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PubMed2005

Modelling of HLA-DQ2 and its interaction with gluten peptides to explain molecular recognition in celiac disease.

Celiac disease (CD) is sustained by abnormal intestinal mucosal T-cell response to gluten and it is strongly associated with HLA class II molecules encoded by DQA1*0501/DQB1*02 (DQ2) or DQA1*03/DQB1*0302 (DQ8). The in vitro stimulatory activity of gliadin increases after treatment with tissue transglutaminase (tTG) which catalyses the deamidation of specific residues of glutamine to glutamate that can serve as anchors for binding to DQ2 as well as to DQ8 molecules. We modelled the three-dimensional structure of the DQ2 dimer protein, the most frequent in celiac patients, by using a homology modelling strategy, and deposited the model in the Protein Data Bank (PDB). Then, we simulated the interactions of DQ2 with different gluten peptides and the deamidation of specific peptide glutamines in the known p4, p6, p7 and p9 anchor positions, as well as in p1 and p5 positions, and other substitutions for which experimental effects on binding are available by previous experimental studies. By evaluating the energy of interaction and the H-bond interactions, we were able to distinguish what substitutions improve the interaction peptide-DQ2, in agreement with previously published experimental data. By analysing the peptide-DQ2 complex at the atom level, we observed that these glutamate side chains can interact with specific positively charged amino acids of DQ2, absent in other HLA alleles not related to celiac disease. The simulation was also extended to other peptides, related to celiac disease but for which no experimental data exists about the effects of glutamine deamidation. Our results give an interpretation at the molecular level of previously reported binding experimental data and open a new window to gain further insights about peptide recognition in celiac disease.

Alleles↗
PubMed2005

Improving on nature: antibiotics that target the ribosome.

Antibiotic resistance, along with the resolution of antibiotic-ribosomal subunit complexes at the atomic level, has provided new insights into modifications of clinically relevant antimicrobials that target the ribosome. Modifications to the aminoglycoside or negamycin scaffolds have been reported in the past, but few derivatives appear to be greatly improved compared to their parent compound. Computational and/or traditional screening efforts have yielded novel compounds that bind to the decoding site of the small (30S) ribosomal subunit; naphthyridones appear to bind only in the presence of poly(U) and tRNA(Phe), whereas quinolines bind in a similar manner to aminoglycosides. Streptogramin B analogs were designed that have an amide replacement of the labile ester bond. The resultant molecules were not substrates for the inactivating lyase, but were no longer inhibitors of translation. The synthesis of 16-membered macrolides that are modified at the C6 position with peptidyl moieties as well as conjugates of chloramphenicol to either nucleotide groups or pyrene have been described, but no antibacterial activity has been reported. X-ray crystal structures are now available that can be used to improve on natural or synthetic antibiotics that bind to either the 30S or the 50S ribosomal subunit.

Amino Acids, Diamino↗
PubMed2006

Spectral characterization of novel ternary zinc(II) complexes containing 1,10-phenanthroline and Schiff bases derived from amino acids and salicylaldehyde-5-sulfonates.

A series of new ternary zinc(II) complexes [Zn(L(1-10))(phen)], where phen is 1,10-phenanthroline and H(2)L(1-10)=tridentate Schiff base ligands derived from the condensation of amino acids (glycine, l-phenylalanine, l-valine, l-alanine, and l-leucine) and salicylaldehyde-5-sulfonates (sodium salicylaldehyde-5-sulfonate and sodium 3-methoxy-salicylaldehyde-5-sulfonate), have been synthesized. The complexes were characterized by elemental analysis, IR, UV-vis, (1)H NMR, and (13)C NMR spectra. The IR spectra of the complexes showed large differences between nu(as)(COO) and nu(s)(COO), Deltanu (nu(as)(COO)-nu(s)(COO)) of 191-225 cm(-1), indicating a monodentate coordination of the carboxylate group. Spectral data showed that in these ternary complexes the zinc atom is coordinated with the Schiff base ligand acts as a tridentate ONO moiety, coordinating to the metal through its phenolic oxygen, imine nitrogen, and carboxyl oxygen, and also with the neutral planar chelating ligand, 1,10-phenanthroline, coordinating through nitrogens.

