detection of higher-energy substates by the conventional NMR is obvious, as the equilibrium populations of such higher-energy substates are extremely low. Hydrostatic pressure gives a general solution to this problem. The partial molar volumes of proteins at higher-energy states, being functionally relevant most of the time, are generally smaller than those at the basic folded ones, therefore, pressure can shift the equilibrium toward the former substantially, and allows their detection at elevated pressure. Recently, owing to the development of the high pressure NMR and multidimensional NMR technologies, and substantial development of protein structure and dynamics study itself, high pressure NMR spectroscopy is being paid more and more attention. In this review, the history, concepts, techniques, and applications of high-pressure NMR are presented with future prospects.
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Compact ESR Equipment
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Yury V. BOGACHEV, Mikhail N. KNYAZEV, Yaroslav Yu. MARCHENKO
Chinese Journal of Magnetic Resonance, 2016, 33(1): 27-36.
DOI: 10.11938/cjmr20160102
In this paper we represent our original developments of a compact electron spin resonance (ESR) instrument, which is featured with high performance, low cost, reliability and simplicity, open architecture, small size, and a wide range of functional modules and units. Various constructions of the ESR spectrometer microwave units were analyzed. An optimal two-cavity construction for autodyne type ESR spectrometers were finally developed and investigated experimentally. The ESR instrumentation presented also involved compact magnet systems based on electromagnets and permanent magnets with high uniformity of magnetic field. The specifications of the compact ESR instrument developed, as well as a list of applications, are presented. Some special applications of compact ESR spectrometers are discussed.
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A High-Speed Driver for NMR T/R Switch
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DIAO Yu-jian, XIE Jun-yao, XU Jun-cheng, JIANG Yu
Chinese Journal of Magnetic Resonance, 2016, 33(1): 37-43.
DOI: 10.11938/cjmr20160103
T/R switch is a device that switches between the radio frequency (RF) transmission path and the signal reception path, and enables rapid tuning and detuning of RF coils. PIN diodes are widely utilized in modern T/R switch and tunable coil configurations, given that they operate as variable resistors controlled by DC current at RF frequencies. Since the PIN diode can only work with a driver providing the forward or reverse bias supply, its performance is significantly influenced by the capability of the driver. This paper presents a driver design with high driving speed, and high voltage and current driving capabilities. In this design, the control signal was separated from the high power driving supplies. The driver had a switching time within 500 ns with an output voltage over 400 V and an output current over 10 A. It can be applied to drive fast and high-power T/R switches.
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A Single-Sided NMR Sensor: Design and Applications
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JI Yong-liang, CUI Xian-jun, HOU Xing-zhe, WU Gao-ling, WANG Qian, LI Long, XU Zheng
Chinese Journal of Magnetic Resonance, 2016, 33(1): 66-76.
DOI: 10.11938/cjmr20160106
Single-sided NMR sensors are especially suitable for nondestructive examination of large samples, due to their features such as small size, low cost, and open structure. This paper presents the design and applications of a single-sided NMR sensor with relatively high field uniformity. The uniformity of B 0 was estimated to be 338×10-6 in an area of 10 mm×10 mm in the horizontal direction; while there was a constant gradient of 4.6 T/min the vertical direction. According to the distribution of the magnetic field gradient, a signal processing method based on FFT and band-pass filter was proposed to extract NMR signals from a thin layer of the samples. The one-dimensional resolution in the depth direction was about 50 μ m. Application experiments are presented, including assessing the aging status of polymer composite insulator, measuring the diffusion coefficient of liquids, and analyzing the withering process of plant leaves. It is concluded that the single-sided NMR sensor developed may have potential applications in many fields.
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Divalent Metal Ion Binding to the Response Regulator YycFN Studied by NMR Spectroscopy
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LIU Ting, LIU Mai-li, JIANG Ling
Chinese Journal of Magnetic Resonance, 2016, 33(1): 77-88.
