Biomedical subjects

K K Kim

Publications and source records attributed to K K Kim.

At least 37 records · Page 2Linked to original sources

PubMed2000

Identification of a brain specific protein that associates with a refsum disease gene product, phytanoyl-CoA alpha-hydroxylase.

Refsum disease is an autosomal recessive neurologic disorder of the lipid metabolism. Major diagnostic clinical findings include retinitis pigmentosa, peripheral polyneuropathy, cerebellar ataxia, increased cerebrospinal fluid protein without pleocytosis, nerve deafness, and cardiac involvement. We have identified a novel protein (PAHX-AP #1) associated with phytanoyl-CoA alpha-hydroxylase (PAHX), a Refsum disease gene product, using the yeast-based two-hybrid assay. The middle portion (amino acids 83-264) of PAHX was used as a bait and a mouse brain cDNA library was searched. The ability of PAHX-AP #1 to interact with PAHX was confirmed using immunoprecipitation and Western blot studies in NIH3T3 cells which stably expressed both PAHX and PAHX-AP #1. Northern and Western blot analyses demonstrated a unique pattern of developmental PAHX-AP #1 expression which was targeted to the adult brain, but ubiquitous expressions of PAHX were observed in all examined tissues. In situ hybridization analyses of the brain showed specific localization of PAHX-AP #1 to the supragranular layer in the cerebral cortex, dentate gyrus, hippocampus, Purkinje cell layer, deep cerebellar nucleus, trigeminal nucleus, abducent nucleus, facial nucleus, cochlear and vestibular nucleus, ganglion cell and nuclear layer of the retina. These data indicate that localization of PAHX-AP #1 in the brain is correlated with central neurologic symptoms of Refsum disease such as retinitis pigmentosa, cerebellar ataxia, nerve deafness and suggest that PAHX-AP #1 may be involved in the development of the central neurologic deficits of Refsum disease.

3T3 Cells↗

PubMed2000

Crystal structure of a fibrillarin homologue from Methanococcus jannaschii, a hyperthermophile, at 1.6 A resolution.

Fibrillarin is a phylogenetically conserved protein essential for efficient processing of pre-rRNA through its association with a class of small nucleolar RNAs during ribosomal biogenesis. The protein is the antigen for the autoimmune disease scleroderma. Here we report the crystal structure of the fibrillarin homologue from Methanococcus jannaschii, a hyperthermophile, at 1.6 A resolution. The structure consists of two domains, with a novel fold in the N-terminal region and a methyltransferase-like domain in the C-terminal region. Mapping temperature-sensitive mutations found in yeast fibrillarin Nop1 to the Methanococcus homologue structure reveals that many of the mutations cluster in the core of the methyltransferase-like domain.

Amino Acid Sequence↗

PubMed2000

Identification of four novel mutations in five unrelated Korean families with Fabry disease.

Fabry disease is a X-linked recessively inherited metabolic disorder, which results from the deficient activity of the lysosomal hydrolase alpha-galactosidase A leading to the systemic deposition of glycosphingolipids with terminal alpha-galactosyl moieties. Single-strand conformation polymorphism (SSCP) analysis was performed, followed by DNA sequencing of PCR amplified exons of the human alpha-galactosidase A gene in 5 unrelated Korean patients with classic Fabry disease. Five different mutations were identified; two nonsense mutations (Y86X and R342X), one missense mutation (D266N), and two small deletions (296del2 and 802del4). Except for R342X mutation, four were novel mutations (Y86X, D266N, 296del2, 802del4). A T to G transversion at nucleotide position 5157 in exon 2 caused a tyrosine-to-stop substitution at codon 86. A G to A transition at position 10287 in exon 5 substituted an asparagine for an aspartate at codon 266. Mutation 296del2 in exon 2 resulted in a frame shift with a stop signal at the 22th codon downstream from the mutation, whereas mutation 802del4 resulted in a stop codon at the site of 4 bp deletion. In addition, the 802del4 was found to be a de novo mutation. This is the first report on mutation analysis of the human alpha-galactosidase A gene in Korean patients with Fabry disease.

Adolescent↗

PubMed2000

The lateralizing and surgical prognostic value of a single 2-hour EEG in mesial TLE.

