bluuebunny/crossref_metadata_2025_split huggingface dataset:
Primary Structure of Escherichia coli Ribosomal Protein S1 and Features of Its Functional Domains
Authors: KIMURA Makoto , FOULAKI Kirani , SUBRAMANIAN Alap‐Raman , WITTMANN‐LIEBOLD Brigitte 
Published: March 2005

The complete covalent structure of ribosomal protein S1 of Eschericlziu coli has been determined and predictions made of its secondary structure. Protein S1 (E. coli MRE 600) is a single‐chain, acidic protein with 557 amino acid residues of the composition Asp43, Asn23, Thr25, Ser25, Glu60, Glnl4, Pro10, Gly48, Ala48, Val67, Met6, Ile30, Leu45, Tyr6, Phe17, His8, LYS43, Arg30, Trp7, Cys2 and an Mr, of 61159. The two ‐SH groups of S1 are located in the central region of the chain at positions 292 and 349, the latter being the reactive group whose modification results in the reported loss of the nucleic‐acid‐unfolding ability of S1, The central region also contains the majority of the tryptophan, histidine and methionine residues of S1 and is predicted to have a secondary structure dominated by β‐sheets and turns. A direct proof for the location of the nucleic‐acid‐binding domain of S1 in the central region has recently been obtained [Subramanian et al. (1981) Eur. J. Biochem. 119, 245‐249], The N‐terminal region of S1, which contains the ribosome‐binding domain has a relatively high predicted α‐helix content and no preponderance of basic amino acids. The facile trypsin‐sensitive site in S1 is located at Arg‐171, approximately at the border between the N‐terminal and central regions. The acidic and basic amino acids of S1 (32.8% of all residues) are distributed throughout the chain, often in small clusters of between two and six residues.The amino acid sequence of S1 contains three 24‐residue stretches with strong internal homology. Two of the stretches are located in the central, RNA‐binding region, suggesting a possible role in the RNA‐binding and helix‐destabilizing functions of S1. A fragment of Mr, 104 from the central region of S1 gives an anomalously high apparent Mr, by dodecylsulfate gel electrophoresis, indicating a stable structural element therein and accounting for the apparent high Mr, of S1 as determined by gel electrophoresis.
C1 Proteins: a Class of High‐Mobility‐Group Non‐histone Chromosomal Proteins from the Fruit Fly Ceratitis capitata
Authors: MARQUEZ Gabriel , MORAN Federico , MONTERO Francisco , FRANCO Luis 
Published: March 2005

CM‐cellulose chromatography of a fraction soluble in 5% perchlorice acid from Ceratitis capitata chromatin yields three proteins, C1a1, C1a2 and C1b, which bave been purified to electrophorecal homogeneity.
C1a1, C1a2 and C1b analyse like high mobility group (HMG) non‐histone chromosomal proteins, although they do not exactly correspond with those from vertebrates. It is proposed that C1 proteins, as well as Dosophilia D1 [Rodriguez Alfageme et al. (1980) Chromosoma, 78, 1‐31] are representative of a class of insect‐specific HMG proteins. Tryptic fingerprints show that C1a1 and C1a2 are very similar, but C1b is a somewhat distinct protein. Circular dichroism studies have shown that these preparations do not appreciably fold on increasing ionic strength.
The interactions between DNA and C1 proteins have been studied. These proteins precipitate DNA in 0.15 M NaCl, 0.015 M sodium citrate and the precipitation curves are cooperative. Soluble complexes between C1 proteins and DNA could be prepared in low ionic strength media and their thermal denaturation profiles obtained. C1 proteins do not destabilize DNA under the conditions used to prepare the complexes but the three proteins stabilize DNA to a different degree. From these studies it has been concluded that the association constant of C1b to DNA is smaller than that of C1a1 and C1a2.
Photochemical Inactivation of Lactoperoxidase Sensitized by Carbonyl Compounds
Authors: MÁKINEN Kauko K. , MÁKINEN Pirkko‐Liisa 
Published: March 2005

