Rapid mass spectrometric determination of disulfide connectivity in peptides and proteins

Disulfide crosslinks are ubiquitous in natural peptides and proteins, providing rigidity to polypeptide scaffolds. The assignment of disulfide connectivity in multiple crosslinked systems is often difficult to achieve. Here, we show that rapid unambiguous characterisation of disulfide connectivity can be achieved through direct mass spectrometric CID fragmentation of the disulfide intact polypeptides. The method requires a direct mass spectrometric fragmentation of the native disulfide bonded polypeptides and subsequent analysis using a newly developed program, DisConnect. Technical difficulties involving direct fragmentation of proteins are surmounted by an initial proteolytic nick and subsequent determination of the structures of these proteolytic peptides through DisConnect. While the connectivity in proteolytic fragments containing one cystine is evident from the MS profile alone, those with multiple cystines are subjected to subsequent mass spectrometric fragmentation. The wide applicability of this method is illustrated using examples of peptide hormones, peptide toxins, proteins, and disulfide foldamers of a synthetic analogue of a marine peptide toxin. The method, coupled with DisConnect, provides an unambiguous, straightforward approach, especially useful for the rapid screening of the disulfide crosslink fidelity in recombinant proteins, determination of disulfide linkages in natural peptide toxins and characterization of folding intermediates encountered in oxidative folding pathways.

Cyclic AMP-dependent protein lysine acylation in mycobacteria regulates fatty acid and propionate metabolism

Acetylation of lysine residues is a posttranslational modification that is used by both eukaryotes and prokaryotes to regulate a variety of biological processes. Here we identify multiple substrates for the cAMP-dependent protein lysine acetyltransferase from Mycobacterium tuberculosis (KATmt). We demonstrate that a catalytically important lysine residue in a number of FadD (fatty acyl CoA synthetase) enzymes is acetylated by KATmt in a cAMP-dependent manner and that acetylation inhibits the activity of FadD enzymes. A sirtuin-like enzyme can deacetylate multiple FadDs, thus completing the regulatory cycle. Using a strain deleted for the KATmt ortholog in Mycobacterium bovis Bacillus Calmette-Guerin (BCG), we show for the first time that acetylation is dependent on intracellular cAMP levels. KATmt can utilize propionyl CoA as a substrate and, therefore, plays a critical role in alleviating propionyl CoA toxicity in mycobacteria by inactivating acyl CoA synthetase (ACS). The precision by which mycobacteria can regulate the metabolism of fatty acids in a cAMP-dependent manner appears to be unparalleled in other biological organisms and is ideally suited to adapt to the complex environment that pathogenic mycobacteria experience in the host.

Analysis of designed beta-hairpin peptides: molecular conformation and packing in crystals

The crystal structures of several designed peptide hairpins have been determined in order to establish features of molecular conformations and modes of aggregation in the crystals. Hairpin formation has been induced using a centrally positioned (D)Pro-Xxx segment (Xxx = (L)Pro, Aib, Ac(6)c, Ala; Aib = alpha-aminoisobutyric acid; Ac(6)c = 1-aminocyclohexane-1-carboxylic acid). Structures of the peptides Boc-Leu-Phe-Val-(D)Pro-(L)Pro-Leu-Phe-Val-OMe (1), Boc-Leu-Tyr-Val-(D)Pro-(L)Pro-Leu-Phe-Val-OMe (2, polymorphic forms labeled as 2a and 2b), Boc-Leu-Val-Val-(D)Pro-(L)Pro-Leu-Val-Val-OMe (3), Boc-Leu-Phe-Val-(D)Pro-Aib-Leu-Phe-Val-OMe (4, polymorphic forms labeled as 4a and 4b), Boc-Leu-Phe-Val-(D)Pro-Ac(6)c-Leu-Phe-Val-OMe (5) and Boc-Leu-Phe-Val-(D)Pro-Ala-Leu-Phe-Val-OMe (6) are described. All the octapeptides adopt type II' beta-turn nucleated hairpins, stabilized by three or four cross-strand intramolecular hydrogen bonds. The angle of twist between the two antiparallel strands lies in the range of -9.8 degrees to -26.7 degrees. A detailed analysis of packing motifs in peptide hairpin crystals is presented, revealing three broad modes of association: parallel packing, antiparallel packing and orthogonal packing. An attempt to correlate aggregation modes in solution with observed packing motifs in crystals has been made by indexing of crystal faces in the case of three of the peptide hairpins. The observed modes of hairpin aggregation may be of relevance in modeling multiple modes of association, which may provide insights into the structure of insoluble polypeptide aggregates.

