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Lange R, Elter P, Biala K, Matschegewski C, Stählke S, Löffler R, Fleischer M, Nebe JB, Kern D, Beck U. Titanium surfaces structured with regular geometry-material investigations and cell morphology. SURF INTERFACE ANAL 2010. [DOI: 10.1002/sia.3320] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Fourcade O, Sanchez P, Kern D, Mazoit JX, Minville V, Samii K. Propacetamol and ketoprofen after thyroidectomy. Eur J Anaesthesiol 2005; 22:373-7. [PMID: 15918387 DOI: 10.1017/s0265021505000645] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
BACKGROUND AND OBJECTIVE The combination of non-opioid analgesic drugs, though widely used, has been rarely evaluated. The aim of this study was to compare the efficacy of propacetamol and the non-steroidal analgesic drug ketoprofen, alone or in combination, on pain relief after thyroid surgery performed using remifentanil. METHODS Ninety-seven patients were randomly allocated to one of the three groups: propacetamol 2 g (32), ketoprofen 100 mg (33) and propacetamol 2 g + ketoprofen 100 mg (32). Each regimen was administered intravenously (i.v.) 30 min before the end of surgery and then every 6 h. If pain was not relieved, patients received an i.v. bolus of tramadol 100 mg. Tramadol consumption and pain intensity using a visual analogue scale was recorded at 1, 2, 8 and 14 h after the end of surgery. RESULTS Pain scores were significantly higher with propacetamol compared with ketoprofen 2 h after surgery (35 +/- 3.7, 21 +/- 2.6, respectively; P < 0.01). The number of patients receiving tramadol was higher with propacetamol alone compared with the two other groups, 1 h (14/32, 4/33, 2/32, respectively; P > 0.01) and 2 h (24/32, 6/33, 8/32, respectively; P < 0.01) after surgery. There was no difference between ketoprofen alone and ketoprofen plus propacetamol, and there was no difference between the three groups from the 8th hour onward. CONCLUSIONS In the immediate postoperative period after thyroid surgery performed using remifentanil, the concomitant use of propacetamol and ketoprofen does not improve analgesia compared with ketoprofen alone.
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Fabre S, Vaysse F, Carpentier C, Kern D, Fourcade O. [Is premixed 50% nitrous oxide and oxygen an alternative to general anaesthesia for dental care in children?]. ACTA ACUST UNITED AC 2004; 23:72-3. [PMID: 14980330 DOI: 10.1016/j.annfar.2003.11.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Sacrista S, Kern D, Fourcade O, Izard P, Galinier P, Samii K, Cathala B. Spinal anaesthesia in a child with hypoplastic left heart syndrome. Paediatr Anaesth 2003; 13:253-6. [PMID: 12641689 DOI: 10.1046/j.1460-9592.2003.00961.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Hypoplastic left heart syndrome (HLHS), a complex congenital heart disease, is the most common lethal cardiac defect in neonates. Its treatment includes cardiac transplantation and/or surgical palliation. Associated extracardiac congenital abnormalities are exceptional. We report the case of a neonate with HLHS and anorectal atresia who required urgent surgical management to relieve intestinal obstruction. The surgery was successfully performed under spinal anaesthesia.
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Branch WT, Kern D, Haidet P, Weissmann P, Gracey CF, Mitchell G, Inui T. The patient-physician relationship. Teaching the human dimensions of care in clinical settings. JAMA 2001; 286:1067-74. [PMID: 11559292 DOI: 10.1001/jama.286.9.1067] [Citation(s) in RCA: 193] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Despite repeated calls to emphasize the humanistic dimensions of care during medical education, these are few known techniques for effective teaching of humanism. We describe the barriers that inhibit humanistic teaching and suggest pragmatic teaching methods to overcome such barriers and teach humanistic care in clinical settings. We began by asking participants at a conference on patient-physician communications sponsored by the American Academy on Physician and Patient in June 1998, "What can we do in the patient's presence to improve and teach the human dimensions of care? Please provide one or more examples of approaches you found to be effective." We augmented this information with suggestions from a number of colleagues in other settings. In a series of iterations, we analyzed all their suggestions to identify key teaching methods. We found that barriers to teaching humanism largely consist of elements of the informal and hidden curricula in medical schools. We then defined methods to help teachers overcome these barriers. Specific methods fall into the 3 categories of taking advantage of seminal events, role modeling, and using active learning skills. We believe that formal courses and other well-motivated endeavors that take place away from patients fail to foster humanistic care. In contrast, we present pragmatic teaching methods that can be used in the fast-paced setting of the clinical environment.
