Biomedical subjects

M Delepierre

Publications and source records attributed to M Delepierre.

At least 55 records · Page 3Linked to original sources

PubMed1996

An insect-specific toxin from Centruroides noxius Hoffmann. cDNA, primary structure, three-dimensional model and electrostatic surface potentials in comparison with other toxin variants.

Scorpion toxins acting on sodium channels differ in their specificity. Toxic peptides specific towards mammals and arthropods (insects and/or crustaceans) have been described. Because of the similar three-dimensional fold of these peptides, the molecular base of their specificity is thought to reside in certain differences at the level of amino acid residues especially within or near the binding site of the toxin to the particular ion channel. The cDNA, amino acid sequence and biological activity of an insect-specific toxin, Cn10, from the scorpion Centruroides noxius Hoffmann is reported. The electrostatic potential surface around a three-dimensional model of Cn10 was calculated. It revealed that residues Tyr4, Lys13, Ile18, Leu19, Gly20, Lys43, Leu44, Thr57, Tyr58, Pro59, Thr64 and Cys65, situated at the side of the toxin proposed in the literature to bind to the sodium channel, constitute a positive surface region. Therefore, they may form the site that binds to the channel. Cn10 was included in a comparative analysis of two groups of natural variants, highly similar peptides of the genus Centruroides with specificities towards mammals or arthropods. A number of surface-accessible residues, consistently different between the two groups and situated near the putative binding site, may be of importance for the specificity of the analyzed toxins.

Amino Acid Sequence↗

PubMed1996

A novel beta-(1-3)-glucanosyltransferase from the cell wall of Aspergillus fumigatus.

Cell wall transferases utilizing beta-(1-3)-glucan chains as substrates may play important roles in cell wall assembly and rearrangement, as beta-(1-3)-glucan is a major structural component of the cell wall of many fungi. A novel beta-(1-3)-glucanosyltransferase was purified to apparent homogenei ty from an autolysate of the cell wall of Aspergillus fumigatus. The enzyme had a molecular mass of 49 kDa and contained approximately 5 kDa of N-linked carbohydrate. The enzyme catalyzed an initial endo-type splitting of a beta-(1-3)-glucan molecule, followed by linkage of the newly generated reducing end to the nonreducing end of another beta-(1-3)-glucan molecule. Laminarioligosaccharides of size G10 and greater were donor substrates for the transferase. Laminarioligosaccharides of size G5 and greater formed acceptors. The enzyme was able to reuse initial transferase products as donors and acceptors in extended incubations, resulting in the formation of increasingly larger transferase products until they became insoluble. The major initial products from an incubation of the transferase with borohydride-reduced G11 (rG11) were rG6 and rG16. 1H NMR analysis of the rG16 transferase product showed it was a laminarioligosaccharide, indicating that the enzyme forms a beta-(1-3)-linkage during transfer. The enzyme may have a key function in vivo by allowing the integration of newly synthesized glucan into the wall and promoting cell wall expansion during cell growth.

Aspergillus fumigatus↗

PubMed1996

Isolation and characterization of an endogenous peptide from rat brain interacting specifically with the serotonergic 1B receptor subtypes.

The existence of endogenous compounds interacting with the serotonergic system was previously postulated. In the present work, rat brain tissues were extracted by acidic and organic procedures. The resulting extract was tested for its capacity to interact with the binding of [3H]5-hydroxytryptamine ([3H]5-HT) to 5-HT1 receptors. Compounds responsible for the observed inhibitory activities were isolated and purified by high pressure liquid chromatography. A tetrapeptide corresponding to a novel amino acid sequence Leu-Ser-Ala-Leu (LSAL) was identified. It reduces the binding of [3H]5-HT to 5-HT1 receptors at low concentration (IC50 = 10(-10) M). This effect corresponds to a specific interaction at 5-HT1B receptors since LSAL does not significantly affect other neurotransmitter bindings. LSAL appears heterogeneously distributed throughout the brain (hippocampus > cerebellum > striatum > brain stem) and in peripheral tissues (kidney > lung > stomach > blood > liver > spleen). Two other peptides, Leu-Ser (LS) and Ala-Leu (AL), were also purified. They hardly affected [3H]5-HT binding compared with LSAL. They presumably represent degradation products of the functional peptide LSAL. The fact that LSAL interacts specifically with 5-HT1B receptors that inhibit the release of neurotransmitters and particularly that of 5-HT itself suggests that this peptide may be involved in mechanisms controlling 5-HT neurotransmission and, accordingly, may play an important role in pathophysiological functions related to 5-HT activity.