Aldehydes↗
PubMed2001

Sample treatment in chromatography-based speciation of organometallic pollutants.

Speciation analysis is nowadays performed routinely in many laboratories to control the quality of the environment, food and health. Chemical speciation analyses generally include the study of different oxidation state of elements or individual organometallic compounds. The determination of the different chemical forms of elements is still an analytical challenge, since they are often unstable and concentrations in different matrices of interest are in the microg l(-1) or even in the ng l(-1) range (e.g., estuarine waters) or ng g(-1) in sediments and biological tissues. For this reason, sensitive and selective analytical atomic techniques are being used as available detectors for speciation, generally coupled with chromatography for the time-resolved introduction of analytes into the atomic spectrometer. The complexity of these instrumental couplings has a straightforward consequence on the duration of the analysis, but sample preparation to separate and transfer the chemical species present in the sample into a solution to be accepted readily by a chromatographic column is the more critical step of total analysis, and demands considerable operator skills and time cost. Traditionally, liquid-liquid extraction has been employed for sample treatment with serious disadvantages, such as consumption, disposal and long-term exposure to organic solvent. In addition, they are usually cumbersome and time-consuming. Therefore, the introduction of new reagents such as sodium tetraethylborate for the simultaneous derivatization of several elements has been proposed. Other possibilities are based in the implementation of techniques for efficient and accelerated isolation of species from the sample matrix. This is the case for microwave-assisted extraction, solid-phase extraction and microextraction, supercritical fluid extraction or pressurized liquid extraction, which offer new possibilities in species treatment, and the advantages of a drastic reduction of the extraction time and the embodiment into on-line flow analysis systems. This new generation of treatment techniques constitutes a good choice as fast extraction methods for feasible species-selective analysis of organometallic compounds under the picogram level, that can be used for national regulatory agencies, governmental and industrial quality control laboratories, and consequently, for manufacturers of analytical instrumentation.

Chromatography↗
PubMed2003

Aptamer affinity chromatography for rapid assay of adenosine in microdialysis samples collected in vivo.

An anti-adenosine aptamer was evaluated as a stationary phase in packed capillary liquid chromatography. Using an aqueous mobile phase containing 20 mM Mg2+, adenosine was strongly retained on the column. A gradient of increasing Ni2+ (to 18 mM), which is presumed to complex with nitrogen atoms in adenosine involved in binding to the aptamer, eluted adenosine in a narrow zone. Up to 6 microl of 1.2 microM adenosine could be injected onto the 150-microm I.D. x 7 cm long column without loss of adenosine. With UV absorbance detection, the detection limit was 30 nM or 120 fmol (4 microl injected). Samples could be repetitively injected with 4.6% relative standard deviation in peak area. Columns were stable to at least 200 injections. The adenosine assay, which required no sample preparation, was used on microdialysis samples collected from the somatosensory cortex of chloral hydrate anesthetized rats. Total analysis times were short enough that dialysate samples could be injected every 5 min. Basal dialysate concentrations of adenosine stabilized at 87+/-10 nM (n=5) with the probe operated at 0.6 microl/min.

Adenosine↗
PubMed2002

The inherent properties of DNA four-way junctions: comparing the crystal structures of holliday junctions.

Holliday junctions are four-stranded DNA complexes that are formed during recombination and related DNA repair events. Much work has focused on the overall structure and properties of four-way junctions in solution, but we are just now beginning to understand these complexes at the atomic level. The crystal structures of two all-DNA Holliday junctions have been determined recently from the sequences d(CCGGGACCGG) and d(CCGGTACCGG). A detailed comparison of the two structures helps to distinguish distortions of the DNA conformation that are inherent to the cross-overs of the junctions in this crystal system from those that are consequences of the mismatched dG.dA base-pair in the d(CCGGGACCGG) structure. This analysis shows that the junction itself perturbs the sequence-dependent conformational features of the B-DNA duplexes and the associated patterns of hydration in the major and minor grooves only minimally. This supports the idea that a DNA four-way junction can be assembled at relatively low energetic cost. Both structures show a concerted rotation of the adjacent duplex arms relative to B-DNA, and this is discussed in terms of the conserved interactions between the duplexes at the junctions and further down the helical arms. The interactions distant from the strand cross-overs of the junction appear to be significant in defining its macroscopic properties, including the angle relating the stacked duplexes across the junction.