2,3‐Butanedione was found to be a poor noncompetitive inhibitor (Ki∼ 0.1 M) of bovine milk lacto‐peroxidase. Irradiation of an incubation mixture of these two substances in the visible region led, however, to an irreversible loss of enzyme activity. The inactivation rates were dependent on light intensity, light wavelength and sensitizer concentration. Maximal rate of inactivation occurred at 400‐420 nm. Other dicarbonyl compounds which caused a similar photodestruction of lactoperoxidase in the visible region were 2,3‐pentanedione and 1‐phenyl‐1,2‐propanedione, the following compounds being without effect: phenylglyoxal, methylglyoxal, glyoxal, 1,2‐cyclohexanedione and acetone. Of the latter, however, 1,2‐cyclohexanedione, phenylglyoxal, methylglyoxal and acetone inactivated lactoperoxidase at 254 nm.
The butanedione‐sensitized photochemical inactivation of lactoperoxidase was prevented by the presence of free radical scavengers and singlet oxygen quenchers, the best protectors being the histidine derivatives L‐3‐methylthistidine, L‐1‐methylhistidine and L‐thiol‐2‐histidine, which displayed dual quenching ability. No photochemical inactivation off lactoperoxidase occurred in anoxic media even in the presence of high butanedione concentration and strong illumination.
The butanedione‐sensitized photochemical inactivation of lactoperoxidase was accompanied by extensive changes in the ultraviolet absorption spectra of the enzyme. Simultaneously, a dramatic loss in tryptophan fluorescence occurred. All spectral and fluorescence changes were prevented by the above protectors. The sensitized enzyme inactivation was shown to be an all‐or‐none type of reaction; no partially inactivated enzymes existed.
Amino acid analysis of native and butanedione light‐treated lactoperoxidase showed that the treated enzyme contained considerably less of the following amino acids than the native enzyme: methonine, arginine, tyrosine, aspartic acid, serine, glutamic acid. Histidine residues were probably attacked also. Inhibition and modification studies showed that the activity of the enzyme was not based on arginyl and tryptophyl residues.
These results suggest that 2,3‐butanedione, 1,2‐cyclohexanedione, phenylglyoxal and related dicarbonyl compounds, which have previously been used as relatively specific probes for the active arginyl residues of enzymes, cause under suitable modification conditions extensive change in the structure of an enzyme by affecting a multitude of amino acid residues. These compounds can totally inactivate an enzyme regardless of the essentiality or inessentiality of arginyl residues for enzyme activity. The present results warn against drawing conclusions from modification studies with dicarbonyl compounds unless the irradiation conditions are carefully considered.
Preferred Solution Conformation of des‐Arg9‐Bradykinin and Analysis of Structure‐Conformation‐Activity Relationships in the Series [Alan]des‐Arg9‐Bradykinin
Authors: DIVE Vincent , LINTNER Karl , FERMANDJIAN Serge , ST. PIERRE Serge , REGOLI Domenico 
Published: March 2005

This paper describes the solution conformation of the vasoactive peptide hormone des‐Arg9‐bradykinin (Arg‐Pro‐Pro‐Gly‐Phe‐Ser‐Pro‐Phe).

By 1H‐NMR spectroscopy we studied des‐Arg9‐bradykinin and its fragments bradykinin‐(1‐5), bradykinin‐(1‐6) in aqueous solution as a function of pH (titration) and in dimethylsulfoxide solution at two ionic states (cation and neutral ion species).
The preferred solution conformation which is most strongly stabilized in dimethylsulfoxide in the neutral ion species includes a distorted β‐turn II involving the N‐terminal sequence of Pro2‐Pro3‐Gly4‐Phe5 and most likely a C7‐type bend in the C‐terminal part Ser‐Pro‐Phe.
A complete series of analogous ([Alan]des Arg9‐bradykinin, with n= 1,2 … 8) was then investigated by circular dichroism and 1‐H‐NMR spectroscopy in order to study the conformational role played by each residue and to delineate the local and the long‐range effects on conformational brought about by the Xaa→Ala substitutions. Chosen spectral parameters (circular dichroic spectra, chemical shift variations and vicinal coupling constants) characteristic of the preferred solution conformation of the native sequence of des‐Arg9‐bradykinin are followed from analogue to analogue. The important conformational role of the arginine‐1 side chain and its positive charge and the spatial proximity of the N‐terminal and C‐terminal groups, i.e. the folded structure of the peptide can be inferred from these data.
A comparison of the biological activities of the analogues with the conformative perturbations caused by the chemical alterations shows des‐Arg9‐bradykinin conformation and receptor affinity to be equally sensitive to single‐residue substitutions. The correct orientation of the arginine‐1 side chain, the precise geometry of the turn involving residues 2‐5 and of the C‐terminal Pro‐Phe sequence are of primary importance.
Polymerization/Excision Kinetics of Escherichia coli DNA Polymerase I
Authors: SAGHI Mohammed , DORIZZI Mireille 
Published: March 2005

