Biomedical subjects

A Aubry

Publications and source records attributed to A Aubry.

At least 37 records · Page 2Linked to original sources

PubMed2000

Crystallization and preliminary X-ray diffraction studies of the peptide methionine sulfoxide reductase from Escherichia coli.

Peptide methionine sulfoxide reductase mediates the reduction of protein sulfoxide methionyl residues back to methionines and could thus be implicated in the antioxidant defence of organisms. Hexagonal crystals of the Escherichia coli enzyme (MsrA) were obtained by the hanging-drop vapour-diffusion technique. They belong to space group P6(5)22, with unit-cell parameters a = b = 102.5, c = 292.3 A, gamma = 120 degrees. A native data set was collected at 1.9 A resolution. Crystals of selenomethionine-substituted MsrA were also grown under the same crystallization conditions. A three-wavelength MAD experiment has led to the elucidation of the positions of the Se atoms and should result in a full structure determination.

Crystallization↗

PubMed2000

Antibiotic susceptibility pattern of Mycobacterium marinum.

In vitro activities of 17 antibiotics against 53 clinical strains of Mycobacterium marinum, an atypical mycobacterium responsible for cutaneous infections, were determined using the reference agar dilution method. Rifampin and rifabutin were the most active drugs (MICs at which 90% of the isolates tested were inhibited [MIC(90)s], 0.5 and 0.6 microgram/ml, respectively). MICs of minocycline (MIC(90), 4 microgram/ml), doxycycline (MIC(90), 16 microgram/ml), clarithromycin (MIC(90), 4 microgram/ml), sparfloxacin (MIC(90), 2 microgram/ml), moxifloxacin (MIC(90), 1 microgram/ml), imipenem (MIC(90), 8 microgram/ml), sulfamethoxazole (MIC(90), 8 microgram/ml) and amikacin (MIC(90), 4 microgram/ml) were close to the susceptibility breakpoints. MICs of isoniazid, ethambutol, trimethoprim, azithromycin, ciprofloxacin, ofloxacin, and levofloxacin were above the concentrations usually obtained in vivo. For each drug, the MIC(50), geometric mean MIC, and modal MIC were very close, showing that all the strains had a similar susceptibility pattern. Percent agreement (within +/-1 log(2) dilution) between MICs yielded by the Etest method and by the agar dilution method used as reference were 83, 59, 43, and 24% for minocycline, rifampin, clarithromycin, and sparfloxacin, respectively. Reproducibility with the Etest was low, in contrast to that with the agar dilution method. In conclusion, M. marinum is a naturally multidrug-resistant species for which the agar dilution method is more accurate than the Etest for antibiotic susceptibility testing.

Anti-Bacterial Agents↗

PubMed1999

Apo and holo crystal structures of an NADP-dependent aldehyde dehydrogenase from Streptococcus mutans.

The aldehyde dehydrogenases (ALDHs) are a superfamily of multimeric enzymes which catalyse the oxidation of a broad range of aldehydes into their corresponding carboxylic acids with the reduction of their cofactor, NAD or NADP, into NADH or NADPH. At present, the only known structures concern NAD-dependent ALDHs. Three structures are available in the Protein Data Bank: two are tetrameric and the other is a dimer. We solved by molecular replacement the first structure of an NADP-dependent ALDH isolated from Streptococcus mutans, in its apo form and holo form in complex with NADP, at 1.8 and 2.6 A resolution, respectively. Although the protein sequence shares only approximately 30 % identity with the other solved tetrameric ALDHs, the structures are very similar. However, a large local conformational change in the region surrounding the 2' phosphate group of the adenosine moiety is observed when the enzyme binds NADP, in contrast to the NAD-dependent ALDHs. Structure and sequence analyses reveal several properties. A small number of residues seem to determine the oligomeric state. Likewise, the nature (charge and volume) of the residue at position 180 (Thr in ALDH from S. mutans) determines the cofactor specificity in comparison with the structures of NAD-dependent ALDHs. The presence of a hydrogen bond network around the cofactor not only allows it to bind to the enzyme but also directs the side-chains in a correct orientation for the catalytic reaction to take place. Moreover, a specific part of this network appears to be important in substrate binding. Since the enzyme oxidises the same substrate, glyceraldehyde-3-phosphate (G3P), as NAD-dependent phosphorylating glyceraldehyde-3-phosphate dehydrogenases (GAPDH), the active site of GAPDH was compared with that of the S. mutans ALDH. It was found that Arg103, Arg283 and Asp440 might be key residues for substrate binding.

