Biomedical subjects

S W Suh

Publications and source records attributed to S W Suh.

At least 19 recordsLinked to original sources

PubMed2003

The TB structural genomics consortium: a resource for Mycobacterium tuberculosis biology.

The TB Structural Genomics Consortium is an organization devoted to encouraging, coordinating, and facilitating the determination and analysis of structures of proteins from Mycobacterium tuberculosis. The Consortium members hope to work together with other M. tuberculosis researchers to identify M. tuberculosis proteins for which structural information could provide important biological information, to analyze and interpret structures of M. tuberculosis proteins, and to work collaboratively to test ideas about M. tuberculosis protein function that are suggested by structure or related to structural information. This review describes the TB Structural Genomics Consortium and some of the proteins for which the Consortium is in the progress of determining three-dimensional structures.

Amino Acid Sequence↗

PubMed2002

Nitric oxide causes apparent release of zinc from presynaptic boutons.

One of us showed previously [Cuajungco and Lees (1998) Brain Res. 799, 188-129] that nitric oxide injected into the cerebrum in vivo causes zinc staining to appear in the somata of neurons and suggested that this staining of somata might be accompanied by a depletion (release) of zinc from axon terminals. In the present study, we confirm earlier results and report that there is a dramatic loss (apparent release) of histologically reactive zinc from the boutons of zinc-containing axons induced by infusion of nitric oxide into the brain in vivo. Rats were anesthetized with halothane and a cannula was inserted into the hippocampus. Either nitric oxide donor (spermineNONOate, 100 mM/2 microl) or control (spermine, 100 mM/2 l) was infused into the hippocampus or the cerebellar cortex. Two hours after infusion, N-(6-methoxy-8-quinolyl)-para-toluenesulfonamide (TSQ) staining for zinc in the brains revealed that sperminenitric oxide, but not control (spermine only) produced up to 95% depletion of zinc staining from the zinc-containing boutons. TSQ-positive neurons were also conspicuous throughout injection sites, in both the cerebral cortex and in the cerebellar cortex, where the Purkinje neurons were especially vivid, despite the scarcity of zinc-containing axonal boutons. It is suggested that the TSQ-stainable zinc in somata might represent intracellular stores mobilized from within or permeating extracellular stores.

Animals↗

PubMed2001

Crystallization and preliminary X-ray studies of Trp138Phe/Val185Thr xylose isomerases from Thermotoga neapolitana and Thermoanaerobacterium thermosulfurigenes.

Xylose isomerases from Thermotoga neapolitana (TNXI) and Thermoanaerobacterium thermosulfurigenes (TTXI) share 70.4% sequence identity and are thermostable. The double mutants Trp138Phe/Val185Thr of TNXI and TTXI have higher catalytic efficiencies than TNXI and TTXI, respectively. The Trp138Phe/Val185Thr TNXI and TTXI mutants were overexpressed in Escherichia coli strain BL21(DE3) and purified. Crystals of the two proteins were grown with polyethylene glycol 8000 as the major precipitant by the hanging-drop vapour-diffusion method. Crystals of the TNXI mutant were obtained in the absence of substrate, in complex with glucose and in complex with fructose. Crystals of the TTXI mutant were obtained complexed with glucose. Diffraction data were collected at 1.9, 2.1 and 2.1 A resolution for the fructose-TNXI mutant, glucose-TNXI mutant and substrate-unbound TNXI mutant, respectively. The diffraction data for the glucose-TTXI mutant were collected at 2.0 A resolution. The crystals belong to the orthorhombic space groups C222(1) (TNXI mutant) and P2(1)2(1)2(1) (TTXI mutant). The TNXI and TTXI mutant crystals contain two and four monomers in the asymmetric unit, respectively.

Aldose-Ketose Isomerases↗

PubMed2001

Hydrolysis of plasmid DNA catalyzed by Co(III) complex of cyclen attached to polystyrene.

Reactivity of the Co(III) complex of cyclen (CoCyc) in the hydrolytic cleavage of supercoiled pUC18 DNA leading to the formation of the corresponding open circular form was enhanced by >200 times upon attachment of CoCyc to cross-linked polystyrenes. Thus, half-lives as short as 40 min were achieved by the resin-based CoCyc in cleavage of the supercoiled DNA at 4 degrees C.