Amino Acid Sequence↗

PubMed1995

Chemical structure and translation inhibition studies of the antibiotic microcin C7.

Escherichia coli microcin C7 (MccC7) is an antibiotic that inhibits protein synthesis in vivo. It is a heptapeptide containing unknown modifications at the N and C termini (García-Bustos, J. F., Pezzi, N., and Méndez, E. (1985) Antimicrob. Agents Chemoth. 27, 791-797). The chemical structure of MccC7 has been characterized by use of 1H homonuclear and heteronuclear (13C, 15N, 31P) nuclear magnetic resonance spectroscopy as well as mass spectrometry (1177 +/- 1 Da). The heptapeptide Met-Arg-Thr-Gly-Asn-Ala-Asp is substituted at the N terminus by a N-formyl group. The C-terminal substituent consists of the phosphodiester of 5'-adenylic acid and n-aminopropanol (AMPap), which is linked via the phosphorus atom to an amide group, thus forming a phosphoramide. The main chain carbonyl of the C-terminal aspartic acid residue is connected via this amide bond to the modified nucleotide unit. MccC7 and the peptide unit inhibit protein translation in vitro while a synthetic analog of the AMPap substituent is not active. Neither the peptide nor the AMPap molecule has an effect on the growth of MccC7-sensible cells. Our results strongly suggest that the peptide is responsible for MccC7 antibiotic activity while the C-terminal substituent is needed for MccC7 transport. Implications of the structure determined in this work for MccC7 synthesis and mode of action are discussed.

Amino Acid Sequence↗

PubMed1995

Phosphorylation mechanism of nucleoside diphosphate kinase: 31P-nuclear magnetic resonance studies.

The phosphorylation mechanism of Dictyostelium discoideum nucleoside diphosphate (NDP) kinase was investigated by NMR. 31P chemical shifts were measured on both native and denatured enzyme. In the enzymatically phosphorylated enzyme denatured by 9 M urea or 7 M guanidine hydrochloride, the NDP kinase phosphohistidine signal appeared between the signals of N delta and N epsilon free monophosphohistidines used as reference compounds and added to the sample. A signal with the same intermediate position was also observed in the pronase digest of the alkaline-denatured phosphorylated enzyme. However, when phosphohistidines of the phosphorylated synthetic peptide pGlu-His-Gly were taken as references, the NDP kinase and the N delta peptide phosphohistidine signals were shown to be identical, providing evidence that phosphorylation occurs on the N delta of the active site histidine residue. Moreover, the rate of hydrolysis of the histidine-bound phosphate is in agreement with a modification at the N delta position. Phosphorylation of the NDP kinase by phosphoramidate provided a result similar to that of the enzymatic phosphorylation. In both cases, phosphorylation could not be detected on any amino acid other than histidine. Particularly, no phosphoserine residue was observed.

Animals↗

PubMed1995

Solution structure of a homopyrimidine: homopurine dodecamer encoded by the HIV-1 envelope gene: NMR and molecular simulation studies.

The solution structure of the nonpalindromic dodecanucleotide homopyrimidine:homopurine, d(5'-TTTCTCCTTTCT):d(5'-AGAAAGGAGAAA), was determined by two-dimensional nuclear magnetic resonance spectroscopy combined with molecular simulation. The dodecamer sequence studied was found within the HIV-1 envelope sequence and had all four Gs substituted by A in two hypermutants. A set of low-energy B-DNA conformations satisfying the quantitative NOE data were obtained. These highly related structure had neither peculiar helical parameters for the base pairs nor axis curvature. Analysis of the dihedral angles (epsilon-zeta) suggests that the A stretches flanking the GpA dinucleotides were more flexible.

Base Sequence↗

PubMed1995

Protein folding intermediates with rapidly exchangeable amide protons contain authentic hydrogen-bonded secondary structures.

Recent studies on protein folding intermediates by pulsed amide proton exchange and by far-ultraviolet circular dichroism have shown important discrepancies between the secondary structure contents estimated by these two methods at early folding stages. To solve these apparent discrepancies, structural studies have been performed on the isolated, 101 residue long, C-terminal proteolytic domain (F2) of the Escherichia coli tryptophan synthase beta chain, which had previously been reported to behave as an early folding intermediate [Chaffotte, A. F., Cadieux, C., Guillou, Y., & Goldberg, M. E. (1992) Biochemistry 31, 4303-4308]. The secondary structure of F2 has been investigated by far-UV circular dichroism (CD), Fourier transform infrared (FTIR) spectroscopy, and NMR. The CD and FTIR spectra clearly indicate that isolated F2 has about 30-45% of its residues involved in secondary structures stabilized by conventional hydrogen bonds. The characteristics of the NMR spectrum (line broadening, absence of structure-induced chemical shifts, absence of nuclear Overhauser effects in the amide region, few dipolar interactions between the side-chain protons) suggest that isolated F2 is oscillating between several conformations in rapid equilibrium. The rate of amide proton exchange has been studied by one-dimensional NMR, which indicates a significant extent of proton protection, with, however, protection factors that can be estimated to be at most 60 and more probably closer to 10. Thus, F2 appears to exist as a molten globule that exhibits very low amide proton protection and yet contains a large fraction of its residues involved in authentic secondary structures stabilized by hydrogen bonds. Such a state is likely to correspond to the earliest structured folding intermediates thus far characterized.