The incorporation and excision kinetics of Escherichia coliDNA polymerase I in the replication of (dA)n with dUTP and (dI)n with dCTP was studied at various temperatures and pH. When the incorporation/excision ratio (dy/dx) is plotted against the concentration of deoxynucleoside triphosphate [S] two kinds of curves are obtained. With (dI)n, dy/dx increases with [S], then reaches an asymptotic value. This behaviour, consistent with a kinetic amplification or kinetic proofreading mechanism, is observed at all temperatures and pH. With (dA)n, dy/dx increases with [S] but in a convex, instead of a concave manner. In this case, we approximated the curves by straight lines at the origin, in conformity with the prediction of the frayed‐unfrayed model. Again a single behaviour is consistently observed at all temperatures and pH.
The data were analyzed in terms of ratios or products of three kinetic constants: ki for incorporation, ke for excision and, in the (dI)n system, θ for the processing of the incoming dNTP. The dNMP production in the (dI)n system is dominated by the keθ term which increases with temperature and pH. Temperature and pH. Temperature influences excision more than incorporation. The net result being a linear decrease of ki/ke with temperature. The effect is more pronounced with (dI)n than with (dA)n and is probably related to the stability of the template‐primer complex. The ki/ke term shows a bell‐shaped dependency with pH in the (dI)n system. With (dA)n it remains constant between pH 7.5 and 8.5 then decreases with a transition midpoint at pH 9.0. We suggest that the pH profiles may reflect the ionization of the template in the first case, and of the substrate in the second.
Inhibition of Mitochondrial Protein Synthesis and Energy Coupling by Fragment A of Diphtheria Toxin
Authors: ABRAHAM Abraham K. , FLATMARK Torgeir , TANGERÅS Arild , PIHL Alexander 
Published: March 2005

The effect of intact diphtheria toxin and its fragment A on energy‐dependent functions in mouse liver mitochondria/mitoplasts has been studied. Fragment A was found to inhibit protein synthesis in mitoplasts to the same extent (approximately 80%) as the uncoupler carbonylcyanide p‐trifluoromethoxyphenylhydrazone, but had no similar effect in lysed mitoplasts. Intact diphtheria toxin had no effect in either case.Fragment A was found to function as a potent uncoupler in isolated mitochondria and mitoplasts, inhibiting oxidative phosphorylation by approximately 80% at a concentration (2 μg fragment A/mg of protein) that did not inhibit protein synthesis. In contrast, intact toxin slightly increased the tightness of energy coupling in isolated mitoplasts. 125I‐labelled intact diphtheria toxin was bound to mitoplasts to about the same extent as labelled fragment A.At concentrations which efficiently inhibited mitochondrial protein synthesis, fragment A had no effect on the intramitochondrial concentration of nicotinamide adenine dinucleotides, nor was it capable of ADP‐ribosylating mitochondrial proteins, indicating that the well known enzymatic activity of fragment A is not involved in the observed effect in mitochondria.The results indicate that fragment A of diphtheria toxin inhibits protein synthesis in mitochondria and mitoplasts by inhibiting mitochondrial energy transduction. The detailed mechanism of the uncoupling effect and its possible significance in intact cells remain to be elucidated.
Positive and Negative cAMP‐Mediated Control of Tyrosine Aminotransferase Synthesis in Reuber H35 Hepatoma Cells
Authors: SNOEK Gerry T. , VOORMA Harry O. , VAN WIJK Roel 
Published: March 2005

Induction of L‐tyrosine:2‐oxoglutarate aminotransferase (EC 2.6.1.5) by N6, O2′‐dibutyryl‐adenosine 3′,5′‐ monophosphate (Bt2cAMP) in Reuber H35 hepatoma cells reaches a maximum value between 3‐5 h after addition of Bt2cAMP and subsequently decreases in the continuous presence of Bt2cAMP. We have investigated the kinetics of the increase, i.e. induction, and the decrease, i.e. the repressed state, of the tyrosine‐aminotransferase‐synthesizing system under these conditions.Our experimental results are as follows. 1. The repressed state of the tyrosine‐aminotransferase‐synthesizing system is not caused by a decrease in the intracellular cAMP concentration. 2. The repressed state is inhibited by actinomycin D (while induction is not inhibited). 3. During the repressed state no effect of dexamethasone on tyrosine aminotransferase synthesis is found, while during induction Bt2cAMP and dexamethasone act synergistically. 4. Longer starvation of the cells in serum‐free medium has no influence on the kinetics of the induction/repressed state curve.From these results we have concluded that the machanism of the transition to the repressed state of the tyrosine‐aminotransferase‐synthesizing system is essentially different from the mechanism of deinduction which occurs after removal of the inducer. Moreover, the repressed state of the system is a phenomenon which is induced by Bt2cAMP separately from induction at a different level of protein synthesis.
Analysis of Mycolic Acids from a Group of Corynebacteria by Capillary Gas Chromatography and Mass Spectrometry
Authors: GAILLY Chantal , SANDRA Patrick , VERZELE Maurice , COCITO Carlo 
Published: March 2005