Cobalt↗

PubMed2001

Crystallization and preliminary X-ray crystallographic analysis of deoxyuridine triphosphate nucleotidohydrolase from Saccharomyces cerevisiae.

Deoxyuridine triphosphate nucleotidohydrolase (dUTPase) from Saccharomyces cerevisiae is essential for cell viability. It has been overexpressed in Escherichia coli and has been crystallized at 296 K using polyethylene glycol (PEG) 1500 as a precipitant. The crystals belong to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 59.48, b = 138.54, c = 157.91 A, alpha = beta = gamma = 90 degrees. Two molecules of trimeric dUTPase from S. cerevisiae are present in the asymmetric unit, giving a crystal volume per protein mass (V(M)) of 3.36 A(3) Da(-1) and a solvent content of 63%. The diffraction limit of the crystals could be significantly extended by the crystal-annealing procedure. A set of native data extending to 2.7 A resolution has been collected at 100 K using synchrotron X-rays.

Crystallization↗

PubMed2001

Loss of vesicular zinc and appearance of perikaryal zinc after seizures induced by pilocarpine.

The condition of status epilepticus induced by systemic administration of kainic acid (KA) causes an apparent translocation of vesicular zinc from presynaptic boutons into postsynaptic neurons. The accumulation of zinc in the somata has been identified as a contributing cause of neuronal injury. We show here that another form of status epilepticus, induced by administration of the muscarinic agonist pilocarpine, produces changes in zinc that are essentially the same as those produced by the kainic acid-induced seizures. Moreover, neurons that develop zinc staining after pilocarpine seizures are the same that shown degenerative changes. This result suggests that the loss of zinc from presynaptic boutons and the appearance of zinc in postsynaptic somata may both occur in seizures per se, regardless of etiology.

Aminoquinolines↗

PubMed2001

Structural basis of non-specific lipid binding in maize lipid-transfer protein complexes revealed by high-resolution X-ray crystallography.

Non-specific lipid-transfer proteins (nsLTPs) are involved in the movement of phospholipids, glycolipids, fatty acids, and steroids between membranes. Several structures of plant nsLTPs have been determined both by X-ray crystallography and nuclear magnetic resonance. However, the detailed structural basis of the non-specific binding of hydrophobic ligands by nsLTPs is still poorly understood. In order to gain a better understanding of the structural basis of the non-specific binding of hydrophobic ligands by nsLTPs and to investigate the plasticity of the fatty acid binding cavity in nsLTPs, seven high-resolution (between 1.3 A and 1.9 A) crystal structures have been determined. These depict the nsLTP from maize seedlings in complex with an array of fatty acids.A detailed comparison of the structures of maize nsLTP in complex with various ligands reveals a new binding mode in an nsLTP-oleate complex which has not been seen before. Furthermore, in the caprate complex, the ligand binds to the protein cavity in two orientations with equal occupancy. The volume of the hydrophobic cavity in the nsLTP from maize shows some variation depending on the size of the bound ligands. The structural plasticity of the ligand binding cavity and the predominant involvement of non-specific van der Waals interactions with the hydrophobic tail of the ligands provide a structural explanation for the non-specificity of maize nsLTP. The hydrophobic cavity accommodates various ligands from C10 to C18. The C18:1 ricinoleate with its hydroxyl group hydrogen bonding to Ala68 possibly mimics cutin monomer binding which is of biological importance. Some of the myristate binding sites in human serum albumin resemble the maize nsLTP, implying the importance of a helical bundle in accommodating the non-specific binding of fatty acids.

Binding Sites↗

PubMed2001

Crystal structure of the MJ0490 gene product of the hyperthermophilic archaebacterium Methanococcus jannaschii, a novel member of the lactate/malate family of dehydrogenases.