Aldehyde Oxidoreductases↗

PubMed1999

Crystallization and preliminary X-ray diffraction studies of D-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaeon Methanothermus fervidus.

The homotetrameric holo-D-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaeon Methanothermus fervidus has been crystallized in the presence of NADP+ using the hanging-drop vapour-diffusion method. Crystals grew from a solution containing 2-methyl-2,4-pentanediol and magnesium acetate. A native data set has been collected to 2.1 A using synchrotron radiation and cryocooling. Diffraction data have been processed in the orthorhombic system (space group P21212) with unit-cell dimensions a = 136.7, b = 153.3, c = 74.9 A and one tetramer per asymmetric unit.

Archaea↗

PubMed1998

Transferability of multipole charge-density parameters: application to very high resolution oligopeptide and protein structures.

Crystallography at sub-atomic resolution permits the observation and measurement of the non-spherical character of the electron density (parameterized as multipoles) and of the atomic charges. This fine description of the electron density can be extended to structures of lower resolution by applying the notion of transferability of the charge and multipole parameters. A database of such parameters has been built from charge-density analysis of several peptide crystals. The aim of this study is to assess for which X-ray structures the application of transferability is physically meaningful. The charge-density multipole parameters have been transferred and the X-ray structure of a 310 helix octapeptide Ac-Aib2-L-Lys(Bz)-Aib2-L-Lys(Bz)-Aib2-NHMe refined subsequently, for which diffraction data have been collected to a resolution of 0.82 A at a cryogenic temperature of 100 K. The multipoles transfer resulted in a significant improvement of the crystallographic residual factors wR and wR free. The accumulation of electrons in the covalent bonds and oxygen lone pairs is clearly visible in the deformation electron-density maps at its expected value. The refinement of the charges for nine different atom types led to an additional improvement of the R factor and the refined charges are in good agreement with those of the AMBER molecular modelling dictionary. The use of scattering factors calculated from average results of charge-density work gives a negligible shift of the atomic coordinates in the octapeptide but induces a significant change in the temperature factors (DeltaB approximately 0.4 A2). Under the spherical atom approximation, the temperature factors are biased as they partly model the deformation electron density. The transfer of the multipoles thus improves the physical meaning of the thermal-displacement parameters. The contribution to the diffraction of the different components of the electron density has also been analyzed. This analysis indicates that the electron-density peaks are well defined in the dynamic deformation maps when the thermal motion of the atoms is moderate (B typically lower than 4 A2). In this case, a non-truncated Fourier synthesis of the deformation density requires that the diffraction data are available to a resolution better than 0.9 A.

Crystallography, X-Ray↗

PubMed1998

The crystal state conformation of Aib-rich segments of peptaibol antibiotics.

Ac-(Aib-Ala)3-OH (a protected segment of the peptaibols gliodeliquescin and paracelsin), Z-Leu-Aib-Val-Aib-Gly-OtBu (a segment of [Leu]7-gliodeliquescin), Z-Val-Aib-Aib-Gln-OtBu (a common segment of alamethicin, paracelsin, and hypelcin), and Ac-Aib-Pro-(Aib-Ala)2-OMe and Z-Aib-Pro-(Aib-Ala)2-OMe, which represent differently N(alpha)-protected 1-6 segments of alamethicin and hypelcin, have been synthesized by solution methods. The crystal-state conformations of these five Aib-containing peptides have been determined by X-ray diffraction analysis. We have confirmed that the 3(10)-helical structure is preferentially adopted by Aib-rich short peptides. An experimentally unambiguous proof for the 3(10)-->alpha-helix conversion has been provided by the two differently N-blocked -Aib-Pro-(Aib-Ala)2-OMe hexapeptides. The beta-bend ribbon conformation, commonly observed in the (Aib-Pro)n sequential oligopeptides, is not found in the -Aib-Pro-Aib-Ala-Aib-Ala-sequence. As expected on the basis of the L-configuration of the C(alpha)-monoalkylated residues, a right-handed helix screw sense was found in all peptides investigated.

Anti-Bacterial Agents↗

PubMed1998

Azaproline as a beta-turn-inducer residue opposed to proline.

