Chemical and conformational study of the interactions involved in mycotoxin complexation with beta-D-glucans

In a previous paper we reported that beta-D-glucans isolated from Saccharomyces cerevisiae could adsorb zearalenone, reduce its bioavailability in the digestive tract, and protect animals against its adverse effects. We have now investigated, in vitro, the kinetics of the interaction between other mycotoxins and beta-D-glucans from several sources at three pH values found along the digestive tract (3.0, 6.0, and 8.0). Acid and neutral conditions gave the highest affinity rates for aflatoxins B1 > deoxynivalenol > ochratoxin A and involved both the (1 --> 3)-beta-D-glucans and the (1 --> 6)-beta-D-glucans. Alkaline conditions, owing to their destructuring action on glucans, were favorable only for the adsorption of patulin. Using molecular mechanics, we found that hydroxyl, ketone, and lactone groups are involved in the formation of both hydrogen bonds and van der Waals interactions between aflatoxins B1, deoxynivalenol and patulin, and beta-D-glucans. Differences in the binding capacity of the mycotoxins are due to their specific physical and chemical characteristics.     

Solution and conformational properties of wheat beta-D-glucans studied by light scattering and viscometry

The solution properties of wheat beta-glucan were investigated by light scattering and viscometric methods. The hydrodynamic radius (R(h)), weight average molecular weight (M(w)), radius of gyration (R(g)), and the second virial coefficient (A(2)) of wheat beta-glucan were determined by both dynamic and static light scattering methods, whereas the critical concentrations (c) of the solution were derived from [eta] via viscometric method. The structure sensitive parameters, rho (1.52-1.62), the conformation parameter nu (0.62), and the Mark-Houwink-Sakurada exponents alpha (0.78) confirmed the random coil conformation of wheat beta-glucan in 0.5 M NaOH solution. The characteristic ratio (4.97) was obtained by the random flight model, and the statistical segment length (8.83 nm) was derived from the wormlike cylinder model. It was found that the wormlike cylinder model could explain the chain stiffness better than the random flight model, which suggested an extended random coil conformation of wheat beta-glucan in 0.5 M NaOH solution. The study also revealed that the structure feature of wheat beta-glucan; that is, the higher trisaccharide-to-tetrasaccharide ratio contributed to the stiffer chain conformation compared with other cereal beta-glucans.     

lectrochemical and conformational study of the interactions of fibrinogen with acidic polysaccharides

The interactions of fibrinogen wth acidic polysaccharides have been studied in connection with anticoagulant properties of heparin. Despite the high charge density of heparin, a polyelectrolyte complex of fibrinogen and heparin could not be detected at any mixing ratio by the measurement of turbidity, metachromasis with acridine orange, circular dichroism, and viscosity of their mixture solutions. Sodium cellulose sulphate and dextran sulphate, however, which have similar charge densities, formed precipitates of polyelectrolyte complexes with fibrinogen. This difference was presumed to be due to the secondary structure characteristics of heparin in solution as well as the relatively low molecular weight of heparin.     

Raman spectroscopic study of the conformational changes of thyroxine induced by interactions with phospholipid

Comparison of the Raman spectra of thyroxine ( L-3,3',5,5'-tetraiodothyronine) in the pure state and in a 1:5 mixture with phosphatidylcholine reveals spectral differences that reflect structural changes of thyroxine induced by interactions with the phospholipid. These structural changes could be localized in specific parts of the thyroxine molecule on the basis of a vibrational analysis that was carried out by density functional calculations with the B3LYP hybrid functional applying the SDD effective core potential basis set. The calculated (and subsequently scaled) frequencies reveal a good agreement with the experimental data, which together with calculated IR and Raman intensities allow a plausible assignment of most of the IR and Raman bands. Thus, it is found that modes localized in the aromatic beta-ring and in the ether group as well as the C-I stretching modes of ring alpha are affected upon lipid interactions, indicating that thyroxine interacts with the phosphatidylcholine bilayer via penetration of the hydrophobic part of the molecule.     