DOI: 10.11938/cjmr20160107
YycGF, originally identified in Bacillus subtilis , is recognized as a crucial two-component signal transduction system closely associated with cell viability. It is highly conserved in low G+C Gram-positive bacteria, including Staphylococcus aureus , Streptococcus pneumoniae and other human pathogens. The histidine kinase (HK) YycG senses extracellular or intracellular signals and phosphorylates its cognate response regulator (RR) YycF, which in turn recognizes sequence specific regions on the bacterial chromosome and regulates the expression of certain genes. The presence of a divalent metal ion is essential for phosphoryl group transfer. Here, we presented a metal ion binding study of the response regulator YycF (YycFN ) from Bacillus subtilis using NMR spectroscopy. The metal ions Ca2+ and Mg2+ induced severe chemical shift changes in YycF backbone resonances, involving mainly the Asp9, Asp16 and Asp53 residues. Furthermore, the binding affinities of Ca2+ and Mg2+ with YycFN were compared. The results provide important clues for understanding the conformational change of YycFN upon metal ion binding before its phosphorylation.
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4,4,5,5-Tetramethyl-1,3,2-Dioxaborolane Studied by 11 B-NMR and 1 H-11 B HMQC Spectroscopy
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LIU Ya-qin, HE Ling
Chinese Journal of Magnetic Resonance, 2016, 33(1): 89-95.
DOI: 10.11938/cjmr20160108
The NMR detection methods for borane-containing compounds were studied, using 4,4,5,5-tetramethyl-1,3,2-dioxaborolane as an example. We showed that the 11 B-NMR spectrum of 4,4,5,5-tetramethyl-1,3,2-dioxaborolane can be assigned by combining the information provided byone-dimensional boron spectrum and two-dimensional heteronuclear multiple quantum coherence spectroscopy 1 H-11 B HMQC. It is concluded that the methods presented can be used to obtain information of boron atom structure, and to analyze structures of borane-containing compounds.
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Spectral Analysis and Evaluation of Shanshan Coal Tar
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HONG Kun, MA Feng-yun, ZHAO Xin, ZHONG Mei, LIU Jing-mei, LIU Yue-e, HE Lu
Chinese Journal of Magnetic Resonance, 2016, 33(1): 96-105.
DOI: 10.11938/cjmr20160109
The composition and structure parameters of coal tar distilled from the coal of the Shanshan area, Xinjiang were studied by NMR spectroscopy and Fourier transform infrared (FT-IR) spectrometry. With the structure parameters calculated from the spectra, and coalification degree and hydrocarbon generation capacity of the crude coal were evaluated. The result showed that the average rate of aromatic carbon (f ar C ) was 0.44, carbon number (N ) was 2.87, replace index (s ) was 0.33 and condensation index (Q ) was 0.74. It was found that there were many alkyl-side chains connecting to the condensation aromatic nuclei. Five IR parameters (B 1 ~B 5 ) were chosen to process the spectra with vector normalization and integral in the Ominic software. The NMR and IR data indicated that the crude coal is medium in metamorphic grade, and belongs to humic coal mainly composed of vitrinite. The oxygen-containing functional groups exist mainly in the form of aryl ethers. Carboxyl and methoxy groups either fall out or disappear. According to the hydrocarbon generation mechanism, these data indicated that the gas potentiality of the coal tar is higher than its oil potential; and the gas potential carbon is mainly the methyl units.
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Changes of Chemical Constitution in Alismatis rhizoma after Saline Processing as Revealed by 1 H NMR Analysis
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HAN Wei-jian, LIN Xiao-tong, GUO Na, CHEN Qiao, ZHANG Ting-ting, XU Nan
Chinese Journal of Magnetic Resonance, 2016, 33(1): 117-124.
DOI: 10.11938/cjmr20160111
As a commonly used traditional Chinese medicine (TMC), Alismatis rhizoma is the main ingredient of many classical formulas, such as Wu Ling San, Long Dan Xie Gan Wan and Liu Wei Di Huang Wan. Both the raw slices of Alismatis rhizoma and the slices processed with saline arelisted are prescription drugs in the Pharmacopoeia of People's Republic of China. TMC theory thinks the raw and processed slices of Alismatis rhizoma are different in function. The raw slices are emphasized on its actions of alleviating water retention and dispersing heat, whiles the processed slices are thought ineffective in these respects. The active components in these two types of Alismatis rhizoma slices remained poorly understood, making standardizing the saline processing procedure and quality control difficult. In this paper, we applied 1 H NMR based metabonomic approach to investigate the difference of chemical constitution between the raw and salt-processed slices of Alismatis rhizome . The result showed that the chemical constitution of the Alismatis rhizoma slices changed significantly after salt-processing, and such changes were influenced by the length of processing time. In PLS-DA analysis, the signals of alisols at δ 3.82, 3.78, 3.66, 1.34, 0.94, and 1.30 changed significantly under different processing conditions, indicating that alisols were perhaps the chemical fingreprints contributing the different functions of raw and salt-processed Alismatis rhizoma slices.