Amides↗

PubMed1995

Cloning and characterization of the cDNAs encoding Na+ channel-specific toxins 1 and 2 of the scorpion Centruroides noxius Hoffmann.

Using a cDNA library prepared from venomous glands of the Mexican scorpion Centruroides noxius Hoffmann the genes that encode toxins 1 and 2 were identified, cloned and sequenced. In view of the proposed mechanism for processing the mature peptides coded by these two genes, the corresponding peptide-toxins were sequenced de novo. Mass spectrometric and 1H-NMR analyses of the C-terminal peptide produced by enzymatic digestion of both toxins indicated that the last residue is serine-amide. Sequence comparison revealed that these two genes have a similarity of 56% and 80% at the amino acid and nucleotide levels, respectively. Small corrections to the published primary structures were introduced: Cn toxin 1 has an extra serine residue at position 65 and the residue in position 60 is a proline, while the amino acids at positions 34 and 35 of Cn 2 are, respectively, tyrosine and glycine. Sequence comparison of toxins from the genus Centruroides suggests the presence of at least three classes of distinct peptides in these venoms.

Amino Acid Sequence↗

PubMed1995

Conformational behaviour of a synthetic peptide of the C-terminus of villin that interacts with actin: an NMR, CD and stimulated annealing study.

The solution structure of a synthetic 22-amino acid peptide (P1) corresponding to the extreme C-terminal end and one of the F-actin binding sites of villin has been determined by 1H NMR and CD spectroscopy. The structure of this peptide was compared to that of a peptide in which lysine to glutamic acid substitutions were introduced at positions 17 and 19 (P11), abolishing F-actin binding. Both peptides are largely unstructured in aqueous solution. Changes observed in the NMR and CD spectra of both peptides are consistent with alpha-helix formation in trifluoroethanol/water mixtures. A set of 189 interproton distances derived from nuclear Overhauser enhancement (NOE) measurements, 17 phi-angle constraints obtained from 3JNH alpha coupling constants, as well as about 10 N ... O distance restraints deduced from amide proton exchange kinetics with deuterium, were used for the structure determination. The three-dimensional structure of P1 and P11 is characterized by two helical regions, one extending from residues 2 to 5 and a second covering residues 7 to 17. The central fragment, ranging from Leu-7 to Leu-15, is more stable. The C-terminal residues are less structured, particularly within peptide P11. The significance of these structural results is discussed in relation to the biological activity of villin.

Actins↗

PubMed1994

Primary and NMR three-dimensional structure determination of a novel crustacean toxin from the venom of the scorpion Centruroides limpidus limpidus Karsch.

A crustacean-specific toxin from the Mexican scorpion Centruroides limpidus limpidus was purified, and its primary sequence was determined, including disulfide bonds. This toxin has 66 amino acid residues and is stabilized by four disulfide bridges (Cys12-Cys65, Cys16-Cys41, Cys25-Cys46, and Cys29-Cys48). A detailed nuclear magnetic resonance structure of this protein was obtained using a combination of two-dimensional proton NMR experiments. The NMR parameters that gave 69 dihedral restraints and 418 distance constraints were used in molecular dynamics calculations in order to determine the solution conformation of the toxin. It is composed of a short alpha-helix and a three-stranded antiparallel beta-sheet. Although the regular secondary structure of this crustacean toxin is common to the structural motif of other scorpion toxins, detailed conformational analysis was performed in order to highlight structural features that might be responsible for the differential modulation of the toxin on sodium channels of distinct tissues: mammalian versus crustacean.

Amino Acid Sequence↗

PubMed1994

C-terminal secretion signal of an Erwinia chrysanthemi protease secreted by a signal peptide-independent pathway: proton NMR and CD conformational studies in membrane-mimetic environments.