Parameter optimized surfaces (POPS): analysis of key interactions and conformational changes in the ribosome

We present a new method for the calculation of solvent accessible surface areas at the atomic and residue levels, which we call parameter optimized surfaces (POPS-A and POPS-R ). Atomic and residue areas (the latter simulated with a single sphere centered at the C^αs atom for amino acids and at the P atom for nucleotides) have been optimized versus accurate all-atoms methods. We concentrated on an analytical formula for the approximation of solvent accessibilities. The formula is simple, easily derivable and fast to compute, therefore it is practical for use in molecular dynamics simulations as an approximation to the first solvation shell. The residue based approach POPS-R has been derived as a useful tool for the analysis of large macromolecular assemblies like the ribosome, and is especially suited for use in refinement of low resolution structures. The structures of the 70S, 50S and 30S ribosomes have been analyzed in detail and most of the interactions within the subunits and at their interfaces were clearly identified. Some interesting differences between 30S alone and within the 70S have been highlighted. Owing to the presence of the P-tRNA in the 70S ribosome, localized conformational rearrangements occur within the subunits, exposing Arg and Lys residues to negatively charged binding sites of P-tRNA. POPS-R also allows for estimates of the loss of free energy of solvation upon complex formation, particularly useful in designing new protein–RNA complexes and in suggesting more focused experimental work.     

A study of cell interactions involved in Pleurodeles waltlii epidermal differentiation

Summary A polyclonal antibody (SP-2) has been produced, which recognizes antigens expressed in epidermal cells of Pleurodeles waltlii embryos. The antigens appear first at the end of gastrulation in the external surface of the embryo and are selectively expressed in ectodermally derived epidermal structures. Ectodermal commitment was investigated using cell cultures and blastocoel graft experiments. The four animal blastomeres of the 8-cell stage as well as the animal cap explants of the early gastrula stage cultured in vitro differentiate into epidermis, and SP-2 antigens are expressed. The expression of SP-2-defined antigens is inhibited both in vivo and in vitro by the inductive interaction of chordomesoderm. Once dissociated, ectodermal cells do not react with SP-2. Conversely, the aggregation of ectodermal cells may restore the expression of SP-2 antigens. Transplantation of animal cap explants or isolated ectodermal cells into the blastocoel of a host embryo at the early gastrula stage shows that only cells integrated into the epidermis express the marker antigens. When vegetal cells were dissociated from donor embryos before the mid-blastula stage and implanted into the blastocoel of host embryos at the early gastrula stage, their progeny were found in all germ layers, cells that were found in the host epidermis were stained with SP-2, whereas those contributing to mesoderm and endoderm were not. Thus the acquisition of cell polarity in epidermal differentiation and the organization of cells into epithelial structures are essential for SP-2-defined antigen expression.     

A conductance stopped-flow study of polyelectrolyte systems. Dynamic conformational change of synthetic macroions and their complexation with neutral polymers

Two dynamic phenomena of polyelectrolyte systems, namely the rapid conformational changes of weak polyelectiolytes (polyacrylic acid (HPAA) and polyethylenimine, induced by pH-jump) and the complexation of HPAA with polyvinylpyrrolidone are first investigated by means of the conductance stopped-flow (kappa-SF) technique. The pH-induced relaxations observed by mixing an aqueous solution of HPAA or polyethylenimine with water containing a tiny amount of alkali or acid, are safely ascribed to the conformational transition of the macroions between the compact "coil" and the stretched "rod" forms. The relaxation times are large at high degrees of neutralization and for "rod" conformation. Tentative values for the thermodynamic parameters of the dynamic conformational changes are obtained and discussed. The reaction rates of the polymer complex formation and dissociation of HPAA with polyvinylpyrrolidone are also determined using the kappa-SF method. The association constant and the rates of formation and dissociation are 1.84 x 10(3) M(-1), 9.4 x 10(4) M(-1) s(-1) and 51 s(-1) at 10 degrees C, respectively. We then derive the thermodynamic parameters from the above results.     

Noncovalent interactions of peptides with porphyrins in aqueous solution: conformational study using vibrational CD spectroscopy.

Noncovalent interactions of poly(L-lysine) (PL), oligopeptides L-lysyl-L-alanyl-L-alanine and (L-lysyl-L-alanyl-L-alanine)(2) with meso-tetrakis(4-sulfonatophenyl)porphine (TPPS), and poly(L-glutamic acid) (PLGA) with meso-tetrakis(1-methyl-4-pyridyl)porphine tetra-p-tosylate (TMPyP) in aqueous solutions have been studied using combination of spectroscopic methods: Vibrational circular dichroism (VCD) spectroscopy in the mid-infrared region provides a direct information on conformational changes of the polypeptides and oligopeptides caused by interactions with porphyrins; ultraviolet-visible absorption, fluorescence, and electronic circular dichroism (ECD) reveal the aggregation characterization of the porphyrin part of the complexes. Interactions of TPPS with tripeptide, hexapeptide, and PL containing about ten amino acid residues in the molecular chain are accompanied with the changes of VCD patterns in the amide I' region. In these cases, the conformation of the oligopeptide part of complexes is obviously influenced by interactions with TPPS and partial changes of random coil structure are observed in VCD. When PL was composed of the hundreds of lysine residues, just a weak intensity decrease was detected and the shape of VCD spectrum typical for the random coil structure was preserved. As follows from the uv-vis absorption and fluorescence spectra, porphyrin molecules are attached to peptides by electrostatic interaction as a monomer or dimer and interaction between porphyrin and peptide depends on the polypeptide chain length. For the PLGA-TMPyP system with PLGA containing from tens to hundreds of glutamic acid residues in the chain, the VCD spectra were unchanged when TMPyP was presented in the aqueous solution of PLGA and random coil conformation of PLGA-TMPyP aggregates was preserved.     

