共查询到20条相似文献,搜索用时 0 毫秒
1.
Schroeder SJ Blaha G Tirado-Rives J Steitz TA Moore PB 《Journal of molecular biology》2007,367(5):1471-1479
Crystal structures of the 50 S ribosomal subunit from Haloarcula marismortui complexed with two antibiotics have identified new sites at which antibiotics interact with the ribosome and inhibit protein synthesis. 13-Deoxytedanolide binds to the E site of the 50 S subunit at the same location as the CCA of tRNA, and thus appears to inhibit protein synthesis by competing with deacylated tRNAs for E site binding. Girodazole binds near the E site region, but is somewhat buried and may inhibit tRNA binding by interfering with conformational changes that occur at the E site. The specificity of 13-deoxytedanolide for eukaryotic ribosomes is explained by its extensive interactions with protein L44e, which is an E site component of archaeal and eukaryotic ribosomes, but not of eubacterial ribosomes. In addition, protein L28, which is unique to the eubacterial E site, overlaps the site occupied by 13-deoxytedanolide, precluding its binding to eubacterial ribosomes. Girodazole is specific for eukarytes and archaea because it makes interactions with L15 that are not possible in eubacteria. 相似文献
2.
Halophilic archaea activate acetate via an (acetate)-inducible AMP-forming acetyl-CoA synthetase (ACS), (Acetate + ATP + CoA Acetyl-CoA + AMP + PPi). The enzyme from Haloarcula marismortui was purified to homogeneity. It constitutes a 72-kDa monomer and exhibited a temperature optimum of 41°C and a pH optimum of 7.5. For optimal activity, concentrations between 1 M and 1.5 M KCl were required, whereas NaCl had no effect. The enzyme was specific for acetate (100%) additionally accepting only propionate (30%) as substrate. The kinetic constants were determined in both directions of the reaction at 37°C. Using the N-terminal amino acid sequence an open reading frame — coding for a 74 kDa protein — was identified in the partially sequenced genome of H. marismortui. The function of the ORF as acs gene was proven by functional overexpression in Escherichia coli. The recombinant enzyme was reactivated from inclusion bodies, following solubilization in urea and refolding in the presence of salts, reduced and oxidized glutathione and substrates. Refolding was dependent on salt concentrations of at least 2 M KCl. The recombinant enzyme showed almost identical molecular and catalytic properties as the native enzyme. Sequence comparison of the Haloarcula ACS indicate high similarity to characterized ACSs from bacteria and eukarya and the archaeon Methanosaeta. Phylogenetic analysis of ACS sequences from all three domains revealed a distinct archaeal cluster suggesting monophyletic origin of archaeal ACS. 相似文献
3.
Structure of the base of the L7/L12 stalk of the Haloarcula marismortui large ribosomal subunit: analysis of L11 movements 总被引:1,自引:0,他引:1
Initiation factors, elongation factors, and release factors all interact with the L7/L12 stalk of the large ribosomal subunit during their respective GTP-dependent cycles on the ribosome. Electron density corresponding to the stalk is not present in previous crystal structures of either 50 S subunits or 70 S ribosomes. We have now discovered conditions that result in a more ordered factor-binding center in the Haloarcula marismortui (H.ma) large ribosomal subunit crystals and consequently allows the visualization of the full-length L11, the N-terminal domain (NTD) of L10 and helices 43 and 44 of 23 S rRNA. The resulting model is currently the most complete reported structure of a L7/L12 stalk in the context of a ribosome. This region contains a series of intermolecular interfaces that are smaller than those typically seen in other ribonucleoprotein interactions within the 50 S subunit. Comparisons of the L11 NTD position between the current structure, which is has an NTD splayed out with respect to previous structures, and other structures of ribosomes in different functional states demonstrates a dynamic range of L11 NTD movements. We propose that the L11 NTD moves through three different relative positions during the translational cycle: apo-ribosome, factor-bound pre-GTP hydrolysis and post-GTP hydrolysis. These positions outline a pathway for L11 NTD movements that are dependent on the specific nucleotide state of the bound ligand. These three states are represented by the orientations of the L11 NTD relative to the ribosome and suggest that L11 may play a more specialized role in the factor binding cycle than previously appreciated. 相似文献
4.
