• Proceedings of the Korean Society of Potoscience Conference
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• spring
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• pp.28-28
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• 2004

• Bulletin of the Korean Chemical Society
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• v.21 no.5
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• pp.523-525
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• 2000

• Bulletin of the Korean Chemical Society
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• v.34 no.4
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• pp.1043-1046
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• 2013

Prediction of physicochemical properties of organic molecules is an important process in chemistry and chemical engineering. The MSEP approach developed in our lab calculates the molecular surface electrostatic potential (ESP) on van der Waals (vdW) surfaces of molecules. This approach includes geometry optimization and frequency calculation using hybrid density functional theory, B3LYP, at the 6-31G(d) basis set to find minima on the potential energy surface, and is known to give satisfactory QSPR results for various properties of organic molecules. However, this MSEP method is not applicable to screen large database because geometry optimization and frequency calculation require considerable computing time. To develop a fast but yet reliable approach, we have re-examined our previous work on organic molecules using two semi-empirical methods, AM1 and PM3. This new approach can be an efficient protocol in designing new molecules with improved properties.

• IMMUNE NETWORK
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• v.10 no.2
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• pp.35-45
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• 2010

Background: Expression of recombinant antibodies and their derivatives fused with other functional molecules such as alkaline phosphatase in Escherichia coli is important in the development of molecular diagnostic reagents for biomedical research. Methods: We investigated the possibility of applying a well-known Fos-Jun zipper to dimerize $V_H$ and $V_L$ fragments originated from the Fab clone (SP 112) that recognizes pyruvate dehydrogenase complex-E2 (PDC-E2), and demonstrated that the functional zipFv-112 and its alkaline phosphatase fusion molecules (zipFv-AP) can be produced in the cytoplasm of Origami(DE3) trxB gor mutant E. coli strain. Results: The zipFv-AP fusion molecules exhibited higher antigen-binding signals than the zipFv up to a 10-fold under the same experimental conditions. However, conformation of the zipFv-AP seemed to be influenced by the location of an AP domain at the C-terminus of $V_H$ or $V_L$ domain [zipFv-112(H-AP) or zipFv-112(L-AP)], and inclusion of an AraC DNA binding domain at the C-terminus of VH of the zipFv-112(L-AP), termed zipFv-112(H-AD/L-AP), was also beneficial. Cytoplasmic co-expression of disulfide-binding isomerase C (DsbC) helped proper folding of the zipFv-112(H-AD/L-AP) but not significantly. Conclusion: We believe that our zipFv constructs may serve as an excellent antibody format bi-functional antibody fragments that can be produced stably in the cytoplasm of E. coli.

• Biomaterials and Biomechanics in Bioengineering
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• v.2 no.2
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• pp.97-109
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• 2015

A series of amphiphilic graft copolymers were synthesized by varying the number of graft chains and graft chain lengths. The polarity of the hydrophobic graft chain on the copolymers was varied their solution properties. The glass transition temperature of the copolymers was in the low-temperature region, because of the amorphous nature of poly (trimethylene carbonate) (PTMC). The surface morphology of the lyophilized colloid gel had a bundle structure, which was derived from the combination of poly(N-hydroxyethylacrylamide)( poly(HEAA)) and PTMC. The solution properties were evaluated using dynamic light scattering and fluorescence measurements. The particle size of the graft copolymers was about 30-300 nm. The graft copolymers with a higher number of repeating units attributed to the TMC (trimethylene carbonate) component and with a lower macromonomer ratio showed high thermal stability. The critical association concentration was estimated to be between $2.2{\times}10^{-3}$ and $8.9{\times}10^{-2}mg/mL$, using the pyrene-based fluorescence probe technique. These results showed that the hydrophobic chain of the graft copolymer having a long PTMC segment had a low polarity, dependent on the number of repeating units of TMC and the macromonomer composition ratio. These results demonstrated that a higher number of repeating units of TMC, with a lower macromonomer composition, was preferable for molecular encapsulation.