Energetics and conformational changes upon complexation of a phenothiazine drug with human serum albumin

The interactions and complexation process of the amphiphilic phenothiazine fluphenazine hydrochloride with human serum albumin in aqueous buffered solutions of pH 3.0 and 7.4 have been examined by zeta-potential, isothermal titration calorimetry (ITC), UV-vis spectroscopy, and dynamic light scattering (DLS) techniques with the aim of analyzing the effect of hydrophobic and electrostatic forces on the complexation process and the alteration of protein conformation upon binding. Thus, the energetics and stoichiometry of the binding process were derived from ITC data. The enthalpies of binding obtained are small and exothermic, so the Gibbs energies of binding are dominated by large increases in entropy, consistent with hydrophobic interactions at a acidic pH. However, at physiological pH, binding to the first class of binding sites is dominated by an enthalpic contribution due to the existence of electrostatic interactions and probably some hydrogen bonding. Binding isotherms were obtained from microcalorimetric data by using a theoretical model based on the Langmuir isotherm. zeta-Potential data showed a reversal in the sign of the protein charge at pH 7.4, as a consequence of the binding of the drug to the protein. Gibbs energies of drug binding per mole of drug were also derived from zeta-potential data. On the other hand, binding of the phenothiazine that causes a conformational transition on the protein structure was followed as a function of drug concentration using UV-vis spectroscopy, and the data were analyzed to obtain the Gibbs energy of the transition in water (deltaG(degree)w) and in a hydrophobic environment (deltaG(degree)hc). Finally, the population distribution of the different species in solution and the size of the complexes were analyzed through dynamic light scattering. The existence of an aggregation process of drug/protein complexes, as a consequence of the expanded structure of the protein induced by the drug and subsequent further binding, is in agreement with ITC data. In addition, detection of drug aggregates at concentrations below the drug critical micelle concentration was also detected by this technique.     

Characterization of two polyketide synthase genes involved in zearalenone biosynthesis in Gibberella zeae

Zearalenone, a mycotoxin produced by several Fusarium spp., is most commonly found as a contaminant in stored grain and has chronic estrogenic effects on mammals. Zearalenone is a polyketide derived from the sequential condensation of multiple acetate units by a polyketide synthase (PKS), but the genetics of its biosynthesis are not understood. We cloned two genes, designated ZEA1 and ZEA2, which encode polyketide synthases that participate in the biosynthesis of zearalenone by Gibberella zeae (anamorph Fusarium graminearum). Disruption of either gene resulted in the loss of zearalenone production under inducing conditions. ZEA1 and ZEA2 are transcribed divergently from a common promoter region. Quantitative PCR analysis of both PKS genes and six flanking genes supports the view that the two polyketide synthases make up the core biosynthetic unit for zearalenone biosynthesis. An appreciation of the genetics of zearalenone biosynthesis is needed to understand how zearalenone is synthesized under field conditions that result in the contamination of grain.     

Motifs involved in protein-protein interactions

Summary Interactions between proteins are extremely variable. However, in the dimeric proteins comprised of regular motifs, interface interactions are similar to those that stabilize monomers. Additional stability is gained by converting loops within motifs or domains to linkers across interfaces. In multi-domain proteins, interactions can be greatly effected by the conformation of linkers between domains. Complex association of subunits, involving higher rotational symmetry or cubic symmetry, frequently involves motif sharing across interfaces.     

Tachykinins and conformational aspects of their interactions with receptors]

Several peptides of the tachykinin family are reviewed. Special attention is spared to mammalian tachykinins as peptide neurotransmitters. Conformational possibilities of the tachykinins are considered in connection with their ability to interact with specific receptors. The results of theoretical and experimental studies suggest a significant identity of spatial structures of the tachykinins and explain the absence of the strict specificity in tachykinin-receptor interactions.     

