Biomedical subjects

Dong Young Kim

Publications and source records attributed to Dong Young Kim.

18 recordsLinked to original sources

PubMed2006

Ultrasensitive chemiresistors based on electrospun TiO2 nanofibers.

Nanostructured semiconducting metal oxides and particularly single nanowire devices offer exceptional gas sensitivity but at the expense of statistical variations and excessive noise levels. In this study TiO2/poly(vinyl acetate) composite nanofiber mats were directly electrospun onto interdigitated Pt electrode arrays, hot pressed at 120 degrees C, and calcined at 450 degrees C. This resulted in a novel multiple nanowire network composed of sheaths of 200-500 nm diameter cores filled with readily gas accessible approximately 10 nm thick single-crystal anatase fibrils. TiO2 nanofiber sensors tested for NO2, in dry air, exhibited exceptional sensitivity showing with, for example, a 833% increase in sensor resistance when exposed to 500 ppb NO2 at 300 degrees C, consistent with a detection limit estimated to be well below 1 ppb. Unusual response patterns were observed at high NO2 concentrations (> 12.5 ppm), consistent with n to p inversion of the surface-trap limited conduction facilitated by the high surface-to-volume ratio of this material.

Crystallization↗

PubMed2005

Structure of inorganic pyrophosphatase from Helicobacter pylori.

Inorganic pyrophosphatase (PPase) is a ubiquitous cytosolic enzyme which catalyzes the hydrolysis of inorganic pyrophosphate (PPi) to orthophosphate (Pi). The crystal structure of inorganic pyrophosphatase from Helicobacter pylori (H-PPase) has been solved by MAD and refined to an R factor of 20.6% at 2.6 A resolution. The crystallographic asymmetric unit contains a homohexameric H-PPase arranged as a dimer of trimers. While most of the structural elements of PPases are highly conserved in H-PPase, some unique structural features are localized in the flexible loops near the active site, suggesting that the structural flexibility of these loops is required for the catalytic efficiency of PPase.

Amino Acid Sequence↗

PubMed2005

Structure and function of HtrA family proteins, the key players in protein quality control.

High temperature requirement A (HtrA) and its homologues constitute the HtrA family proteins, a group of heat shock-induced serine proteases. Bacterial HtrA proteins perform crucial functions with regard to protein quality control in the periplasmic space, functioning as both molecular chaperones and proteases. In contrast to other bacterial quality control proteins, including ClpXP, ClpAP, and HslUV, HtrA proteins contain no regulatory components or ATP binding domains. Thus, they are commonly referred to as ATP-independent chaperone-proteases. Whereas the function of ATP-dependent chaperone-proteases is regulated by ATP hydrolysis, HtrA exhibits a PDZ domain and a temperature-dependent switch mechanism, which effects the change in its function from molecular chaperone to protease. This mechanism is also related to substrate recognition and the fine control of its function. Structural and biochemical analyses of the three HtrA proteins, DegP, DegQ, and DegS, have provided us with clues as to the functional regulation of HtrA proteins, as well as their roles in protein quality control at atomic scales. The objective of this brief review is to discuss some of the recent studies which have been conducted regarding the structure and function of these HtrA proteins, and to compare their roles in the context of protein quality control.

Amino Acid Sequence↗

PubMed2005

Optimal recovery of high-purity rutin crystals from the whole plant of Fagopyrum esculentum Moench (buckwheat) by extraction, fractionation, and recrystallization.

Rutin, one of the flavonoids derived from plants, is increasingly in demand in the food, pharmaceutical, and cosmetic industries due to its various biological and physiological activities including antioxidation, anti-inflammation, and anti-hypertension. The whole plant of buckwheat (Fagopyrum esculentum Moench) is a major source of natural rutin. This study developed a low-cost process encompassing the efficient extraction, fractionation, and recrystallization to obtain high-purity rutin from buckwheat, and it could improve the economic utilization of this abundant low-value agricultural product. The sequential separation and purification procedures established in this study involved extraction with 50% (v/v) aqueous ethanol at 80 degrees C for 1 h followed by elution with water and aqueous ethanols at 20% and 30% (v/v) on a styrene-based resin column, and recrystallization at 4 degrees C for 12 h. These conditions resulted in the recovery of 92% of total rutin with over 95% purity. In the present study, high-purity rutin was obtained from whole buckwheat through low-cost processes, the separation and purification strategy established in this study could provide valuable information to the relevant industries.

Chemical Fractionation↗

PubMed2005

The target of RNAIII-activating protein (TRAP) from Staphylococcus aureus: purification, crystallization and preliminary X-ray analysis.