Liquid chromatography tandem mass spectrometry coupling is a highly sensitive and specific technique allowing molecule detection in the femtomolar range. This article introduces a straightforward approach to apply this technique in 13C metabolic flux analysis. Based on a theoretical analysis of the correlation between molecule ions and corresponding fragments, a method was developed to determine the carbon labeling of intracellular metabolites without increasing the number of measurements per metabolite compared with direct molecule ion analysis. The method was applied to phosphorylated metabolites because their fragmentation results in high yields of [PO3]- and/or [H2PO4]- ions. Comparing the accuracy of the carbon labeling determination of phosphorylated metabolites between direct analysis of the molecule ions with that of corresponding phosphate fragment ions, it could be demonstrated that the introduced approach resulted in significantly higher accuracy and sensitivity for all tested metabolites. When applying the techniques to Escherichia coli cell extracts, 2 microg cell dry weight per injection was sufficient to determine the natural abundances of the carbon fractions m and m+1 from six phosphorylated metabolites with high accuracy, predestining the approach for very small cultivation volumes in the microliter range. 相似文献
5.
Campeol E Flamini G Cioni PL Morelli I D'Andrea F Cremonini R 《Carbohydrate research》2004,339(16):2731-2732
1,5-Anhydroxylitol, a compound never found previously in the vegetal kingdom was obtained from Olea europaea leaves in approximately 0.5-1% yield. 相似文献
6.
O-acetylated glucomannans were isolated from aspen and birch wood employing two different procedures and thereafter subjected to carbohydrate analysis by NMR spectroscopy and MALDI mass spectrometry. In one of the isolation procedures, acetone-extracted aspen or birch wood meal was extracted with dimethyl sulfoxide and then with hot water. Fractionation of the hemicellulose-containing extracts by size-exclusion chromatography was subsequently performed. In the other procedure, fractional precipitation with ethanol was used to isolate glucomannans from lyophilized process water produced by mechanical pulping of aspen. The aspen and birch glucomannans are O-acetylated at the C-2 or C-3 position of some of the mannose residues (random distribution), with a degree of acetylation of approx 0.3. In both cases the degree of polymerization was approx 16, indicating that low-molecular mass fractions of the glucomannans in hardwood have been isolated here. 相似文献
7.
Truhlar SM Cervantes CF Torpey JW Kjaergaard M Komives EA 《Protein science : a publication of the Protein Society》2008,17(9):1636-1639
Advances in NMR spectroscopy have enabled the study of larger proteins that typically have significant overlap in their spectra. Specific (15)N-amino acid incorporation is a powerful tool for reducing spectral overlap and attaining reliable sequential assignments. However, scrambling of the label during protein expression is a common problem. We describe a rapid method to evaluate the fidelity of specific (15)N-amino acid incorporation. The selectively labeled protein is proteolyzed, and the resulting peptides are analyzed using MALDI mass spectrometry. The (15)N incorporation is determined by analyzing the isotopic abundance of the peptides in the mass spectra using the program DEX. This analysis determined that expression with a 10-fold excess of unlabeled amino acids relative to the (15)N-amino acid prevents the scrambling of the (15)N label that is observed when equimolar amounts are used. MALDI TOF-TOF MS/MS data provide additional information that shows where the "extra" (15)N labels are incorporated, which can be useful in confirming ambiguous assignments. The described procedure provides a rapid technique to monitor the fidelity of selective labeling that does not require a lot of protein. These advantages make it an ideal way of determining optimal expression conditions for selectively labeled NMR samples. 相似文献
8.
Characterization of O-acetyl-(4-O-methylglucurono)xylan isolated from birch and beech 总被引:6,自引:0,他引:6
The structures of water-soluble birch and beech xylans, extracted from holocellulose using dimethyl sulfoxide, were determined employing 1H and 13C NMR spectroscopy together with chemical analysis. These polysaccharides were found to be O-acetyl-(4-O-methylglucurono)xylans containing one 4-O-methylglucuronic acid substituent for approximately every 15 D-xylose residues. The average degree of acetylation of the xylose residues in these polymers was 0.4. The presence of the structural element -->4)[4-O-Me-alpha-D-GlcpA-(1-->2)][3-O-Ac]-beta-D-Xylp-(1--> was demonstrated. Additional acetyl groups were present as substituents at C-2 and/or C-3 of the xylopyranosyl residues. Utilizing size-exclusion chromatography in combination with mass spectroscopy, the weight-average molar masses (and polydispersities) were shown to be 8000 (1.09) and 11,100 (1.08) for birch and beech xylan, respectively. 相似文献
9.