We investigated 109 patients who received anterior temporal lobectomy for intractable mTLE by post-operative follow-up for at least 11/2 years. We reviewed pre-operative 2-hour interictal EEGs, counted interictal epileptiform discharges (IEDs), and compared the lateralization of IEDs with the side of surgery and surgical outcome. Twenty of 22 patients who had no spikes and 44 of 51 who had unitemporal spikes became seizure free after surgical resection. The correct lateralization of the epileptogenic side was possible in 90. 9% of the patients with unitemporal IEDs. In 12 seizure-free patients of 15 patients with less than 70% predominance of IED in one temporal lobe, the positive predictive value of the lateralization was 41.7%. In 16 seizure-free patients of 21 with more than 70% preponderance of IED in one lobe, the positive predictive value was 81.3%. Surgical outcome of patients with unitemporal and bitemporal IEDs were not significantly different. Interictal scalp EEG can be used as a lateralizing tool in mTLE when the temporal IEDs appear with more than 70% preponderance in one side. Although the presence of bitemporal IEDs often causes confusion in terms of the correct lateralization, it does not affect the surgical outcome.

Adult↗

PubMed2000

Crystallization and preliminary X-ray diffraction analysis of Saccharomyces cerevisiae Ygr203p, a homologue of Acr2 arsenate reductase.

Ygr203p, a 148-residue protein encoded by the ygr203w gene of Saccharomyces cerevisiae, is a homologue of the yeast Acr2 arsenate reductase encoded by the acr2 (or ypr200c) gene. It also shows significant sequence similarity to the human cell-cycle control Cdc25 phosphatase family. It has been overexpressed in soluble form in Escherichia coli with a His(6) tag at its C-terminus. The recombinant protein has been crystallized at 296 K using sodium chloride as precipitant. The crystals belong to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 40.48, b = 50.95, c = 91.95 A. The asymmetric unit contains a monomer, giving a crystal volume per protein mass (V(m)) of 2.61 A(3) Da(-1) and a solvent content of 53.8%. The crystals diffract to better than 1.9 A resolution with Cu Kalpha X-rays. They are therefore suitable for high-resolution structure determination.

Adenosine Triphosphatases↗

PubMed2000

Nucleoside diphosphate kinase from the hyperthermophilic archaeon Methanococcus jannaschii: overexpression, crystallization and preliminary X-ray crystallographic analysis.

Nucleoside diphosphate (NDP) kinase is a key enzyme in maintaining cellular pools of all nucleoside triphosphates. NDP kinase from the hyperthermophilic archaebacterium Methanococcus jannaschii has been overexpressed in Escherichia coli and crystallized at 297 K using polyethylene glycol 4000 as precipitant. The crystal is hexagonal, belonging to the space group P6(3), with unit-cell parameters a = b = 72.89, c = 100.87 A. The asymmetric unit contains two subunits of NDP kinase, with a corresponding crystal volume per protein mass (V(M)) of 2.38 A(3) Da(-1) and a solvent content of 48.3%. Native X-ray diffraction data to 2.30 A resolution have been collected using synchrotron X-rays.

Crystallization↗

PubMed2000

Crystallization and preliminary crystallographic studies of ribosome recycling factor from Escherichia coli.

Ribosome recycling factor (RRF) catalyzes the disassembly of a termination complex during the final stage of protein synthesis. RRF from Escherichia coli has been crystallized with PEG 400 as precipitant at 287 K. The crystal belongs to the trigonal space group P3(1)21 (or P3(2)21), with unit-cell parameters a = b = 48.08, c = 141.67 A. Native data were collected from a frozen crystal to a resolution of 3.0 A on a Cu Kalpha rotating-anode X-ray source.

Bacterial Proteins↗

PubMed2000

Clinicopathologic analysis of 124 biopsy-proven peripheral nerve diseases.

We reviewed dinical, histological and ultrastructural findings of 124 cases of sural nerve biopsy specimens to delineate the trends of peripheral nerve diseases in our institute. Eighty-one were men and 43 were women. We categorized them into five groups: specific diagnosis (66 cases, 53.2%), axonal degeneration type (47 cases, 37.9%), demyelinating type (4 cases, 3.2%), mixed axonal degeneration-demyelinating type (6 cases, 4.8%) and normal (1 case, 0.9%). Cases with specific diagnosis included 21 inflammatory demyelinating polyneuropathy (15 chronic inflammatory demyelinating polyradiculoneuropathy, 6 Guillain-Barre disease), 13 hereditary motor and sensory neuropathy (7 Charcot-Marie-Tooth type I, 6 Charcot-Marie-Tooth type II), 10 vasculitis, 6 toxic neuropathy, 4 leprosy, 3 diabetic neuropathy, 2 alcoholic neuropathy, 1 Fabry's disease and other specific diseases (5 cases). In our cases, the proportion of specific diagnoses was higher, while the proportion of demyelinating peripheral neuropathies and normal were lower than those of Western series. The results of this study indicate that 1) a dose clinicopathologic correlation is important to make a precise diagnosis of peripheral nerve biopsy, 2) Biopsy under strict indication may reduce unnecessary histologic examination, 3) There is no difference in disease pattern of peripheral neuropathy between Western people and Koreans.