Comparative study on conformational stability and subunit interactions of two bacterial asparaginases.

The denaturation and reconstitution of Erwinia carotovora and Escherichia coli L-asparaginases has been followed by optical rotatory dispersion, circular dichroism and analytical ultracentrifugation. Denaturation in urea results in dissociation of the native enzyme (mol. wt. 140 000 approx.) to produce unfolded subunits (mol. wt. 35 000 approx.); the Erwinia L-asparaginase subunits can be refolded by dilution or dialysis in alkaline conditions, pH 10.5, without aggregation to the active tetramer, to give a rather unstable solution of a monomer possibly in equilibrium with dimer. These alkaline-reconstituted subunits undergo a conformational change to a more ordered state in the presence of sodium dodecylsulphate, similar to those produced by the action of sodium dodecylsulphate on the native enzyme. If the denatured subunits are reconstituted in the pH range 5.0-7.5, the enzymically active tetramer is reformed in up to 80% yield, depending upon the conditions of temperature and concentration. Kinetic data for these various transitions suggest that dissociation is a rate-limiting step while conformational changes of the polypeptide chains are relatively much more rapid. The possible significance of these different rates of change to therapeutic considerations is discussed.     

Urinary zearalenone measured with ELISA as a biomarker of zearalenone exposure in pigs

The suitability to assess zearalenone (ZEA) exposure in pigs of a commercial ELISA kit for ZEA analysis in urine was tested. A daily dose of 0, 5, 10, 20 and 40 μg synthetic ZEA per kilogram BW was administered via the feed to four gilts per dose group, and after 3 and after 7 days of ZEA intake, urine samples were assayed with the ELISA which has a relative cross-reactivity of 42 % with α-zearalenol. The concentration of urinary ZEA equivalents (ZEA plus 42 % of α-zearalenol present) did not differ between day 4 and day 8 (P?=?0.50) within each dose group. The urinary ZEA equivalent/creatinine ratio was tightly correlated with ZEA intake (r?=?0.95). The urinary ZEA equivalent/creatinine values at 0 and 40 μg/kg BW were distinctly different from those of the intermediate dose levels, whereas there was some overlapping of the individual values at the dose levels 5, 10 and 20 μg/kg BW. The urinary ZEA equivalent/creatinine ratio can be used as a biomarker for ZEA exposure in pigs provided that urine samples of several animals receiving the same diet are assayed, either separately or after pooling.     

A DFT investigation of conformational geometries and interconversion equilibria of phenylthiosemicarbazone and its complexation with zinc

The geometrical structures of phenylthiosemicarbazone (HAPhTSC) conformers have been obtained by geometry optimizations using density functional theory (DFT) calculations at the B3LYP/6-31G(d) and B3LYP/6-311G(d,p) levels of theory. Six thioamino and 24 thioimino tautomers of HAPhTSC have been found. Six tautomerization reactions between thioamino and thioimino tautomers occurring via transition states and their corresponding activation energies have been obtained. Conformational pathways for tautomerizations and interconversions of HAPhTSC conformers have been presented. Tautomerization between the most stable species of thioamino (Atttcc) and its thioimino (Itttcct) tautomer is an endothermic reaction, H⁰=18.17 kcal mol^–1 and its log K=–13.74, at 298.15 K. Thermodynamic quantities of tautomerizations, interconversions of HAPhTSC conformers and their equilibrium constants are reported. The geometry of the zinc complex with HAPhTSC, found as a Zn(HAPhTSC)₂Cl₂ structure, has been obtained using B3LYP/6-31G(d) calculations. Binding of the Zn(HAPhTSC)₂Cl₂ complex is an exothermic and spontaneous reaction.Figure Conformational notation defined as a name consisting of a letter A for a thioamino tautomer followed by c for cis or t for trans isomerism of five dihedral angles of (C4-C3-C2-N3), (C3-C2-N3-N2), (C2-N3-N2-C1), (N3-N2-C1-N1) and (N2-C1-N1-H2), serially, or a letter I for b thioimino tautomer followed by c for cis or t for trans isomerism of six dihedral angles of (C4-C3-C2-N3), (C3-C2-N3-N2), (C2-N3-N2-C1), (N3-N2-C1-N1), (N2-C1-N1-H2) and (N2-C1-S-H1), serially.Electronic Supplementary Material Supplementary material is available for this article at     

Nucleotide analogs and molecular modeling studies reveal key interactions involved in substrate recognition by the yeast RNA triphosphatase

