• Journal of the Korean Magnetic Resonance Society
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• v.26 no.1
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• pp.1-9
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• 2022

There are two distinct approaches to improving the quality of protein NMR structures during refinement: all-atom force fields and accumulated knowledge-assisted methods that include Rosetta. Mao et al. reported that, for 40 proteins, Rosetta increased the accuracies of their NMR-determined structures with respect to the X-ray crystal structures (Mao et al., J. Am. Chem. Soc. 136, 1893 (2014)). In this study, we calculated 32 structures of those studied by Mao et al. using all-atom force field and implicit solvent model, and we compared the results with those obtained from Rosetta. For a single protein, using only the experimental NOE-derived distances and backbone torsion angle restraints, 20 of the lowest energy structures were extracted as an ensemble from 100 generated structures. Restrained simulated annealing by molecular dynamics simulation searched conformational spaces with a total time step of 1-ns. The use of GPU-accelerated AMBER code allowed the calculations to be completed in hours using a single GPU computer-even for proteins larger than 20 kDa. Remarkably, statistical analyses indicated that the structures determined in this way showed overall higher accuracies to their X-ray structures compared to those refined by Rosetta (p-value < 0.01). Our data demonstrate the capability of sophisticated atomistic force fields in refining NMR structures, particularly when they are coupled with the latest GPU-based calculations. The straightforwardness of the protocol allows its use to be extended to all NMR structures.

• Carbon letters
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• v.16 no.3
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• pp.192-197
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• 2015

In the present work, we propose a molecule (C₁₄H₁₄) that can be used as a building block of hexagonal diamond-type crystals and nanocrystals, including wurtzite structures. This molecule and its combined blocks are similar to diamondoid molecules that are used as building blocks of cubic diamond crystals and nanocrystals. The hexagonal part of this molecule is included in the C₁₂ central part of this molecule. This part can be repeated to increase the ratio of hexagonal to cubic diamond and other structures. The calculated energy gap of these molecules (called hereafter wurtzoids) shows the expected trend of gaps that are less than that of cubic diamondoid structures. The calculated binding energy per atom shows that wurtzoids are tighter structures than diamondoids. Distribution of angles and bonds manifest the main differences between hexagonal and cubic diamond-type structures. Charge transfer, infrared, nuclear magnetic resonance and ultraviolet-visible spectra are investigated to identify the main spectroscopic differences between hexagonal and cubic structures at the molecular and nanoscale. Natural bond orbital population analysis shows that the bonding of the present wurtzoids and diamondoids differs from ideal sp³ bonding. The bonding for carbon valence orbitals is in the range (2s^0.982p^3.213p^0.02)-(2s^0.942p^3.313p^0.02) for wurtzoid and (2s^0.932p^3.293p^0.01)-(2s^0.992p^3.443p^0.01) for diamantane.

• Journal of Microbiology and Biotechnology
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• v.17 no.3
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• pp.530-533
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• 2007

It has been well known that the use of Saccharomyces cerevisiae can cause fungemia in critically ill patients and flavone shows an antimicrobial effect on S. cerevisiae. Therefore, we have investigated the activities of thirteen flavone analogues on S. cerevisiae in our studies. Because flavonoids including flavones have antioxidative effects, we try to carry out the activity studies of flavone analogues in vitro and in vivo. In addition, the relationships between the structures of flavone analogues and their biological activities, such as antimicrobial and antioxidative effects, were elucidated using Comparative Molecular Field Analysis calculations. Of the flavone analogues tested here, 3,2'-dihydroxyflavone showed both good antimicrobial and antioxidative activities.

• 한국정보디스플레이학회:학술대회논문집
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• 2004.08a
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• pp.899-902
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• 2004

The molecular reorientations and surface morphologies of rubbed films formed from atactic polystyrene (PS) samples with various molecular weights were investigated in detail. Previously unknown surface topography features were newly discovered in rubbed films, depending on molecular weights: submicroscale groove-like meandering structures composed of fine-grooves like pebbles in tens nanometers are present, oriented perpendicular to the rubbing direction. The vinyl main chains, however, were preferentially reoriented along the rubbing direction and the planes of the phenyl side groups were preferentially reoriented perpendicular to the rubbing direction with para-directions that were positioned nearly normal to the film plane. Nematic liquid crystal (LC) molecules were found to always align on the rubbed PS surfaces along the orientation direction of the submicroscale grooves generated by rubbing.

• Journal of the Korean Wood Science and Technology
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• v.48 no.6
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• pp.769-779
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• 2020

This study investigates the selective fractionation of lignin with uniform structures and lower molecular weight. Lignin solubilization was first performed using a solution of acetic acid (AA) and hydrogen peroxide (HP) (4:1, (v/v)) to form peracetic acid (PAA), which is a strong oxidant. After the PAA-induced solubilization that occurred at 80℃, totally soluble lignin was extracted by ethyl acetate (EA) and divided into organic- and water-soluble fractions. The EA fraction was then fractionated by open-column using three solutions (chloroform-ethyl acetate, methanol, and water) sequentially. With an increase in the solvent polarity during the fractionation step, the molecular weight of the lignin-derived compounds in the fraction increased. Remarkably, some lignin fractions did not have aromatic structures. These fractions were identified as carboxylic acid-containing polymers like poly-carboxylates. These results conclude that the selective production of lignin-derived polymers with specific molecular weight and structural characteristics could be possible through open-column fractionation.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.5-5
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• 2003