The MJ0490 gene, one of the only two genes of Methanococcus jannaschii showing sequence similarity to the lactate/malate family of dehydrogenases, was classified initially as coding for a putative l-lactate dehydrogenase (LDH). It has been re-classified as a malate dehydrogenase (MDH) gene, because it shows significant sequence similarity to MT0188, MDH II from Methanobacterium thermoautotrophicum strain DeltaH. The three-dimensional structure of its gene product has been determined in two crystal forms: a "dimeric" structure in the orthorhombic crystal at 1.9 A resolution and a "tetrameric" structure in the tetragonal crystal at 2.8 A. These structures share a similar subunit fold with other LDHs and MDHs. The tetrameric structure resembles typical tetrameric LDHs. The dimeric structure is equivalent to the P-dimer of tetrameric LDHs, unlike dimeric MDHs, which correspond to the Q-dimer. The structure reveals that the cofactor NADP(H) is bound at the active site, despite the fact that it was not intentionally added during protein purification and crystallization. The preference of NADP(H) over NAD(H) has been supported by activity assays. The cofactor preference is explained by the presence of a glycine residue in the cofactor binding pocket (Gly33), which replaces a conserved aspartate (or glutamate) residue in other NAD-dependent LDHs or MDHs. Preference for NADP(H) is contributed by hydrogen bonds between the oxygen atoms of the monophosphate group and the ribose sugar of adenosine in NADP(H) and the side-chains of Ser9, Arg34, His36, and Ser37. The MDH activity of MJ0490 is made possible by Arg86, which is conserved in MDHs but not in LDHs. The enzymatic assay showed that the MJ0490 protein possesses the fructose-1,6-bisphosphate-activated LDH activity (reduction). Thus the MJ0490 gene product appears to be a novel member of the lactate/malate dehydrogenase family, displaying an LDH scaffold and exhibiting a relaxed substrate and cofactor specificities in NADP(H) and NAD(H)-dependent malate and lactate dehydrogenase reactions.

Allosteric Regulation↗

PubMed2001

Adrenalectomy causes loss of zinc ions in zinc-enriched (ZEN) terminals and decreases seizure-induced neuronal death.

Chelatable zinc ions from synaptic vesicles have been suggested to be involved in neuronal death caused by stroke, epilepsy and head trauma. Elevated glucocorticoid concentration exacerbates such neuron loss, while low levels protect. We have tested the notion that the neuroprotective effect of prior glucocorticoid reduction is mediated by a reduction of zinc ions contained in zinc-enriched (ZEN) synaptic vesicles. The level of vesicular zinc ions was evaluated by toluene sulfonamide quinoline (TSQ) fluorometry and zinc autometallography (ZnS(AMG)) 10 and 30 days, respectively, after adrenalectomy. The hippocampus showed significant vesicular zinc ion depletion following adrenalectomy. After the kainate injection, adrenalectomized rats showed proconvulsive seizure behavior, i.e. shortened latency to seizure onset time and increased seizure score. Additionally they showed decreased hippocampal CA3 neuronal death as compared to control animals. The present data suggest that zinc ions released from damaged ZEN terminals are involved in seizure-induced neuronal death.

Adrenalectomy↗

PubMed2001

Malignant esophagogastric junction obstruction: palliative treatment with an antireflux valve stent.

The authors assessed the efficacy of an antireflux valve stent in the palliation of malignant esophagogastric junction (EGJ) obstruction after in vitro testing of the stent. Seventeen patients with inoperable malignant EGJ obstruction were treated. Antireflux valves, made of three polyurethane leaflets, were attached to the distal part of the stent to prevent reflux. When the flow rate of normal saline was 100 mL/sec in the forward direction, the valve fully opened at a pressure of 10 mm Hg. When the flow rate of normal saline was 0.35 mL/sec in the backward direction, the valve nearly completely closed at a pressure of 10 mm Hg. Stent placement was successful in all patients without complications. The median dysphagia score decreased significantly, from 3.0 (dysphagia to liquids) to 1.0 (dysphagia to normal solid food) (P < .0005). No patients experienced reflux symptoms. There was one case of stent migration. A valve stent that can prevent major reflux is an effective device for the palliation of malignant EGJ obstruction.

Aged↗

PubMed2001

Crystal structure and functional analysis of the SurE protein identify a novel phosphatase family.