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Charron C, Roy H, Lorber B, Kern D, Giegé R. Crystallization and preliminary X-ray diffraction data of the second and archaebacterial-type aspartyl-tRNA synthetase from Thermus thermophilus. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2001; 57:1177-9. [PMID: 11468411 DOI: 10.1107/s0907444901009611] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2001] [Accepted: 06/11/2001] [Indexed: 11/10/2022]
Abstract
The archaebacterial-type aspartyl-tRNA synthetase (AspRS2) from the thermophilic eubacterium Thermus thermophilus was crystallized using the hanging-drop vapour-diffusion method. Crystals grew at pH 9.5 in the presence of PEG 8000 and NaCl. A native diffraction data set has been collected at 2.5 A resolution using synchrotron radiation and cryocooling. Crystals belong to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 57.3, b = 121.9, c = 166.9 A and V(M) = 3.03 A(3) Da(-1). There is one dimer of M(r) 96 000 per asymmetric unit. A molecular-replacement analysis gave solutions for the rotation and translation functions.
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Suc A, Mariotti M, Lestrade C, Kern D, Izard P, Marmet T, Vignes M, Raynaud JP. [Children also die]. Arch Pediatr 2001; 8:751-3. [PMID: 11484460 DOI: 10.1016/s0929-693x(00)90311-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Palliative care has recently been developed in adults. However, children die as well and quite a few articles have been published on this special issue. The object of this article is to summarize the available literature in order to call for the development of clinical policies and minimum standards adapted to French pediatrics.
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Abstract
Protein actions are usually discussed in terms of static structures, but function requires motion. We find a strong correlation between phosphorylation-driven activation of the signaling protein NtrC and microsecond time-scale backbone dynamics. Using nuclear magnetic resonance relaxation, we characterized the motions of NtrC in three functional states: unphosphorylated (inactive), phosphorylated (active), and a partially active mutant. These dynamics are indicative of exchange between inactive and active conformations. Both states are populated in unphosphorylated NtrC, and phosphorylation shifts the equilibrium toward the active species. These results support a dynamic population shift between two preexisting conformations as the underlying mechanism of activation.
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Becker HD, Min B, Jacobi C, Raczniak G, Pelaschier J, Roy H, Klein S, Kern D, Söll D. The heterotrimeric Thermus thermophilus Asp-tRNA(Asn) amidotransferase can also generate Gln-tRNA(Gln). FEBS Lett 2000; 476:140-4. [PMID: 10913601 DOI: 10.1016/s0014-5793(00)01697-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Thermus thermophilus strain HB8 is known to have a heterodimeric aspartyl-tRNA(Asn) amidotransferase (Asp-AdT) capable of forming Asn-tRNA(Asn) [Becker, H.D. and Kern, D. (1998) Proc. Natl. Acad. Sci. USA 95, 12832-12837]. Here we show that, like other bacteria, T. thermophilus possesses the canonical set of amidotransferase (AdT) genes (gatA, gatB and gatC). We cloned and sequenced these genes, and constructed an artificial operon for overexpression in Escherichia coli of the thermophilic holoenzyme. The overproduced T. thermophilus AdT can generate Gln-tRNA(Gln) as well as Asn-tRNA(Asn). Thus, the T. thermophilus tRNA-dependent AdT is a dual-specific Asp/Glu-AdT resembling other bacterial AdTs. In addition, we observed that removal of the 44 carboxy-terminal amino acids of the GatA subunit only inhibits the Asp-AdT activity, leaving the Glu-AdT activity of the mutant AdT unaltered; this shows that Asp-AdT and Glu-AdT activities can be mechanistically separated.