The target of the RNAIII-activating protein (TRAP) is a 21 kDa protein in which phosphorylation is activated by the RNAIII-activating protein (RAP), which causes an increase in RNAII and RNAIII synthesis and the production of the virulence factors. In an attempt to examine the structural role of TRAP in the signal transduction pathway, TRAP from Staphylococcus aureus was overexpressed, purified and crystallized using PEG 8000 and 5% Jeffamine M600 (pH 7.0), as precipitants by hanging-drop vapour diffusion methods at 287 K. The crystals belong to the orthorhombic space group, P2(1)2(1)2(1), with unit cell parameters of a=39.68, b=50.41, c=85.45 A. There is one monomer of TRAP per crystallographic asymmetric unit with a crystal volume per protein mass (V(M)) of 2.06 A(3) Da(-1) and a solvent content of 40.3%. A complete data set diffracting to 1.9 A resolution was collected from a single crystal at 100 K using a synchrotron-radiation source.

Adaptor Proteins, Signal Transducing↗

PubMed2005

Single-walled carbon nanotube network with bimodal pore structures of uniform microporosity and mesoporosity.

We characterized single-walled carbon nanotubes before and after HNO3/H2SO4 treatments for different times by scanning electron microscopy, Raman spectroscopy, and N2 adsorption at 77 K. Single-walled carbon nanotube assembly revealed a bimodal pore structure of microporosity (surface area of 476 m2 g(-1)) and mesoporosity (surface area of 476 m2 g(-1)) with a high total surface area of 1048 m2g(-1). The microporosity increased prominently after HNO3/H2SO4 treatments, whereas the mesoporosity decreased progressively with the treatment time. The HNO3/H2SO4 treatment of nanotubes induced an aggregation and alignment that should transform larger mesopores of nanotube assemblies into smaller ones, and smaller mesopores into micropores, resulting in the decrease of external surface area. This effect was attributed to the presence of abundant defects on the tube wall that were saturated by functional groups during the acid treatment of the single-walled carbon nanotubes.

Adsorption↗

PubMed2005

Electrophoretic and dynamic light scattering in evaluating dispersion and size distribution of single-walled carbon nanotubes.

We have introduced both electrophoretic and dynamic light scattering to evaluate the polydispersity, nanodispersity, and stability of single-walled carbon nanotubes (SWNTs) in distilled water with surfactants. By controlling the sodium dodecyl sulfate composition and some pretreatment by sonication, we were able to achieve nanodispersion (dispersion into individual nanotubes). The polydispersity was well described by combining both methods. We further showed that the nanodispersion and length distribution observed in the dynamic light scattering spectra were clearly identified by atomic force microscopy. Although surfactants with aliphatic groups can nanodisperse SWNT bundles, the dispersivity and stability depended seriously on the sample preparation process. Our measurements showed that a combination of electrophoretic and dynamic light scattering can provide a convenient and robust means of measuring polydispersity, nanodispersity, and stability of SWNTs in various solutions.

Electrophoresis↗

PubMed2004

Beneficial role of cetyltrimethylammonium bromide in the enhancement of photovoltaic properties of dye-sensitized rutile TiO2 solar cells.

A new approach involving the introduction of the common cationic surfactant cetyltrimethylammonium bromide (CTAB) for modifying a rutile TiO2 film during its formation from hydrolyzed TiCl4 solution has been adopted, intending to improve the photoelectrochemical properties of the pertinent dye-sensitized solar cell. CTAB-routed films were found to consist of smaller clusters of near-spherical TiO2 particles, compared with larger clusters of long rod-shaped particles in the absence of CTAB. As a consequence, the photocurrent and photovoltage of the cell fabricated by using CTAB have increased significantly, leading to a conversion efficiency increase, compared with those of the cell prepared without CTAB. On the basis of FE-SEM, BET, and XRD analyses, the increases are attributed to decreased particle size, improved interparticle connectivity, and enhanced crystallinity of the CTAB-promoted TiO2 particles and decreased void volume in the film. Faster growth of the TiO2 film was another beneficial effect of CTAB. A mechanism is proposed for the beneficial role of CTAB during the film formation.

Journal Article↗

PubMed2004

Crystallization and preliminary X-ray crystallographic study of UDP-glucose pyrophosphorylase (UGPase) from Helicobacter pylori.

UDP-glucose pyrophosphorylase (UGPase) catalyzes the synthesis of UDP-glucose, an essential metabolite in all living organisms. An X-ray crystallographic study of UGPase from Helicobacter pylori has been performed in order to elucidate its role in the regulation of this important metabolic pathway. UGPase was crystallized from 0.1 M sodium acetate trihydrate pH 4.6, 2.0 M ammonium sulfate and 0.1 M guanidine-HCl. According to diffraction data collected at a resolution of 2.9 A using a synchrotron-radiation source, the crystal belongs to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 91.47, b = 98.61, c = 245.70 A, alpha = beta = gamma = 90.0 degrees.

