Sequencing of T-superfamily conotoxins from Conus virgo: Pyroglutamic acid identification and disulfide arrangement by MALDI mass spectrometry

De novo mass spectrometric sequencing of two Conus peptides, Vi1359 and Vi1361, from the vermivorous cone snail Conus virgo, found off the southern Indian coast, is presented. The peptides, whose masses differ only by 2 Da, possess two disulfide bonds and an amidated C-terminus. Simple chemical modifications and enzymatic cleavage coupled with matrix assisted laser desorption ionization (MALDI) mass spectrometric analysis aided in establishing the sequences of Vi1359, ZCCITIPECCRI-NH2, and Vi1361, ZCCPTMPECCRI-NH2, Which differ only at residues 4 and 6 (Z = pyroglutamic acid). The presence of the pyroglutamyl residue at the N-terminus was unambiguously identified by chemical hydrolysis of the cyclic amide, followed by esterification. The presence of Ile residues in both the peptides was confirmed from high-energy collision induced dissociation (CID) studies, using the observation Of W-n- and d(n)-ions as a diagnostic. Differential cysteine labeling, in conjunction with MALDI-MS/MS, permitted establishment of disulfide connectivity in both peptides as Cys2-Cys9 and Cys3-Cys10. The cysteine pattern clearly reveals that the peptides belong to the class of T-superfamily conotoxins, in particular the T-1 superfamily.

Unfolding of Plasmodium falciparum Triosephosphate Isomerase in Urea and Guanidinium Chloride: Evidence for a Novel Disulfide Exchange Reaction in a Covalently Cross-Linked Mutant†

The conformational stability of Plasmodium falciparum triosephosphate isomerase (TIMWT) enzyme has been investigated in urea and guanidinium chloride (GdmCl) solutions using circular dichroism, fluorescence, and size-exclusion chromatography. The dimeric enzyme is remarkably stable in urea solutions. It retains considerable secondary, tertiary, and quaternary structure even in 8 M urea. In contrast, the unfolding transition is complete by 2.4 M GdmCl. Although the secondary as well as the tertiary interactions melt before the perturbation of the quaternary structure, these studies imply that the dissociation of the dimer into monomers ultimately leads to the collapse of the structure, suggesting that the interfacial interactions play a major role in determining multimeric protein stability. The C-m(urea)/C-m(GdmCl) ratio (where C-m is the concentration of the denaturant required at the transition midpoint) is unusually high for triosephosphate isomerase as compared to other monomeric and dimeric proteins. A disulfide crosslinked mutant protein (Y74C) engineered to form two disulfide cross-links across the interface (13-74') and (13'-74) is dramatically destablized in urea. The unfolding transition is complete by 6 M urea and involves a novel mechanism of dimer dissociation through intramolecular thiol-disulfide exchange.

Structural Ordering of Disordered Ligand-Binding Loops of Biotin Protein Ligase into Active Conformations as a Consequence of Dehydration

Mycobacterium tuberculosis (Mtb), a dreaded pathogen, has a unique cell envelope composed of high fatty acid content that plays a crucial role in its pathogenesis. Acetyl Coenzyme A Carboxylase (ACC), an important enzyme that catalyzes the first reaction of fatty acid biosynthesis, is biotinylated by biotin acetyl-CoA carboxylase ligase (BirA). The ligand-binding loops in all known apo BirAs to date are disordered and attain an ordered structure only after undergoing a conformational change upon ligand-binding. Here, we report that dehydration of Mtb-BirA crystals traps both the apo and active conformations in its asymmetric unit, and for the first time provides structural evidence of such transformation. Recombinant Mtb-BirA was crystallized at room temperature, and diffraction data was collected at 295 K as well as at 120 K. Transfer of crystals to paraffin and paratone-N oil (cryoprotectants) prior to flash-freezing induced lattice shrinkage and enhancement in the resolution of the X-ray diffraction data. Intriguingly, the crystal lattice rearrangement due to shrinkage in the dehydrated Mtb-BirA crystals ensued structural order of otherwise flexible ligand-binding loops L4 and L8 in apo BirA. In addition, crystal dehydration resulted in a shift of similar to 3.5 angstrom in the flexible loop L6, a proline-rich loop unique to Mtb complex as well as around the L11 region. The shift in loop L11 in the C-terminal domain on dehydration emulates the action responsible for the complex formation with its protein ligand biotin carboxyl carrier protein (BCCP) domain of ACCA3. This is contrary to the involvement of loop L14 observed in Pyrococcus horikoshii BirA-BCCP complex. Another interesting feature that emerges from this dehydrated structure is that the two subunits A and B, though related by a noncrystallographic twofold symmetry, assemble into an asymmetric dimer representing the ligand-bound and ligand-free states of the protein, respectively. In-depth analyses of the sequence and the structure also provide answers to the reported lower affinities of Mtb-BirA toward ATP and biotin substrates. This dehydrated crystal structure not only provides key leads to the understanding of the structure/function relationships in the protein in the absence of any ligand-bound structure, but also demonstrates the merit of dehydration of crystals as an inimitable technique to have a glance at proteins in action.

