bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conformation of human IgG subclasses in solution
Authors: KILÁR Ferenc , SIMON István , LAKATOS Susan , VONDERVISZT Ferenc , MEDGYESI György A. , ZÁVODSZKY Péter 
Published: March 2005

The structure of six human myeloma proteins: IgG1(Bal), IgG2(Klu), IgG3(Bak), IgG3(Het), IgG4(Kov) and IgG4(Pol), was studied in solution using small‐angle X‐ray scattering and hydrodynamic methods. For IgG1(Bal) and IgG3(Het) the experimental data, including radius of gyration (R°g), radii of gyration of the cross‐section (Rq1, Rq2), intrinsic viscosity [η], sedimentation coefficient (S320,w) and molecular mass, were interpreted in terms of structural models based on the Fab and Fc conformations, observed in crystal, by varying the relative positions of the Fab and Fc parts, i.e. their relative angles and distances.The values R°g= (6.00 ± 0.05) nm, S°20,W= (6.81 ± 0.10) S and [η] = 0.0062 ± 0.0005 cm3/mg obtained for IgG1(Bal) are compatible with a planar model in which the angle between the Fab arms is about 120°. For IgG3(Het) the following data were obtained: R°g= (4.90 ± 0.05) nm, S°20,W= (6.32 ± 0.01) S and [η] = (0.0065 ± 0.0005) cm3/mg. The apparent contradiction between the higher molecular mass and lower R°g and S°20,W values for IgG3(Het) in comparison to IgG1(Bal) can be resolved by proposing a “non‐planar” (tetrahedral) molecular shape, in which the long hinge peptide is in a folded conformation and the two Fab and Fc parts are in a closely packed arrangement. In this model the angle between the two Fab arms is about 90°, in the average position.The X‐ray scattering and hydrodynamic behaviour of the IgG2 and IgG4 types of antibodies appeared to be similar to IgG1(Bal). The parameters of the two IgG3 proteins are similar while they are different to the others.
Structural studies on the linkage unit between poly(galactosylglycerol phosphate) and peptidoglycan in cell walls of Bacillus coagulans
Authors: KAYA Shunji , ARAKI Yoshio , ITO Eiji 
Published: March 2005

Structural studies were carried out on the linkage units in the teichoic‐acid–glycopeptide complexes isolated from lysozyme digests of the cell walls of Bacillus coagulans AHU 1366. On treatment with 47% hydrogen fluoride, the complexes gave a disaccharide characterized as glucosyl(β1→4)N‐acetylglucosamine together with major fragments, galactosyl(α1→2)glycerol. By means of Smith degradation and partial acid hydrolysis, the teichoic acid chain was shown to be composed of the repeating units, galactosyl(α1→2)glycerol‐3(1)‐phosphate, which were joined by phosphodiester bonds at C‐6 of the galactose residues.The mild alkaline hydrolysis of teichoic‐acid‐linked glycan fragments yielded teichoic acid chains and disaccharide‐linked glycan fragments, from which the disaccharide, glucosyl(β1→4)N‐acetylglucosamine, was liberated by mild acid hydrolysis, whereas the same disaccharide linked to the teichoic acid chain was obtained by direct heating of the cell walls at pH 2.5. In addition, the presence of specialized glycerol phosphate units in the linkage region was shown by the isolation of tris(glycerol phosphate)‐3‐glucosyl(β1→4)N‐acetylglucosamine from the products of the Smith degradation of the teichoic‐acid–glycopeptide complexes. Thus, it is concluded that the poly(galactosylglycerol phosphate) chain in the cell walls of B. coagulans AHU 1366 is linked to peptidoglycan through a novel linkage unit, bis(glycerol phosphate)‐3‐glucosyl(β1→4)N‐acetylglucosamine.
Presence of hormonogenic and repetitive domains in the first 930 amino acids of bovine thyroglobulin as deduced from the cDNA sequence
Authors: MERCKEN Luc , SIMONS Marie‐Jeanne , DE MARTYNOFF Guy , SWILLENS Stéphane , VASSART Gilbert 
Published: March 2005

