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NMR in Fragment Based Lead Discovery
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RUAN Ke, GAO Jia, MA Rong-Sheng
Chinese Journal of Magnetic Resonance, 2012, 29(2): 163-181.
The fragment based drug screening and design emerged in the past decade, and has gained important applications. Many fragmentderived drugs have entered clinical trials. Probing the weak interactions between the target protein and small molecule fragments Modern NMR techniques play a vital role in fragment based lead discovery. In this article, the basic procedures of NMR fragment screening and the relevant key concepts (i.e., target validation, fragment library design, quality control and prevailing NMR fragment screening techniques) were first introduced. The theoretical framework of the NMR techniques commonly used in fragment based lead discovery stage, including chemical shift perturbation, intermolecular NOE, residual dipolar coupling and paramagnetic spin label etc., were also reviewed. Examples were given to show how these techniques can be used to resolve the structure of target/ligand complexs. Strategies of fragment growth, linking and merging were also discussed.
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Protein-Protein Interactions Studied by NMR——A Review Using the Ubiquitin-Proteasome
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ZHANG Nai-Xia, WU Juan, ZHANG Hua-Qun, LIU Xia
Chinese Journal of Magnetic Resonance, 2012, 29(2): 182-189.
Protein-protein interactions (PPIs) play key roles in multiple cellular processes. Both X-ray crystallography and NMR techniques are commonly used to illustrate the structural basis of PPIs. Although most of the available structures of protein complexes are determined by X-ray crystallography, NMR proves to be the technique of choice under special circumstances such as crystallization-resistance, weak binding, and complicated dynamic behavior presented by protein complexes. Chemical shift perturbation analysis, inter-molecular NOE detection, paramagnetic relaxation enhancement and residual dipolar coupling detection are the four major NMR techniques used for studing PPI. The principles and strengths of these NMR techniques and their applications in studying the ubiquitin-proteasome pathway are reviewed in this article.
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Two-Dimensional NMR Spectroscopy for Observing Rock Wettability
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MENG Xiao-Hai, JIANG Zhi-Min, SHI Jing-Sheng, QU Yan-Tao, WANG Wei-Min
Chinese Journal of Magnetic Resonance, 2012, 29(2): 190-200.
Wettability is an important parameter reflecting the water/oil distribution in reservoirs. Studying the surface wettability of the rocks in the reservoir is important for oil recovery. Compared to one-dimensional relaxation spectroscopy, two-dimensional diffusion-relaxation correlation spectroscopy showed greatly improved capability in distinguishing oil and water. In this article, we showed that two-dimensional diffusion-relaxation correlation spectroscopy can be used to measure the surface wettability of glass beads and artificial cores under oilwater coexistence. It was shown that oil/water separation in artificial cores could only be achieved by two-dimentional spectroscopy, but not by traditional 1D NMR relaxation spectroscopy. In conclusion, two-dimensional diffusion-relaxation correlation spectroscopy is an important tool to measure rock surface wettability.
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Design of An FPGA-Based Control Logic in NMR Logging Tool
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YU Hui-Jun, XIAO Li-Zhi, V. Anferov, S. Anferova, ZHU Wan-Li, LIU Hua-Bing, GUO Bao-Xin
Chinese Journal of Magnetic Resonance, 2012, 29(2): 201-208.
Using a CPMG pulse sequence, NMR logging tool transmits high-power radiofrequency (RF) pulses, receives weak echo signals following timing schedule of the CPMG pulse sequence, and dissipates energy stored in the antenna after transmitting the RF pulse. In this article, the control logic of the NMR logging tool is introduced. Field programmable gate array (FPGA) was used to control the timing of the CPMG pulse. The principles and timing requirement of transmitter, Q-switch and de-coupler were given. Simulation results were provided. The control logic introduced was used in a prototype NMR logging tool successfully.
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Quantitative Evaluation of Water-Flooded Zone Using Magnetic Resonance Measurements for Mud Logging (MR-ML) Technology
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XU Xiao-Qiong, WANG Zhi-Zhan,CI Xing-Hua
Chinese Journal of Magnetic Resonance, 2012, 29(2): 209-215.