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Becker HD, Roy H, Moulinier L, Mazauric MH, Keith G, Kern D. Thermus thermophilus contains an eubacterial and an archaebacterial aspartyl-tRNA synthetase. Biochemistry 2000; 39:3216-30. [PMID: 10727213 DOI: 10.1021/bi992573y] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Thermus thermophilus possesses two aspartyl-tRNA synthetases (AspRSs), AspRS1 and AspRS2, encoded by distinct genes. Alignment of the protein sequences with AspRSs of other origins reveals that AspRS1 possesses the structural features of eubacterial AspRSs, whereas AspRS2 is structurally related to the archaebacterial AspRSs. The structural dissimilarity between the two thermophilic AspRSs is correlated with functional divergences. AspRS1 aspartylates tRNA(Asp) whereas AspRS2 aspartylates tRNA(Asp), and tRNA(Asn) with similar efficiencies. Since Asp bound on tRNA(Asn) is converted into Asn by a tRNA-dependent aspartate amidotransferase, AspRS2 is involved in Asn-tRNA(Asn) formation. These properties relate functionally AspRS2 to archaebacterial AspRSs. The structural basis of the dual specificity of T. thermophilus tRNA(Asn) was investigated by comparing its sequence with those of tRNA(Asp) and tRNA(Asn) of strict specificity. It is shown that the thermophilic tRNA(Asn) contains the elements defining asparagine identity in Escherichia coli, part of which being also the major elements of aspartate identity, whereas minor elements of this identity are missing. The structural context that permits expression of aspartate and asparagine identities by tRNA(Asn) and how AspRS2 accommodates tRNA(Asp) and tRNA(Asn) will be discussed. This work establishes a distinct structure-function relationship of eubacterial and archaebacterial AspRSs. The structural and functional properties of the two thermophilic AspRSs will be discussed in the context of the modern and primitive pathways of tRNA aspartylation and asparaginylation and related to the phylogenetic connexion of T. thermophilus to eubacteria and archaebacteria.
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Cura V, Moras D, Kern D. Sequence analysis and modular organization of threonyl-tRNA synthetase from Thermus thermophilus and its interrelation with threonyl-tRNA synthetases of other origins. EUROPEAN JOURNAL OF BIOCHEMISTRY 2000; 267:379-93. [PMID: 10632708 DOI: 10.1046/j.1432-1327.2000.01011.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The gene encoding threonyl-tRNA synthetase (Thr-tRNA synthetase) from the extreme thermophilic eubacterium Thermus thermophilus HB8 has been cloned and sequenced. The ORF encodes a polypeptide chain of 659 amino acids (Mr 75 550) that shares strong similarities with other Thr-tRNA synthetases. Comparative analysis with the three-dimensional structure of other subclass IIa synthetases shows it to be organized into four structural modules: two N-terminal modules specific to Thr-tRNA synthetases, a catalytic core and a C-terminal anticodon-binding module. Comparison with the three-dimensional structure of Escherichia coli Thr-tRNA synthetase in complex with tRNAThr enabled identification of the residues involved in substrate binding and catalytic activity. Analysis by atomic absorption spectrometry of the enzyme overexpressed in E. coli revealed the presence in each monomer of one tightly bound zinc atom, which is essential for activity. Despite strong similarites in modular organization, Thr-tRNA synthetases diverge from other subclass IIa synthetases on the basis of their N-terminal extensions. The eubacterial and eukaryotic enzymes possess a large extension folded into two structural domains, N1 and N2, that are not significantly similar to the shorter extension of the archaebacterial enzymes. Investigation of a truncated Thr-tRNA synthetase demonstrated that domain N1 is not essential for tRNA charging. Thr-tRNA synthetase from T. thermophilus is of the eubacterial type, in contrast to other synthetases from this organism, which exhibit archaebacterial characteristics. Alignments show conservation of part of domain N2 in the C-terminal moiety of Ala-tRNA synthetases. Analysis of the nucleotide sequence upstream from the ORF showed the absence of both any anticodon-like stem-loop structure and a loop containing sequences complementary to the anticodon and the CCA end of tRNAThr. This means that the expression of Thr-tRNA synthetase in T. thermophilus is not regulated by the translational and trancriptional mechanisms described for E. coli thrS and Bacillus subtilis thrS and thrZ. Here we discuss our results in the context of evolution of the threonylation systems and of the position of T. thermophilus in the phylogenic tree.