The sequence of the first 2831 nucleotides of bovine thyroglobulin mRNA has been determined from the analysis of a cDNA clone. Following a 41‐nucleotide 5′ untranslated sequence, a single open‐reading frame encoding 930 amino acids was observed. This corresponds to the aminoterminal third of thyroglobulin, preceded by a putative signal peptide of 19 amino acids. The protein sequence was found to be essentially made of the sevenfold repetition of a 60‐amino‐acid‐long building unit, interrupted at fixed positions by unrelated segments of variable length. The presence of an internal homology within the repetitive unit itself suggests that the 5′ region of the thyroglobulin gene has evolved from the initial duplication of a relatively short sequence, followed by the serial duplication of the resulting unit.The tyrosine residue at position five has been assigned an important hormonogenic function [Mercken, L., Simons, M.‐J. and Vassart, G. (1982) FEBS Lett. 149, 285–287]. This residue is flanked by sequence elements related to the repeated unit, suggesting that the hormonogenic domain evolved also from the basic ancestor sequence.
The sub‐cellular localisation and regulatory properties of pyruvate carboxylase from Rhizopus arrhizus
Authors: OSMANI Stephen A. , SCRUTTON Michael C. 
Published: March 2005

Cell‐free extracts of Rhizopus arrhizus contain exclusively cytosolic pyruvate carboxylase and NAD‐glutamate dehydrogenase, a single mitochondrial isoenzyme of NADP‐isocitrate dehydrogenase, and both mitochondrial and cytosolic isoenzymes of NADP‐malate dehydrogenase (decarboxylating). Other enzymes examined have sub‐cellular localisations similar to those characteristic of mammalian liver.
Purified preparations of R. arrhizus pyruvate carboxylase are subject to partial regulatory inhibition by L‐aspartate and 2‐oxoadipate. L‐Glutamate acts as a less effective analogue of L‐aspartate while 2‐oxoaglutarate is ineffective. Competition studies indicate the presence of separate inhibitory sites for L‐aspartate and 2‐oxoadipate.
Under routine assay conditions R. arrhizus pyruvate carboxylase shows significant activation by acyl derivatives of coenzyme A with long chain acyl CoA being more effective than acetyl‐CoA. This activation is no longer observed in the presence of high concentrations of pyruvate, MgATP2‐ and HCO−3.
The concentrations of L‐aspartate and 2‐oxoadipate required to give 50% inhibition ([I]0.5), and the maximal extents of inhibition, are increased by addition of acetyl‐CoA. Acetyl‐CoA increases the sigmoidal character of the relationship: initial rate/[L‐aspartate], but decreases this parameter for the relationship: initial rate/ [2‐oxoadipate].
The studies indicate that R. arrhizus possesses an entirely cytosolic pathway for the conversion of glucose to fumaric acid and that both the organisation of pyruvate metabolism and the regulation of pyruvate carboxylase differ significantly in this organism as compared to that proposed previously for Aspergillus nidulans.
Quaternary structure of chloroplast F1‐ATPase in solution
Authors: WAGNER Richard , ENGELBRECHT Siegfried , ANDREO Carlos S. 
Published: March 2005

