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Biomedical subjects

S W Suh

Publications and source records attributed to S W Suh.

At least 37 records · Page 2Linked to original sources

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↗

Structural and mechanistic conservation in DNA ligases.

DNA ligases are enzymes required for the repair, replication and recombination of DNA. DNA ligases catalyse the formation of phosphodiester bonds at single-strand breaks in double-stranded DNA. Despite their occurrence in all organisms, DNA ligases show a wide diversity of amino acid sequences, molecular sizes and properties. The enzymes fall into two groups based on their cofactor specificity, those requiring NAD(+) for activity and those requiring ATP. The eukaryotic, viral and archael bacteria encoded enzymes all require ATP. NAD(+)-requiring DNA ligases have only been found in prokaryotic organisms. Recently, the crystal structures of a number of DNA ligases have been reported. It is the purpose of this review to summarise the current knowledge of the structure and catalytic mechanism of DNA ligases.

Adenosine Triphosphate↗

Release of synaptic zinc is substantially depressed by conventional brain slice preparations.

Research on synaptically-released zinc is frequently done in vitro with acute brain slice preparations. We show here the in vitro hippocampal slice preparation has two major pitfalls for zinc research. First, up to 50% of the synaptic zinc is lost during slice cutting and/or the first 10 min of slice incubation, with the losses being most pronounced on the edges of the slice. Second, the release of the remaining zinc from a slice is substantially depressed (up to 50%) at the low temperatures (32 degrees C) typically used for brain slice studies. In concert, these effects reduce zinc release about 75% in vitro, compared to in vivo. Implications for research on synaptically-released zinc are discussed.

Animals↗

Crystal structure of Escherichia coli CyaY protein reveals a previously unidentified fold for the evolutionarily conserved frataxin family.

Friedreich ataxia is an autosomal recessive neurodegenerative disease caused by defects in the FRDA gene, which encodes a mitochondrial protein called frataxin. Frataxin is evolutionarily conserved, with homologs identified in mammals, worms, yeast, and bacteria. The CyaY proteins of gamma-purple bacteria are believed to be closely related to the ancestor of frataxin. In this study, we have determined the crystal structure of the CyaY protein from Escherichia coli at 1.4-A resolution. It reveals a protein fold consisting of a six-stranded antiparallel beta-sheet flanked on one side by two alpha-helices. This fold is likely to be shared by all members of the conserved frataxin family. This study also provides a framework for the interpretation of disease-associated mutations in frataxin and for understanding the possible functions of this protein family.

Amino Acid Sequence↗

HBV polymerase interacts independently with N-terminal and C-terminal fragments of Hsp90beta.

Hsp90 is an abundant chaperone protein that assists the folding of specific proteins, such as steroid receptors, protein kinases, and so on, for their proper function. TP and RT domains of HBV polymerase have been also shown to be associated with Hsp90. Therefore, the identification of the binding sites within Hsp90, responsible for forming Hsp90/HBV Pol complex, is important for the understanding of HBV replication. In this study, cotransfection and immunoprecipitation experiments were performed to localize the binding sites of HBV pol to Hsp90. Our data show that HBV pol interact independently with both N-terminal and C-terminal fragments of Hsp90. Further analysis showed that N-terminal fragment (1-302) of Hsp90 interacts with both TP and RT domains of HBV pol, whereas C-terminal fragment (438-723) interacts with only RT domain. In conclusion, we showed that HBV pol independently interacts with N-terminal and C-terminal fragments, but not the middle fragment (327-438) of Hsp90.

Animals↗

Crystal structure of the ribosome recycling factor from Escherichia coli.

We have determined the crystal structure of the Escherichia coli ribosome recycling factor (RRF), which catalyzes the disassembly of the termination complex in protein synthesis. The L-shaped molecule consists of two domains: a triple-stranded antiparallel coiled-coil and an alpha/beta domain. The coil domain has a cylindrical shape and negatively charged surface, which are reminiscent of the anticodon arm of tRNA and domain IV of elongation factor EF-G. We suggest that RRF binds to the ribosomal A-site through its coil domain, which is a tRNA mimic. The relative position of the two domains is changed about an axis along the hydrophobic cleft in the hinge where the alkyl chain of a detergent molecule is bound. The tRNA mimicry and the domain movement observed in RRF provide a structural basis for understanding the role of RRF in protein synthesis.

Amino Acid Sequence↗

Crystal structure of NAD(+)-dependent DNA ligase: modular architecture and functional implications.

DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor. Despite the difference in cofactor specificity and limited overall sequence similarity, the two classes of DNA ligase share basically the same catalytic mechanism. In this study, the crystal structure of an NAD(+)-dependent DNA ligase from Thermus filiformis, a 667 residue multidomain protein, has been determined by the multiwavelength anomalous diffraction (MAD) method. It reveals highly modular architecture and a unique circular arrangement of its four distinct domains. It also provides clues for protein flexibility and DNA-binding sites. A model for the multidomain ligase action involving large conformational changes is proposed.

Amino Acid Sequence↗

Evidence that synaptically-released zinc contributes to neuronal injury after traumatic brain injury.

Prior evidence indicates that synaptically-released zinc enters postsynaptic neurons in toxic excess during ischemia and seizures. In addition, prevention of this zinc translocation has been shown to be neuroprotective in both ischemia and seizures. Here we show evidence that the same translocation of zinc from presynaptic boutons into postsynaptic neurons occurs after mechanical injury to the brain. Specifically, using a rat model of traumatic brain injury, we show that trauma is associated with (i) loss of zinc from presynaptic boutons (ii) appearance of zinc in injured neurons, and (iii) neuroprotection by intraventricular administration of a zinc chelator just prior to brain impact. The possible use of zinc chelators for neuroprotection after head trauma is considered.

Aminoquinolines↗

Histochemically-reactive zinc in amyloid plaques, angiopathy, and degenerating neurons of Alzheimer's diseased brains.

Excess brain zinc has been implicated in Alzheimer's neuropathology. Here we evaluated that hypothesis by searching the brains of Alzheimer's patients for abnormal zinc deposits. Using histochemical methods, we found vivid Zn2+ staining in the amyloid deposits of dense-core (senile) plaques, in the amyloid angiopathy surrounding diseased blood vessels, and in the somata and dendrites of neurons showing the characteristic neurofibrillary tangles (NFT) of Alzheimer's. In contrast, brains from age-matched, non-demented subjects showed only occasional staining for Zn2+ in scattered neurons and possible plaques. A role of abnormal zinc metabolism in Alzheimer's neuropathology is suggested.

Aged↗

Computational studies of essential dynamics of Pseudomonas cepacia lipase.

In order to investigate the interfacial activation of a lipase from Pseudomonas cepacia (PcL), molecular dynamics (MD) simulations and essential dynamics (ED) analysis were performed in different solvent environments: vacuum and explicit water solvents. Starting from the active (open) structure of PcL, the essential dynamics analysis of the simulations revealed large correlated motions, which may be responsible for the activation of the enzyme. Fluctuations in the U1 (active-site lid) and U2 domains are found to be important in the activation of PcL. In contrast, the catalytic triad exhibits very little displacement. These results are consistent with the previous X-ray structural determination. A combined analysis of the trajectories showed some differences for the simulations in different solvent environments. It was found that the region around the helix alpha5 showed larger displacements in the water simulations. It can be concluded that the open structure of PcL becomes unstable in water solvents, leading to the closing of the so-called 'lid' region. The simulations and ED analysis on the closed structure of PgL provided additional information concerning the structural changes involved in the activation of the lipases. It was found that structural changes for PcL and PgL, which are responsible for the essential motions of the protein, showed contrasting behavior in the different solvent environments.

Binding Sites↗

Importance of zinc in the central nervous system: the zinc-containing neuron.

Zinc is essential to the structure and function of myriad proteins, including regulatory, structural and enzymatic. It is estimated that up to 1% of the human genome codes for zinc finger proteins. In the central nervous system, zinc has an additional role as a neurosecretory product or cofactor. In this role, zinc is highly concentrated in the synaptic vesicles of a specific contingent of neurons, called "zinc-containing" neurons. Zinc-containing neurons are a subset of glutamatergic neurons. The zinc in the vesicles probably exceeds 1 mmol/L in concentration and is only weakly coordinated with any endogenous ligand. Zinc-containing neurons are found almost exclusively in the forebrain, where in mammals they have evolved into a complex and elaborate associational network that interconnects most of the cerebral cortices and limbic structures. Indeed, one of the intriguing aspects of these neurons is that they compose somewhat of a chemospecific "private line" of the mammalian cerebral cortex. The present review outlines (1) the methods used to discover, define and describe zinc-containing neurons; (2) the neuroarchitecture and synaptology of zinc-containing neural circuits; (3) the physiology of regulated vesicular zinc release; (4) the "life cycle" and molecular biology of vesicular zinc; (5) the importance of synaptically released zinc in the normal and pathological processes of the cerebral cortex; and (6) the role of specific and nonspecific stressors in the release of zinc.