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Kern D, Volkman BF, Luginbühl P, Nohaile MJ, Kustu S, Wemmer DE. Structure of a transiently phosphorylated switch in bacterial signal transduction. Nature 1999; 402:894-8. [PMID: 10622255 DOI: 10.1038/47273] [Citation(s) in RCA: 166] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Receiver domains are the dominant molecular switches in bacterial signalling. Although several structures of non-phosphorylated receiver domains have been reported, a detailed structural understanding of the activation arising from phosphorylation has been impeded by the very short half-lives of the aspartylphosphate linkages. Here we present the first structure of a receiver domain in its active state, the phosphorylated receiver domain of the bacterial enhancer-binding protein NtrC (nitrogen regulatory protein C). Nuclear magnetic resonance spectra were taken during steady-state autophosphorylation/dephosphorylation, and three-dimensional spectra from multiple samples were combined. Phosphorylation induces a large conformational change involving a displacement of beta-strands 4 and 5 and alpha-helices 3 and 4 away from the active site, a register shift and an axial rotation in helix 4. This creates an exposed hydrophobic surface that is likely to transmit the signal to the transcriptional activation domain.
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Mazauric MH, Roy H, Kern D. tRNA glycylation system from Thermus thermophilus. tRNAGly identity and functional interrelation with the glycylation systems from other phylae. Biochemistry 1999; 38:13094-105. [PMID: 10529180 DOI: 10.1021/bi991392t] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The systems of tRNA glycylation belong to the most complex aminoacylation systems since neither the oligomeric structure of glycyl-tRNA synthetases (GlyRS) nor the discriminator bases in tRNAGly are conserved in the phylae. To better understand the structure-function relationship in glycylation systems of various origins and the functional peculiarities related to their structural divergences, the elements in tRNA conferring its glycine identity in Thermus thermophilus were characterized and compared to those of other systems. Thermophilic identity is conferred by the G1-C72, C2-G71, G3-C70, and C50-G64 pairs together with the G10, U16, C35, and C36 single residues. In contrast to most other aminoacylation systems, the discriminator base is not directly involved in identity. Transplantation of these elements in tRNAAsp and tRNAPhe converts specificity toward glycine albeit conservation of nucleotide 73. Analysis of the functional interrelation of the identity elements shows coupling in synthetase recognition of the elements from anticodon and G10 whereas those from acceptor arm are recognized independently. Despite nondirect implication in identity, the discriminator base contributes cooperatively with C36 in specificity of glycylation. The link between the structural heterogeneity and the functional divergence of the glycylation systems and the phylogenic interrelation of these systems were approached by comparing the ability of GlyRSs of various phylae to glycylate heterologous tRNAGly. Dimeric GlyRSs from mammalian and archaebacteria acylate efficiently only eukaryotic and archaebacterial tRNAGly with a discriminatory A73, whereas tetrameric Escherichia coli GlyRS acylates only eubacterial tRNAGly with a discriminatory U73. In contrast, dimeric yeast GlyRS acylates efficiently both eukaryotic and archaebacterial tRNAGly as well as peculiar prokaryotic isoacceptors. Species specificity is lost with the dimeric GlyRS from Thermus thermophilus that acylates efficiently eubacterial, archaebacterial, and eukaryotic tRNAGly. These features are discussed in the context of the evolution of the glycylation systems and the phylogenic interrelation of the organisms.