Crystal structure of dimeric FabZ of Plasmodium falciparum reveals conformational switching to active hexamers by peptide flips

The crystal structure of beta-hydroxyacyl acyl carrier protein dehydratase of Plasmodium falciparum (PfFabZ) has been determined at a resolution of 2.4 angstrom. PfFabZ has been found to exist as a homodimer (d-PfFabZ) in the crystals of the present study in contrast to the reported hexameric form (h-PfFabZ) which is a trimer of dimers crystallized in a different condition. The catalytic sites of this enzyme are located in deep narrow tunnel-shaped pockets formed at the dimer interface. A histidine residue from one subunit of the dimer and a glutamate residue from the other subunit lining the tunnel form the catalytic dyad in the reported crystal structures. While the position of glutamate remains unaltered in the crystal structure of d-PffabZ compared to that in b-PfFabZ, the histidine residue takes up an entirely different conformation and moves away from the tunnel leading to a His-Phe cis-trans peptide flip at the histidine residue. In addition, a loop in the vicinity has been observed to undergo a similar flip at a Tyr-Pro peptide bond. These alterations not only prevent the formation of a hexamer but also distort the active site geometry resulting in a dimeric form of FabZ that is incapable of substrate binding. The dimeric state and an altered catalytic site architecture make d-PfFabZ distinctly different from the FabZ structures described so far. Dynamic light scattering and size exclusion chromatographic studies clearly indicate a pH-related switching of the dimers to active hexamers. (c) 2006 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserv.

Amino acid sequence of the winged bean (Psophocarpus tetragonolobus) basic lectin. Adenine binding and identification of the active-site tryptophan residue

The complete amino acid sequence of winged bean basic agglutinin (WBA I) was obtained by a combination of manual and gas-phase sequencing methods. Peptide fragments for sequence analyses were obtained by enzymatic cleavages using trypsin and Staphylococcus aureus V8 endoproteinase and by chemical cleavages using iodosobenzoic acid, hydroxylamine, and formic acid. COOH-terminal sequence analysis of WBA I and other peptides was performed using carboxypeptidase Y. The primary structure of WBA I was homologous to those of other legume lectins and more so to Erythrina corallodendron. Interestingly, the sequence shows remarkable identities in the regions involved in the association of the two monomers of E. corallodendron lectin. Other conserved regions are the double metal-binding site and residues contributing to the formation of the hydrophobic cavity and the carbohydrate-binding site. Chemical modification studies both in the presence and absence of N-acetylgalactosamine together with sequence analyses of tryptophan-containing tryptic peptides demonstrate that tryptophan 133 is involved in the binding of carbohydrate ligands by the lectin. The location of tryptophan 133 at the active center of WBA I for the first time subserves to explain a role for one of the most conserved residues in legume lectins.

Reaction of carbon disulfide with azide ion

Carbon disulfide reacts with azide ion to form the 1,2,3,4-thiatriazolinethionate ion and not the acyclic azido dithiocarbonate ion as previously reported. A series of salts of thiatriazoline have been prepared and none shows evidence for the presence of the azido group. Esters of thiatriazolinethione prepared by the reaction of the sodium salt with alkyl or acyl halides have been found to be either 5-(substituted) mercapto-1,2,3,4-thiatriazoles or 4-substituted 1,2,3,4-thiatriazoline-5-thiones. These structures have been assigned on the basis of degradative and spectroscopic evidence. The chemistry of the so-called azidodithiocarbonates has been reinterpreted in terms of the thiatriazole structure.