Base Pair Mismatch↗
PubMed2002

Determination of lignocaine and amprolium in pharmaceutical formulations using AAS.

The ion-associate complexes of lignocaine hydrochloride (Lig.Cl) with ammonium reineckate (Rk) or sodium cobaltithiocyanate, and that of amprolium hydrochloride (Amp.Cl) with ammonium reineckate, have been prepared. The precipitated ion-associates were subjected to elemental analyses, infrared and nuclear magnetic resonance spectroscopy and determination of the metal content for elucidation of their structures. The solubilities of the solid ion-associate complexes have been studied and their solubility products were determined at different temperatures at the optimum pH for their quantitative precipitation. The thermodynamic parameters DeltaH, DeltaG and DeltaS for the dissolution of the ion-associate complexes were calculated. These ion-associate complexes have been used for the quantitative determination of the above mentioned drugs by precipitating them with an excess of the inorganic metal complex ions and determining the excess metal complex ions using atomic absorption spectrometry. The method was applied for the determination of the above drugs in pure solution and pharmaceutical preparations. 0.135-135.4 and 0.158-157.6 mg of lignocaine and amprolium, respectively, can be determined with mean relative standard deviations (R.S.D.) 0.92-1.20% and recovery values of 99.18+/-0.48 to 100.12+/-0.34% indicating high precision and accuracy.

Amprolium↗
PubMed2000

The surface structure of catalysts activated with hydrogen donors as elucidated by multinuclear solid-state NMR.

1H, 27Al and 31P MAS, and 13C and 29Si CP/MAS NMR spectroscopies, were used to characterize catalysts of Pd supported on various solids including SiO2, AlPO4 and Mg3(PO4)2 that were activated with the chiral hydrogen-donor limonene. The above-mentioned techniques were used to check for the formation of an organopalladium complex between Pd2+ atoms and the olefin bonds in the limonene molecule on the catalyst surface. The results are compared with those obtained for catalysts activated in a hydrogen stream.

Aluminum↗
PubMed1999

Free and protein-bound carbohydrate structures.

Several areas of research in the study of the structure and dynamics of free and protein-bound carbohydrates have experienced considerable advances during the past year. These include the application of state-of-the-art NMR techniques using (13)C-labeled sugars to obtain conformational information, the full structural characterization of several saccharides that either form part of glycoproteins or form noncovalent complexes, both in solution and in the solid state, the description of several enzyme-carbohydrate complexes at the atomic level and last, but not least, the development and analysis of calculation protocols to predict the dynamical and conformational behavior of oligosaccharides.

Carbohydrate Conformation↗
PubMed1997

Selectivity of F8-actinomycin D for RNA:DNA hybrids and its anti-leukemia activity.