The purple acid phosphatases comprise a family of binuclear metal-containing enzymes. The metal centre contains one ferric ion and one divalent metal ion. Spectroscopic studies of the monomeric, ${\sim}$36 kDa mammalian purple acid phosphatases reveal the presence of an Fe(III)Fe(II) centre in which the metals are weakly antiferromagnetically coupled, whereas the dimeric, ${\sim}$110 000 kDa plant enzymes contain either Fe(III)Zn(II) or Fe(III)Mn(II). The three dimensional structures of the red kidney bean and pig enzymes show very similar arrangements of the metal ligands but some significant differences beyond the immediate vicinity of the metals. In addition to the catalytic domain, the plant enzyme contains a second domain of unknown function. A search of sequence databases was undertaken using a sequence pattern which includes the conserved metal-binding residues in the plant and animal enzymes. The search revealed the presence in plants of a 'mammalian-type' low molecular weight purple acid phosphatase, a high molecular weight form in some fungi, and a homologue in some bacteria. The catalytic mechanism of the enzyme has been investigated with a view to understanding the marked difference in specificity between the Fe-Mn sweet potato enzyme, which exhibits highly efficient catalysis towards both activated and unactivated phosphate esters, and other PAPs, which hydrolyse only activated esters. Comparison of the active site structures of the enzymes reveal some interesting differences between them which may account for the difference. The implications fur understanding the physiological functions of the enzymes will be discussed.

• Applied Microscopy
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• v.46 no.3
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• pp.134-139
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• 2016

Detailed structural and molecular imaging of intact organs has incurred academic interest because the associated technique is expected to provide innovative information for biological investigation and pathological diagnosis. The conventional methods for volume imaging include reconstruction of images obtained from serially sectioned tissues. This approach requires intense manual work which involves inevitable uncertainty and much time to assemble the whole image of a target organ. Recently, effective tissue clearing techniques including CLARITY and ACT-PRESTO have been reported that enables visualization of molecularly labeled structures within intact organs in three dimensions. The central principle of the methods is transformation of intact tissue into an optically transpicuous and macromolecule permeable state without loss of intrinsic structural integrity. The rapidly evolving protocols enable morphological analysis and molecular labeling of normal and pathological characteristics in large assembled biological systems with single-cell resolution. The deep tissue volume imaging will provide fundamental information about mutual interaction among adjacent structures such as connectivity of neural circuits; meso-connectome and clinically significant structural alterations according to pathologic mechanisms or treatment procedures.

• Proceedings of the Korean Vacuum Society Conference
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• 2011.02a
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• pp.310-310
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• 2011

Morphological evolution of amorphous carbon film is investigated by molecular dynamics simulation. Here, energetic carbon atoms (75 eV) are deposited on the diamond (001) substrate to find effect of incidence angles. At normal and near-normal incidences ($0^{\circ}{\sim}30^{\circ}$) atomically smooth surfaces are observed during their growth. However, rough surfaces emerge and develop into a ripple structure at grazing incidences ($60^{\circ}{\sim}70^{\circ}$). The different growth modes according to the incidence angles can be described by impact-induced displacements of atoms. Downhill transport along any sloped surfaces is predominant for the case of normal incidence. As the incidence angles become grazing, uphill transport is allowed along the surfaces, which have smaller slopes than incidence angle, so the surface features can be amplified. Impact-induced transport and self-shadowing effect can be responsible to the initial growth of seeding structures at a grazing incidence, which would be grown up as tilted columnar structures in further depositions.

• Korean Journal of Materials Research
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• v.16 no.2
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• pp.92-98
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• 2006

Molecular dynamics simulations were performed to study interface structures between an $Al_2O_3$ crystalline phase and a interface phase of $CaAl_2Si_2O_8$. We calculated atomic structures and excess interface energies in systems with different thicknesses of the interface film. It was found that excess interface energies at first readily decreased with increasing film thickness, but increased for larger thicknesses of more than 2 nm. The excess energies of $Al_2O_3/CaAl_2Si_2O_8$ interfaces exhibit a minimum at a thickness around 1 nm. In this range of film thicknesses, the atoms in the interface film show a short-range ordered structure and slow diffusion rather than the random structure and rapid diffusion expected to an observation of an equilibrium thickness for interface films in ceramics.

• Transactions of the Korean Society of Automotive Engineers
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• v.12 no.1
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• pp.106-113
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• 2004

Most of mechanical structures are composed of many substructures connected to one another by various types of mechanical joints. In automotive engineering, it is important to study these connected structures under various dynamic forces for the evaluations of fatigue life and stress concentration exactly. In this study, the dynamic response of vehicle structure to external forces is classified an inverse problem involving strains from the experiment and the analysis. The practical dynamic forces are determined by the combination of the analytical and experimental method with analyzed strain by quasi-static finite element analysis under unit force and with measured strain by a strain gage under driving load, respectively. In a stressed body, inter-molecular chemical bonds are failed beyond the certain magnitude. The failure of molecular structure in material is considered as a time process of which rate is determined by mechanical stress. That is, the failure of inter-molecular chemical bonds is the fatigue lift of material. This kinetic concept is expressed as lethargy coefficient. And S-N curve is obtained with the lethargy coefficient from quasi-static tensile test. Equivalent practical dynamic force is obtained from the identification of practical dynamic force for one loading point. Using the practical dynamic force and S-N curve, fatigue life of a window pillar is analyzed with FEM under the identified force by the procedure of above mentioned.