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Biomedical subjects

Isabel Usón

Publications and source records attributed to Isabel Usón.

At least 19 recordsLinked to original sources
PubMed2006

Tri-[Pt2Tl]3- and polynuclear chain [Pt-Tl]infinity- complexes based on nonbridged Pt(II)-Tl(I) bonds: solid state and frozen solution photophysical properties.

Treatment of (NBu4)2[PtR4] (R = C6F5) with 1 or 0.5 equiv of TlNO3 in EtOH/H(2)O produces colorless crystals of trinuclear complex (NBu4)3[Tl{PtR4}2], 1, in which the Tl+ center is complexed by two [PtR4]2- fragments (Pt-Tl = 2.9777(4) and 3.0434(4) A). The expected mixed complex with a Pt/Tl composition of 1:1, 2, is generated as an orange microcrystalline solid by treating [PtR4]2- with a large excess of TlNO3 (approximately 8 equiv). Crystallographic analysis of 2 reveals the formation of a novel one-dimensional (1D) heterometallic linear chain (NBu4)(infinity)[Tl{PtR4}](infinity), 2, formed by alternating a [PtR4]2- fragment and a Tl+ center with a uniform Pt-Tl bond separation along the chain of 3.0321(2) A. Surprisingly, treatment of (NBu4)2[PtR4] with 1 equiv of TlPF6 in EtOH yields pale greenish-yellow needles of an unusual adduct, 2.{(NBu4)(PF6)}(infinity) (3), which was found to form a similar extended linear chain, {TlPtR4}(infinity), constructed by two alternating Pt-Tl separations, a shorter (3.1028(6) A) one and a longer (3.2306(6) A) one. The solid state and solution photophysical properties have been examined. While complex 1 shows a high-energy MM'CT blue phosphorescence (450 nm), the extended chain in 2 exhibits a lower-energy emission (582 nm) than that in adduct 3 (505 nm). For products 2 and 3, interesting luminescence thermochromism is observed in frozen solutions. The emissions are found to be strongly dependent on the solvent, concentration, and excitation wavelength.

Journal Article↗
PubMed2006

Three-dimensional crystal structure and enzymic characterization of beta-mannanase Man5A from blue mussel Mytilus edulis.

Endo-beta-1,4-d-mannanase is the key depolymerizing enzyme for beta-1,4-mannan polymers present in the cell walls of plants and some algae, as well as in some types of plant seeds. Endo-1,4-beta-mannanase from blue mussel Mytilus edulis (MeMan5A) belongs to the glycoside hydrolase (GH) family 5 enzymes. The MeMan5A structure has been determined to 1.6A resolution using the multiple-wavelength anomalous dispersion method at the selenium K edge with selenomethionyl MeMan5A expressed in the yeast Pichia pastoris. As expected for GH 5 enzymes, the structure showed a (betaalpha)(8)-barrel fold. An unusually large number of histidine side-chains are exposed on the surface, which may relate to its location within the crystalline style of the digestive tract of the mussel. Kinetic analysis of MeMan5A revealed that the enzyme requires at least six subsites for efficient hydrolysis. Mannotetraose (M4) and mannopentaose (M5) were shown to interact with subsites -3 to +1, and -3 to +2, respectively. A clear kinetic threshold was observed when going from M4 to M5, indicating that the +2 subsite provides important interaction in the hydrolysis of short oligomeric mannose substrates. The catalytic centre motif at subsite -1 found in superfamily GH clan A is, as expected, conserved in MeMan5A, but the architecture of the catalytic cleft differs significantly from other GH 5 enzyme structures. We therefore suggest that MeMan5A represents a new subfamily in GH 5.

Amino Acid Sequence↗
PubMed2006

Kettapeptin: isolation, structure elucidation and activity of a new hexadepsipeptide antibiotic from a terrestrial Streptomyces sp.