The detailed structure of a 68-residue chimeric peptide encompassing the 56 last C-terminal residues of Erwinia chrysanthemi protease G has been investigated by using circular dichroism and NMR spectroscopies. The peptide which contains the secretion signal of PrtG was solubilized either in aqueous solvent, in trifluoroethanol (TFE)/H2O mixtures, or in dodecyl beta-D-maltoside detergent. The peptide helical content increases upon TFE and detergent additions. A stable conformation is reached at 40% TFE (v:v) and at a micelle to peptide ratio higher than 1. The 1H NMR spectrum has been assigned in TFE/H2O, 2:1 (v:v), and it is shown that residues 26-29 and 50-62 form a relatively stable helix although a conformational equilibrium between a helix and probably a more random structure is observed throughout fragment 13-63. Comparison of the CterG conformation with results obtained by deletion approach could lead to the hypothesis that the C-terminal secretion signal is composed of an alpha-helix located close to the essential C-terminal tetrapeptide D65VIV.

Amino Acid Sequence↗

PubMed1994

[Epitopes of the envelope of the hepatitis B virus: a structural approach].

Hepatitis B is a major public health problem. More than 300 million people are chronically infected by the virus. During infection very large quantities of complete virions and empty envelopes, consisting of spherical or filamentous lipoprotein particles, are present in the blood. DNA genome coding for envelopes is divided into three domains, preS1, preS2 and S. All available data suggest that the preS1 and preS2 products are exposed at the surface of the virions. These proteins are more immunogenic than S in terms of in vivo antibody response and the number of epitopes identified. The three dimensional mapping of antigenic sites of the HBV will provide important strategic information for vaccine development and identification of targets for immunorecognition or immunoregulation of the disease.

Epitopes↗

PubMed1993

Sequence of a staphylococcal gene, vat, encoding an acetyltransferase inactivating the A-type compounds of virginiamycin-like antibiotics.

The Staphylococcus aureus plasmids, pIP680 and pIP1156, which confer resistance to A-type compounds of virginiamycin-like antibiotics (Vml: streptogramin A, pristinamycin IIA, virginiamycin M) and to synergistic mixtures of the A and B compounds of Vml antibiotics, were shown to direct the modification of A-type compounds by acetylation. The vat gene, encoding the acetyltransferase modifying A-type compounds, was isolated from plasmid pIP680 and sequenced. This gene potentially encodes a 219-amino-acid (aa) protein, VAT, of 24 330 Da showing at least 38% aa identity with two chloramphenicol acetyltransferases encoded by cat genes isolated from Escherichia coli and Agrobacterium tumefaciens. Resistance to A-type compounds of Vml antibiotics conferred to S. aureus by vat was not expressed in E. coli, although a protein having a M(r) similar to that encoded by this gene was detected in E. coli minicells. The vat gene was detected by the polymerase chain reaction in two chromosomally located staphylococcal conjugative elements and in the conjugative plasmid, pIP1156, conferring resistance to A-type compounds.

Acetyltransferases↗

PubMed1993

Binomial frequency response to non-binomial pulse sequences for efficient water suppression.

This article reports on the use of short-hard pulse and spin-lock pulse combinations giving a binomial-like frequency response for the measurement of NMR spectra in aqueous solutions of quite dilute samples. The pulse sequence proposed provides excellent water suppression and does not introduce any linear or higher order phase errors. Application to the measurement of 2D NOESY data of a 0.25 mM solution of a double-stranded DNA fragment is presented.

Base Sequence↗

PubMed1992

Zinc, a novel structural element found in the family of bacterial adenylate kinases.

The adk gene from Bacillus stearothermophilus was cloned and overexpressed in Escherichia coli under the control of the lac promoter. The primary structure of B. stearothermophilus adenylate kinase exhibited 76% identity with the enzyme from Bacillus subtilis, 60% identity with the enzyme from Lactococcus lactis, and 42% identity with the enzyme from E. coli. The most striking property of the adenylate kinase from B. stearothermophilus is the presence of a structural zinc atom bound to four cysteines in a zinc finger-like fashion. The ability to coordinate zinc is predicted also for a number of other isoforms of bacterial adenylate kinases. Furthermore, the tightly bound metal ion contributes to the high thermodynamic stability of adenylate kinase from B. stearothermophilus.

Adenylate Kinase↗

PubMed1991

1H-NMR conformational analysis of a high-affinity antigenic 11-residue peptide from the tryptophan synthase beta 2 subunit.