Crystallization↗

PubMed2004

Crystallization and preliminary X-ray crystallographic study of the leech protease inhibitor guamerin and its complex with bovine pancreatic chymotrypsin.

Guamerin, a small peptide inhibitor of the serine protease from Hirudo nipponia, was expressed in yeast and crystallized using the vapor diffusion method, with MPD as precipitant. The crystal was found to belong to the monoclinic P2(1) space group with unit cell parameters a=136.06, b=206.59, c=227.39 A, beta=105.03 degrees. The guamerin/bovine pancreatic chymotrypsin complex was also crystallized using PEG 8K as precipitant. The space group was identified as P2(1)2(1)2(1) with unit cell parameters of a=44.01, b=44.30, c=122.47 A. The diffraction data of the complex were collected up to a resolution of 2.4 A using a synchrotron-radiation source under cryogenic condition.

Animals↗

PubMed2004

Polysomnographic effects of nasal surgery for snoring and obstructive sleep apnea.

OBJECTIVE: It has been hypothesized that nasal obstruction causes an increase in negative pressure in the upper airway and induces an inspiratory collapse at the pharyngeal level. We used portable polysomnography (PSG) to assess the efficacy of nasal surgery for snoring and obstructive sleep apnea (OSA). MATERIAL AND METHODS: We reviewed 21 patients who presented with nasal obstruction and snoring. Septal surgery with or without inferior turbinectomy was performed. Each patient was assessed pre- and postoperatively using PSG. We measured the respiratory distress index (RDI), apnea index (AI), oxygen saturation index (OSI) and the duration of snoring. Selection criteria were an RDI of > 15 as determined by PSG and clinical nasal obstruction and a deviated nasal septum as determined by physical examination. RESULTS: Nasal surgery had the following effects: RDI decreased from 39 to 29 (p = 0.0001), AI decreased from 19 to 16 (p = 0.0209), OSI decreased from 48 to 32 (p = 0.0001) and the duration of snoring decreased from 44% to 39% (p = 0.1595). Snoring and OSA were completely relieved in 4 patients (19%) who did not require any additional surgical therapy. CONCLUSION: Snoring and OSA may be corrected merely by septal surgery in some patients, and secondary surgery (uvulopalatoplasty) may be considered after a thorough evaluation by means of postoperative PSG.

Adult↗

PubMed2003

Crystal structure of ClpX molecular chaperone from Helicobacter pylori.

ClpX, a heat shock protein 100 chaperone, which acts as the regulatory subunit of the ATP-dependent ClpXP protease, is responsible for intracellular protein remodeling and degradation. To provide a structural basis for a better understanding of the function of the Clp ATPase family, the crystal structures of Helicobacter pylori ClpX, lacking an N-terminal Cys cluster region complexed with ADP, was determined. The overall structure of ClpX is similar to that of heat shock locus U (HslU), consisting of two subdomains, with ADP bound at the subdomain interface. The crystal structure of ClpX reveals that a conserved tripeptide (LGF) is located on the tip of ClpP binding loop extending from the N-terminal subdomain. A hexameric model of ClpX suggests that six tripeptides make hydrophobic contacts with the hydrophobic clefts of the ClpP heptmer asymmetrically. In addition, the nucleotide binding environment provides the structural explanation for the hexameric assembly and the modulation of ATPase activity.

ATPases Associated with Diverse Cellular Activitie↗

PubMed2003

Purification, crystallization and preliminary X-ray studies of ClpX from Helicobacter pylori.

ClpX, a member of the HSP (heat-shock protein) 100 family, functions as a molecular chaperone and is a regulatory subunit of the ClpXP protease. To understand the chaperone and regulatory mechanisms of ClpX, Helicobacter pylori ClpX has been overexpressed in Escherichia coli and crystallized at 295 K using (NH(4))(2)HPO(4) as precipitant. X-ray diffraction data have been collected to 2.6 A resolution using a synchrotron-radiation source. The crystals belong to the hexagonal space group P6(5) or P6(1), with unit-cell parameters a = b = 78.52 (04), c = 131.51 (09) A, alpha = beta = 90, gamma = 120 degrees. The crystallographic asymmetric unit contains one molecule of ClpX, with a corresponding V(M) of 2.78 A(3) Da(-1) and a solvent content of 55.8%.

ATPases Associated with Diverse Cellular Activitie↗

PubMed2003

Antimicrobial peptide LL-37 is upregulated in chronic nasal inflammatory disease.