Takatoshi Matsuo Akiko Ikeda Hiroto Seki Toshiaki Ichimata Daisuke Sugimori Satoshi Nakamura 《Biometals》2001,14(2):135-142
The gene encoding a ferredoxin (Fd) from Haloarcula japonica strain TR-1 was cloned and sequenced. Sequence analysis of the cloned Ha. japonica Fd gene revealed that the structural gene consisted of an open reading frame of 387 nucleotides encoding 129 amino acids. The deduced amino acid sequence of Ha. japonica Fd showed 84 to 98% identity with corresponding sequences in other extremely halophilic archaea. The Ha. japonica Fd gene was inserted into the shuttle vector pWL102 and used to transform Ha. japonica. Ha. japonica Fd could then be produced as a fusion with HisTag (6xHis) in Ha. japonica host cells. The absorption and ESR spectra of the Fd/HisTag fusion protein revealed the presence of a [2Fe-2S] cluster which is characteristic of native Ha. japonica Fd. 相似文献
10.
The syntheses of new oxamide derivatives of methyl 2-amino-2-deoxy-alpha-D-glucopyranoside and amino acid or peptide esters are presented. The reaction of methyl 3,4,6-tri-O-acetyl-2-acetamido-2-deoxy-alpha-D-glucopyranoside and oxalyl chloride gave N-(methyl 3,4,6-tri-O-acetyl-2-deoxy-alpha-D-glucopyranosid-2-yl) oxamic acid chloride which on reaction with the ester of Gly, L-Ala, L-Phe, GlyGly, Gly-L-Phe and Gly-L-Ala afforded N-(methyl 3,4,6-tri-O-acetyl-2-deoxy-alpha-D-glucopyranosid-2-yl), N'-oxalyl-amino acid or dipeptide esters. The structure of the oxamides was studied using 1H, 13C NMR in solution and solid state. 相似文献
11.
Chemical components and molecular mass of six polysaccharides isolated from the sclerotium of Poria cocos 总被引:1,自引:0,他引:1
Wang Y Zhang M Ruan D Shashkov AS Kilcoyne M Savage AV Zhang L 《Carbohydrate research》2004,339(2):327-334
Six polysaccharides were extracted sequentially from the fresh sclerotium of Poria cocos cultivated in China using 0.9% NaCl (PCS1), hot water (PCS2), 0.5M NaOH (PCS3-I and PCS3-II), and 88% formic acid (PCS4-I and PCS4-II). Their chemical and physical characteristics were determined using infrared spectroscopy (IR), gas chromatography (GC), GC-MS methylation analysis, 13C NMR spectroscopy, elementary analysis (EA), protein analysis, size exclusion chromatography combined with laser light scattering (SEC-LLS), light scattering (LS), and viscometry. The results indicated that the polysaccharides PCS1, PCS2, and PCS3-I were heteropolysaccharides containing D-glucose, D-galactose, D-mannose, D-fucose, and D-xylose; the predominant monosaccharide was D-glucose except for PCS1 where it was D-galactose. PCS3-II, the main component of the sclerotium of P. cocos, was a linear (1-->3)-beta-D-glucan of high purity. PCS4-I consisted of (1-->3)-beta-D-glucan with some beta-(1-->6) linked branches. PCS4-II was mainly composed of (1-->3)-beta-D-glucan containing some glucose branches. The M(w) values of the six polysaccharides PCS1, PCS2, PCS3-I, PCS4-I in 0.2M NaCl aqueous solution, PCS3-II, and PCS4-II in dimethyl sulfoxide (Me(2)SO) were determined to be 11.6 x 10(4), 20.8 x 10(4), 17.1 x 10(4), 9.1 x 10(4), 12.3 x 10(4), and 21.1 x 10(4), respectively. The six polysaccharides in aqueous solution or Me(2)SO exist as flexible chains. 相似文献
12.