The cell wall of leprosy‐derived corynebacteria (a group of ‘diphtheroids’ isolated from human leprosy lesions and patients' blood) was previously shown to contain, in addition to peptidoglycan and arabinogalactan, mycolic acids. These α‐branched β‐hydroxy fatty acids were attributed to the corynomycolic group, according to their RF in monodimensional thin‐layer chromatography. In the present work, mycolic acids from leprosy‐derived and reference corynebacteria have been fractionated by monodimensional and bidimensional thin‐layer chro‐ matography and by gas chromatography. Pyrolyzed mycolic acids have been analysed on conventional packed columns, whereas intact methyl esters of mycolic acids with free and silylated β‐hydroxyl group have been analyzed on capillary columns, and their structure has been established by mass spectrometry.In all leprosy‐derived corynebacteria, some 20 components containing 24‐ 36 carbon atoms and 0‐4 double bonds were obtained. The three major groups had 32, 34 and 36 carbons, and the frequency of unsaturated versus saturated chains increased proportionally to the molecular weight. For comparison, the main components of a reference corynebacterium, Corynebacterium diphtheriae PW8, had 30 and 32 carbons, and their hydro‐ carbon chains were essentially saturated. This work confirms the relative chemical homogeneity of different leprosy‐derived corynebacteria and describes some peculiar traits in the chemical structure of this group of organisms. In addition, it shows the complexity of the mycolic acid fraction of corynebacterial cell wall and suggests that the mycolic acid pattern is a sort of fingerprint of each bacterial strain grown under standard conditions. Finally, the fractionation of intact corynomycolic acid methyl esters with free or silylated β‐hydroxyl group by capillary gas chromatography proved to be the best analytical procedure at present available for resolving this complex mixture of corynomycolate isomers. Structural determination of silylated samples by mass spectrometry is preferred because they have more diagnostic fragments.
Agonist‐Mediated Conformational Changes of Muscarinic Receptors in Rat Brain
Authors: VAUQUELIN Georges , ANDRÉ Claudine , DE BACKER Jean‐Paul , LADURON Pierre , STROSBERG A. Donny 
Published: March 2005

Muscarinic acetylcholine receptors were identified in the microsomal P fraction of rat forebrain by the specific binding of the radiolabeled antagonist [3H]dexetimide. Binding occurred to a single class of non cooperative sites (3.25 μmol/mg protein) with an equilibrium dissociation constant of 1.1 nM. Agonist/[3H]‐ dexetimide competition binding experiments allowed the distinction between two major muscarinic receptor subpopulations, having respectively high affinity (20 % of the total receptor population) and low affinity for agonists, but with the same affinity for antagonists. A 610‐fold difference in affinity was calculated for carbamoyl‐ choline, the agonist extensively investigated in this study.The alkylating reagent N‐ethylmaleimide did not affect the total receptor number, antagonist binding to the high‐affinity and low‐affinity sites, nor agonist binding to the high‐affinity sites. The reagent, however, caused a net increase in agonist affinity for the low‐affinity sites. This process was dependent on time and dose of N‐ethylmaleimide, until a maximal increase in affinity (fourfold increase for carbamoylcholine) was attained. This suggests a quanta1 conversion of the low‐affinity sites by the reagent into an alkylated form, which possesses a higher affinity for agonists but an unchanged affinity for antagonists. The rate of alkylation was enhanced by the presence of agonists but not of antagonists, which is indicative for the ability of agonists to mediate a conformational change of these sites. The close correlation between the N‐ethylmaleimide‐mediated increase in drug affinity for the low‐affinity sites and the ability of the drugs to enhance alkylation of these sites by N‐ethylmaleimide can be explained by the ability of (a) muscarinic drugs to interact with the low‐ affinity sites according to the Monod‐Wyman‐Changeux ‘Plausible Model’ and (b) N‐ethylmaleimide to freeze these sites in the ‘active’ conformation by alkylation.
Purification and Characterization of the CytochromecOxidase fromRhodopseudomonas sphaeroides
Authors: GENNIS Robert B. , CASEY Robert P. , AZZI Angelo , LUDWIG Bernd 
Published: March 2005

