• Proceedings of the KSME Conference
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• 2007.05a
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• pp.527-531
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• 2007

The classical continuum theory-based thin film model is independent of their size and the surface effect can be ignored. But the surface to bulk ratio becomes very large in nano-size structures such as nano film, nano wire and nano beam. In this case, surface effect plays an important role and its contribution of the surface effect must be considered. Molecular dynamics simulation has been a conventional way to analyze these ultra-thin structures but structures in the range between submicro and micro are difficult to analyze by classical molecular dynamics due to the restriction of computing resources and time. Therefore, in present study, the continuum-based method is considered to predict the overall physical and mechanical properties of the structures in nano-scale, especially, for the thin-film. The proposed continuum based-thin plate finite element is efficient and reliable for the prediction of nano-scale film behavior.

• Applied Microscopy
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• v.47 no.4
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• pp.226-232
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• 2017

Electron microscopy and X-ray diffraction have together played a key role in our understanding of the molecular structure and mechanism of contraction of muscle. This review highlights the role of electron microscopy, from early insights into thick and thin filament structure by negative staining, to studies of single myosin molecule structure, and finally to recent high-resolution structures by cryo-electron microscopy. Muscle filaments are designed for movement. Their labile structures thus present challenges to obtaining near-atomic detail, which are also discussed.

• Bulletin of the Korean Chemical Society
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• v.10 no.2
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• pp.185-190
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• 1989

Geometries for a number of representative ${\beta}$ -lactam antibiotics (penams, cephems and monobactams) have been calculated by computer graphics/molecular mechanics energy minimization procedures using both MM2 and AMBER force fields. The calculated geometries have been found in reasonable agreement with the geometries reported in the X-ray crystal structures, especially in terms of the pyramidal character of the amide nitrogen in the ${\beta}$-lactam ring and the Cohen distance. Based on these calculations, it is suggested that the nitrogen atom in the monobactams may also have pyramidal geometries in the biologically active conformations.

• Bulletin of the Korean Chemical Society
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• v.11 no.4
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• pp.313-317
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• 1990

Geometries for several representative quinolone carboxylate type antibacterials have been calculated by computer graphics/molecular mechanics energy minimization procedures using both MM2 and AMBER force fields. The calculated geometries were found to be in reasonable agreements with the corresponding X-ray crystal structures. It has been pointed out that notwithstanding the weaknesses associated with calculating the resonance and hydrogen bonding contributions, the employed methods are capable of generating credible ring geometries and torsional angle dispositions of N(1)-ethyl and 3-carboxylate substituents of the quinolones.

• Proceedings of the Korean Biophysical Society Conference
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• 1998.06a
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• pp.10-10
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• 1998

IMPs are important to cells in functions such as transport, energy transduction and signalling. Three dimensional molecular structures of such proteins at atomic level are needed to understand such processes. Prediction of such structures (and functions) is necessary especially because there are only a small number of membrane protein structures determined in atomic resolution.(omitted)

• Bulletin of the Korean Chemical Society
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• v.30 no.3
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• pp.623-629
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• 2009

We have performed replica-exchange molecular dynamics simulations on 41 residue peptide mainly composed of NAC (non A$\beta$ component) sequence in $\alpha$-Synuclein. To investigate conformational characteristics of intrinsically unstructured peptides, we carried out structural analysis on the ‘representative structures’ for ensemble of structures occurring at different temperatures. The secondary structure profile obtained from our simulations suggests that the NAC region of $\alpha$-synuclein can be divided into roughly three helical-like segments. It is found that the overall helix-turn-helix like topology is conserved even though the conformational fluctuations grow as the temperature increases. The coordinate-based and the distance-based representative structures exhibit noticeable differences at higher temperatures while they are similar at lower temperatures. It is found that structural variations for the coordinate-based representative structures are much larger, suggesting that distance-based representative structures provide more reliable information concerning characteristic features of intrinsically unstructured proteins. The present analysis also indicates that the conformational features of representative structures at high temperatures might be related to those in membrane or low pH environment.