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Sauter C, Lorber B, Kern D, Cavarelli J, Moras D, Giegé R. Crystallogenesis studies on yeast aspartyl-tRNA synthetase: use of phase diagram to improve crystal quality. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 1999; 55:149-56. [PMID: 10089405 DOI: 10.1107/s0907444998010890] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/1998] [Accepted: 08/14/1998] [Indexed: 11/10/2022]
Abstract
Aspartyl-tRNA synthetase (AspRS) extracted from yeast is heterogeneous owing to proteolysis of its positively charged N-terminus; its crystals are of poor quality. To overcome this drawback, a rational strategy was developed to grow crystals of sufficient quality for structure determination. The strategy is based on improvement of the protein homogeneity and optimization of crystallization, taking advantage of predictions from crystal-growth theories. An active mutant lacking the first 70 residues was produced and initial crystallization conditions searched. The shape and habit of initial crystals were improved by establishing a phase diagram of protein versus crystallizing-agent concentrations. Growth of large well faceted crystals takes place at low supersaturations near the isochronic supersolubility curve. Further refinement led to reproducible growth of two crystalline forms of bipyramidal (I) or prismatic (II) habit. Both diffract X-rays better than crystals previously obtained with native AspRS. Complete data sets were collected at 3 A resolution for form I (space group P41212) and form II (space group P3221) and molecular-replacement solutions were found in both space groups.
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Becker HD, Kern D. Thermus thermophilus: a link in evolution of the tRNA-dependent amino acid amidation pathways. Proc Natl Acad Sci U S A 1998; 95:12832-7. [PMID: 9789000 PMCID: PMC23616 DOI: 10.1073/pnas.95.22.12832] [Citation(s) in RCA: 129] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Thermus thermophilus possesses an aspartyl-tRNA synthetase (AspRS2) able to aspartylate efficiently tRNAAsp and tRNAAsn. Aspartate mischarged on tRNAAsn then is converted into asparagine by an omega amidase that differs structurally from all known asparagine synthetases. However, aspartate is not misincorporated into proteins because the binding capacity of aminoacylated tRNAAsn to elongation factor Tu is only conferred by conversion of aspartate into asparagine. T. thermophilus additionally contains a second aspartyl-tRNA synthetase (AspRS1) able to aspartylate tRNAAsp and an asparaginyl-tRNA synthetase able to charge tRNAAsn with free asparagine, although the organism does not contain a tRNA-independent asparagine synthetase. In contrast to the duplicated pathway of tRNA asparaginylation, tRNA glutaminylation occurs in the thermophile via the usual pathway by using glutaminyl-tRNA synthetase and free glutamine synthesized by glutamine synthetase that is unique. T. thermophilus is able to ensure tRNA aminoacylation by alternative routes involving either the direct pathway or by conversion of amino acid mischarged on tRNA. These findings shed light on the interrelation between the tRNA-dependent and tRNA-independent pathways of amino acid amidation and on the processes involved in fidelity of the aminoacylation systems.
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Hübner G, Tittmann K, Killenberg-Jabs M, Schäffner J, Spinka M, Neef H, Kern D, Kern G, Schneider G, Wikner C, Ghisla S. Activation of thiamin diphosphate in enzymes. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1385:221-8. [PMID: 9655909 DOI: 10.1016/s0167-4838(98)00070-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Activation of the coenzyme ThDP was studied by measuring the kinetics of deprotonation at the C2 carbon of thiamin diphosphate in the enzymes pyruvate decarboxylase, transketolase, pyruvate dehydrogenase complex, pyruvate oxidase, in site-specific mutant enzymes and in enzyme complexes containing coenzyme analogues by proton/deuterium exchange detected by 1H-NMR spectroscopy. The respective deprotonation rate constant is above the catalytic constant in all enzymes investigated. The fast deprotonation requires the presence of an activator in pyruvate decarboxylase from yeast, showing the allosteric regulation of this enzyme to be accomplished by an increase in the C2-H dissociation rate of the enzyme-bound thiamin diphosphate. The data of the thiamin diphosphate analogues and of the mutant enzymes show the N1' atom and the 4'-NH2 group to be essential for the activation of the coenzyme and a conserved glutamate involved in the proton abstraction mechanism of the enzyme-bound thiamin diphosphate.