Isothermal transformation of beta-phase in Cu-rich Cu-Al-Sn alloys

Microstructural changes resulting from isothermal decomposition of the beta-phase have been studied in Cu-rich binary Cu-Al and ternary Cu-Al-Sn alloys containing up to 3 at.% Sn at temperatures from 873 to 673 K. Results are presented as TTT diagrams. The decomposition occurs in several stages, each of which involves the establishment of metastable equilibrium between beta and one or more of the product phases alpha, beta(1) and gamma(2). Addition of Sn has been shown to increase the stability of the ordered beta(1)-phase in relation to beta. In alloys containing more than 2 at.% Sn, the beta(1) emerges as a stable phase. At low Sn concentrations beta(1) is metastable. An important new finding is the existence of three-phase equilibrium microstructure containing alpha, beta(1) and gamma(2). Increasing addition of Sn alters the morphology of beta(1) from rosettes to dendrites and finally to Widmanstatten needles.

Effect of thermal and thermo-mechanical cycling on the microstructure of Ni-rich NiTi shape memory alloys

Microstructural changes of Ni-rich NiTi shape memory alloy during thermal and thermo-mechanical cycling have been investigated using Electron Back Scattered Diffraction. A strong dependence of the orientation of the prior austenite grain on the misorientation development has been observed during thermal cycling and thermo-mechanical cycling. This effect is more pronounced at the grain boundaries compared to grain interior. At a larger applied strain, the volume fraction of stabilized martensite phase increases with increase in the number of cycling. Deformation within the martensite leads to stabilization of martensitic phase even at temperatures slightly above the austenite finish temperature. Modulus variation with respect to temperature has been explained on the basis of martensitic transformation.

Electron microscopy of microstructural transformation in electrodeposited Ni-rich, Ag-Ni film

Ag-Ni films were electrodeposited over a Cu substrate. Structural characterization revealed a fibrous microstructure with an amorphous structure for the as-deposited film. Isothermal annealing at 400 degrees C of the film inside transmission electron microscope led to amorphous-to-crystalline transition along with the evolution of nano-sized particles in the microstructure. The crystalline phase was Ni-Ag solid solution. The relative volume fraction of the nano-sized particles increased gradually with time. There was however no detectable decomposition of solid solution phase till about 4 h of annealing. Beyond 4 h phase separation initiated and pure Ag and Ni phases formed in the film. This study provides a methodology by which microstructural engineering of as-electrodeposited amorphous Ag-Ni films can be conducted to isolate a particular microstructure in order to tap specific potentially usable functionalities. (C) 2013 Elsevier B.V. All rights reserved.

Transmission electron microscopy study of Ni-rich, Ag-Ni nanowires

Present work provides an electrodeposition based methodology for synthesizing Ni-rich, Ag-Ni nanowires using an alumina template. Ag-Ni system shows negligible solid solubility in the bulk. Detailed structural and compositional characterization of as-synthesized nanowires using transmission electron microscopy technique revealed a two phase microstructure. Regions along and near the nanowire axis contained crystalline Ag-Ni solid solution phase with Ag-rich composition. Whereas, regions away from the axis and near the nanowire boundary predominantly contained nanocrystalline Ni-rich, Ni-Ag solid solution phase. (C) 2013 Elsevier B. V. All rights reserved.

An electron rich porous extended framework as a heterogeneous catalyst for Diels-Alder reactions

An electron rich porous metal-organic framework (MOF) has been synthesized, which acts as an effective heterogeneous catalyst for Diels-Alder reactions through encapsulation of the reactants in confined nano-channels of the framework.

