• Journal of the Korean Magnetic Resonance Society
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• v.17 no.1
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• pp.11-18
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• 2013

Rapid advances of computational power and method have made it practical to apply the time-consuming calculations with all-atom force fields and sophisticated potential energies into refining NMR structure. Added to the all-atom force field, generalized-Born implicit solvent model (GBIS) contributes substantially to improving the qualities of the resulting NMR structures. GBIS approximates the effects that explicit solvents bring about even with fairly reduced computational times. Although GBIS is employed in the final stage of NMR structure calculation with experimental restraints, the effects by GBIS on structures have been reported notable. However, the detailed effect is little studied in a quantitative way. In this study, we report GBIS refinements of ubiquitin and GB1 structures by six GBIS models of AMBER package with experimental distance and backbone torsion angle restraints. Of GBIS models tested, the calculations with igb=7 option generated the closest structures to those determined by X-ray both in ubiquitin and GB1 from the viewpoints of root-mean-square deviations. Those with igb=5 yielded the second best results. Our data suggest that the degrees of improvements vary under different GBIS models and the proper selection of GBIS model can lead to better results.

• Journal of the Korean Magnetic Resonance Society
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• v.9 no.1
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• pp.29-37
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• 2005

Intra-cellular drug uptake in Xenopus laevis oocyte has been elucidated using localized MR spectroscopy (MRS) and PFG NMR techniques at a 600 $MH_z$(Bruker, 14.1 T) NMR spectrometer. The localized MRS has been done with a homemade probe, and shows the intra-cellular uptake of nicotinamide. The self-diffusion of the molecule in Xenopus oocyte was obtained by PFG NMR technique. The measured data are well fitted with a linear combination of two exponential functions, which shows that there are two types of drug molecules, intra-and extra-cellular molecules. Diffusion coefficients of intra- and extra-cellular drug molecules are 3.7 $\times$ $10^{-11}$ $\m^{2}/s$and 6.4 $\times$ $10^{-10}$ $\m^{2}/s$, respectively. In the weighting factors there is shown that about 5% of drug molecule is inside the cells. These techniques can be used for drug screening in molecule-, cell-, and tissue-based preclinical test.

• Bulletin of the Korean Chemical Society
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• v.34 no.3
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• pp.823-826
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• 2013

A low-${\varepsilon}$ solid-state NMR(Nuclear Magnetic Resonance) probe was developed for the spectroscopic analysis of two-dimensional $^{15}N-^1H$ heteronuclear dipolar coupling in dilute membrane proteins oriented in hydrated and dielectrically lossy lipid environments. The system employed a 800 MHz narrow-bore magnet. A solenoid coil strip shield was used to reduce deleterious RF sample heating by minimizing the conservative electric fields generated by the double-tuned resonator at high magnetic fields. The probe's design, construction, and performance in solid-state NMR experiments at high magnetic fields are described here. Such high-resolution solid-state NMR spectroscopic analysis of static oriented samples in hydrated phospholipid bilayers or bicelles could aid the structural analysis of dilute biological membrane proteins.

• Bulletin of the Korean Chemical Society
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• v.34 no.5
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• pp.1467-1472
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• 2013

Metabolomics is a field that studies systematic dynamics and secretion of metabolites from cells to understand biological pathways based on metabolite changes. The metabolic profiling of intact human colorectal tissues was performed using high-resolution magic angle spinning (HR-MAS) NMR spectroscopy, which was unnecessary to extract metabolites from tissues. We used two different groups of samples, which were defined as normal and cancer, from 9 patients with colorectal cancer and investigated the samples in NMR experiments with a water suppression pulse sequence. We applied target profiling and multivariative statistical analysis to the analyzed 1D NMR spectra to identify the metabolites and discriminate between normal and cancer tissues. Cancer tissue showed higher levels of arginine, betaine, glutamate, lysine, taurine and lower levels of glutamine, hypoxanthine, isoleucine, lactate, methionine, pyruvate, tyrosine relative to normal tissue. In the OPLS-DA (orthogonal partial least square discriminant analysis), the score plot showed good separation between the normal and cancer groups. These results suggest that metabolic profiling of colorectal cancer could provide new biomarkers.

• Journal of the Korean Magnetic Resonance Society
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• v.10 no.2
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• pp.197-202
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• 2006

[ $^{11}B$ ] nuclear magnetic resonance (NMR) measurements were performed on the single crystals of $TbB_4$ to investigate local electronic structure and 4f spin dynamics. $^{11}B$ NMR spectrum, Knight shift, spin-lattice and spin-spin relaxation rates were measured down to 4K at 8T. $^{11}B$ NMR shift and linewidth are huge and strongly temperature dependent due to the 4f moments. In addition, both are proportional to magnetic susceptibility, indicating that the hyperfine field at the boron site originates from the 4f spins of Tb. Below $T_N$, the single broad resonance peak of $^{11}B$ NMR splits into several peaks reflecting the local magnetic fields due to antiferromagnetic spin arrangements. The longitudinal and the transverse relaxation rates, $1/T_1\;and\;1/T_2$, independent of temperature above $T_N$, decreases tremendously confirming huge suppression of spin fluctuation below $T_N$.