Adult↗

PubMed2000

A case of myasthenia gravis proven by ultrastructural study.

Although light microscopic features of muscle are not pathognomonic in most cases of myasthenia gravis (MG), careful examination of neuromuscular junction by electron microscopy (EM) can reveal important clues for this disease. We report here a case of MG confirmed by EM study to emphasize that tissue diagnosis is still the best adjuvant to confirm the diagnosis. An 18-year-old female visited our hospital complaining of progressive muscle weakness for 3 years. She had difficulty in running, going upstairs and doing routine activities. Symptoms were aggravated with continuous work and resolved after rest. She had weakness of bilateral masseter and facial muscles and proximal portions of extremities without definite diurnal variation. Electromyography showed myopathic changes in proximal muscles of extremities. MG was considered but tensilon test was equivocal. Repetitive nerve stimulation tests revealed 20-30 percent decrease in responses to low and high rate stimulation. Muscle biopsy revealed selective type 2 atrophy. Ultrastructurally, abnormalities of neuromuscular junctions, i.e., wide primary synaptic cleft, and wide and shallow secondary synaptic clefts with mild myopathic features were present. These findings were pathognomonic for MG. Later, her symptoms were improved completely 3 months after thymectomy. The histologic finding of thymus was follicular hyperplasia.

Adolescent↗

PubMed2000

Isolation and identification of antifungal N-butylbenzenesulphonamide produced by Pseudomonas sp. AB2.

An antifungal bacterial strain, isolated from a greenhouse soil sample, inhibits growth of microflora nearby. It was selected for further studies of bacterial antifungal properties. This isolate was identified as a Pseudomonas sp. based on carbohydrate utilization, and other biochemical and physiological tests. Petri plate assay revealed that the Pseudomonas sp. exhibited antifungal activity against the plant pathogens, Pythium ultimum, Rhizoctonia solani, Phytophthora capsici, Botrytis cinerea and Fusarium oxysporum. Using direct inhibition bioassay on TLC plates after ethyl acetate extraction of the culture filtrate, we correlated antifungal activity with production of antifungal compounds. An antifungal antibiotic was isolated from the culture filtrate and was identified as N-butylbenzenesulphonamide. ED50, values of the N-butylbenzenesulphonamide against P. ultimum, P. capsici, R. solani, and B. cinerea were 73, 41, 33 and 102 ppm, respectively.

Antifungal Agents↗

PubMed2000

Activation of c-Jun N-terminal kinase and activator protein 1 by receptor activator of nuclear factor kappaB.

Receptor activator of nuclear factor kappaB (RANK), a lately identified member of the tumor necrosis factor receptor superfamily, plays important roles both in osteoclastogenesis and in lymph node development. Previously, we and others showed that RANK could stimulate the activity of c-Jun N-terminal kinase (JNK). In this study, we investigated the mechanism by which RANK activates JNK. We found that N-terminal deletion mutants of tumor necrosis factor receptor-associated factor 2 and 6 were inhibitory to RANK activation of JNK. The JNK activation by RANK was also reduced by cotransfection of kinase-inactive mutants of apoptosis signal-regulating kinase 1, MAPK/ERK kinase kinase 1, and nuclear factor kappaB-inducing kinase. In addition, dominant negative mutants of Rac and Ras decreased the RANK stimulation of JNK activity. Furthermore, we determined whether the RANK engagement of JNK signaling pathways could lead to the activation of the activator protein 1 (AP-1) transcription factor, one of the potential downstream targets of activated JNK. RANK was found to activate AP-1 in a manner dependent on the signaling molecules involved in the JNK activation by this receptor. Furthermore, the activation of JNK and ERK, but not that of p38, appeared to be involved in the AP-1 activation by RANK. Thus, RANK may use both JNK and ERK pathways to signal to the AP-1 transcription factor.

Animals↗

PubMed1999

Four-helical-bundle structure of the cytoplasmic domain of a serine chemotaxis receptor.