Li3MRuO5 (M = Co, Ni), new lithium-rich layered oxides related to LiCoO2: promising electrochemical performance for possible application as cathode materials in lithium ion batteries

We describe the synthesis and crystal structure of Li3MRuO5 (M = Co and Ni), new rock salt related oxides. Both the oxides crystallize in the layered LiCoO2 (alpha-NaFeO2) structure, as revealed by powder XRD data. Magnetic susceptibility data suggest that the oxidation states of transition metals are Li3Co3+(ls)Ru4+(ls) O-5 (ls = low spin) for the M = Co compound and Li3Ni2+Ru5+O5 for the M = Ni compound. Electrochemical investigations of lithium deintercalation-intercalation behaviour reveal that both Co and Ni phases exhibit attractive specific capacities of ca. 200 mA h g(-1) at an average voltage of 4 V that has been interpreted as due to the oxidation of Co3+ and Ru4+ in Li3CoRuO5 and Ni2+ to Ni4+ in the case of Li3NiRuO5. Thus, a different role of Ru ions is played in the isostructural oxides. Finally, in both cases evidence of irreversible behaviour above 4.2 V is observed and interpreted as formation of high valent ions or alternatively oxidation of oxide ions.

Biological sulfate reduction of a sulfate-rich industrial waste liquor using sulfate reducing bacteria

An industrial waste liquor having high sulfate concentrations was subjected to biological treatment using the sulfate-reducing bacteria (SRB) Desulfovibrio desulfuricans. Toxicity levels of different sulfate, cobalt and nickel concentrations toward growth of the SRB with respect to biological sulfate reduction kinetics was initially established. Optimum sulfate concentration to promote SRB growth amounted to 0.8 - 1 g/L. The strain of D. desulfuricans used in this study initially tolerated up to 4 -5 g/L of sulfate or 50 mg/L of cobalt and nickel, while its tolerance could be further enhanced through adaptation by serial subculturing in the presence of increasing concentrations of sulfate, cobalt and nickel. From the waste liquor, more than 70% of sulfate and 95% of cobalt and nickel could be precipitated as sulfides, using a preadapted strain of D. desulfuricans. Probable mechanisms involving biological sulfide precipitation and metal adsorption onto precipitates and bacterial cells are discussed.

Single crystalline magnetite, maghemite, and hematite nanoparticles with rich coercivity

One-pot synthesis of amorphous iron oxide nanoparticles with two different dimensions (<5 nm and 60 nm) has been achieved using the reverse micelle method, with <5 nm nanoparticles separated from the stable colloid by exploiting their magnetic behaviour. The transformation of the as-prepared amorphous powders into Fe3O4 and Fe2O3 phases (gamma and alpha) is achieved by carrying out controlled annealing at elevated temperatures under different optimized conditions. The as-prepared samples resulting from micellar synthesis and the corresponding annealed ones are thoroughly characterized by powder X-ray diffraction, transmission electron microscopy (TEM), and by Raman and X-ray photoelectron spectroscopies. Expectedly, the magnetic characteristics of Fe3O4 and Fe2O3 phase (gamma and alpha) nanoparticles are found to have strong dependence on their phase, dimension, and morphology. The coercivity of Fe3O4 and Fe2O3 (gamma and alpha) nanoparticles is reasonably high, even though high resolution TEM studies bring out that these nanoparticles are single crystalline. This is in contrast with previous reports wherein poly-crystallinity of iron oxides nanoparticles has been regarded as a prerequisite for high coercivity.

Oxy-steam gasification of biomass for hydrogen rich syngas production using downdraft reactor configuration