Two synthetic peptides from the beta 2 subunit of tryptophan synthase have been studied by 1H-NMR spectroscopy at 300 MHz. One peptide, His-Gly-Arg-Val-Gly-Ile-Tyr-Phe-Gly-Met-Lys (peptide 11; Ile, isoleucine) is antigenic and binds with a high affinity to a monoclonal antibody that recognizes the native beta 2 subunit. The second peptide, His-Gly-Arg-Val-Gly-Ile-Tyr-Phe (peptide 8) reacts very weakly with the antibody. The 1H-NMR spectra of the two peptides have been assigned from two-dimensional techniques in H2O, 2H2O and (2H6) dimethyl sulfoxide [(2H6)Me2SO]. The structure has been evaluated through analysis of nuclear Overhauser effects, coupling constants, amide-proton exchange rates and their temperature coefficients, and chemical shifts. In aqueous solvent, the C-terminal part of peptide 11 presents some structure centered around residues Phe-Gly-Met. The relationship between the structure found in peptide 11 and its antigenic nature is discussed.

Amino Acid Sequence↗

PubMed1991

The isolated C-terminal (F2) fragment of the Escherichia coli tryptophan synthase beta 2-subunit folds into a stable, organized nonnative conformation.

Proteolysis of the beta 2-subunit of Escherichia coli tryptophan synthase by the endoproteinase Glu C from Staphylococcus aureus V8 yields a peptide, F2, corresponding to the C-terminal 101 residues of the beta-chain. The conformation and stability of isolated F2 in phosphate buffer at pH 7.8 (where native beta 2 is stable) have been investigated. Circular dichroism spectra in the far-UV showed the presence of large amounts of secondary structure (19% alpha-helices, 34% extended beta-structures). Circular dichroism spectra in the near-UV and sedimentation velocity studies indicated an open globular structure with the aromatic side chains in a symmetric (or disordered) environment. NMR spectra and rates of amide proton exchange showed that F2 fluctuates rapidly between several conformations. The thermal denaturation of F2 observed by the loss of far-UV circular dichroism with increasing temperature appeared noncooperative, and indicates a high thermal stability (Tm = 70 degrees C). Differential scanning microcalorimetry confirmed the absence of cooperativity and indicated a very low value for the calorimetric enthalpy of denaturation (delta H = 17 kJ/mol). All these properties were compatible with a molten globule. However, the low sedimentation coefficient of F2 suggested a very hydrated and/or expanded structure, and the secondary structure content of isolated F2 (see above) differed widely from that reported in the literature for F2 within the context of native beta 2 (49% alpha-helices and 13% extended beta-structures). Thus, neither the secondary nor the tertiary structure of isolated F2 resembled those of native F2. In this respect, isolated F2 is not a "molten globule".(ABSTRACT TRUNCATED AT 250 WORDS)

Circular Dichroism↗

PubMed1991

1H- and 31P-NMR studies of ditercalinium binding to a d(GCGC)2 and d(CCTATAGG)2 minihelices: a sequence specificity study.

The structures of the complexes formed in aqueous solution between ditercalinium, a bis-intercalating drug, and both the self-complementary tetranucleotide d(GCGC)2 and octanucleotide d(CCTATAGG)2, have been investigated by 400-MHz 1H-nmr and 162-MHz 31P-nmr. All the nonexchangeable protons, as well as the exchangeable imino protons and the phosphorus signals, have been assigned. Both oligonucleotides have been shown to adopt a right-handed B-DNA type structure. The addition of ditercalinium to the oligonucleotides lead to the formation of complexes in slow exchange at the nmr time scale with the free helices. At all drug-to-helix ratios studied, the ditercalinium was found in the bound form, whereas free and complexed oligonucleotides were in slow exchange, allowing resonance assignments through two-dimensional chemical exchange experiments. for d(GCGC)2 the strong upfield shifts induced on all aromatic protons of both the bases and the drug by complexation with ditercalinium suggest an interaction by intercalation of the two rings. However, the loss of twofold symmetry upon binding, as well as the chemical shift variation of the drug proton signals of one of the chromophores with temperature and concentration, favor a model in which the drug-nucleotide complexes have one ring of the drug intercalated and the other stacked on top of the external base pair. The intermolecular contacts between drug protons and nucleotide protons give a defined geometry for complexation that is consistent with the proposed model. In contrast, with d(CCTATAGG)2 several drug-nucleotide complexes were formed and a large increase in line broadening was observed at high drug-to-DNA ratios, precluding a detailed analysis of these complexes. However, the large upfield shift in the imino proton resonances together with the shielding of the ditercalinium ring protons favor a model with bis-intercalation of ditercalinium. This model is supported by the downfield shift of at least 4 out of 14 phosphorus signals. The results are compared with those obtained on ditercalinium binding to the homologous sequences d(CGCG)2 and d(TTCGCGAA)2, and discussed in terms of sequence specificity.

Antineoplastic Agents↗