Azaproline (AzPro) is an analogue of proline containing a nitrogen atom in place of the C(alpha)H group. AzPro has been introduced in various model peptides, and especially in the Boc-Ala-AzPro-Ala-NHiPr tripeptide. The structural consequence of that modification has been investigated in solution by using IR and 1H NMR, with reference to the cognate proline-containing peptide. Contrary to proline, which induces beta-folding of the Pro-Ala sequence, azaproline apparently favors betaVI-folding of the Ala-AzPro one with high occurrence. Opening of the AzPro pyrazolidine ring to get N-methylazaalanine fundamentally does not change the structural properties of the azatripeptide, but allows the existence of open conformers to an extent depending on the solvent.

Aza Compounds↗

PubMed1997

A crystallographic comparison between mutated glyceraldehyde-3-phosphate dehydrogenases from Bacillus stearothermophilus complexed with either NAD+ or NADP+.

Mutations have been introduced in the cytosolic glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Bacillus stearothermophilus in order to convert its cofactor selectivity from a specificity towards NAD into a preference for NADP. In the B-S mutant, five mutations (L33T, T34G, D35G, L187A, P188S) were selected on the basis of a sequence alignment with NADP-dependent chloroplastic GAPDHs. In the D32G-S mutant, two of the five mutations mentioned above (L187A, P188S) have been used in combination with another one designed from electrostatic considerations (D32G). Both mutants exhibit a dual-cofactor selectivity at the advantage of either NAD (B-S) or NADP (D32G-S). In order to analyse the cofactor-binding site plasticity at the molecular level, crystal structures of these mutants have been solved, when complexed with either NAD+ (D32G-Sn, resolution 2.5 A, R = 13.9%; B-Sn, 2.45 A, 19.3%) or NADP+ (D32G-Sp, 2.2 A, 19.2%; B-Sp, 2.5 A, 14.4%). The four refined models are very similar to that of the wild-type GAPDH and as expected resemble more closely the holo form than the apo form. In the B-S mutant, the wild-type low affinity for NADP+ seems to be essentially retained because of repulsive electrostatic contacts between the extra 2'-phosphate and the unchanged carboxylate group of residue D32. Such an antideterminant effect is not well compensated by putative attractive interactions which had been expected to arise from the newly-introduced side-chains. In this mutant, recognition of NAD+ is slightly affected with respect to that known on the wild-type, because mutations only weakly destabilize hydrogen bonds and van der Waals contacts originally present in the natural enzyme. Thus, the B-S mutant does not mimic efficiently the chloroplastic GAPDHs, and long-range and/or second-layer effects, not easily predictable from visual inspection of three-dimensional structures, need to be taken into account for designing a true "chloroplastic-like" mutant of cytosolic GAPDH. In the case of the D32G-S mutant, the dissociation constants for NAD+ and NADP+ are practically reversed with respect to those of the wild-type. The strong alteration of the affinity for NAD+ obviously proceeds from the suppression of the two wild-type hydrogen bonds between the adenosine 2'- and 3'-hydroxyl positions and the D32 carboxylate group. As expected, the efficient recognition of NADP+ is partly promoted by the removal of intra-subunit electrostatic repulsion (D32G) and inter-subunit steric hindrance (L187A, P188S). Another interesting feature of the reshaped NADP+-binding site is provided by the local stabilization of the extra 2'-phosphate which forms a hydrogen bond with the side-chain hydroxyl group of the newly-introduced S188. When compared to the presently known natural NADP-binding clefts, this result clearly demonstrates that an absolute need for a salt-bridge involving the 2'-phosphate is not required to switch the cofactor selectivity from NAD to NADP. In fact, as it is the case in this mutant, only a moderately polar hydrogen bond can be sufficient to make the extra 2'-phosphate of NADP+ well recognized by a protein environment.

Binding Sites↗

PubMed1997

Aza-peptides. II. X-ray structures of aza-alanine and aza-asparagine-containing peptides.