Alzheimer Disease↗

Crystallization and preliminary x-ray crystallographic analysis of NAD+-dependent DNA ligase from Thermus filiformis.

A highly thermostable DNA ligase from Thermus filiformis has been crystallized at room temperature using methoxypolyethylene glycol 5000 as a precipitant. The crystal belongs to the monoclinic space group P2(1), with unit-cell parameters a = 90.63, b = 117.80, c = 98. 65 A, beta = 115.56 degrees. Two molecules of DNA ligase are present in the asymmetric unit, giving a crystal volume per protein mass (V(m)) of 3.1 A(3) Da(-1) and a solvent content of 61%. A native data set extending to 3.0 A resolution has been collected at 100 K using synchrotron X-rays.

Bacterial Proteins↗

Overexpression, crystallization and preliminary X-ray crystallographic analysis of dihydrofolate reductase from bacteriophage T4.

Dihydrofolate reductase (DHFR) from bacteriophage T4 is a homodimer consisting of 193-residue subunits. It has been crystallized in the presence of the cofactor (NADPH) and an inhibitor (aminopterin) at 296 K using sodium chloride as precipitant. The crystals are tetragonal, belonging to the space group P4(1)22 (or P4(3)22), with unit-cell parameters a = b = 61.14, c = 123.23 A under cryogenic conditions. The asymmetric unit contains a single subunit, with a corresponding V(m) of 2.65 A(3) Da(-1) and a solvent content of 53. 6%. Native data have been collected from a crystal to 1.9 A resolution using synchrotron X-rays.

Bacteriophage T4↗

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↗

Crystallization and preliminary X-ray crystallographic analysis of Escherichia coli CyaY, a structural homologue of human frataxin.

CyaY is a 106-residue protein from Escherichia coli. It shows amino-acid sequence similarity to human frataxin and a frataxin homologue in Saccharomyces cerevisiae, Yfh1p. The former is associated with the disease Friedreich ataxia and the latter plays a key role in iron homeostasis in mitochondria. CyaY has been overexpressed in soluble form in E. coli. The recombinant protein with a His(6) tag at its C-terminus has been crystallized at 296 K using polyethylene glycol (PEG) 4000 as a precipitant. Native diffraction data have been collected to 1.8 A using Cu Kalpha X-rays. The crystals belong to the trigonal space group P3(1)21 (or P3(2)21), with unit-cell parameters a = b = 44.66, c = 99.87 A, alpha = beta = 90.0, gamma = 120.0 degrees. The asymmetric unit contains one molecule of recombinant CyaY, with a corresponding V(m) of 2.13 A(3) Da(-1) and solvent content of 42.3%.

Bacterial Proteins↗

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↗

Lactate dehydrogenase from the hyperthermophilic archaeon Methanococcus jannaschii: overexpression, crystallization and preliminary X-ray analysis.

L(+)-Lactate dehydrogenase (LDH) is a key enzyme in anaerobic metabolism which converts pyruvate to lactate. LDH from the hyperthermophilic archaebacterium Methanococcus jannaschii has been overexpressed in Escherichia coli and crystallized in two crystal forms at 297 K using 2-methyl-2,4-pentanediol as precipitant. Type I crystals grew rapidly and diffracted to at least 2.8 A Bragg spacing upon exposure to Cu Kalpha X-rays. X-ray diffraction data to 2.9 A have been collected from a native crystal. The type I crystal is tetragonal, belonging to the space group P4(2)2(1)2, with unit-cell parameters a = b = 99.74, c = 170.00 A. The asymmetric unit contains two LDH subunits, with a corresponding crystal volume per protein mass (V(m)) of 3.05 A(3) Da(-1) and a solvent content of 59.7%. Type II crystals, which grew more slowly, diffracted to at least 1.8 A Bragg spacing upon exposure to Cu Kalpha X-rays. X-ray diffraction data to 1.9 A have been collected from a native crystal. The type II crystal is orthorhombic, belonging to the space group P2(1)2(1)2, with unit-cell parameters a = 47.65, b = 125.10, c = 58.08 A. The asymmetric unit contains a single LDH subunit, with a corresponding crystal volume per protein mass (V(m)) of 2.50 A(3) Da(-1) and a solvent content of 50.8%. Therefore, the type II crystal is more suitable for high-resolution structure determination than the type I crystal.

Cloning, Molecular↗

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↗