Water production rate is a key parameter for classifying flooding level in water-flooded zone. How to calculate water production rate from water saturation index is a main problem in evaluating water-flooded zone. In this work, rocks with different water production rate were first produced with the water-injection preperation commonly used for evaluating oil/water relative permeability, and then analyzed by steadystate magnetic resonance measurements for mud logging (MR-ML) spectroscopy. Based on the response characterisics of the rocks, an empirical formula to calculate water production rate from the water saturation index was proposed, which takes advantage of the oil production test data and oil/water relative permeability curve from sealed core analysis. The feasibility of using the water production rate derived to evaluate flooding level was investigated. The results from practical applications showed that MR-ML spectroscopy can be used for rapid identification of water flooded layer, classifying water flooding level, with high accuracy.
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Structural Dependence of 13 C Chemical Shifts in Solid Hydroxy- and Amino-Butyrate Metabolites
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REN Ping-Ping, HUANG Jing, ZHANG Li-Min, TANG Hui-Ru
Chinese Journal of Magnetic Resonance, 2012, 29(2): 231-238.
Butyrate metabolites are present in animals, plants and some microorganisms with various important biological functions. Many molecular features of the metabolites remain to be fully understood, including the characteristics of their structures in the solid states, molecular dynamics and the relationships between these two aspects. In this paper, the 13 C chemical shifts of a series of amino- and hydroxylbutyrate metabolites were analyzed with 13 C CP MAS NMR spectroscopy. Some structure-property relationships were observed. These metabolites had significant differences for their 13 C chemical shifts in solution and the solid state. In the solid state, the presence of amino and hydroxyl groups had obvious contributions to such differences due to their participation in hydrogen-bonding whereas participation of methyl groups in hydrophobic interactions also had observable effects. These findings provide essential basic information for further understanding the structures, molecular dynamics and perhaps polymorphisms for these metabolites.
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An FPGA-Based Multi-Channel Receiver Module for Magnetic Resonance Imaging
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WANG Hong, SUN Hong-Yu, TANG Wei-Nan, LIN Xian-Chai, WANG Wei-Min
Chinese Journal of Magnetic Resonance, 2012, 29(2): 239-247.
A field programmable gate array (FPGA)-based multi-channel receiver module was developed for magnetic resonance imaging (MRI), with its performance evaluated by MRI experiments. Based on a single FPGA, this apparatus operates direct sampling, digital down conversion and data flow control for multi-channel MR signals. The system-level digital signal processing (DSP) development tools offered by Xilinx company——System Generator was used for FPGA function modeling, simulation and automatic code generation of HDL. The sampling rate of this module is 80 MSPS and the receiver bandwidth can be varied between 1 kHz and 1 MHz, thus the module is suitable for an MRI system with a magnetic field lower than 1 T. Inside the FPGA, digital quadrature demodulation, decimation filtering and data stream processing of one to four channels of sampled signals are performed, and the module is expandable to 8 channels. This module has features of small size, highly integrated and reconfigurable and low cost, providing a high-performance digital solution for multi-channel reception system of an MRI spectrometer.
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NMR Study on Multiple Environmental Response Behaviors of Poly[2-(diethylamino)ethylmethacry-late](PDMAEMA)
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XU Yang-Lin, LUO Jing-Ming, RU Ge-Ying, FENG Ji-Wen
Chinese Journal of Magnetic Resonance, 2012, 29(2): 278-287.
Poly[2-(diethylamino)ethylmethacry-late](PDMAEMA) with narrow molecular-weight distribution was synthesized by the atom transfer radical polymerization (ATRP) method. The thermo-sensitive, pH-sensitive and ionic sensitive behaviors of PDMAEMA chains in D2 O solution were investigated by measuring 1 H NMR spectra and relaxation times. It was found that the mobility, temperature-induced lower critical solution temperature (LCST) transition and ionic-strength- induced phase separation of PDMAEMA chains depend on pH of the solution. The mobility of PDMAEMA chains decreased with increasing pH value at room temperature. Ionic-strength-induced phase separation was observed at lower pH values, but not LCST transition. On the contrary, the LCST transition occurred at higher pH values, but not the ionic-strength-induced phase separation.