The hydrodynamic properties of isolated ATPases were studied via their rotational diffusion in buffer solution. Chloroplast F1‐ATPase (CF1) and Escherichia coli F1‐ATPase (EF1) were covalently labeled with eosin‐isothiocyanate and then investigated by polarized laser spectroscopy.The rotational correlation time in aqueous buffer of latent (five‐subunit) CF1 was 390 ns. Four‐subunit (δ‐deficient) CF1 showed the same correlation time, however, for three‐subunit (δ, ɛ‐deficient) CF1 the rotational correlation time was more than eight times larger (3200 ns).The rotational correlation time of activated CF1 was three times larger than the one of latent CF1. These large changes in the rotational correlation times are directly related to changes in the quaternary structure of CF1 upon activation. EF1 was found to behave essentially as activated CF1.Based on the observed rotational correlation times we concluded that the mass distributions of latent CF1 and of δ‐deficient CF1 resemble a dimeric arrangement. The structure of δ,ɛ‐deficient CF1 more likely resembles a hexagon, the mass centers of the six main subunits lie in one plane. The structure of the activated forms of CF1 can be described best as an intermediate between the dimeric arrangement of latent CF1 and an octahedron. The large changes in the quaternary structure of isolated CF1 are reversed when the activation of the enzyme is reversed.
Influence of dA · dT and d(2aminoA) · dT base pairs on the B⇄Z transition of DNA fragments
Authors: CAVAILLÈS Jean‐Aristide , NEUMANN Jean‐Michel , TRAN‐DINH Son , HUYNH‐DINH Tam , d'ESTAINTOT Bétrice Langlois , IGOLEN Jean 
Published: March 2005

The Helical structures of d(C‐G‐C‐A‐m5C‐G‐T‐G‐m5C‐G), d(m5C‐G‐C‐A‐m5C‐G‐T‐G‐C‐G) and d(C‐2aminoA‐C‐G‐T‐G) were studied in aqueous solution at various salt concentrations and temperatures by 1H‐NMR spectroscopy. In 0.1 M NaCl solution only the B form was evidenced for these DNA fragments whereas in 4 M NaCl both B and Z forms, in slow exchange on the NMR time scale, were observed. Under these conditions the Z form accounted for less than 60% of the decamer conformation; conversely d(C‐G)3 hexamers containing methylated cytidines were predominantly in the Z form (>90%) [Tran‐Dinh et al. (1984) Biochemistry 23, 1362; Cavaillès et al. (1984) J. Biomol. Struct. Dyn. 1, 1347–1371]. On the other hand, d(C‐2aminoA‐C‐G‐T‐G) in which the d(2aminoA) · dT base pair forms three hydrogen bonds, was found to adopt the Z conformation in 4M NaCl solution which was not the case for d(C‐A‐C‐G‐T‐G) (unpublished results).The present study shows that the B⇄Z transition in solution is highly sequence‐dependent and that correlation exists between the stability of the duplexes (essentially governed by the number of hydrogen bonds between complementary bases) and their ability to adopt the Z conformation.
Mitochondrial transcription and processing of transcripts during release from glucose repression in ‘resting cells’ of Saccharomyces cerevisiae
Authors: ZENNARO Elisabetta , GRIMALDI Luca , BALDACCI Giuseppe , FRONTALI Laura 
Published: March 2005

Mitochondrial transcription and processing of transcripts have been investigated at different stages of release from glucose repression in resting cells of Saccharomyces cerevisiae.Transcripts were identified by hybridization with nick‐translated or terminally labelled gene‐specific probes. This allowed the determination of the steady‐state levels of individual transcripts in the mitochondrial RNA population.Results showed different gene‐specific patterns of response to respiratory induction: no increase in the level of transcripts (oxi2); a rapid increase in the steady‐state levels of all transcripts (cob); a very strong increase in the processing of the high‐molecular‐mass precursors (oxi3 and oli2); an increase in the level of stable circular transcripts (oxi3). As a whole the results indicate specific and differentiated effects of release from glucose repression on the expression of the different mitochondrial genes and demonstrate the importance of processing events in mitochondrial regulation.
Modification of the carbohydrate in ricin with metaperiodate — cyanoborohydride mixtures
Authors: THORPE Philip E. , DETRE Simone I. , FOXWELL Brian M. J. , BROWN Alex N. F. , SKILLETER David N. , WILSON Glynn , FORRESTER J. Anthony , STIRPE Fiorenzo 
Published: March 2005