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Kern D. For the children of the mountains. ADVANCE FOR NURSE PRACTITIONERS 1998; 6:56-8. [PMID: 9708057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Hirai A, Takemoto K, Nishino K, Watanabe N, Anderson E, Attwood D, Kern D, Hettwer M, Rudolph D, Aoki S, Nakayama Y, Kihara H. Imaging soft X-ray microscope at Rits Synchrotron Radiation Center. JOURNAL OF SYNCHROTRON RADIATION 1998; 5:1102-1104. [PMID: 15263759 DOI: 10.1107/s0909049597018529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/1997] [Accepted: 12/01/1997] [Indexed: 05/24/2023]
Abstract
An imaging soft X-ray microscope with zone plates has been installed at Rits SR Center (Ritsumeikan University, Kusatsu, Japan). With this microscope, specimens were set in air, which made it possible to investigate the specimens without breaking the vacuum of the microscope. The specimens can be prefocused with an optical microscope. Dry and wet biospecimens in air were observed. A new optical system was designed to improve the resolution.
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Mazauric MH, Keith G, Logan D, Kreutzer R, Giegé R, Kern D. Glycyl-tRNA synthetase from Thermus thermophilus--wide structural divergence with other prokaryotic glycyl-tRNA synthetases and functional inter-relation with prokaryotic and eukaryotic glycylation systems. EUROPEAN JOURNAL OF BIOCHEMISTRY 1998; 251:744-57. [PMID: 9490048 DOI: 10.1046/j.1432-1327.1998.2510744.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The tRNA glycylation system is amongst the most complex aminoacylation systems since neither the oligomeric structure of the enzymes nor the discriminator base in tRNAs are conserved in the phylae. To understand better this structural diversity and its functional consequences, the prokaryotic glycylation system from Thermus thermophilus, an extreme thermophile, was investigated and its structural and functional inter-relations with those of other origins analyzed. Alignments of the protein sequence of the dimeric thermophilic glycyl-tRNA synthetase (Gly-tRNA synthetase) derived from its gene with sequences of other dimeric Gly-tRNA synthetases revealed an atypical character of motif 1 in all these class 2 synthetases. Interestingly, the sequence of the prokaryotic thermophilic enzyme resembles eukaryotic and archaebacterial Gly-tRNA synthetases, which are all dimeric, and diverges drastically from the tetrameric enzymes from other prokaryotes. Cross aminoacylations with tRNAs and synthetases of different origins provided information about functional interrelations between the glycylation systems. Efficient glycylations involving partners from T. thermophilus and Escherichia coli showed conservation of the recognition process in prokaryotes despite strong structural variations of the synthetases. However, Gly-tRNA synthetase from T. thermophilus acylates eukaryotic tRNA(Gly) while the charging ability of the E. coli enzyme is restricted to prokaryotic tRNA(Gly). A similar behaviour is found in eukaryotic systems where the restricted species specificity for tRNA glycylation of mammalian Gly-tRNA synthetase contrasts with the relaxed specificity of the yeast enzyme. The consensus sequence of the tRNAs charged by the various Gly-tRNA synthetases reveals conservation of only G1-C72 in the acceptor arm, C35 and C36 in the anticodon, and the (G10-Y25)-G45 triplet involved in tRNA folding. Conservation of these nucleotides indicates their key role in glycylation and suggests that they were part of the ancestral glycine identity set. These features are discussed in the context of the phylogenic connections between prokaryotes, eukaryotes, and archaebacteria, and of the particular place of T. thermophilus in this phylogeny.