Although many compounds have been found that bind to DNA in various ways and exhibit various biological activities, few compounds that specifically bind to RNA or RNA:DNA hybrids are known, even though such compounds are expected to have important biological properties. For example, one characteristic function of the retroviruses, which is generally not found in eukaryotic cells, is the production of an RNA:DNA hybrid in the viral replication phase. If an agent is designed to bind only to an RNA:DNA hybrid, and not to DNA or to RNA, such an agent might be able to inhibit specifically the RNase H activity of retroviral reverse transcriptase, and therefore suppress viral replication. Actinomycin D is known to bind to double-stranded DNA, but not to RNA, because steric hindrance between the 2-amino group of the phenoxazone ring and the 2'-hydroxyl group of RNA prevents intercalation of the compound. However, if the > C-H moiety at the 8-position of the phenoxazone ring is replaced by a > C-F, a possible hydrogen-bond acceptor, this analogue (8-fluoro-actinomycin D, F8AMD) might be able to bind intercalatively to an RNA:DNA hybrid by forming an additional hydrogen bond between F8 and the 2'-hydroxyl group of the guanosine ribose. To test this hypothesis, the crystal structure of d(GAAGCTTC)2-F8AMD has been determined at 3.0 A resolution. Based on this crystal structure, a model in which F8AMD binds into the hybrid r(GAAGCUUC):d(GAAGCTTC) has been built using molecular mechanics and dynamic methods. These structural studies indicate that F8AMD binds intercalatively to a B-form double-stranded DNA whereas the drug intercalates into an RNA:DNA hybrid taking an A-form conformation. In the RNA:DNA hybrid complex, the F8 atom is located so as to be able to interact to an O2' hydroxyl group with either an O-H...F hydrogen bond or H+...F- electrostatic interaction. This interaction might stabilize the F8AMD molecule in the RNA:DNA hybrid. A binding study indicates that both actinomycin D (AMD) and F8AMD bind intercalatively not only to double-stranded DNAs, but also to RNA:DNA hybrids. Although the overall binding capacity of F8AMD (k = 4.5 x 10(5) M-1) is reduced slightly in comparison with AMD itself (k = 1.8 x 10(6) M-1), F8AMD tends to bind relatively more favorably than AMD to the RNA:DNA hybrids. The drugs' effects on RNA synthesis in HeLa cells indicates that the binding capacities of AMD and F8AMD correlates strongly to their RNA synthesis inhibitory activities. F8AMD required a concentration of 78 nM to inhibit RNA polymerase activity in HeLa cells by 50%, whereas AMD reached the same inhibitory level at 30 nM. Surprisingly, F8AMD exhibits unique selectivity against leukemia cells as does another C8-derivatized AMD analogue, N8AMD. F8AMD inhibits 50% of leukemia cell growth at less than 1.0 nM whereas 10- to 130-fold-higher drug concentrations are required to inhibit the growth of other tumor cell lines by 50%. The GI50 value of F8AMD for leukemia cells is the lowest among the GI50 values for all other AMD derivatives tested. By contrast, AMD is quite potent and kills most cells at less than 50 nM concentration, but it does not show any selectivity for certain cell lines. This indicates that AMD should have very limited use as an antitumor agent. It is difficult to rationalize why F8AMD and N8AMD show such strong selectivity against leukemia cells. However, this study and our previous study (J. Am. Chem. Soc. 1994, 116, 7971) indicated that F8AMD and N8AMD tended to bind more favorably to RNA:DNA hybrids. Thus, the unique antileukemia selectivity shown by F8AMD and N8AMD might be used by the agents binding to RNA:DNA hybrids rather than to double-stranded DNA.

Antineoplastic Agents↗
PubMed2003

Analysis of underivatized amino acids and their D/L-enantiomers by sheathless capillary electrophoresis/electrospray ionization mass spectrometry.

Capillary electrophoresis/electrospray ionization-mass spectrometry (CE/ESI-MS) was applied to the analysis of underivatized amino acids and the separation of their D/L-enantiomers. Under full-scan mode, all standard protein amino acids were separated and detected at low-femtomole levels using a 130-cm-long, 20-microm-i.d., 150-microm-o.d. underivatized fused-silica capillary with 1 M formic acid as the background electrolyte. The CE/ESI-MS technique was also applied to the separation of L-arginine from L-canavanine (a close analogue of arginine where the terminal methylene linked to the guanidine group of arginine is replaced by an oxygen atom) in a complex mixture containing all standard protein amino acids. The utility of CE/ESI-MS in the analysis of real-world samples was demonstrated by the identification of two metabolic diseases (PKU and tyrosinemia) through blood analysis with minimal sample preparation. In addition, the on-line separation of 11 underivatized L-amino acids from their D-enantiomers was achieved by using a 30 mM solution of (+)-(18-crown-6)-2,3,11,12-tetracarboxylic acid as the background electrolyte.

Amino Acids↗
PubMed2005

Crystal structure of Escherichia coli penicillin-binding protein 5 bound to a tripeptide boronic acid inhibitor: a role for Ser-110 in deacylation.