Attempts to target antibody‐ricin conjugates (immunotoxins) to designated cell types in vivo may be thwarted by their rapid clearance by hepatic reticuloendothelial cells which have receptors that recognise oligosaccharide side chains on the toxin. The B‐chain of ricin contains high mannose type oligosaccharides and the A‐chain contains a complex unit (GlcNAc)2‐Fuc‐Xyl‐(Man)4–6, all of which potentially could be recognised by the reticuloendothelial system.Treatment of ricin with a mixture of sodium metaperiodate and sodium cyanoborohydride at pH 3.5 resulted in oxidative cleavage of the carbohydrates and reduction of the aldehyde groups thus formed to primary alcohols. By conducting the modification procedure at acidic pH, both the possibility of Schiff's base formation between the aldehyde groups and amino groups in the protein and the possibility of non‐specific oxidation of amino acids were minimised. The extent of the carbohydrate modification depended on the duration of treatment, resulting maximally in the destruction of 13 of the 18 mannose residues and of all xylose and fucose.The toxicity of the modified toxin to cells in culture declined by up to 90% as the carbohydrate was destroyed. This was not due to a reduced ability of the B‐chain to bind to cells or of the A‐chain to inactivate ribosomes. In contrast to the in vitro results, the toxicity of the modified toxin to mice and rats was elevated by up to fourfold. The modification greatly reduced the clearance of the toxin by non‐parenchymal cells in the liver and prevented the damage to hepatic Kupffer and sinusoidal cells and to the red pulp of the spleen that is inflicted by the native toxin. The elevated toxicity to animals appears to be because the modified toxin evades the reticuloendothelial system and persists in the bloodstream for longer periods, thus resulting in lethal damage to vital tissues in the animal at lower dosage.The results suggest that immunotoxins prepared from modified ricin would not be readily cleared by the reticuloendothelial system and so be more effective at killing their target cells.
Isolation and characterization of cytoplasmic poly(A) polymerase from cryptobiotic gastrulae of Artemia salina
Authors: ROGGEN Erwin , SLEGERS Herman 
Published: March 2005

Poly(A) polymerase has been purified to near homogeneity from the cytoplasm of Artemia salina cryptobiotic gastrulae by ion‐exchange chromatography on DEAE‐cellulose, DEAE‐Sepharose CL‐6B and phosphocellulose P11, gel filtration on CL‐Sepharose 6B, affinity chromatography on poly(A)‐Sepharose 4B and ATP‐agarose. The enzyme is fully dependent on exogeneous oligo(riboadenylic acid) and is free of any nuclease or other enzyme activities. In standard assay conditions the enzyme preparation has a specific activity of 5.6 μmol AMP · h−1· (mg protein)−1.Sodium dodecyl sulphate/polyacrylamide gel electrophoresis reveals the presence of only two proteins with Mr 94000 and 70000. The Mr‐70000 protein has been identified as poly(A) polymerase.The enzyme is exclusively activated by Mn2+. Addition of Ca2+, Mg2+, Zn2+, NH+4, K+ or Na+ inhibits the enzymatic reaction. The activity is specific for ATP and competitive inhibition is observed in the presence of other ribonucleoside 5′‐triphosphates. AMP incorporation is time‐dependent and is increased non‐linearly with protein and primer concentration.
Coenzymic activity of NADP derivatives alkylated at 2′‐phosphate and 6‐amino groups
Authors: OKUDA Keiko , URABE Itaru , OKADA Hirosuke 
Published: March 2005