RNA triphosphatases (RTPases) are involved in the addition of the distinctive cap structure found at the 5′ ends of eukaryotic mRNAs. Fungi, protozoa and some DNA viruses possess an RTPase that belongs to the triphosphate tunnel metalloenzyme family of enzymes that can also hydrolyze nucleoside triphosphates. Previous crystallization studies revealed that the phosphohydrolase catalytic core is located in a hydrophilic tunnel composed of antiparallel β-strands. However, all past efforts to obtain structural information on the interaction between RTPases and their substrates were unsuccessful. In the present study, we used computational molecular docking to model the binding of a nucleotide substrate into the yeast RTPase active site. In order to confirm the docking model and to gain additional insights into the molecular determinants involved in substrate recognition, we also evaluated both the phosphohydrolysis and the inhibitory potential of an important number of nucleotide analogs. Our study highlights the importance of specific amino acids for the binding of the sugar, base and triphosphate moieties of the nucleotide substrate, and reveals both the structural flexibility and complexity of the active site. These data illustrate the functional features required for the interaction of an RTPase with a ligand and pave the way to the use of nucleotide analogs as potential inhibitors of RTPases of pathogenic importance.     

Heterophilic interactions of DM-GRASP: GRASP-NgCAM interactions involved in neurite extension

DM-GRASP is an immunoglobulin superfamily cell adhesion molecule that is expressed in both the developing nervous and immune system. Specific populations of neurons respond to DM-GRASP substrates appears to require homophilic interactions between DM-GRASP molecules. We were interested in determining whether DM-GRASP interacts heterophilically with other ligands as well. We have found that eleven proteins from embryonic chick brain membranes consistently bind to and elute from a DM-GRASP-Sepharose affinity column. One of these proteins is DM-GRASP itself, consistent with its known homophilic binding. Another protein, at 130 kD, is immunoreactive with monoclonal antibodies to NgCAM. Other neural cell adhesion molecules were not detected in the eluate. The DM- GRASP-Sepharose eluate also contains a potent neurite stimulating activity, which cannot be accounted for by either DM-GRASP or NgCAM. To investigate the interaction of DM-GRASP and NgCAM, antibodies against DM-GRASP were added to neuronal cultures extending neurites on an NgCAM substrate. The presence of antibodies to DM-GRASP decreased neurite extension on laminin, suggesting that the antibody is not toxic or generally inhibiting motility. We present two possible models for the DM-GRASP-NgCAM association and a hypothesis for neural cell adhesion function that features the dimerization of cell adhesion molecules.     

Synaptic vesicles: key organelles involved in neurotransmission

1. This article summarizes some of the recent advances in the understanding of structural and functional properties of isolated small synaptic vesicles (SSV) from mammalian brain. 2. SSV contain a set of integral membrane proteins which are highly specific for this organelle and which occur on all SSV of the central and peripheral nervous system irrespective of their transmitter content. In contrast, these proteins are absent from the membrane of peptide-containing large dense-core vesicles indicating that the two types of organelle have a different membrane composition. The availability of antibodies for these proteins has allowed the evaluation of the purity of vesicle preparations which is instrumental for functional studies. 3. Recent advances in the study of neurotransmitter uptake have revealed that SSV contain specific carrier systems for glutamate and GABA. They are different from the transporters of the plasma membrane, and are dependent on the energy of a proton electrochemical gradient. The uptake of glutamate has been characterized in some detail and the mechanistic and physiological implications of these findings are discussed.     

Identification of key proteins involved in the anammox reaction

Bacteria performing anaerobic ammonium oxidation (anammox) are key players in the global nitrogen cycle due to their inherent ability to convert biologically available nitrogen to N₂. Anammox is increasingly being exploited during wastewater treatment worldwide, and about 50% of the total N₂ production in marine environments is estimated to proceed by the anammox pathway. To fully understand the microbial functionality and mechanisms that control environmental feedbacks of the anammox reaction, key proteins involved in the reaction must be identified. In this study we have utilized an analytical protocol that facilitates detection of proteins associated with the anammoxosome, an intracellular membrane compartment within the anammox bacterium. The protocol enabled us to identify several key proteins of the anammox reaction including a hydrazine hydrolase producing hydrazine, a hydrazine-oxidizing enzyme converting hydrazine to N₂ and a membrane-bound ATP synthase generating ATP from the gradients of protons formed in the anammox reaction. We also performed immunogold labelling electron microscopy to determine the subcellular location of the hydrazine hydrolase. The results from our study support the hypothesis that proteins associated with the anammoxosome host the complete suite of reactions during anammox.