The ethyl acetate extract of the Streptomyces sp. isolate GW99/1572 exhibited significant biological activity against Gram-positive bacteria and delivered kettapeptin (1), a new hexadepsipeptide antibiotic of the azinothricin type. The structure was elucidated by various 1D and 2D NMR techniques, mass spectrometry and by comparison of the NMR data with those of closely related antibiotics. The absolute configuration of the compound was derived by crystal structure analysis and by comparison with the optical rotation data of related compounds.

Anti-Infective Agents↗
PubMed2005

Crystal and solution structures of 7-amino-actinomycin D complexes with d(TTAGBrUT), d(TTAGTT) and d(TTTAGTTT).

The formation of the complex of 7-amino-actinomycin D with potentially single-stranded DNA has been studied by X-ray crystallography in the solid state, by NMR in solution and by molecular modelling. The crystal structures of the complex with 5'-TTAG[Br(5)U]T-3' provide interesting examples of MAD phasing in which the dispersive component of the MAD signal was almost certainly enhanced by radiation damage. The trigonal and orthorhombic crystal modifications both contain antibiotic molecules and DNA strands in the form of a 2:4 complex: in the orthorhombic form there is one such complex in the asymmetric unit, while in the trigonal structure there are four. In both structures the phenoxazone ring of the first drug intercalates between a BrU-G (analogous to T-G) wobble pair and a G-T pair where the T is part of a symmetry-related molecule. The chromophore of the second actinomycin intercalates between the BrU-G and G-BrU wobble pairs of the partially paired third and fourth strands. The base stacking also involves (A*T)*T triplets and Watson-Crick A-T pairs and leads to similar complex three-dimensional networks in both structures, with looping-out of unpaired bases. Although the available NOE constraints of a solution containing the antibiotic and d(TTTAGTTT) strands in the ratio 1:1 are insufficient to determine the structure of the complex from the NMR data alone, they are consistent with the intercalation geometry observed in the crystal structure. Molecular-dynamics (MD) trajectories starting from the 1:2 complexes observed in the crystal showed that although the thymines flanking the d(AGT) core are rather flexible and the G-T pairing is not permanently preserved, both strands remain bound to the actinomycin by strong interactions between it and the guanines between which it is sandwiched. Similar strong binding (hemi-intercalation) of the actinomycin to a single guanine was observed in the MD trajectories of a 1:1 complex. The dominant interaction is between the antibiotic and guanine, but the complexes are stabilized further by promiscuous base-pairing.

Antibiotics, Antineoplastic↗
PubMed2004

Succinate complex crystal structures of the alpha-ketoglutarate-dependent dioxygenase AtsK: steric aspects of enzyme self-hydroxylation.

The alkylsulfatase AtsK from Pseudomonas putida S-313 is a member of the non-heme iron(II)-alpha-ketoglutarate-dependent dioxygenase superfamily. In the initial step of their catalytic cycle, enzymes belonging to this widespread and versatile family coordinate molecular oxygen to the iron center in the active site. The subsequent decarboxylation of the cosubstrate alpha-ketoglutarate yields carbon dioxide, succinate, and a highly reactive ferryl (IV) species, which is required for substrate oxidation via a complex mechanism involving the transfer of radical species. Non-productive activation of oxygen may lead to harmful side reactions; therefore, such enzymes need an effective built-in protection mechanism. One of the ways of controlling undesired side reactions is the self-hydroxylation of an aromatic side chain, which leads to an irreversibly inactivated species. Here we describe the crystal structure of the alkylsulfatase AtsK in complexes with succinate and with Fe(II)/succinate. In the crystal structure of the AtsK-Fe(II)-succinate complex, the side chain of Tyr(168) is co-ordinated to the iron, suggesting that Tyr(168) is the target of enzyme self-hydroxylation. This is the first structural study of an Fe(II)-alpha-ketoglutarate-dependent dioxygenase that presents an aromatic side chain coordinated to the metal center, thus allowing structural insight into this protective mechanism of enzyme self-inactivation.

Bacterial Proteins↗
PubMed2004

Solution and structure of an alternating D,L-peptide.