Coenzymic activities of the following NADP derivatives were investigated: 2′‐O‐(2‐carboxyethyl)phosphono‐NAD (I), N6‐(2‐carboxyethyl)‐NADP (II), 2′‐O‐(2‐carboxyethyl)phosphono‐N6‐(2‐carboxyethyl)‐NAD (III), 2′‐O‐[N‐(2‐aminoethyl)carbamoylethyl]phosphono‐NAD (IV), N6‐[N‐(2‐aminoethyl)carbamoylethyl]‐NADP (Va), 2′, 3′‐cyclic NADP, and 3′‐NADP. Derivatives I and IV show the effects of modification at the 2′‐phosphate group, and derivatives II and Va show those at the 6‐amino group of NADP. As for enzymes, alcohol, isocitrate, 6‐phosphogluconate, glucose, glucose‐6‐phosphate, and glutamate dehydrogenases were used. These enzymes were grouped, and derivatives II and Va show those at the 6‐amino group of NADP. As for enzymes, alcohol, isocitrate, 6‐phosphogluconate, glucose, glucose‐6‐phosphate, and glutamate dehydrogenases were used. These enzymes were grouped on the basis of the ratio of the activities for NAD and NADP into NADP‐specific enzymes (ratio <0.01), NAD(P)‐specific enzymes (0.01 < ratio < 100), and NAD‐specific enzymes (ratio > 100).For NADP‐specific enzymes, modifications at the 2′‐phosphate group of NADP caused great loss of cofactor activity. The relative cofactor activities (NADP = 100%) of derivatives I and IV for these enzymes were 0.5–20 and 0.01 – 0.5%, respectively. On the other hand, NAD(P)‐specific enzymes showed several types of responses to the NADP derivatives. The relative cofactor activities of I and IV for Leuconostoc mesenteroides and Bacillus stearothermophilus glucose‐6‐phosphate dehydrogenases and beef liver glutamate dehydrogenase were 60 – 200%; whereas, for B. megaterium glucose dehydrogenase and L. mesenteroides alcohol dehydrogenase, the values were 0.8–8%. For NAD‐specific enzymes, these values were 20–50%. The relative cofactor activities of 2′,3′‐cyclic NADP and 3′‐NADP were very low (less than 0.2%) except for beef liver glutamate dehydrogenase, B. stearothermophilus glucose‐6‐phosphate dehydrogenase, and horse liver alcohol dehydrogenase. Kinetic studies showed that the losses of the cofactor activity of NADP by these modifications were mainly due to the increase of the Km value. The mechanisms of coenzyme specificity of dehydrogenases are discussed.Unlike the 2′‐phosphate group, the 6‐amino group is common to NAD and NADP, and the effects of modification at the 6‐amino group were independent of the coenzyme specificity of enzymes used for the assay. Derivatives II and Va had high relative cofactor activities (65 – 130%) for most of the enzymes except for isocitrate and glucose dehydrogenases (less than 1%) and L. mesenteroides alcohol dehydrogenase (20–60%). The cofactor activity of derivative III was generally lower than those of I and II.
Further characterisation of the FAD and Fe2S2 redox centres of component C, the NADH: acceptor reductase of the soluble methane monooxygenase of Methylococcus capsulatus (Bath)
Authors: LUND John , DALTON Howard 
Published: March 2005

The absorbance contributions of the FAD and Fe2S2 redox centres of component C of the soluble methane monooxygenase complex have been resolved, using mersalyl to destroy the Fe2S2 centre. The Fe2S2 seems to be very similar to that of spinach ferredoxin, by its absorbance and electron paramagnetic resonance (EPR) spectra, and the FAD semiquinone is a neutral semiquinone. Spectrophotometry near room temperature and EPR spectroscopy near liquid‐helium temperature allow the three redox couples of component C to be ordered. Component C can exist in Oe−1 (oxidised), 1e−1 (semiquinone), 2e−1 (mostly semiquinone and reduced Fe2S2), and 3e−1 forms (dihydroquinone and reduced Fe2S2), under equilibrium conditions. The ability of component C to support odd‐electron forms is consistent with its proposed role as a 2e−1/1e−1 transformase, splitting electron pairs from NADH for passage to component A in one‐electron steps. (The FAD appears to interact with NADH, and transfers single electrons to the Fe2S2, for donation to component A at a constant redox potential.)The mid‐point potentials of component C were found using redox dyes and EPR spectroscopy and were: FAD/FAD·, Em= ‐150 mV; Fe2S2/Fe2·S2, Em=−220 mV; FAD·/FAD·, Em=−260 mV. the presence of NADH did not alter these mid‐point potentials. These mid‐point potentials are consistent with the role of component C as the NADH:component A reductase, passing electrons from NADH (Em=−320 mV) onto component A (Em=+150 m V and Em=−150 m V). The reducing power from NADH appears to be required by component A to acitvate one atom of oxygen, to insert into methane, and the reducing equivalents derived from NADH end up with the other oxygen atom, as water.
Characterization and primary structures of DNA‐binding HU‐type proteins from Rhizobiaceae
Authors: KHANAKA Hussain , LAINE Bernard , SAUTIERE Pierre , GUILLAUME Jean 
Published: March 2005