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MESH Headings
- Amino Acid Sequence
- Animals
- Base Sequence
- Cloning, Molecular
- Consensus Sequence
- DNA Primers
- Genetic Variation
- Glycine-tRNA Ligase/biosynthesis
- Glycine-tRNA Ligase/chemistry
- Glycine-tRNA Ligase/genetics
- Humans
- Mammals
- Molecular Sequence Data
- Mutagenesis, Site-Directed
- Polymerase Chain Reaction
- Prokaryotic Cells
- RNA, Transfer, Gly/biosynthesis
- RNA, Transfer, Gly/chemistry
- RNA, Transfer, Gly/genetics
- Recombinant Proteins/biosynthesis
- Recombinant Proteins/chemistry
- Sequence Alignment
- Sequence Homology, Amino Acid
- Sequence Homology, Nucleic Acid
- Thermus thermophilus/enzymology
- Thermus thermophilus/genetics
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Nohaile M, Kern D, Wemmer D, Stedman K, Kustu S. Structural and functional analyses of activating amino acid substitutions in the receiver domain of NtrC: evidence for an activating surface. J Mol Biol 1997; 273:299-316. [PMID: 9367763 DOI: 10.1006/jmbi.1997.1296] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The bacterial enhancer-binding protein NtrC activates transcription when phosphorylated on aspartate 54 in its amino (N)-terminal regulatory domain or when altered by constitutively activating amino acid substitutions. The N-terminal domain of NtrC, which acts positively on the remainder of the protein, is homologous to a large family of signal transduction domains called receiver domains. Phosphorylation of an aspartate residue in a receiver domain modulates the function of a downstream target, but the accompanying structural changes are not clear. In the present work we examine structural and functional differences between the wild-type receiver domain of NtrC and mutant forms carrying constitutively activating substitutions. Combinations of such substitutions resulted in both increased structural changes in the N-terminal domain, monitored by NMR chemical shift differences, and increased transcriptional activation by the full-length protein. Structural changes caused by substitutions outside the active site (D86N and A89T) were not only local but extended over a substantial portion of the N-terminal domain including the region from alpha-helix 3 to beta-strand 5 ("3445 face") and propagating to the active site. Interestingly, the activating substitution of glutamate for aspartate at the site of phosphorylation (D54E) also triggered structural changes in the 3445 face. Thus, the active site and the 3445 face appear to interact. Implications with respect to how phosphorylation may affect the structure of receiver domains and how structural changes may be communicated to the remainder of NtrC are discussed.
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Becker HD, Reinbolt J, Kreutzer R, Giegé R, Kern D. Existence of two distinct aspartyl-tRNA synthetases in Thermus thermophilus. Structural and biochemical properties of the two enzymes. Biochemistry 1997; 36:8785-97. [PMID: 9220965 DOI: 10.1021/bi970392v] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Two aspartyl-tRNA synthetases (AspRSs) were isolated from Thermus thermophilus HB8. Both are alpha2 dimers but differ in the length of their polypeptide chains (AspRS1, 68 kDa; and AspRS2, 51 kDa). Both chains start with Met and are deprived of common sequences to a significant extent. This rules out the possibility that AspRS2 is derived from AspRS1 by proteolysis, in agreement with specific recognition of each AspRS by the homologous antibodies. DNA probes derived from N-terminal amino acid sequences hybridize specifically to different genomic DNA fragments, revealing that the two AspRSs are encoded by distinct genes. Both enzymes are present in various strains from T. thermophilus and along the growth cycle of the bacteria, suggesting that they are constitutive. Kinetic investigations show that the two enzymes are specific for aspartic acid activation and tRNAAsp charging. tRNA aspartylation by the thermostable AspRSs is governed by thermodynamic parameters which values are similar to those measured for mesophilic aspartylation systems. Both thermophilic AspRSs are deprived of species specificity for tRNA aspartylation and exhibit N-terminal sequence signatures found in other AspRSs, suggesting that they are evolutionarily related to AspRSs from mesophilic prokaryotes and eukaryotes. Comparison of the efficiency of tRNA aspartylation by each enzyme under conditions approaching the physiological ones suggests that in vivo tRNAAsp charging is essentially ensured by AspRS1, although AspRS2 is the major species. The physiological significance of the two different AspRSs in T. thermophilus is discussed.