Cloning,overexpression and purification of functionally active Saccharomyces cerevisiae Hop1 protein from scherichia coli

One of the major limitations to the application of high-resolution biophysical techniques such as X-crystallography and spectroscopic analyses to structure-function studies of Saccharomyces cerevisiae Hop1 protein has been the non-availability of sufficient quantities of functionally active pure protein. This has, indeed, been the case of many proteins, including yeast synaptonemal complex proteins. In this study, we have performed expression screening in Escherichia coli host strains, capable of high-level expression of soluble S. cerevisiae Hop1 protein. A new protocol has been developed for expression and purification of S. cerevisiae Hop1 protein, based on the presence of hexa-histidine tag and double-stranded DNA-Cellulose chromatography. Recombinant S. cerevisiae Hop1 protein was >98% pure and exhibited DNA-binding activity with high-affinity to the Holliday junction. The availability of the recombinant HOP1 expression vector and active Hop1 protein would facilitate structure-function investigations as well as the generation of appropriate truncated and site-directed mutant proteins, respectively. (C) 2010 Elsevier Inc. All rights reserved.

Pd and Pt ions as highly active sites for the water-gas shift reaction over combustion synthesized zirconia and zirconia-modified ceria

Noble metal substituted ionic catalysts were synthesized by solution combustion technique. The compounds were characterized by X-ray diffraction, FT-Raman spectroscopy, and X-ray photoelectron spectroscopy. Zirconia supported compounds crystallized in tetragonal phase. The solid solutions of ceria with zirconia crystallized in fluorite structure. The noble metals were substituted in ionic form.The water-gas shift reaction was carried out over the catalysts.Negligible conversions were observed with unsubstituted compounds. The substitution of a noble metal ion was found to enhance the reaction rate. Equilibrium conversion was obtained below 250 degrees C in the presence of Pt ion substituted compounds. The formation of Bronsted acid-Bronsted base pairs was proposed to explain the activity of zirconia catalysts. The effect of oxide ion vacancies on the reactions over substituted ceria-zirconia solid solutions was established. (c)2010 Elsevier B.V. All rights reserved.

Polarographic and redox potential studies on copper(I) and copper(II) and their complexes. Part III. Copper (I and II)-ethylene diamine and edta complexes and theory of formation of step reduction waves in cupric copper systems

Polarographic and redox potential measurements on the cupric and cuprous complexes of ethylenediamine and EDTA have been carried out. From the ratio of the stability constants of the cupric and cuprous complexes, and the stability constant of the cupric complex, the stability constant of the cuprous-ethylenediamine complex is obtained. In the case of the EDTA complex it has been possible to obtain only βic/β2ous from the equilibrium concentrations of the cuprous and cupric complexes and the disproportionation constant. The inequalities for the appearance of step reduction waves have been given. The values of the stability constants of the cupric and cuprous complexes determined by the polarographic-redox potential method have been used to explain the appearance of step reduction waves in some systems and the non-appearance in other systems.

Polarographic and redox potential studies on copper(I) and copper(II) and their complexes. Part I. Copper(I and II)-ammonia and methylamine complexes

The equilibrium between cuprous ion, cupric ion and metallic copper has been studied using polarographic and redox potential measurements, by reducing cupric ion with copper gauze until equilibrium. Using the well-defined anodic diffusion current plateau, an amperometric method for estimating cuprous copper based on the titration of cuprous ion with dichromate or permanganate has been developed. The diffusion current constant and the disproportionation constant of cuprous ion and the standard potential for the reduction reaction of Cu2+ → Cu+ have been determined. Polarograms have been taken after reducing cupric complexes of ammonia and methylamine with copper until equilibrium. In the case of the copper-ammonia system, reduction to the cuprous state is practically complete while in the case of the cupric-methylamine system, the first cathodic wave occurs to some extent. A new method, called the polarographic-redox potential method, for determining the stability constants of cuprous and cupric complexes has been developed. The method depends upon the determination of the concentration of complexes by polarographic wave heights, and free cupric anc cuprous ions by redox potentials. The stability constants of the following complexes have been obtained: Cu(NH3)2+4, Cu(NH3)+2, Cu(CH3NH2)2(OH)2, Cu(CH3NH2)+2. The stability constants determined by the new method and the half-wave potential shift method agree and the value for the cupric-ammonia complex is in good agreement with Bjerrum method, indicating the reliability of this method.

Ultrasonic studies in chemically active liquid media (1) aqueous solution of N2O4

Using a pulse method the ultrasonic absorption has been studied in the frequency range of 2 to 10 Mc/s in dilute aqueous solutions of nitrogen tetroxide gas at room temperature. The absorption peaks (αλ vs frequency) observed in this study are attributed to the ionic dissociation reaction of the nitrous acid into its constituent ions. The rate constants of the forward and backward reactions are calculated using the theory of Tabuchi. The variation of the logarithm of the rate constant of the bimolecular ionic reaction, namely, log10 kb, with the square root of ionic strength qualitatively follows Brönsted's theory for ionic reactions in solutions.