The DNA‐binding HU‐type proteins from several species of Rhizobiaceae including Rhizobium meliloti, two strains of Rhizobium leguminosarum with highly different phenotypic characters and Agrobacterium tumefaciens, were characterized and their amino acid sequences were determined.HU‐type proteins isolated from R. leguminosarum L18 and A. tumefaciens are identical and show slight differences with the R. meliloti HU‐type protein. On the other hand the R. leguminosarum L53 HU‐type protein is quite different from the proteins cited above; several amino acid substitutions encountered in this protein result in significant changes in the folding of the polypeptide chain.The biochemical characteristics of these proteins are in good agreement with the respective position of these bacteria in the phylogeny determined by numerical taxonomy.
Primary structure of histone H2B from gonads of the starfish Asterias rubens
Authors: MARTINAGE Arlette , BRIAND Gilbert , VAN DORSSELAER Alain , TURNER Christopher H. , SAUTIERE Pierre 
Published: March 2005

The complete amino acid sequence (121 residues) of histone H2B from gonads of the starfish Asterias rubens has been established from structural data obtained essentially from large fragments generated by cleavage of histone H2B at aspartyl residues and by limited hydrolysis of the dimer H2A‐H2B with mouse submaxillary gland protease.No real sequence homology can be found between the amino‐terminal sequence (residues 1–21) of starfish and calf H2B. One non‐conservative substitution (serine‐32 in calf → lysine‐28 in starfish) leads to the presence of a cluster of eight basic residues (sequence 23 – 30) and to the disappearance of a potential site of phosphorylation.A particular structural feature of starfish histone H2B is the presence of N‐dimethylproline at its aminoterminal end. By comparison with N‐terminal acetylation, which is commonly found in histones, N‐terminal methylation is rarely observed. At the present time the functional significance of the N‐terminal methylation as well as that of the proline‐rich nature of the amino‐terminal sequence of the starfish histone H2B remain to be defined.
Intracellular calcium fluxes in human platelets
Authors: THOMPSON Neil T. , SCRUTTON Michael C. 
Published: March 2005

Fluorescence changes and secretory recretory responses have been measured on addition of various excitatory agonists to platelets loaded with the cytosolic Ca2+ probe, Quin 2 or with chlortetracycline as a probe for membraneassociated Ca2+.
When extracellular [Ca2+] is decreased to less than 0.1 μM by addition of EGTA a linear correlation is observed between the extent of increase in cytosolic [Ca2+] and the extent of mobilisation of membrane‐associated Ca2+ on stimulation by maximal doses of five excitatory agonists. A similar linear correlation between the increase in cytosolic [Ca2+] and the extent of ATP secretion is observed over the thrombin dose/response curve.
Similar EC50 values are observed for ATP secretion, the increase in cytosolic [Ca2+] and the decrease in chlortetracycline fluorescence induced by thrombin. However, the decrease in chlortetracycline fluorescence shows a sigmoidal relationship with the increase in cytosolic [Ca2+] and a hyperbolic relationship with ATP secretion over this dose/response curve.
Addition of prostaglandin D2 prior to thrombin causes parallel inhibition of the increase in cytosolic [Ca2+] and the decrease in chlortetracycline fluorescence induced by this agonist. However, addition of prostaglandin D2 after thrombin reverses the increase in cytosolic [Ca2+] induced by this agonist but fails to cause a similar reversal of the decrease in chlortetracycline fluorescence.
The data provide further evidence supporting the proposal that chlortatracycline can be used as a probe to monitor mobilisation of membrane‐associated Ca2+ but suggest that, in platelets stimulated in the effective absence of extracellular Ca2+, both Ca2+ mobilisation and Ca2+ removal can under some conditions involve sites which are not monitored by this probe.