In order to determine the structural consequences of the N alpha/C alpha H exchange in aza-peptides, we have solved the crystal molecular structures of some derivatives containing the aza-analogue of asparagine [Z-AzAsn(Me)-NMe2 (1), Z-AzAsn(Me)-Pro-NHiPr (2) and Piv-Pro-AzAsn(Me)-NHiPr (5)], aspartic acid [Z-AzAsp(OEt)-Pro-NHiPr (3) and alanine (Boc-AzAla-Pro-NHiPr (4)], by using X-ray diffraction. They reveal that the alpha-nitrogen accommodates a pyramidal (1-4) or planar (5) structure depending on the sequence. When pyramidal, the alpha-nitrogen assumes the R (D-like) chirality. All of the derivatives but 1 adopt either a beta 1-folded (2-4) or beta n-folded (5) structure in which the (AzAsn)N3H bond is intramolecularly hydrogen-bonded to the alpha-nitrogen.

Alanine↗

PubMed1997

Aza-peptides. III. Experimental structural analysis of aza-alanine and aza-asparagine-containing peptides.

To determine the structural perturbations induced by the C alpha H-->N alpha exchange in aza-peptides, we have examined by 1H NMR and IR spectroscopy various derivatives of the aza-analogues of alanine, aspartic acid and asparagine in different organic solvents with increasing polarity. Their general formulas are: R1-AzXaa-NR2R3, R1-Pro-AzXaa-NR2R3 and R1-AzXaa-Pro-NR2R3 (where AzXaa denotes the aza-analogue of the amino acid residue Xaa = Ala, Asp, Asn; R1 = Boc, Z; R2, R3 = H, Me, iPr). The aza-analogue of an amino acid residue appears to be a strong beta-turn-inducing motif, and the AzAsn carboxamide side-chain is capable of interacting, as a proton donor, with the preceding peptide carbonyl group.

Alanine↗

PubMed1997

X-ray structures of aza-proline-containing peptides.

The aza-analogue of proline (AzPro) contains a nitrogen atom in place of the CH alpha of the cognate residue. The resolution of the crystal structures of seven AzPro-containing peptides, presenting a set of ten AzPro motifs, reveals the structural properties of this particular aza-residue. Because of sterical hindrances, both nitrogen atoms are out of planarity, and the reduced electronic conjugation in the two AzPro-adjacent amide groups probably explains the longer amide bond distances and the weak proton-accepting character of the two pyrazolidine nitrogens. The absolute configuration of both AzPro nitrogens depends on the chemical nature of the sequence. In all cases, the AzPro residue assumes the same intrinsic three-dimensional structure and presents folding tendencies opposed to those induced by proline.

Aza Compounds↗

PubMed1996

Crystal structures of peptides and modified peptides.

The X-ray diffraction experiments on peptides and related molecules which have been carried out in Western Europe, except Italy, in the last eight years are reviewed. The crystal structures of some bioactive peptides such as Leu-enkephalin (a neurotransmitter), cyclosporin A (an immunomodulator in both the free and protein-bound state), balhimycin (an antibiotic) and octreotide (a somatostatin analogue) are briefly presented. Crystallized N- and C-protected model peptides have given an insight into the folding tendency and folding modes depending on the peptide sequences. The crystal structures of various pseudopeptide molecules reveal how the three-dimensional structure of peptide analogues can be modulated by substituting non-peptide groups for the peptide bond. A few examples of structural mimetics of the beta- and gamma-turns, and of templates for alpha-helix induction are also presented.

Amino Acid Sequence↗

PubMed1995

The three-dimensional structure of thymidine kinase from herpes simplex virus type 1.

Recombinant thymidine kinase from Herpes simplex virus type 1 (ATP:thymidine 5'-phosphotransferase; EC 2.7.1.21), an enzyme of therapeutic importance, was purified and crystallized in an N-terminally truncated but still fully active form. The three-dimensional structure was solved by X-ray diffraction analysis at 3.0 A resolution using isomorphous replacement. The chain fold is presented together with the bound substrates thymidine and ATP. Three chain segments at the surface could not be located. The chain fold, the location of the substrates and presumbly also the catalytic mechanism resemble the well-known adenylate kinases.

Amino Acid Sequence↗

PubMed1994

Onset of the fully extended conformation in (alpha Me)Leu derivatives and short peptides.