Homologs of the Escherichia coli surE gene are present in many eubacteria and archaea. Despite the evolutionary conservation, little information is available on the structure and function of their gene products. We have determined the crystal structure of the SurE protein from Thermotoga maritima. The structure reveals the dimeric arrangement of the subunits and an active site around a bound metal ion. We also demonstrate that the SurE protein exhibits a divalent metal ion-dependent phosphatase activity that is inhibited by vanadate or tungstate. In the vanadate- and tungstate-complexed structures, the inhibitors bind adjacent to the divalent metal ion. Our structural and functional analyses identify the SurE proteins as a novel family of metal ion-dependent phosphatases.

Acid Phosphatase↗

PubMed2001

Trigger digits in children.

Seven thousand, seven hundred newborn children were examined prospectively to determine the congenital incidence of trigger thumb and finger. No cases were found. The case histories of 43 trigger digit cases (35 trigger thumbs and eight trigger fingers) noted in 40 children diagnosed at our center between 1995 and 1998 were reviewed with special reference to the spontaneous recovery rate, treatment outcome, and age at presentation. Of the 35 thumb cases, 23 underwent surgical release and all responded satisfactorily to surgical treatment. Spontaneous recovery was noted in 12 trigger thumb cases and in all eight trigger finger cases. Trigger finger developed earlier in life than trigger thumb and the spontaneous recovery rate was higher in trigger finger than trigger thumb.

Child, Preschool↗

PubMed2001

Crystallization and preliminary X-ray crystallographic analysis of the TM1442 gene product from Thermotoga maritima, a homologue of Bacillus subtilis anti-anti-sigma factors.

A 110-residue protein encoded by the TM1442 gene of Thermotoga maritima shows amino-acid sequence similarity to Bacillus subtilis anti-anti-sigma factors RsbV and SpoIIAA. It has been overexpressed in Escherichia coli and the recombinant protein exists primarily as both a monomer and a dimer in solution. The dimeric form has been crystallized using polyethylene glycol (PEG) 8000 as a precipitant. Native X-ray diffraction data have been collected at 100 K to 2.0 A resolution. The crystals are monoclinic, belonging to the space group P2(1), with unit-cell parameters a = 31.54 (13), b = 116.83 (37), c = 31.39 (7) A, alpha = 90, beta = 119.84 (9), gamma = 90 degrees. The asymmetric unit contains two monomers of the recombinant polypeptide, with a corresponding V(M) of 2.24 A(3) Da(-1) and a solvent content of 45.0%.

Bacillus subtilis↗

PubMed2001

Crystallization and preliminary X-ray crystallographic analysis of type II dehydroquinase from Helicobacter pylori.

The enzyme 3-dehydroquinase catalyzes the interconversion of 3-dehydroquinate and 3-dehydroshikimate. The enzymes are classified into two groups, type I and type II, which have different biochemical and biophysical properties and act with different mechanisms. The type II dehydroquinase of Helicobacter pylori, a dodecameric enzyme, was overexpressed in Escherichia coli. The recombinant protein has been crystallized at 296 K using polyethylene glycol (PEG) 4000 as a precipitant. Native X-ray diffraction data have been collected to 2.5 A resolution using synchrotron radiation. The crystals are cubic and belong to the space group P4(2)32, with unit-cell parameters a = b = c = 98.91 A. The asymmetric unit contains one subunit of recombinant type II dehydroquinase, with a corresponding V(M) of 2.18 A(3) Da(-1) and a solvent content of 43.6%.

Cloning, Molecular↗

PubMed2001

Crystallization and preliminary X-ray crystallographic analysis of RNase HIII from Bacillus subtilis.