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Spectrum Characteristics and Filtering Effect of 87 Rb-Ar Spectrum Lamp
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XU Feng, HAO Qiang, HE Sheng-guo, MEI Gang-hua
Chinese Journal of Magnetic Resonance, 2016, 33(1): 125-132.
DOI: 10.11938/cjmr20160112
Via hyperfine spectral profile measurements, the spectrum characteristics and isotope filtering effect of the rubidium spectrum lamp were studied under the circumstance that both the lamp bulb and the filtering cell are filled with argon buffer gas. Spectral profile distortion of the 87 Rb-Ar spectrum lamp was observed, and it was found that a lower temperature in the lamp bulb could minimize the distortion. The results also showed that the pressure, length and operation temperature of the filtering cell have evident influences on the filtering effect. After design and operation parameters being optimized, the spectrum lamp and the filtering cell were used in a rubidium frequency standard, and the short-term frequency stability was greatly improved.
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Spectroscopy Study on Synthesis of Diisopropyl Coumarin-3-Phosphate by 31 P NMR
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LI Yuan-zhe, QIU Li, YIN Qiu-yue, MAO Pu, XIAO Yong-mei, QU Ling-bo, YUAN Jin-wei
Chinese Journal of Magnetic Resonance, 2016, 33(1): 133-141.
DOI: 10.11938/cjmr20160113
Synthesis of diisopropyl coumarin-3-phosphate was tracked by 31 P NMR, and the reaction mechanism was discussed using the materials of coumarin and diisopropyl H -phosphite and AgNO3 as the catalyst. The reaction conditions are optimized, and the regioselectivity of the reaction site is analyzed.
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Spectral Analysis of Fungicide Cyflufenamid
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LIU De-yun, WANG Ya-ru, WEI Hai-feng, XIA Gao-feng, YANG Xiao-yun
Chinese Journal of Magnetic Resonance, 2016, 33(1): 142-152.
DOI: 10.11938/cjmr20160114
Cyflufenamid is an excellent fungicide with novel molecular structure. In this paper, one-dimensional and two-dimensional NMR spectroscopy, combined with mass spectrometry (MS), ultraviolet spectroscopy (UV) and infrared spectroscopy (IR), were used to elucidate the structure of cyflufenamid. NMR chemical shifts of the compound were assigned. The correspondences between the UV/IR absorption peaks and the functional groups in this compoundwere discussed. The effects of the fluorine atoms in the compound on the 1 H and 13 C NMR chemical shifts were investigated, as well as the possible fragmentation patterns of the compound.
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Application of NMR in the Studies of Structure and Interactions of α -Synuclein
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DAI Chen-ye, ZHANG Ze-ting, LIU Mai-li, LI Cong-gang
Chinese Journal of Magnetic Resonance, 2016, 33(1): 153-167.
DOI: 10.11938/cjmr20160115
α -synuclein (AS) is natively unfolded protein, and has the potential to aggregate and assemble into fibrils. AS fibril is the major component of Lewy bodies (LB), the hallmark of neurodegenerative diseases such as Parkinson's disease (PD). Many previous studies have studied the structure and functions of AS, hoping toshed a light on the pathogenesis of PD. Compared to the other methods, nuclear magnetic resonance (NMR) has many advantages in studying natively unfolded proteins, and can provide atom-level structural and dynamic information of these proteins. This review focuses on the applications of NMR, combined with other techniques, in the studies on the structure, aggregation mechanisms, membrane interactions, metal ion interactions, and protein interactions of AS.