When grown aerobically in the dark,Rhodopseudomonas sphaeroidesdevelops a respiratory chain similar to that in mitochondria and the photosynthetic apparatus is suppressed. The aa3‐type cytochrome c oxidase fromRps. sphaeroideshas been purified in Triton X‐100 by affinity chromatography with Sepharose 4B coupled to yeast cytochromec. The oxidase contains 14 nmol heme a/mg protein and is composed of three polypeptide subunits with relative molecular masses of 45000, 37000 and 35000. The enzyme is highly active in the presence of detergents, with a maximal velocity of 300s−1/mol oxidase using either yeast or horse‐heart cytochromec.TheRps. sphaeroides oxidaseis cross‐reactive with antibodies directed against the oxidases fromParacoccus denitrificansandSaccharomyces cerevisiae. A particularly close relationship is indicated in the case ofP. denitrificans. TheRps. sphaeroidesoxidase has been incorporated into phospholipid vesicles. The resulting oxidase in these vesicles demonstrates high enzymatic activity and a respiratory control ratio of 5. Using these vesicles, no evidence for proton extrusion accompanying cytochrome c oxidation was observed. The data suggest that theRps. sphaeroides oxidasedoes not function as a proton pump.
The Reaction of Bovine Glutamate Dehydrogenase with Periodate‐Oxidised ADP
Authors: FAVILLA Roberto , BAYLEY Peter M. 
Published: March 2005

The reactive analogue oADP produced by periodate oxidation of ADP has been studied as a potential affinity label for the enzyme bovine glutamate dehydrogenase, using circular dichroism (CD) difference spectroscopy to monitor specific binding.
The analogue binds stoichiometrically, rapidly and reversibly to the adenine nucleotide binding site with Kd∼ 12 μM (20°C, pH 7) with characteristic intensification of the adenine nucleotide CD at 260 nm.
This complex is unstable and decays with a half‐life of about 1.5 h; the analogue then becomes attached as a Schiff base to a number of subsidiary sites, including the enzyme active site, with partial inactivation of the enzyme.
Depending upon initial concentration of oADP, the enzyme activity is progressively lost during the slow reaction; following borohydride reduction, up to four molecules of analogue are bound/subunit.
Protection against loss of enzyme activity is afforded by the coenzyme NAD+ plus glutarate or l‐hydroxyglutarate (an effective inhibitor), or by glutarate alone, but not by NADNAD+ alone.
Spectroscopic and protection studies indicate that after the decay of the specific CD signal, the enzyme retains the capacity to bind ADP, but that this is progressively lost in parallel with decay of enzymic activity.
The results are consistent with proximity or functional interaction between the adenine nucleotide site and the coenzyme binding portion of the active site.
Thus oADP does not act as a true affinity label for the adenine nucleotide binding site, but the reaction subsequent to binding at that site shows some specificity directed towards the active site.
Somatic Antigens of Pseudomonas aeruginosa
Authors: DMITRIEV Boris A. , KOCHAROVA Nyna A. , KNIREL Yuriy A. , SHASHKOV Alexander S. , KOCHETKOV Nikolay K. , STANISLAVSKY Evgeny S. , MASHILOVA Galina M. 
Published: March 2005

An O‐antigenic lipopolysaccharide, manifesting a high serological activity in the reaction of passive haemag‐glutination and its inhibition, was isolated from Pseudomonas aeruginosa O:6 cells (Lanyi). Splitting‐off of the lipid component by mild acid hydrolysis resulted in the polysaccharide deprived of O‐specific activity.The polysaccharide chain of the lipopolysaccharide was made up exclusively of the residues of amino sugars, among which have been identified: 2‐acetamido‐2‐deoxy‐d‐galactose (GalNAc), 2‐acetamido‐2,6‐dideoxy‐d‐ glucose (QuiNAc), 2‐acetamido‐2,6‐dideoxy‐d‐galactose (FucNAc) as well as 2,3‐diacetamido‐2,3‐dideoxy‐d‐glucuronic acid [Glc(NAc)2A] found naturally for the first time. The principal methods of establishing the polysaccharide structure were 13C nuclear magnetic resonance, methylation analysis and solvolysis with hydrogen fluoride. Depending on solvolysis conditions, a disaccharide or a trisaccharide containing the diacetamidouronic acid residue was formed.From the results obtained it followed that the polysaccharide chain of the O‐antigenic Ps. aeruginosa O:6 lipopolysaccharide represents an acidic hexosaminoglycan constructed of the repeating tetrasaccharide units of the following structure:→4)dGalNAc(αl→4)dGlc(NAc)2A(β1 →3)dFucNAc(α1→3)dQuiNAc(α1→.