• Bulletin of the Korean Chemical Society
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• v.15 no.10
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• pp.852-856
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• 1994

A series of aliphatic hydrocarbons, methane to hexane in the liquid state, are modeled with the molecular mechanical potential parameters treating all hydrogen degrees of freedom explicitly. Thermodynamic properties (heat capacities and heats of vaporization) are calculated from relatively short (20ps) molecular dynamics trajectories. The liquid state structures are also examined through various radial distribution functions. Molecular dynamics simulations reproduce experimentally measured properties within a few percent errors, thus indicate that the present set of all-hydrogen parameters is suitable for simulating macromolecular systems in bulk.

• Bulletin of the Korean Chemical Society
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• v.32 no.7
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• pp.2325-2331
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• 2011

Human CDX1 and CDX2 genes play important roles in the regulation of cell proliferation and differentiation in the intestine. Hox genes clustered on four chromosomal regions (A-D) specify positional signaling along the anterior-posterior body axis, including intestinal development. Using glutathione S-transferase (GST) pulldown assays, molecular interaction measurements, and fluorescence measurements, we found that the homeodomains (HDs) of CDX1 and CDX2 directly interact with that of HOXD8 in vitro. CDX1 showed significant affinity for HOXD8, but CDX2 showed weak affinity for HOXD8. Thus far, three-dimensional structures of CDX1/2 and HOXD8 have not been determined. In this study, we developed a molecular docking model by homology modeling based on the structures of other HD members. Proteins with mutations in the HD of CDX1 (S185A, N190A, T194A, and V212A) also bound to the HD of HOXD8. Our study suggests that the HDs of CDX1/2 resemble those of HOXD8, and we provide the first insight into the interaction between the HDs of CDX1/2 proteins and those of HOXD8.

• Bulletin of the Korean Chemical Society
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• v.27 no.4
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• pp.568-572
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• 2006

To study the effect of sequence on DNA structure, the two decamer crystal structures one alternating,d(GTACGCGTAC), and the other non-alternating, d(GGCCGCGGCC), were solved. Crystals of both decamers belong to the hexagonal space group $P6_122$, with one strand in the asymmetric unit. The unit cell constants of the alternating decamer are a = b = 39.26 $\AA$, c = 77.70 $\AA$. The structure was refined with 1,828 reflections from 8.0 to 2.0 Aresolution to an R value of 21.3% with all DNA atoms and 63 water molecules. The isomorphous non-alternating decamer had unit cell dimensions of a = b = 39.05 $\AA$, c = 82.15 $\AA$. The structure was refined with 2,423 reflections from 8.0 to 2.0 $\AA$ resolution to a final R value of 22.2% for all DNA atoms and 65 water molecules. Although the average helical parameters of the decamers are typical of A-DNAs, there are some minor differences between them. The helical twist, rise, x-displacement, inclination and roll alternate in the alternating decamer, but do not in the non-alternating decamer. The backbone conformations in both structures show some differences; the residue G(7) of the alternating decamer is trans for $\alpha$ and $\gamma$ while the trans conformations are observed at the residue G(8) of the non-alternating decamer.

• Bulletin of the Korean Chemical Society
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• v.33 no.12
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• pp.4084-4092
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• 2012

Theoretical calculations based on density functional theory (DFT) were performed to study the substituent effect on the geometric and electronic structures as well as the biological behavior of technetium-99m-labeled diphosphonate complexes. Optimized structures of these complexes are surrounded by six ligands in an octahedral environment with three unpaired 4d electrons ($d^3$ state) and the optimized geometry of $^{99m}Tc$-MDP agrees with experimental data. With the increase of electron-donating substituent or tether between phosphate groups, the energy gap between frontier orbitals increases and the probability of non-radiative deactivation via d-d electron transfer decreases. The charge distribution reflects a significant ligand-to-metal electron donation. Based on the calculated geometric and electronic structures and biologic properties of $^{99m}Tc$-diphosphonate complexes, several structure-activity relationships (SARs) were established. These results may be instructive for the design and synthesis of novel $^{99m}Tc$-diphosphonate bone imaging agent and other $^{99m}Tc$-based radiopharmaceuticals.