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Moss P, Charmley P, Mulvihill E, Ziegler S, Raugi GJ, Kern D, Piepkorn M, Gelinas R. The repertoire of T cell antigen receptor beta-chain variable regions associated with psoriasis vulgaris. J Invest Dermatol 1997; 109:14-9. [PMID: 9204948 DOI: 10.1111/1523-1747.ep12276338] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We investigated whether the pattern of T-cell receptors expressed by T cells in inflamed psoriatic skin differed substantially from the pattern seen in T cells from the peripheral blood. A bias or restriction in the repertoire of T-cell receptors found in the lesional skin of different patients might imply that specific subsets of T cells were causally associated with initiating or maintaining the lesions. By using a polymerase chain reaction-based assay of T-cell receptor beta-chain variable region mRNA, we found that the patterns of beta-chain mRNAs displayed in 14 samples of lesional skin or six samples of noninvolved skin were not significantly less diverse than the patterns found in matched peripheral blood samples. There was no evidence that the active lesions of multiple patients showed overexpression of T cells expressing one or a few T-cell receptor forms. The pattern of T-cell receptors displayed in clinically normal skin from normal control individuals showed about the same diversity as normal blood. While these results may not exclude either classical antigen or superantigen-based T-cell activation mechanisms in active plaques, the absence of a simple pattern of Vbeta usage in different patients suggests than other aspects of T-cell biology including trafficking, proliferation, co-stimulation, or responses to cytokines must also be considered.
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Markson L, Clark J, Glantz L, Lamberton V, Kern D, Stollerman G. The doctor's role in discussing advance preferences for end-of-life care: perceptions of physicians practicing in the VA. J Am Geriatr Soc 1997; 45:399-406. [PMID: 9100706 DOI: 10.1111/j.1532-5415.1997.tb05162.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
OBJECTIVES Although previous studies have shown physicians support advance directives, little is known about how they actually participate in decision-making. This study investigate (1) how much experience physicians have had discussing and following advance preferences and (2) how physicians perceive their role in the advance decision-making process. DESIGN Mail survey conducted in 1993. SETTING The Department of Veterans Affairs. PARTICIPANTS A national probability sample of 1050 VA internists, family physicians, and generalists. MEASUREMENTS AND MAIN RESULTS Questionnaires were returned by 67% of participants. In the last year, 79% stated they had discussed advance preference with at least one patient, and 19% had talked to more than 25. Seventy-three percent had used a written directive to make decisions for at least one incompetent patient. Younger age, board certification, spending less time in the outpatient setting, and personal experience with advance decision-making, were all associated independently with having advance preference discussions. Among physicians who had discussions, 59% said they often initiated the discussion, 55% said discussions often occurred in inpatient settings, and 31% said discussions often occurred in outpatient settings. Eighty-two percent of those responding thought physicians should be responsible for initiating discussions. Most would try to persuade a patient to change a decision that was not well informed (91%), not medically reasonable (88%), or not in the patient's best interest (88%); few would attempt to change decisions that conflicted with their own moral beliefs (14%). CONCLUSIONS Physicians report that they are actively involved with their patients in making decisions about end-of-life care. Most say they have had recent discussions with at least some of their patients and feel that as physicians they should play a large and important role in soliciting and shaping patient preferences.
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Kern D, Kern G, Neef H, Tittmann K, Killenberg-Jabs M, Wikner C, Schneider G, Hübner G. How thiamine diphosphate is activated in enzymes. Science 1997; 275:67-70. [PMID: 8974393 DOI: 10.1126/science.275.5296.67] [Citation(s) in RCA: 237] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The controversial question of how thiamine diphosphate, the biologically active form of vitamin B1, is activated in different enzymes has been addressed. Activation of the coenzyme was studied by measuring thermodynamics and kinetics of deprotonation at the carbon in the 2-position (C2) of thiamine diphosphate in the enzymes pyruvate decarboxylase and transketolase by use of nuclear magnetic resonance spectroscopy, proton/deuterium exchange, coenzyme analogs, and site-specific mutant enzymes. Interaction of a glutamate with the nitrogen in the 1'-position in the pyrimidine ring activated the 4'-amino group to act as an efficient proton acceptor for the C2 proton. The protein component accelerated the deprotonation of the C2 atom by several orders of magnitude, beyond the rate of the overall enzyme reaction. Therefore, the earlier proposed concerted mechanism or stabilization of a C2 carbanion can be excluded.
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Kern D, Baker J. A comparison of a mind/body approach versus a conventional approach to aerobic dance. Womens Health Issues 1997; 7:30-7. [PMID: 9009863 DOI: 10.1016/s1049-3867(96)00065-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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