The bacterial chemotaxis receptors are transmembrane receptors with a simple signalling pathway which has elements relevant to the general understanding of signal recognition and transduction across membranes, how signals are relayed between molecules in a pathway, and how adaptation to a persistent signal is achieved. In contrast to many mammalian receptors which signal by oligomerizing upon ligand binding, the chemotaxis receptors are dimeric even in the absence of their ligands, and their signalling does not depend on a monomer-dimer equilibrium. Bacterial chemotaxis receptors are composed of a ligand-binding domain, a transmembrane domain consisting of two helices TM1 and TM2, and a cytoplasmic domain. All known bacterial chemotaxis receptors have a highly conserved cytoplasmic domain, which unites signals from different ligand domains into a single signalling pathway to flagella motors. Here we report the crystal structure of the cytoplasmic domain of a serine chemotaxis receptor of Escherichia coli, which reveals a 200 A-long coiled-coil of two antiparallel helices connected by a 'U-turn'. Two of these domains form a long, supercoiled, four-helical bundle in the cytoplasmic portion of the receptor.

Chemotaxis↗

PubMed1999

Molecular cloning and characterization of splice variants of human RAD50 gene.

In this report, splice variants of human RAD50 (hRAD50) were cloned and characterized. A Northern blot survey identified two transcripts that hybridized to a hRAD50 cDNA clone, an upper faint band (5.9kb) and lower dense band (4.6kb). cDNA clones (hRAD50-2, 4.6kb) encompassing the entire hRAD50 transcript but having a shorter 3'-untranslated region (3'UTR) than the previously reported hRAD50-1 cDNA (5.9kb; Dolganov, G.M., Maser, R.S., Novikov, A., Tosto, L., Chong, S., Bressan, D.A., Petrini, J.H.J., 1996. Human Rad50 is physically associated with human Mre11: Identification of a conserved multiprotein complex implicated in recombinational DNA repair. Mol. Cell. Biol. 16, 4832-4841.) were isolated. The presence of AU-rich sequences in the 3'UTR of hRAD50-1, which define mRNA instability and Northern results, suggest that hRAD50-2 is the major transcript of hRAD50. A third alternative splice variant that lacks the ATP-binding domain was also identified (hRAD50-3, approximately 4.5kb). Expression of hRAD50-3 transcript was detected in all tissues examined by RT-PCR (reverse transcriptase-polymerase chain reaction) and nested DNA-PCR analyses. Expression of hRAD50 partially rescued the MMS (methyl methanesulfonate)-sensitive phenotype in rad50 mutant yeast, whereas hRAD50-3 did not show complementation. These data suggest that the hRAD50-3 does not repair DNA double-strand breaks most likely due to its inability to bind ATP, and to bind damaged DNA. The existence of these alternative splice forms is potentially important in regulation of the biological activity of the DNA recombinational repair gene, hRAD50.

3' Untranslated Regions↗

PubMed1999

Prognostic factors in anterior temporal lobe resections for mesial temporal lobe epilepsy: multivariate analysis.

PURPOSE: Even though there have been several studies on the prognostic factors of temporal lobe epilepsy (TLE) after lobectomy, no studies have been performed for homogeneous mesial TLE. Furthermore, most studies on the predictors of outcome of epileptic surgery were based on univariate analyses and did not consider modern epileptic surgery investigation modalities such as brain magnetic resonance imaging (MRI) and positron emission tomography (PET). We attempted to identify the prognostic factors in anterior temporal lobectomy (ATL) for mesial TLE with multivariate analysis. METHODS: Ninety-three patients with mesial TLE (54 men and 39 women, mean age at surgery, 28.3 +/- 8.2 years) were included in the study. The primary outcome variable was the status of patients in the second postoperative year, classified as either seizure free (except aura), or not seizure free. Clinical, electroencephalographic, MRI, PET, Wada test, and pathological data were considered. RESULTS: Seventy-eight (84.0%) patients had remission of seizures. With univariate analysis, age at surgery (p < 0.001), epilepsy duration before surgery (p = 0.04), and ipsilateral hippocampal sclerosis on MRI (p = 0.02) were found to be significant. By using multivariate analysis, age at surgery (p = 0.001) and ipsilateral hippocampal sclerosis on MRI (p = 0.03) were found to be the most significant prognostic factors. CONCLUSIONS: Age at surgery and hippocampal sclerosis are independent prognostic factors for ATL in mesial TLE. These findings suggest that mesial TLE may be a progressive disorder, and surgical outcome is better when early ATL is performed.

Adolescent↗

PubMed1999

Increase in extracellular glutatione peroxidase in plasma and lungs of mice exposed to hyperoxia.