The crystal structure of H-(L-Tyr-D-Tyr)(4)-L-Lys-OH has been determined to 1.3 A resolution. The D,L-alternating peptide crystallizes in the tetragonal system, space group P4(3)2(1)2, with unit-cell parameters a = b = 27.99 (3), c = 78.93 (8) A. The crystals contain two molecules in the asymmetric unit that form a double-stranded right-handed antiparallel beta-helix. The structure has been solved by SIRAS using a crystal soaked in an iodide-containing solution for 1 min. The programs SHELXD and SHELXE were used to determine the iodide substructure and also the experimental electron-density map. Using the coordinates of known D,L-peptides deposited in the PDB, several attempts were made to solve the structure by molecular-replacement techniques. Although the backbone of the MR model selected shows great similarity and was used to trace the actual peptide structure in the map, it was not possible to obtain the correct solution before the experimental phases became available. The correct fragment orientations are easily determined, but the same does not apply to the translation search. Nevertheless, insights into fragment search and expansion were gained from the tests described in this paper. The correlation coefficient calculated with the resolution shell of data around 2.4 A, a distance corresponding to most 1-3 interatomic vectors, is a particularly good discriminator of correct orientations in the rotation search of small fragments.

Crystallography, X-Ray↗
PubMed2004

A cubic arrangement of DNA double helices based on nickel-guanine interactions.

DNA oligonucleotides can be used in order to assemble highly structured materials. Oligonucleotides with sticky ends can form long linear structures, whereas branching is required to form two- and three-dimensional nanostructures. In this paper, we show that when Ni(2+) is attached to the N7 atom of guanine, it can also act as a branching point. Thus, we have found that the heptanucleotide d(GAATTCG) can assemble into long linear duplex structures, which cross in space to generate a cubic structure. The three-dimensional arrays are stabilized by phosphate-Ni(2+)-guanine interactions. For the first time, the crystallization of a B form DNA oligonucleotide in a cubic system is reported, space group I23. Large solvent cavities are found among the DNA duplexes.

Base Pairing↗
PubMed2004

Inclusion complexes of V-amylose with undecanoic acid and dodecanol at atomic resolution: X-ray structures with cycloamylose containing 26 D-glucoses (cyclohexaicosaose) as host.

Crystal structures are reported of cycloamylose containing 26 D-glucose residues (CA26, cyclohexaicosaose, C156H260O130) in complexes with undecanoic acid (CA26 x 2C10H21COOH x 34.95 H2O, orthorhombic P2(1)2(1)2(1), one CA26 and two bound undecanoic acids F1 and F2 in the asymmetric unit, resolution 0.95 angstroms) and with dodecanol ((CA26)(0.5) x C12H25OH x 32.0H2O, monoclinic C2, half a CA26 binding one dodecanol, A, in the asymmetric unit, resolution 1.0 angstroms). The macrocycle of CA26 is folded like the figure '8' into two 10 D-glucoses long left-handed V-amylose helices forming approximately 5A wide V-channels that are occupied by undecanoic acid (F1, F2) or dodecanol (A) as guest molecules. The functional head groups of the guests near the O(6) ends of the V-channels are hydrogen bonded with d-glucose O(6)n-H; the aliphatic termini beyond C(9) protrude from the O(2), O(3) ends. Parts of the aliphatic chains enclosed in the V-channels are all-trans except for one torsion angle each (approximately 130 degrees ) in undecanoic acid molecules F1 and F2. There are several (guest)C-H...O hydrogen bonds to O(4) and O(6) of CA26 in both complexes, and H...H van der Waals interactions with d-glucose C(3)-H and C(5)-H dominate. C(5)-H determine the position of the aliphatic chains of undecanoic acid F1 and of dodecanol A in contrast to F2 where both C(3)-H and C(5)-H contribute equally, probably because the V-channel is narrower than in F1 and in dodecanol. Complexes of polymeric V-amylose with fatty acids and alcohols studied by X-ray fiber diffraction could not provide the here described high resolution.