Penicillin-binding protein 5 (PBP 5) from Escherichia coli is a well-characterized d-alanine carboxypeptidase that serves as a prototypical enzyme to elucidate the structure, function, and catalytic mechanism of PBPs. A comprehensive understanding of the catalytic mechanism underlying d-alanine carboxypeptidation and antibiotic binding has proven elusive. In this study, we report the crystal structure at 1.6 A resolution of PBP 5 in complex with a substrate-like peptide boronic acid, which was designed to resemble the transition-state intermediate during the deacylation step of the enzyme-catalyzed reaction with peptide substrates. In the structure of the complex, the boron atom is covalently attached to Ser-44, which in turn is within hydrogen-bonding distance to Lys-47. This arrangement further supports the assignment of Lys-47 as the general base that activates Ser-44 during acylation. One of the two hydroxyls in the boronyl center (O2) is held by the oxyanion hole comprising the amides of Ser-44 and His-216, while the other hydroxyl (O3), which is analogous to the nucleophilic water for hydrolysis of the acyl-enzyme intermediate, is solvated by a water molecule that bridges to Ser-110. Lys-47 is not well-positioned to act as the catalytic base in the deacylation reaction. Instead, these data suggest a mechanism of catalysis for deacylation that uses a hydrogen-bonding network, involving Lys-213, Ser-110, and a bridging water molecule, to polarize the hydrolytic water molecule.

Acylation↗
PubMed1996

Metal and pH dependence of heptapeptide catalysis by human matrilysin.

Human matrilysin devoid of its propeptide is expressed in Escherichia coli and purified to homogeneity by heparin chromatography after refolding of the guanidine hydrochloride solubilized protein. Matrilysin autolytically removes its N-terminal tripeptide Met-Tyr-Ser during the refolding process. The enzyme contains 1.91 +/- 0.08 zinc atoms/mol of protein and retains full activity when stored several months at 4 degrees C. It hydrolyzes the fluorescent substrate Dns-PLALWAR at the Ala-Leu bond with a kcat of 3.1 s-1 and K(m) of 1.8 x 10(-5) M at pH 7.5, 37 degrees C, values closely similar to those for the matrilysin produced by activation of the Chinese hamster ovary and E. coli-expressed promatrilysin. The properties of this form of matrilysin demonstrate that the propeptide is not essential for proper folding or stability of the enzyme but likely determines the N-terminal amino acid of the mature enzyme. The pH dependence of kcat/K(m) for Dns-PLALWAR shows that matrilysin has a broad pH optimum (5.0-9.0) and the pKa values obtained are 4.3 and 9.6 at 25 degrees C. The activity is inhibited by several metal binding agents including 1, 10-phenanthroline, OP, but not by the nonchelating isomer, 1,7-phenanthroline. OP inhibits instantaneously by likely forming a transient ternary enzyme.metal.chelator complex. The zinc atom is then removed from the protein in a time-dependent manner. In agreement with the kinetic studies, dialysis in the presence of OP and CaCl2 removes only the catalytic zinc atom. The monozinc enzyme can be reactivated to 90%, 56%, 27%, and 17% of the native activity by addition of zinc, manganese, nickel, and cobalt, respectively. Cadmium, on the other hand, forms an inactive Cd/Zn hybrid. The differences in the chelator accessibility properties of the two zinc sites can thus be exploited to yield metallohybrids of matrilysin.

Amino Acid Sequence↗
PubMed1999

Reactivity of a Vanadium(III) Center over an Oxo Surface Modeled by Calix[4]arene.