Extracellular glutathione peroxidase (E-GPx) is a selenium-dependent enzyme that can reduce hydrogen peroxide and phospholipid hydroperoxides. E-GPx is found in plasma and extracellular fluids such as bronchoalveolar lavage fluid. Because lung is one of the tissues that is capable of synthesizing and secreting E-GPx, the effect of exposure to hyperoxia on E-GPx in plasma and lung were studied in an injury model of hyperoxia exposure in adult mice. Exposure to 100% oxygen for 72 h resulted in an increase of 55% in plasma GPx activity and an increase of 50% in the amount of E-GPx protein in the plasma. Exposure to hyperoxia was also associated with an increase in the amount of E-GPx protein in lungs. The 7-fold increase in the amount of E-GPx protein in lungs was not due to plasma contamination of lungs from mice exposed to hyperoxia. E-GPx in the lung is calculated to account for 10% of lung GPx activity in control mice. However, E-GPx is calculated to account for 45% of lung GPx activity in the lungs of mice exposed to hyperoxia for 72 h. Further studies are needed to determine whether the increase in lung E-GPx is due to changes in translation or stability of E-GPx. The role of E-GPx in protecting the lung from oxidative damage warrants further study.

Animals↗

PubMed1999

Button battery impaction in nasal cavity.

A button battery inserted in the nose of children is an unusual foreign body which is capable of causing extensive tissue damage, resulting from electrical and chemical burns. We report a case of button battery in the nose of a 4-year-old boy presenting with unilateral nasal discharge, and necrosis in the septum and turbinate of the right nasal cavity. Mercury level in concentrated urine was within normal limit. Microscopic examination disclosed extensive liquefaction necrosis with calcification and fibrosis. Numerous dark brown to black granules were noted in the elastic and collagen fibers and interstitium. Dark-field examination of the section revealed brilliantly refractile granules. Polarized microscopy failed to show the granules. Most brown pigments reacted to prussian blue. Tissue mercury analysis yielded a mercury content of 8.01 ppm. We report this case to emphasize the hazards of button battery impaction and to draw attention to the significance of the problem through histopathologic examination.

Child, Preschool↗

PubMed1998

Structure-based assignment of the biochemical function of a hypothetical protein: a test case of structural genomics.

Many small bacterial, archaebacterial, and eukaryotic genomes have been sequenced, and the larger eukaryotic genomes are predicted to be completely sequenced within the next decade. In all genomes sequenced to date, a large portion of these organisms' predicted protein coding regions encode polypeptides of unknown biochemical, biophysical, and/or cellular functions. Three-dimensional structures of these proteins may suggest biochemical or biophysical functions. Here we report the crystal structure of one such protein, MJ0577, from a hyperthermophile, Methanococcus jannaschii, at 1.7-A resolution. The structure contains a bound ATP, suggesting MJ0577 is an ATPase or an ATP-mediated molecular switch, which we confirm by biochemical experiments. Furthermore, the structure reveals different ATP binding motifs that are shared among many homologous hypothetical proteins in this family. This result indicates that structure-based assignment of molecular function is a viable approach for the large-scale biochemical assignment of proteins and for discovering new motifs, a basic premise of structural genomics.

Adenosine Triphosphatases↗

PubMed1998

Crystal structures of eukaryotic translation initiation factor 5A from Methanococcus jannaschii at 1.8 A resolution.

Eukaryotic translation initiation factor 5A (eIF-5A) is a ubiquitous protein found in all eukaryotic cells. The protein is closely associated with cell proliferation in the G1-S stage of the cell cycle. Recent findings show that the eIF-5A proteins are highly expressed in tumor cells and act as a cofactor of the Rev protein in HIV-1-infected cells. The mature eIF is the only protein known to have the unusual amino acid hypusine, a post-translationally modified lysine. The crystal structure of eIF-5A from Methanococcus jannaschii (MJ eIF-5A) has been determined at 1.9 A and 1.8 A resolution in two crystal forms by using the multiple isomorphous replacement method and the multiwavelength anomalous diffraction method for the first crystal form and the molecular replacement method for the second crystal form. The structure consists of two folding domains, one of which is similar to the oligonucleotide-binding domain found in the prokaryotic cold shock protein and the translation initiation factor IF1 despite the absence of any significant sequence similarities. The 12 highly conserved amino acid residues found among eIF-5As include the hypusine site and form a long protruding loop at one end of the elongated molecule.

Amino Acid Sequence↗