ADP-forming acetyl-CoA synthetase (ACD), the novel enzyme of acetate formation and energy conservation in archaea (
), has been studied only in few hyperthermophilic euryarchaea. Here, we report the characterization of two ACDs with unique molecular and catalytic features, from the mesophilic euryarchaeon Haloarcula marismortui and from the hyperthermophilic crenarchaeon Pyrobaculum aerophilum. ACD from H. marismortui was purified and characterized as a salt-dependent, mesophilic ACD of homodimeric structure (166 kDa). The encoding gene was identified in the partially sequenced genome of H. marismortui and functionally expressed in Escherichia coli. The recombinant enzyme was reactivated from inclusion bodies following solubilization and refolding in the presence of salts. The ACD catalyzed the reversible ADP- and Pi-dependent conversion of acetyl-CoA to acetate. In addition to acetate, propionate, butyrate, and branched-chain acids (isobutyrate, isovalerate) were accepted as substrates, rather than the aromatic acids, phenylacetate and indol-3-acetate. In the genome of P. aerophilum, the ORFs PAE3250 and PAE 3249, which code for and subunits of an ACD, overlap each other by 1 bp, indicating a novel gene organization among identified ACDs. The two ORFs were separately expressed in E. coli and the recombinant subunits (50 kDa) and (28 kDa) were in-vitro reconstituted to an active heterooligomeric protein of high thermostability. The first crenarchaeal ACD showed the broadest substrate spectrum of all known ACDs, catalyzing the conversion of acetyl-CoA, isobutyryl-CoA, and phenylacetyl-CoA at high rates. In contrast, the conversion of phenylacetyl-CoA in euryarchaeota is catalyzed by specific ACD isoenzymes.Dedicated to Prof. Dr. Dr. h.c. mult. Hans Günter Schlegel on the occasion of his 80th birthday. 相似文献
13.
Christian Marsching Richard Jennemann Raphael Heilig Hermann-Josef Gr?ne Carsten Hopf Roger Sandhoff 《Journal of lipid research》2014,55(11):2343-2353
Owing to its capability of discriminating subtle mass-altering structural
differences such as double bonds or elongated acyl chains, MALDI-based imaging
MS (IMS) has emerged as a powerful technique for analysis of lipid distribution
in tissue at moderate spatial resolution of about 50 μm. However, it is
still unknown if MS1-signals and ion intensity images correlate with
the corresponding apparent lipid concentrations. Analyzing renal sulfated
glycosphingolipids, sulfatides, we validate for the first time IMS-signal
identities using corresponding sulfatide-deficient kidneys. To evaluate the
extent of signal quenching effects interfering with lipid quantification, we
surgically dissected the three major renal regions (papillae, medulla, and
cortex) and systematically compared MALDI IMS of renal sulfatides with
quantitative analyses of corresponding lipid extracts by on-target MALDI
TOF-MS and by ultra-performance
LC-ESI-(triple-quadrupole)tandem MS. Our results demonstrate a generally strong
correlation (R2 > 0.9) between the local relative sulfatide
signal intensity in MALDI IMS and absolute sulfatide quantities determined by
the other two methods. However, high concentrations of sulfatides in the
papillae and medulla result in an up to 4-fold signal suppression. In
conclusion, our study suggests that MALDI IMS is useful for semi-quantitative
dissection of relative local changes of sulfatides and possibly other lipids in
tissue. 相似文献
14.
Structural features of pectic polysaccharides from the skin of Opuntia ficus-indica prickly pear fruits 总被引:7,自引:0,他引:7
After removal of the mucilage with water at room temperature, pectic polysaccharides were solubilized from Opuntia ficus-indica fruit skin, by sequential extraction with water at 60 degrees C (WSP) and EDTA solution at 60 degrees C (CSP). Polysaccharides with neutral sugar content of 0.48 and 0.36 mol/mol galacturonic acid residue were obtained, respectively, in the WSP and CSP extracts. These pectic polysaccharides were de-esterified and fractionated by anion-exchange chromatography, yielding for each extract five fractions, which were thereafter purified by size-exclusion chromatography. Two of these purified fractions were characterized by sugar analysis combined with methylation and reduction-methylation analysis. The study was then supported by (1)H and (13)C NMR spectroscopy. The results showed that the water-soluble fraction WSP3 and the EDTA soluble fraction CSP3, consisted of a disaccharide repeating unit -->2)-alpha-l-Rhap-(1-->4)-alpha-d-GalpA-(1--> backbone, with side chains attached to O-4 of the rhamnosyl residues. The side chains contained highly branched alpha-(1-->5)-linked arabinan and short linear beta-(1-->4)-linked galactan. 相似文献
15.