The X-ray diffraction crystal structures of the (alpha Me)Leu derivative mClAc-D-(alpha Me) Leu-OH and the terminally protected tripeptide Z-D-(alpha Me) Leu-(L-Ala)2-OMe show the onset of the fully extended (C5) conformation for the (alpha Me) Leu residue in both independent molecules in the asymmetric unit of the former compound and in two out of the four independent molecules in the asymmetric unit of the latter compound. In addition, conformational analysis in CDCl3 solution (using FT-infra-red absorption and 1H nuclear magnetic resonance) revealed the occurrence of a significant population of fully extended conformers throughout the entire sequence of the (alpha Me) Leu homochiral homopeptides pBrBz-[D-(alpha Me) Leu]n-OtBu (from monomer to tetramer). Taken together, these results represent a clear indication that this peptide secondary structure, uncommon for protein amino acids and other C alpha-methylated chiral residues, is not a rare observation in (alpha Me) Leu derivatives and short peptides.

Amino Acid Sequence↗

PubMed1994

Crystal structure analysis of a beta-turn mimic in hydrazino peptides.

The crystal structures of four hydrazino peptides (Piv-Pro-h(N alpha-Bzl)Gly-NHiPr 1, Piv-Pro-hAla-NHiPr 2, Moc-hPro-NHiPr 3, and Boc-hPro-Gly-N(OH)Me 4) deriving from the hydrazino analogues of glycine (hGly), L-alanine (hAla) or L-proline (hPro) have been solved. They reveal a common folded structure of the alpha-hydrazino acid residue characterized by a bifurcated hydrogen bond closing an eight-membered cycle. This folded structure is topologically similar to the beta II'-turn in peptides, and the CO-NH-N hydrazide link can be considered as a good turn-inducer in peptide analogues.

Hydrazines↗

PubMed1994

Turn induction by N-aminoproline. Comparison of the Gly-Pro-Gly and Gly psi [CO-NH-N]Pro-Gly sequences.

The folded structure induced by the N-aminoproline residue (the hydrazino analogue of proline, denoted hPro) in the Boc-Gly1-hPro2-Gly3-NHiPr hydrazino tripeptide has been characterized in the solid state by X-ray diffraction, and compared to the usual beta II-turn structure in the Boc-Gly1-Pro2-Gly36-NHiPr cognate tripeptide. It is stabilized by a bifurcated hydrogen bond in which (Gly3)NH interacts with both (Gly1)CO and (hPro2)N alpha. This conformation is retained in CH2Cl2 and CHCl3 solutions, and allows an overall folded conformation of the hydrazino tripeptide in which (iPr)NH is hydrogen-bonded to (Boc)CO. The hPro alpha-hydrazino acid residue appears to promote a local folded structure, and might behave as a beta-turn mimic.

Amino Acid Sequence↗

PubMed1993

Structures of peptides from alpha-amino acids methylated at the alpha-carbon.

The structural preferences of peptides (and depsipeptides) from the achiral MeAib and Hib residues, and the chiral Iva, (alpha Me) Val, (alpha Me) Leu, and (alpha Me) Phe residues, as determined by conformational energy computations, x-ray diffraction analyses, and 1H-nmr and spectroscopic studies, are reviewed and compared with literature data on Aib-containing peptides. The results obtained indicate that helical structures are preferentially adopted by peptides rich in these alpha-amino acids methylated at the alpha-carbon. Intriguing experimental findings on the impact of the chirality of Iva, (alpha Me) Val, and (alpha Me) Phe residues on helix screw sense are illustrated.

Amino Acid Sequence↗

PubMed1992

Structure of tBuCO-Gly-Gly psi [CH2-N+H2]NHEt.BPh4-.

N-(tert-Butylcarbonylglycylaminoethyl)-N-(ethyl)ammonium tetraphenylborate, C11H24N3O+2.C24H20B-, Mr = 549.57, triclinic, P-1, a = 11.567 (2), b = 11.922 (2), c = 14.484 (3) A, alpha = 70.99 (2), beta = 74.83 (2), gamma = 59.33 (1) degrees, V = 1613.1 A3, Z = 2, D chi = 1.13 g cm-3, lambda(Cu K alpha) = 1.5418 A, mu = 4.69 cm-1, mu Rmax much less than 1, F(000) = 592, T = 293 K, R = 0.058 for 3491 observed reflections. This pseudopeptide is folded by a short N(+)-H ... O = C hydrogen bond (N3 ... O1 = 2.81 A) which closes a ten-membered ring. This results in a beta-turn structure that can be classified as type II on the basis of the conformational angles for the N-terminal glycine. The conformational angles phi 1, psi 1, phi 2 and psi 2 are -53.4 (6), 139.7 (4), 91.5 (5) and -62.6 (6) degrees respectively.

Amino Acid Sequence↗