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.

The Kubo formalism and utilizing the projection operator technique (POT) introduced by Kawabata, the electron spin resonance (ESR) line-shape formula for carbon nanotubes through the hyperfine interaction introduced earlier in terms of POT. We can see that the line-width decreases exponentially as the temperature increases. The spin relaxation time show gradual decrease as magnetic field becomes larger. The analysis reveals the peculiarities in spin relaxation inherent to one dimensional system at low temperature and weak magnetic fields. Thus, the present technique is considered to be more convenient to explain the carbon nanotubes as in the case of other optical transitions.

The structural geometry of $[N(CH_3)_4]_2CdCl_4$ in a hexagonal phase is studied by $^1H$ MAS NMR, $^{13}C$ CP/MAS NMR, and $^{14}N$ NMR. The changes in the chemical shifts for $^{13}C$ and $^{14}N$ in the hexagonal phase are explained by the structural geometry. In addition, the temperature dependencies of the spin-lattice relaxation time in the rotating frame $T_{1{\rho}}$ for $^1H$ MAS NMR and $^{13}C$ CP/MAS NMR are measured.

Four spiroketal sestertepenoids (1 ~ 4) were isolated from the marine sponge Haliclona species. Their planar structures were completely determined from a combination of extensive 1D and 2D NMR experiments, and also the relative stereochemistry on the chiral centers were established by the ROESY experiment. Compounds 1 ~ 3 were determined as the same planar structures with different stereochemistry on the chiral centers C-11 and C-13. Of these, 1 was identified as a new stereoisomer. Four compounds showed the inhibition effect of nitric oxide (NO) production in LPS-stimulated RAW 264.7 cells (0.7~2.0 g/ml).

The microscopic dynamics of $CsH_2PO_4$, with two distinct hydrogen bond lengths, are studied by static nuclear magnetic resonance (NMR) and magic angle spinning (MAS) NMR. The proton dynamics of the two crystallographically inequivalent hydrogen sites were discussed in terms of the $^1H$ NMR and $^1H$ MAS NMR spectra. Although the hydrogen bonds have two inequivalent sites, H(1) and H(2), distinct proton dynamics for the two sites were not found. Further, the $^{133}Cs$ spectrum is more or less continuous near $T_{C1}$ (=153 K). Finally, the phase transition mechanism of $T_{C1}$ in $CsH_2PO_4$ is related to the ordering of protons.

The causative agent of shigellosis, Shigella flexneri, is a Gram-negative anaerobic bacterial pathogen that causes one of the most infectious bacterial dysenteries in humans. It originates infection by invading cells of the colonic epithelium using a type III secretion system. Despite S. flexneri is closely linked with the human disease, structural study is very deficient. Here, we have initiated NMR study of SF1002 which is the uncharacterized protein from S. flexneri strain 5a M90T. Based on a series of triple resonance spectra, sequence-specific assignments of the backbone amide resonances of SF1002 could be completed. This NMR study would contribute to the structural genomics of S.flexneri.

The mannitol transporter Enzyme $II^{Mtl}$ of the bacterial phosphotransferase system has two cytoplasmic phosphoryl transfer domains $IIA^{Mtl}$ and $IIB^{Mtl}$. The two domains are linked by a flexible peptide linker in mesophilic bacterial strains, whereas they are expressed as separated domains in thermophilic strains. Here, we carried out backbone assignment of $IIA^{Mtl}$ from thermophilic Thermoanaerobacter Tencongensis using a suite of heteronuclear triple resonance NMR spectroscopy. We have completed 94% of the backbone assignment, and obtained secondary structural information based on torsion angles derived from the chemical shifts. $IIA^{Mtl}$ of Thermoanaerobacter Tencongensis is predicted to have six ${\beta}$ strands and six ${\alpha}$ helices, which is analogous to $IIA^{Mtl}$ of Escherichia coli.

MRA1997 is a 76-residue conserved hypothetical protein of Mycobacterium tuberculosis H37Ra, one of the most pathogenic bacterial species and the causative agent of tuberculosis. In this study, the sequence-specific backbone resonance assignment of MRA1997 was performed using NMR spectroscopy. Approximately 88.3% of the total resonances could be unambiguously assigned. By analyzing deviations of the $C{\alpha}$ and $C{\beta}$ chemical shift values, the secondary structure of MRA1997 was calculated. The result revealed that secondary structure of MRA 1997 consists of one ${\alpha}$-helix and five ${\beta}$-sheets. Our structural study will be a footstone towards the characterization of the three-dimensional structure of MRA1997.