The genome of Bacillus subtilis contains three different genes encoding RNase H homologs: RNases HI, HII and HIII. RNase HIII from B. subtilis degrades RNA in RNA-DNA hybrids in an Mg(2+)-dependent manner like Escherichia coli RNase HI. However, they belong to different classes; the former belongs to the 'class II' or 'large' RNase H family, while the latter belongs to the 'class I' or 'small' RNase H family. RNase HIII of B. subtilis has been overexpressed in E. coli and crystallized at 296 K using sodium formate as a precipitant. The native X-ray diffraction data have been collected to 2.8 A resolution using synchrotron radiation. The crystals are hexagonal, belonging to the space group P6(1), with unit-cell parameters a = b = 86.89, c = 214.49 A, alpha = beta = 90.0, gamma = 120.0 degrees. A self-rotation function calculation indicated the presence of two monomers of the recombinant RNase HIII in the crystallographic asymmetric unit, giving a V(M) of 3.43 A(3) Da(-1) and a solvent content of 64.2%.

Bacillus subtilis↗

PubMed2001

Crystallization and preliminary X-ray crystallographic analysis of the surE protein from Thermotoga maritima.

The surE protein from Thermotoga maritima is a 247-residue protein of unknown function. Its homologues are well conserved among both the eubacteria and the archaea. It has been overexpressed in soluble form in Escherichia coli. The protein has been crystallized at 296 K using 2-propanol as a precipitant. X-ray diffraction data have been collected to 1.9 A resolution using synchrotron radiation. The crystals belong to the trigonal space group P3(1)21 (or P3(2)21), with unit-cell parameters a = b = 115.96, c = 78.60 A, alpha = beta = 90, gamma = 120 degrees. The asymmetric unit contains two monomers of the surE protein, with a corresponding V(M) of 2.72 A(3) Da(-1) and a solvent content of 54.7%.

2-Propanol↗

PubMed2001

Malignant obstruction of gastric outlet and duodenum: palliation with flexible covered metallic stents.

PURPOSE: To assess the usefulness of flexible covered metallic stents in the palliation of malignant obstruction of the gastric outlet and duodenum. MATERIALS AND METHODS: Twenty-four consecutive patients with malignant obstruction of the gastric outlet (n = 22) or duodenum (n = 2) underwent palliative treatment with self-expandable flexible covered metallic stents. Fourteen patients had advanced gastric carcinoma at the antrum and/or pylorus, and eight had obstruction at the anastomosis site of previous gastrojejunostomy. Complications and clinical status were investigated during the study period. RESULTS: The technical success rate was 75% (18 of 24 patients). Twenty-one stents were placed in 18 patients by using an introducer 6 (n = 7) or 8 mm (n = 14) in diameter. The mean follow-up period was 3.4 months (range, 1 week to 9 months). Symptoms improved in 12 (67%) patients after the procedure. There was no change in symptoms in five and a decrease in one. Twelve patients died during the follow-up period (mean survival, 4.3 months). The complication rate was 25% (six of 24 patients), including stent migration (n = 5) and fracture (n = 3). CONCLUSION: Flexible covered metallic stent placement can be useful for palliation in patients with malignant obstruction of the gastric outlet or duodenum.

Adult↗

PubMed2001

Rapid translocation of Zn(2+) from presynaptic terminals into postsynaptic hippocampal neurons after physiological stimulation.

Zn(2+) is found in glutamatergic nerve terminals throughout the mammalian forebrain and has diverse extracellular and intracellular actions. The anatomical location and possible synaptic signaling role for this cation have led to the hypothesis that Zn(2+) is released from presynaptic boutons, traverses the synaptic cleft, and enters postsynaptic neurons. However, these events have not been directly observed or characterized. Here we show, using microfluorescence imaging in rat hippocampal slices, that brief trains of electrical stimulation of mossy fibers caused immediate release of Zn(2+) from synaptic terminals into the extracellular microenvironment. Release was induced across a broad range of stimulus intensities and frequencies, including those likely to induce long-term potentiation. The amount of Zn(2+) release was dependent on stimulation frequency (1-200 Hz) and intensity. Release of Zn(2+) required sodium-dependent action potentials and was dependent on extracellular Ca(2+). Once released, Zn(2+) crosses the synaptic cleft and enters postsynaptic neurons, producing increases in intracellular Zn(2+) concentration. These results indicate that, like a neurotransmitter, Zn(2+) is stored in synaptic vesicles and is released into the synaptic cleft. However, unlike conventional transmitters, it also enters postsynaptic neurons, where it may have manifold physiological functions as an intracellular second messenger.

Action Potentials↗