• Journal of the Korean Magnetic Resonance Society
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• v.19 no.1
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• pp.1-10
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• 2015

Refinements with atomistic molecular dynamics (MD) simulation have contributed to improving the qualities of NMR structures. In most cases, the calculations with atomistic MD simulation for NMR structures employ generalized-Born implicit solvent model (GBIS) to take into accounts solvation effects. Developments in algorithms and computational capacities have ameliorated GBIS to approximate solvation effects that explicit solvents bring about. However, the quantitative comparison of NMR structures in the latest GBIS and explicit solvents is lacking. In this study, we report the direct comparison of NMR structures that atomistic MD simulation coupled with GBIS and water molecules refined. Two model proteins, GB1 and ubiquitin, were recalculated with experimental distance and torsion angle restraints, under a series of simulated annealing time steps. Whereas the root mean square deviations of the resulting structures were apparently similar, AMBER energies, the most favored regions in Ramachandran plot, and MolProbity clash scores witnessed that GBIS-refined structures had the better geometries. The outperformance by GBIS was distinct in the structure calculations with sparse experimental restraints. We show that the superiority stemmed, at least in parts, from the inclusion of all the pairs of non-bonded interactions. The shorter computational times with GBIS than those for explicit solvents makes GBIS a powerful method for improving structural qualities particularly under the conditions that experimental restraints are insufficient. We also propose a method to separate the native-like folds from non-violating diverged structures.

• Journal of the Korean Magnetic Resonance Society
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• v.13 no.2
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• pp.143-153
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• 2009

Luteinizing Hormone Releasing Hormone (LHRH) is composed of 10 amino acids, and is best known as a neurotransmitter. Because of the 80% homology in animals, much more concerns have focused on the substances that have similar functions or can control LHRH. Ni, Cu-LHRH complexes were synthesized. The degree of complexation was monitored by $^1H,\;^{13}C$-NMR chemical shifts, and final products were identified by ESI-Mass spectrum. Solution-state structure determination of Ni-LHRH complex was accomplished by using NMR results and NMR-based distance geometry (DG). Interproton distances from nuclear Overhauser effect spectroscopy (NOESY) were utilized for the molecular structure determination. Results were compared with previous structures obtained from energy minimization and other spectroscopic methods. Structure obtained in this study has a cyclic conformation which is similar to that of energy minimized, and exhibits a specific a-helical turn with residue numbers (2~7) out of 10 amino acids. Comparison of chemical shifts and EPR studies of Ni, Cu-LHRH complexes exhibit that Ni-LHRH complex has same binding sites with the 4-coordination mode as in Zn-LHRH complex.

• Journal of the Korean Applied Science and Technology
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• v.36 no.1
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• pp.84-89
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• 2019

To characterize the molecular structure of BzO-gal synthesized using Escherichia coli ${\beta}$-gal, NMR ($^1H$- and $^{13}C$-) spectroscopy and mass spectrometry of BzO-gal were conducted. $^1H$ NMR spectrum of BzO-gal showed multiple peaks corresponding to the galactosyl group, which is an evidence of galactosylation on BzOH. Five proton peaks around the aromatic region at ${\delta}_H$ 7.43 ~ 7.24 ppm and 2 peaks from ${\delta}_H$ 4.93 and 4.67 ppm were evidence of the presence of the benzyl group. Seven proton peaks at ${\delta}_H$ 4.32 ~ 3.46 ppm showed the presence of a monosaccharide and were indicative of galactosylation on BzOH. $^{13}C$ NMR spectrum also revealed the presence of 11 carbons suggestive of BzO-gal. The mass value (sodium adduct ion of BzO-gal, m/z = 293.0994) from mass spectrometry analysis of BzO-gal, and $^1H$ and $^{13}C$ NMR spectral data were in good agreement with the expecting structure of BzO-gal. We are expecting that through future study it will eventually be able to develop a new additive of low cytotoxicity.

• Bulletin of the Korean Chemical Society
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• v.29 no.5
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• pp.911-912
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• 2008

• Proceedings of the KSMRM Conference
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• 2002.11a
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• pp.129-129
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• 2002

목적： 초상자성 nano 산화철 입자의 특성을 연구하기 위하여, 여러 다른 자기장 세기에서의 NMR 자기공이완시간(T1/T2)을 측정하고, 초상자성 nano-particle 조영제의 기전에 관한 모델로부터 얻어 진 계산식과 비교해보며, 다양한 온도에서의 EPR spectrum을 이용하여 이들의 전자적 성질을 비교해 보고자 하였다.