Amylose↗
PubMed2004

Crystal structure of the alkylsulfatase AtsK: insights into the catalytic mechanism of the Fe(II) alpha-ketoglutarate-dependent dioxygenase superfamily.

The alkylsulfatase AtsK from Pseudomonas putida S-313 belongs to the widespread and versatile non-heme iron(II) alpha-ketoglutarate-dependent dioxygenase superfamily and catalyzes the oxygenolytic cleavage of a variety of different alkyl sulfate esters to the corresponding aldehyde and sulfate. The enzyme is only expressed under sulfur starvation conditions, providing a selective advantage for bacterial growth in soils and rhizosphere. Here we describe the crystal structure of AtsK in the apo form and in three complexes: with the cosubstrate alpha-ketoglutarate, with alpha-ketoglutarate and iron, and finally with alpha-ketoglutarate, iron, and an alkyl sulfate ester used as substrate in catalytic studies. The overall fold of the enzyme is closely related to that of the taurine/alpha-ketoglutarate dioxygenase TauD and is similar to the fold observed for other members of the enzyme superfamily. From comparison of these structures with the crystal structure of AtsK and its complexes, we propose a general mechanism for the catalytic cycle of the alpha-ketoglutarate-dependent dioxygenase superfamily.

Amino Acid Motifs↗
PubMed2002

Locating the anomalous scatterer substructures in halide and sulfur phasing.

Improved data quality now makes it feasible to exploit the weak anomalous signal derived only from the sulfurs inherent to the protein or in particular from halide ions incorporated by soaking. The latter technique requires the location of a high number of partially occupied halide sites. This number appears to be roughly proportional to the exposed protein surface. This paper explores the application of dual-space ab initio methods as implemented in the program SHELXD to the location of substructures of sulfur in SAD experiments, bromide in SAD and MAD experiments and iodide using SAD and SIRAS to determine the anomalous-atom substructure. Sets of atoms consistent with the Patterson function were generated as a starting point for the dual-space recycling procedure in SHELXD. The substructure is then expanded to the full structure by maximum-likelihood phasing with SHARP and density modification with the program DM. Success in the location of the substructures and subsequent phasing depends critically on the quality of the data and on the extent of the anomalous signal. This varies with each crystal and soak, but for the same crystal the significance of the anomalous signal was found to be highly sensitive to the redundancy of the intensity measurements, which in some cases made all the difference. This is illustrated by the determination of the previously unknown structure of repeat 11 of the human mannose-6-phosphate/insulin-like growth factor II receptor (Man6P/IGFII-receptor), with 310 amino acids in the asymmetric unit, which was phased by soaking the crystals in a cryoprotectant solution containing halide anions.

Amino Acid Sequence↗
PubMed2002

Synthesis and structures of [[HC(CMeNAr)(2)]Ge(S)X] (Ar = 2,6-iPr(2)C(6)H(3), X = F, Cl, Me): structurally characterized examples with a formal double bond between group 14 and 16 elements bearing a halide.

Treatment of [{HC(CMeNAr)2}GeX] (Ar = 2,6-iPr2C6H3, X = Cl (1), F (2)), with elemental sulfur at room temperature smoothly afforded the [{HC(CMeNAr)2}Ge(S)X] (X = Cl (3), F (4)). Compound 4 can also be obtained from 3 with the fluorination reagent Me3SnF. Reaction of 3 with MeLi led to the formation of [{HC(CMeNAr)2}Ge(S)Me] (5). Single-crystal X-ray structural analyses indicate compounds 3-5 are monomeric. The germanium centers adopt four coordinated sites and reside in distorted tetrahedral environment. Compounds 3 and 4 are structurally characterized examples with a formal double bond between group 14 and 16 elements bearing a halide.

Journal Article↗
PubMed2002

Defective oligomerization of arylsulfatase a as a cause of its instability in lysosomes and metachromatic leukodystrophy.