The paper focuses on the use of oxygen and steam as the gasification agents in the thermochemical conversion of biomass to produce hydrogen rich syngas, using a downdraft reactor configuration. Performance of the reactor is evaluated for different equivalence ratios (ER), steam to biomass ratios (SBR) and moisture content in the fuel. The results are compared and evaluated with chemical equilibrium analysis and reaction kinetics along with the results available in the literature. Parametric study suggests that, with increase in SBR, hydrogen fraction in the syngas increases but necessitates an increase in the ER to maintain reactor temperature toward stable operating conditions. SBR is varied from 0.75 to 2.7 and ER from 0.18 to 0.3. The peak hydrogen yield is found to be 104g/kg of biomass at SBR of 2.7. Further, significant enhancement in H-2 yield and H-2 to CO ratio is observed at higher SBR (SBR=1.5-2.7) compared with lower range SBR (SBR=0.75-1.5). Experiments were conducted using wet wood chips to induce moisture into the reacting system and compare the performance with dry wood with steam. The results clearly indicate the both hydrogen generation and the gasification efficiency ((g)) are better in the latter case. With the increase in SBR, gasification efficiency ((g)) and lower heating value (LHV) tend to reduce. Gasification efficiency of 85.8% is reported with LHV of 8.9MJNm(-3) at SBR of 0.75 compared with 69.5% efficiency at SBR of 2.5 and lower LHV of 7.4 at MJNm(-3) at SBR of 2.7. These are argued on the basis of the energy required for steam generation and the extent of steam consumption during the reaction, which translates subsequently in the LHV of syngas. From the analysis of the results, it is evident that reaction kinetics plays a crucial role in the conversion process. The study also presents the importance of reaction kinetics, which controls the overall performance related to efficiency, H-2 yield, H-2 to CO fraction and LHV of syngas, and their dependence on the process parameters SBR and ER. Copyright (c) 2013 John Wiley & Sons, Ltd.

Unconstrained Homooligomeric gamma-Peptides Show High Propensity for C-14 Helix Formation

Monosubstituted gamma(4)-residues (gamma(4)Leu, gamma(4)Ile, and gamma(4)Val) form helices even in short homooligomeric sequences. C-14 helix formation is established by X-ray diffraction in homooligomeric (gamma)(n) tetra-, hexa- and decapeptide sequences demonstrating the high propensity of gamma residues, with proteinogenic side chains, to adopt locally folded conformations.

Effect of chemical treatment on surface characteristics of sputter deposited Ti-rich NiTi shape memory alloy thin-films

NiTi thin-films were deposited by DC magnetron sputtering from single alloy target (Ni/Ti: 45/55 aL.%). The rate of deposition and thickness of sputter deposited films were maintained to similar to 35 nm min(-1) and 4 mu m respectively. A set of sputter deposited NiTi films were selected for specific chemical treatment with the solution comprising of de-ionized water, HF and HNO3 respectively. The influence of chemical treatment on surface characteristics of NiTi films before and after chemical treatment was investigated for their structure, micro-structure and composition using different analytical techniques. Prior to chemical treatment, the composition of NiTi films using energy dispersive X-ray dispersive spectroscopy (EDS), were found to be 51.8 atomic percent of Ti and 48.2 atomic percent of Ni. The structure and morphology of these films were investigated by X-ray diffraction (XRD) and scanning electron microscopy (SEM). XRD investigations, demonstrated the presence of dominant Austenite (110) phase along with Martensite phase, for untreated NiTi films whereas some additional diffraction peaks viz. (100), (101), and (200) corresponding to Rutile and Anatase phase of Titanium dioxide (TiO2) along with parent Austenite (110) phase were observed for chemically treated NiTi films. FTIR studies, it can be concluded that chemically treated films have higher tendency to form metal oxide/hydroxide than the untreated NiTi films. XPS investigations, demonstrated the presence of Ni-free surface and formation of a protective metal oxide (TiO2) layer on the surface of the films, in both the cases. The extent of the formation of surface oxide layer onto the surface of NiTi films has enhanced after chemical treatment. (C) 2014 Elsevier B.V. All rights reserved.

C-12 Helices in Long Hybrid (alpha gamma)(n) Peptides Composed Entirely of Unconstrained Residues with Proteinogenic Side Chains

Unconstrained gamma(4) amino acid residues derived by homologation of proteinogenic amino acids facilitate helical folding in hybrid (alpha gamma)(n) sequences. The C-12 helical conformation for the decapeptide, Boc-Leu-gamma(4)(R)Val](5)-OMe, is established in crystals by X-ray diffraction. A regular C-12 helix is demonstrated by NMR studies of the 18 residue peptide, Boc-Leu-gamma(4)(AR)Val](9)-OMe, and a designed 16 residue (alpha gamma)(n) peptide, incorporating variable side chains. Unconstrained (alpha gamma)(n) peptides show an unexpectedly high propensity for helical folding in long polypeptide sequences.