Kjaergaard M Gårdsvoll H Hirschberg D Nielbo S Mayasundari A Peterson CB Jansson A Jørgensen TJ Poulsen FM Ploug M 《Protein science : a publication of the Protein Society》2007,16(9):1934-1945
The cysteine-rich somatomedin B domain (SMB) of the matrix protein vitronectin is involved in several important biological processes. First, it stabilizes the active conformation of the plasminogen activator inhibitor (PAI-1); second, it provides the recognition motif for cell adhesion via the cognate integrins (alpha(v)beta(3), alpha(v)beta(5), and alpha(IIb)beta(3)); and third, it binds the complex between urokinase-type plasminogen activator (uPA) and its glycolipid-anchored receptor (uPAR). Previous structural studies on SMB have used recombinant protein expressed in Escherichia coli or SMB released from plasma-derived vitronectin by CNBr cleavage. However, different disulfide patterns and three-dimensional structures for SMB were reported. In the present study, we have expressed recombinant human SMB by two different eukaryotic expression systems, Pichia pastoris and Drosophila melanogaster S2-cells, both yielding structurally and functionally homogeneous protein preparations. Importantly, the entire population of our purified, recombinant SMB has a solvent exposure, both as a free domain and in complex with PAI-1, which is indistinguishable from that of plasma-derived SMB as assessed by amide hydrogen ((1)H/(2)H) exchange. This solvent exposure was only reproduced by one of three synthetic SMB products with predefined disulfide connectivities corresponding to those published previously. Furthermore, this connectivity was also the only one to yield a folded and functional domain. The NMR structure was determined for free SMB produced by Pichia and is largely consistent with that solved by X-ray crystallography for SMB in complex with PAI-1. 相似文献
16.
In this paper, we report the structure and apparent molecular weights of bis-(alpha,beta-D-glucopyranosyl)-polyisobutylene (Gluc-PIB-Gluc) aggregates in CDCl(3) by NMR spectroscopy. Analysis of DOSY (diffusion-ordered NMR spectroscopy) experiments of a solution of Gluc-PIB-Gluc showed the presence of aggregates that were corroborated with dynamic light scattering. The structure of the aggregates was also studied by correlation spectroscopy (COSY) and nuclear Overhauser effect spectroscopy (NOESY) experiments. 相似文献
17.
18.
Katzenellenbogen E Zatonsky GV Kocharova NA Bogulska M Korzeniowska-Kowal A Shashkov AS Gamian A Knirel YA 《Carbohydrate research》2002,337(17):1541-1546
The O-specific polysaccharide of Citrobacter gillenii PCM 1542 from serotype O-12a,12 b is composed of one residue each of D-glucose, D-GlcNAc, 2-deoxy-2-[(R)-3-hydroxybutyramido]-D-glucose (D-GlcNAcyl) and two GalNAc residues. On the basis of sugar and methylation analyses of the intact and Smith degraded polysaccharides, along with 1D and 2D 1H and 13C NMR spectroscopy, the following structure of the branched pentasaccharide repeating unit of the O-specific polysaccharide was established:This structure differs significantly from that of the O-specific polysaccharide of C. gillenii PCM 1544 from the same serotype O-12a,12 b, which has been established earlier (Kübler-Kielz.shtsls;b, J. et al. Carbohydr. Res. 2001, 331, 331-336). Serological studies confirmed that the two O-antigens are not related and suggested that strains PCM 1542 and 1544 should be classified into different O-serogroups. 相似文献
19.
C, N CP MAS and high resolution multinuclear NMR study of methyl
Four new derivatives of methyl
were studied by 1H, 13C, 15N NMR in CDCl3 solutions and by 13C, 15N NMR in the solid state. The replacement of one aryl substituent by another has no influence on the proton and carbon chemical shifts within the sugar moiety, in solution. The differences in 13C chemical shifts Δ = δliquid - δsolid are significant for C-3 (deshielding of -3.4 to -3.8 ppm), C-5 and OMe but not observed for C-2, where the ureido substituent is linked, thus indicating that this fragment of the structure is rigid. The values of Δ in 15N chemical shifts of N-3′ are -2.3 to -2.8 ppm (increase of shielding in the solids); the effect of replacement of substituent at aromatic ring is larger than the contribution of intermolecular H-bond interaction. The values of 15.5–16.1 Hz for 1JC-1′-N and 21.2–21.5 Hz for 1JCO-N indicate that the two C---N-3′ bonds are of significant double bond character. 相似文献
Full-size image
20.
The kavalactone, 11-methoxy-5,6-dihydroyangonin, and eight previously reported analogs along with four other aromatic compounds were isolated from the root extracts of Piper methysticum (Kava Kava). Their structural elucidations were made by 1H and 13C NMR spectroscopic assignments using COSY, HMBC and HMQC experiments. 相似文献