In one of the most common mutations causing metachromatic leukodystrophy, the P426L-allele of arylsulfatase A (ASA), the deficiency of ASA results from its instability in lysosomes. Inhibition of lysosomal cysteine proteinases protects the P426L-ASA and restores the sulfatide catabolism in fibroblasts of the patients. P426L-ASA, but not wild type ASA, was cleaved by purified cathepsin L at threonine 421 yielding 54- and 9-kDa fragments. X-ray crystallography at 2.5-A resolution showed that cleavage is not due to a difference in the protein fold that would expose the peptide bond following threonine 421 to proteases. Octamerization, which depends on protonation of Glu-424, was impaired for P426L-ASA. The mutation lowers the pH for the octamer/dimer equilibrium by 0.6 pH units from pH 5.8 to 5.2. A second oligomerization mutant (ASA-A464R) was generated that failed to octamerize even at pH 4.8. A464R-ASA was degraded in lysosomes to catalytically active 54-kDa intermediate. In cathepsin L-deficient fibroblasts, degradation of P426L-ASA and A464R-ASA to the 54-kDa fragment was reduced, while further degradation was blocked. This indicates that defective oligomerization of ASA allows degradation of ASA to a catalytically active 54-kDa intermediate by lysosomal cysteine proteinases, including cathepsin L. Further degradation of the 54-kDa intermediate critically depends on cathepsin L and is modified by the structure of the 9-kDa cleavage product.

Amino Acid Sequence↗
PubMed2002

Structure and biosynthesis of cetoniacytone A, a cytotoxic aminocarba sugar produced by an endosymbiontic Actinomyces.

Cetoniacytone A (1) and some related minor components (2, 6, 7) were produced by Actinomyces sp. (strain Lu 9419), which was isolated from the intestines of a rose chafer (Cetonia aureata). The structures of the novel metabolites were established by detailed spectroscopic analysis. The absolute configuration of 1 was determined by X-ray analysis and derivatisation with chiral acids. 1 exhibits a significant cytotoxicity against selected tumor cell lines. The biosynthesis of 1 was studied by feeding 13C labelled precursors. The results suggest that the characteristic p-C7N skeleton of the aminocarba sugar is formed via the pentose phosphate pathway by cyclisation of a heptulose phosphate intermediate.

Actinomyces↗
PubMed1998

Gallophosphonates Containing Alkali Metal Ions. 2.(1) Synthesis and Structure of Gallophosphonates Incorporating Na(+) and K(+) Ions.

The reactions between t-BuP(O)(OH)(2) and equimolar quantities of MGaMe(4) (M = Na, K) yield ionic and alkali metal containing molecular gallophosphonates [Na(4)(&mgr;(2)-OH(2))(2)(THF)(2)][(Me(2)GaO(3)PBu-t)(2)](2).2THF (2) and [K(THF)(6)][K(5)(THF)(2){(Me(2)GaO(3)PBu-t)(2)}(3)] (3), respectively. Compounds 2 and 3are soluble in common organic solvents and have been characterized by means of analytical and spectroscopic techniques, as well as by single-crystal X-ray diffraction studies. These compounds represent the rare examples of molecular ionic phosphonate cages which contain coordinated Na(+) or K(+) ions. Compound 2 is constructed from two eight-membered Ga(2)O(4)P(2) gallium phosphonate rings which sandwich a central Na(4)(H(2)O)(2) unit. In the case of 3, three eight-membered Ga(2)O(4)P(2) gallium phosphonate units envelope an aggregated K(5) core which exists in the form of a trigonal-bipyramidal polyhedron. The Na(+) and K(+) ions in 2 and 3 are also coordinated by the endocyclic oxygen atoms of the eight-membered gallophosphonate crowns, apart from the regular exocyclic P-O coordination. Unlike the lithium gallophosphonate [Li(4)(THF)(4)][{(MeGaO(3)PBu-t)(3)(&mgr;(3)-O(2))}(2)] (1), compounds 2 and 3 do not undergo any clean cage conversion reaction in the presence of 15-crown-5 and 18-crown-6, respectively.

Journal Article↗