OBJECTIVE: LL-37 is one of the antimicrobial peptides and the only member of the cathelicidin family identified so far in humans. We attempted to find a correlation between LL-37 peptide and inflammation of the nasal mucosa. MATERIAL AND METHODS: Nasal mucosa specimens were obtained from 15 chronic infective rhinitis patients and 6 normal controls. Immunohistochemical staining was used to examine the localization of LL-37 and reverse transcriptase polymerase chain reaction (RT-PCR) was used to determine the levels of LL-37, IL-1beta and IL-8 in tissue. RESULTS: LL-37 peptide was primarily localized in the surface of the epithelia, in the serous and mucous cells of the submucosal glands and in stromal inflammatory cells. The number of LL-37 immunoreactive cells in inflammatory nasal mucosa was significantly increased compared with normal nasal tissue. Using RT-PCR, LL-37 mRNA was detected in 3/6 normal turbinate samples but in all cases with inflammatory nasal tissues. IL-1beta and IL-8 transcripts exhibited a similar pattern to that of LL-37. CONCLUSIONS: We suggest that LL-37 is one of the antimicrobial peptides found in human nasal mucosa and that it participates in the innate immune system of the nasal mucosa.

Adult↗

PubMed2002

Crystal structure of the protease domain of a heat-shock protein HtrA from Thermotoga maritima.

HtrA (high temperature requirement A), a periplasmic heat-shock protein, functions as a molecular chaperone at low temperatures, and its proteolytic activity is turned on at elevated temperatures. To investigate the mechanism of functional switch to protease, we determined the crystal structure of the NH(2)-terminal protease domain (PD) of HtrA from Thermotoga maritima, which was shown to retain both proteolytic and chaperone-like activities. Three subunits of HtrA PD compose a trimer, and multimerization architecture is similar to that found in the crystal structures of intact HtrA hexamer from Escherichia coli and human HtrA2 trimer. HtrA PD shares the same fold with chymotrypsin-like serine proteases, but it contains an additional lid that blocks access the of substrates to the active site. A corresponding lid found in E. coli HtrA is a long loop that also blocks the active site of another subunit. These results suggest that the activation of the proteolytic function of HtrA at elevated temperatures might occur by a conformational change, which includes the opening of the helical lid to expose the active site and subsequent rearrangement of a catalytic triad and an oxyanion hole.

Amino Acid Sequence↗

PubMed2002

Cloning, purification, crystallization and preliminary X-ray studies of RFC boxes II-VIII of replication factor C from Methanococcus jannaschii.

Replication factor C (RFC) is the accessory protein required to load the proliferating cell nuclear antigen (PCNA) onto DNA in replication process. RFC is composed of several subunits and each subunit contains the highly conserved sequences RFC boxes II-VIII. RFC boxes II-VIII of the large subunit of replication factor C from Methanococcus jannaschii has been overexpressed in Escherichia coli, purified and crystallized at 295 K using ammonium sulfate as precipitant. Crystals belong to the space group R32, with unit-cell parameters a = b = 238.23 (5), c = 73.17 (12) A. Native data were collected at 100 K to a resolution of 3.2 A using a synchrotron-radiation source.

Bacterial Proteins↗

PubMed2001

Crystallization and preliminary X-ray studies of the protease domain of the heat-shock protein HtrA from Thermotoga maritima.

HtrA (high-temperature requirement A) is a widely distributed heat-shock protein which has both molecular-chaperone and proteolytic activities. It is composed of two PDZ domains essential for oligomerization and a protease domain. To understand the molecular basis of the dual function of HtrA, the protease domain of T. maritima HtrA has been crystallized. X-ray diffraction data have been collected to 2.7 A resolution using a synchrotron-radiation source. Crystals belong to the cubic space group P2(1)3, with unit-cell parameters a = b = c = 120.55 (8) A. The asymmetric unit contains two protease domains, with a corresponding V(M) of 2.80 A(3) Da(-1) and a solvent content of 56.1%.

Base Sequence↗

PubMedDate not supplied

Reduced expression of coxsackievirus and adenovirus receptor (CAR) in tumor tissue compared to normal epithelium in head and neck squamous cell carcinoma patients.

Even though adenoviral vector is widely used in gene therapy of squamous cell carcinoma of the head and neck (SCCHN), the expression level of Coxsackievirus and adenovirus receptor (CAR) in SCCNH is not clearly defined. To identify this variability, the expression of CAR was measured using SCCHN cell lines and compared with transfection efficiency. It was found by RT-PCR and Western blot analysis that CAR levels varied in SCCHN cell lines. FACS analysis and adenovirus infection assay revealed that there was a good correlation between the level of CAR expression and the transfection efficiency. To identify the actual CAR expression patterns of human SCCHN tissues in vivo, immunohistochemical staining was undertaken on frozen biopsies of six SCCHN patients. In all the patients examined, the normal tissues showed much stronger staining for CAR than the tumor tissues. These results demonstrate that the level of CAR expression of a tumor should be evaluated before clinical application of adenoviral vector for gene therapy in SCCHN.

Adenovirus Infections, Human↗