• Journal of the Korean Magnetic Resonance Society
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• v.28 no.3
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• pp.10-14
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• 2024

Caveolin3, mainly expressed in muscle tissue types, is a structural scaffolding protein of caveolae which are microdomains of plasma membrane. To elucidate the relationship between structure and function, several studies on the structure of caveolins using NMR have been reported. Because the ionic strength can affect the electrostatic-driven association of proteins with ligand and protein structure, the effect of salt in the structural studies has to be considered. In this work, we observed that the chemical shifts of Cav3 in the LPPG detergent change depending on salt concentration. The R2 values also show salt concentration-dependent changes. Specifically, in the N-terminal region where conformational changes and various interactions occur, the R2 values decrease. Interestingly, the R2 values of residues expected to be located in the LPPG detergent are also influenced by the salt concentration. This work suggests that the concentration of NaCl can affect interpretation of NMR data from membrane proteins.

• Journal of the Korean Magnetic Resonance Society
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• v.20 no.4
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• pp.102-108
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• 2016

With the rapid increase of data on protein-protein interactions, the need for delineating the 3D structures of huge protein complexes has increased. The protocols for determining nuclear magnetic resonance (NMR) structure can be applied to modeling complex structures coupled with sparse experimental restraints. In this report, I suggest the use of multiple rigid bodies for improving the efficiency of NMR-assisted structure modeling of huge complexes using CYANA. By preparing a region of known structure as a new type of residue that has no torsion angle, one can facilitate the search of the conformational spaces. This method has a distinct advantage over the rigidification of a region with synthetic distance restraints, particularly for the calculation of huge molecules. I have demonstrated the idea with calculations of decaubiquitins that are linked via Lys6, Lys11, Lys27, Lys29, Lys33, Lys48, or Lys63, or head to tail. Here, the ubiquitin region consisting of residues 1-70 was treated as a rigid body with a new residue. The efficiency of the calculation was further demonstrated in Lys48-linked decaubiquitin with ambiguous distance restraints. The approach can be readily extended to either protein-protein complexes or large proteins consisting of several domains.

• Proceedings of the Korean Biophysical Society Conference
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• 1997.07a
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• pp.14-14
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• 1997

Structure of potent derivatives of gaegurin, an antimicrobial peptide from Korean frog, is studied by CD and NMR spectroscopy. Gaegurin did not show any secondary structure in aqueous environment, but adopted ${\alpha}$-helix in aqueous TFE solution, SDS and liposome buffer. NMR study showed distinct difference in stability near proline residue in helix.(omitted)

• Journal of Magnetics
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• v.21 no.4
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• pp.599-602
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• 2016

Fluoride (F) is an important element for the mineralization of body tissues. The purpose of this study was to administer fluoride prenatally to rats to evaluate its beneficial concentration for rat bone using microstructural analysis, to analyze its effect on the bone structure, and to evaluate the effect of its transfer through rat placenta. Fourier transform infrared spectroscopy (FTIR) and nuclear magnetic resonance spectrometry (NMR) were performed. The $^{19}F$ NMR and $^{31}P$ NMR signals suggested the existence of fluoride ions in the apatite lattice because the signals were caused by the fluoride ions that were coupled to the phosphate atoms and were affected in the phosphate phases other than the element phases in the apatite. Consequently, if it was not affected too much, the desirable concentration of prenatal fluoride treatment could have a helpful effect on the bone crystal structure through placental fluoride transfer.

• Journal of the Korean Magnetic Resonance Society
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• v.22 no.4
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• pp.101-106
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• 2018

Magnetite is the oldest magnet material known to mankind. It is getting attention again from solid state physics researchers now a days because it is one of the most strongly correlated electron systems. Spin, charge, and orbital orders are interplaying with lattice and involved in the Verwey transition where magnetization, conductivity, and structure changes suddenly. The peculiar ordering states above and below the transition temperature mainly originate from the coexistence of $Fe^{2+}$ and $Fe^{3+}$ ions in the B site of the inverse spinel structure. In particular, the state of the charge and orbital order was the oldest and most intriguing problem. NMR has made significant contribution to the investigation of this question. A. Abragam stated that there is no doubt that NMR is a very powerful tool for the study of ferromagnetic and antiferromagnetic materials. In this mini-review, a short history of NMR investigation of magnetite is presented, providing a support to Abragam's claim.

• Journal of the Korean Magnetic Resonance Society
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• v.18 no.1
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• pp.24-29
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• 2014

Atomistic molecular dynamics (MD) simulation has become mature enabling close approximation of the real behaviors of biomolecules. In biomolecular NMR field, atomistic MD simulation coupled with generalized implicit solvent model (GBIS) has contributed to improving the qualities of NMR structures in the refinement stage with experimental restraints. Here all-atom force fields play important roles in defining the optimal positions between atoms and angles, resulting in more precise and accurate structures. Despite successful applications in refining NMR structure, however, the research that has studied the influence of force fields in GBIS is limited. In this study, we compared the qualities of NMR structures of two model proteins, ubiquitin and GB1, under a series of AMBER force fields-ff99SB, ff99SB-ILDN, ff99SB-NMR, ff12SB, and ff13-with experimental restraints. The root mean square deviations of backbone atoms and packing scores that reflect the apparent structural qualities were almost indistinguishable except ff13. Qualitative comparison of parameters, however, indicates that ff99SB-ILDN is more recommendable, at least in the cases of ubiquitin and GB1.

• Journal of the Mineralogical Society of Korea
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• v.24 no.4
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• pp.289-300
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• 2011

Atomistic origins of carbon solubility into silicates are essential to understand the effect of carbon on the properties of silicates and evolution of the Earth system through igneous and volcanic processes. Here, we investigate the atomic structure and NMR properties of dissolved carbon in enstatite using Raman spectroscopy and quantum chemical calculations. Raman spectrum for enstatite synthesized with 2.4. wt% of amorphous carbon at 1.5 GPa and $1,400^{\circ}C$ shows vibrational modes of enstatite, but does not show any vibrational modes of $CO_2$ or ${CO_3}^{2-}$. The result indicates low solubility of carbon into enstatite at a given pressure and temperature conditions. Because $^{13}C$ NMR chemical shift is sensitive to local atomic structure around carbon and we calculated $^{13}C$ NMR chemical shielding tensors for C substituted enstatite cluster as well as molecular $CO_2$ using quantum chemical calculations to give insights into $^{13}C$ NMR chemical shifts of carbon in enstatite. The result shows that $^{13}C$ NMR chemical shift of $CO_2$ is 125 ppm, consistent with previous studies. Calculated $^{13}C$ NMR chemical shift of C is ~254 ppm. The current calculation will alllow us to assign potential $^{13}C$ NMR spectra for the enstatite dissolved with carbon and thus may be useful in exploring the atomic environment of carbon.

• Journal of the Korean Magnetic Resonance Society
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• v.1 no.1
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• pp.45-58
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• 1997

Heteropoly compounds, H3PMo12O40, CsxH3-xPMo12O40, and vanadium containing heteropoly compound were characterized by Solid-state broad line 1H MAS NMR, 31P MAS NMR, and High Speed MAS 51V NMR spectroscopy of quadrupolar nuclei. The effects of calcination, dehydration, and the number of protons on the structure of heteropoly compounds were studied. The results of this study demonstrate that these Solid-state NMR techniques are very useful tools to study heteropoly compounds.

• 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.

• Bulletin of Food Technology
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• v.24 no.2
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• pp.178-186
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• 2011