• Journal of the Korean Chemical Society
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• v.67 no.1
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• pp.13-18
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• 2023

We evaluate electron density functional theories for the computation of 0-1 and 1-2 transition energies of local OH stretching motion of water molecules in condensed phases. By examining thirteen density functionals and nine sets of basis functions, it was found that the optimal combination that predicts the transition energies highly correlated with those calculated by the coupled cluster theory, CCSD(T), is the hybrid density functional theory developed by Head-Gordon group, ωB97X(D)/6-31+G^*.

• Bulletin of the Korean Chemical Society
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• v.32 no.2
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• pp.583-589
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• 2011

Fluorescence correlation spectroscopy (FCS) is a sophisticated and an accurate analytical technique used to study the diffusion of molecules in a solution at the single-molecule level. FCS is strongly affected by many factors such as the stability of the excitation power, photochemical processes, mismatch between the refractive indices, and variations in the cover glass thickness. We have studied FCS near the surface of a cover glass by using rhodamine 123 as a fluorescent probe and have observed that the surface has a strong influence on the measurements. The temporal autocorrelation of FCS decays with two characteristic times when the confocal detection volume is positioned near the surface of the cover glass. As the position of the detection volume is moved away from the surface, the FCS autocorrelation becomes one-component decaying; the characteristic time of the decay is the same as the faster-decaying component in the FCS autocorrelation near the surface. This observation suggests that the faster component can be attributed to the free diffusion of the probe molecules in the solution, while the slow component has its origin from the interaction between the probe molecules and the surface. We have characterized the surface contribution to the FCS measurements near the surface by changing the position of the detection volume relative to the surface. The influence of the surface on the diffusion of the probe molecules was monitored by changing the chemical properties of the surface. The surface contribution to the temporal autocorrelation of the FCS strongly depends on the chemical nature of the surface. The hydrophobicity of the surface is a major factor determining the surface influence on the free diffusion of the probe molecules near the surface.

• Bulletin of the Korean Chemical Society
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• v.32 no.2
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• pp.389-398
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• 2011

Although the currently available surface spectroscopic techniques provide powerful means of studying atoms and simple molecules on surfaces, the identification of complex molecules and functional groups is a major concern in surface analysis. This article describes a recently developed method of surface molecular analysis based on reactive ion scattering (RIS) of low energy (< 100 eV) $Cs^+$ beams. The RIS method can detect surface molecules via a mechanism in which a $Cs^+$ projectile picks up an adsorbate from the surface during the scattering process. The basic principles of the method are reviewed and its applications are discussed by showing several examples from studies of molecules and their reactions on surfaces.

• Molecules and Cells
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• v.44 no.8
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• pp.549-556
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• 2021

Decoding the molecular mechanisms underlying axon guidance is key to precise understanding of how complex neural circuits form during neural development. Although substantial progress has been made over the last three decades in identifying numerous axon guidance molecules and their functional roles, little is known about how these guidance molecules collaborate to steer growth cones to their correct targets. Recent studies in Drosophila point to the importance of the combinatorial action of guidance molecules, and further show that selective fasciculation and defasciculation at specific choice points serve as a fundamental strategy for motor axon guidance. Here, I discuss how attractive and repulsive guidance cues cooperate to ensure the recognition of specific choice points that are inextricably linked to selective fasciculation and defasciculation, and correct pathfinding decision-making.

• Korean Journal of Microbiology
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• v.29 no.4
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• pp.209-214
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• 1991

The PRD1 DNA polymerase is a small multi-functional enzyme containing conserved amino acid sequences shared by family B DNA polymerases. Thus the PRD1 DNA polymerase provides an useful model system with which to study structure-functional relationships of DNA polymerase molecules. In order to investigate the functional and structural roles of the highly conserved amino acid sequences, we have introduced three mutations into a conserved amino acid of the PRD1 DNA polymerase. Genetic complememtation study indicated that each mutation inactivated DNA polymerase catalytic activity.