Metalation of the monomethoxycalix[4]arene [p-Bu(t)-calix[4]-(OMe)(OH)(3)], 1, using [VMes(3).THF] led to the coordinatively unsaturated V(III)-d(2) fragment [p-Bu(t)-calix[4]-(OMe)(O)(3)V] collapsing to the dimer [{&mgr;-p-Bu(t)-calix[4]-(OMe)(O)(3)}V](2), 2, where each calix[4]arene shares a bridging oxygen donor atom. The dimeric complexity remains intact in the reaction with Bu(t)NC and PhCN, which bond to the metal inside the cavity of the calix[4]arene leading to [{&mgr;-p-Bu(t)-calix[4]-(OMe)(O)(3)}(V-L)](2) [L = Bu(t)NC, 3; L = PhCN, 4]. In contrast, the reaction of 2 with pyridine and 4,4'-dipyridyl cleaves the dimeric form into a monomeric complex [{&mgr;-p-Bu(t)-calix[4]-(OMe)(O)(3)}V(Py)], 5, or to a different dimer containing a bridging 4,4'-dipyridyl, [{p-Bu(t)-calix[4]-(OMe)(O)(3)}(2)V(2)(&mgr;-4,4'-dipyridyl)], 6. Complex 2 undergoes one electron oxidation by I(2) to the corresponding vanadium(IV) dimer [{&mgr;-p-Bu(t)-calix[4]-(O)(4)}(2)V(2)], 7, and by p-benzoquinone to [{p-Bu(t)-calix[4]-(OMe)(O)(3)}V](2)(&mgr;-C(6)H(4)O(2)), 8. A two-electron oxidation of the V(III)-d(2) to vanadium(V) derivatives has been achieved using styrene epoxide and diphenyldiazomethane. In the former case the oxovanadium(V) derivative was obtained [p-Bu(t)-calix[4]-(OMe)(O)(3)V=O], 9, and in the latter case a metallahydrazone complex [p-Bu(t)-calix[4]-(OMe)(O)(3)V&tbd1;N-N=CPh(2)], 10. The dimeric d(2) and d(1) derivatives display significant antiferromagnetic couplings between the two metal centers, namely as follows: 2, J = -74.6 cm(-)(1); 3, J = -17 cm(-)(1); 4, J = -33.4 cm(-)(1); 7, J = -131.7 cm(-)(1). The extended Hückel calculations gave an appropriate picture of the two-electron reduction of the diphenyldiazomethane substrate. The proposed structures have been supported by X-ray analyses on 3, 7, 9, and 10.

Journal Article↗
PubMed2002

Hydride donor abilities and bond dissociation free energies of transition metal formyl complexes.

The hydride complex [Pt(dmpe)2H]+ (dmpe = 1,2-bis(dimethylphosphino)ethane) reversibly transfers H- to the rhenium carbonyl complex [CpRe(PMe3)(NO)(CO)]+, giving the formyl CpRe(PMe3)(NO)(CHO). From the equilibrium constant for the hydride transfer (16.2), the DeltaGdegrees for the reaction was determined (-1.6 kcal/mol), as was the hydride-donating ability of the formyl (44.1 kcal/mol). The hydride-donating ability, DeltaGdegrees(H-), is defined as the energy required to release the hydride ion into solution by the formyl complex [i.e. M(CHO) right arrow M(CO)+ + H-]. Subsequently, the hydride-donating ability of a series of formyl complexes was determined, ranging from 44 to 55 kcal/mol. With use of this information, two rhenium carbonyl complexes, [CpRe(NO)(CO)2]+ and [Cp*Re(NO)(CO)2]+, were hydrogenated to formyls, employing [Pt(dmpp)2]2+ and Proton-Sponge. Finally, the E(1/2)(I/0) values for five rhenium carbonyl complexes were measured by cyclic voltammetry. Combined with the known DeltaGdegrees(H-) values for the complexes, the hydrogen atom donating abilities could be determined. These values were all found to be approximately 50 kcal/mol.

Journal Article↗
PubMed2005

Formation of highly stabilized intramolecular dimer radical cation and pi-complex of [3n]cyclophanes (n = 3, 5, 6) during pulse radiolysis.

Formation of radical cation and charge-transfer complex of [3n]cyclophanes (n = 3, 5, 6) was investigated by transient absorption spectroscopy during pulse radiolysis. Radical cations of [3n]cyclophanes showed the charge resonance band around 700 nm which exhibited a blue-shift as the number of trimethylene bridges increased, indicating formation of highly stabilized intramolecular dimer radical cation of [3n]cyclophanes. The absorption peak of the charge-transfer complex with chlorine atom also showed the shift in accord with the oxidation potential of [3n]cyclophanes.

Journal Article↗
PubMed2006

Transannular distance dependence of stabilization energy of the intramolecular dimer radical cation of cyclophanes.

The intramolecular dimer radical cation and charge-transfer complex of various cyclophanes were investigated by using pulse radiolysis measurements. The charge resonance band due to the dimer radical cation of cyclophanes appeared in the near-IR region, which showed a blue-shift as the distance between the two benzene rings of cyclophane decreased. The stabilization energy of the dimer radical cation, which was estimated from the peak position of the charge resonance band, was explained by the exchange interaction, while the substituent effect was small. The absorption peak of the charge-transfer complex with chlorine atom also showed the shift in accordance with the oxidation potential of cyclophanes.

Cations↗