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.

Mass Spectrometry-Based Systems Approach for Identification of Inhibitors of Plasmodium falciparum Fatty Acid Synthase{triangledown}

The emergence of strains of Plasmodium falciparum resistant to the commonly used antimalarials warrants the development of new antimalarial agents. The discovery of type II fatty acid synthase (FAS) in Plasmodium distinct from the FAS in its human host (type I FAS) opened up new avenues for the development of novel antimalarials. The process of fatty acid synthesis takes place by iterative elongation of butyryl-acyl carrier protein (butyryl-ACP) by two carbon units, with the successive action of four enzymes constituting the elongation module of FAS until the desired acyl length is obtained. The study of the fatty acid synthesis machinery of the parasite inside the red blood cell culture has always been a challenging task. Here, we report the in vitro reconstitution of the elongation module of the FAS of malaria parasite involving all four enzymes, FabB/F (β-ketoacyl-ACP synthase), FabG (β-ketoacyl-ACP reductase), FabZ (β-ketoacyl-ACP dehydratase), and FabI (enoyl-ACP reductase), and its analysis by matrix-assisted laser desorption-time of flight mass spectrometry (MALDI-TOF MS). That this in vitro systems approach completely mimics the in vivo machinery is confirmed by the distribution of acyl products. Using known inhibitors of the enzymes of the elongation module, cerulenin, triclosan, NAS-21/91, and (–)-catechin gallate, we demonstrate that accumulation of intermediates resulting from the inhibition of any of the enzymes can be unambiguously followed by MALDI-TOF MS. Thus, this work not only offers a powerful tool for easier and faster throughput screening of inhibitors but also allows for the study of the biochemical properties of the FAS pathway of the malaria parasite.

Mass Spectrometry-Based Systems Approach for Identification of Inhibitors of Plasmodium falciparum Fatty Acid Synthase{triangledown}

The emergence of strains of Plasmodium falciparum resistant to the commonly used antimalarials warrants the development of new antimalarial agents. The discovery of type II fatty acid synthase (FAS) in Plasmodium distinct from the FAS in its human host (type I FAS) opened up new avenues for the development of novel antimalarials. The process of fatty acid synthesis takes place by iterative elongation of butyryl-acyl carrier protein (butyryl-ACP) by two carbon units, with the successive action of four enzymes constituting the elongation module of FAS until the desired acyl length is obtained. The study of the fatty acid synthesis machinery of the parasite inside the red blood cell culture has always been a challenging task. Here, we report the in vitro reconstitution of the elongation module of the FAS of malaria parasite involving all four enzymes, FabB/F (β-ketoacyl-ACP synthase), FabG (β-ketoacyl-ACP reductase), FabZ (β-ketoacyl-ACP dehydratase), and FabI (enoyl-ACP reductase), and its analysis by matrix-assisted laser desorption-time of flight mass spectrometry (MALDI-TOF MS). That this in vitro systems approach completely mimics the in vivo machinery is confirmed by the distribution of acyl products. Using known inhibitors of the enzymes of the elongation module, cerulenin, triclosan, NAS-21/91, and (–)-catechin gallate, we demonstrate that accumulation of intermediates resulting from the inhibition of any of the enzymes can be unambiguously followed by MALDI-TOF MS. Thus, this work not only offers a powerful tool for easier and faster throughput screening of inhibitors but also allows for the study of the biochemical properties of the FAS pathway of the malaria parasite.

Lipopeptides from the Banyan Endophyte, Bacillus subtilis K1: Mass Spectrometric Characterization of a Library of Fengycins

Mass spectrometric analysis of a banyan endophyte, Bacillus subtilis K1, extract showing broad spectrum antifungal activity revealed a complex mixture of lipopeptides, iturins, surfactins, and fengycins. Fractionation by reversed-phase high performance liquid chromatography (HPLC) facilitated a detailed analysis of fengycin microheterogeneity. Matrix assisted laser desorption ionization (MALDI) and electrospray ionization (ESI) mass spectrometric studies permitted the identification of several new fengycin variants. Four major sites of heterogeneity are identified: (1) N-terminus beta-hydroxy fatty acid moiety, where chain length variation and the presence of unsaturation occur, (2) position 6 (Ala/Val/Ile/Leu), (3) position 10 (Val/Ile) within the macrocyclic ring, and (4) Gln to Glu replacement at position 8, resulting in fengycin variants that differ in mass by 1 Da. Diagnostic fragment ions provide a quick method for localizing the sites of variation in the macrocycle or the linear segment. Subsequent establishment of the sequences is achieved by MS/MS analysis of linear fengycin species produced by hydrolysis of the macrocyclic lactone. Unsaturation in the fatty acid chain and the presence of linear precursors in the B. subtilis K1 extract are also established by mass spectrometry. The anomalous distribution of intensities within isotopic multiplets is a diagnostic for Gln/Glu replacements. High resolution mass spectrometry facilitates the identification of fengycin species differing by 1 Da by localizing the variable position (Gln(8)/Glu(8)) in the fengycin variants.

Primary Structural Documentation of the Major Urinary Protein of the Indian Commensal Rat (Rattus rattus) Using a Proteomics Platform

Purpose: A number of proteome studies have been performed recently to identify pheromone-related protein expression and their molecular function using genetically modified rodents' urine. However, no such studies have used Indian commensal rodents; interestingly, in a previous investigation, we confirmed the presence of volatile molecules in commensal rodents urine and these molecules seem to be actively involved in pheromonal communication. Therefore, the present study aims to identify the major urinary protein [MUP] present in commensal rat urine, which will help us to understand the protein's expression pattern and intrinsic properties among the rodents globally. Experimental Design: Initially, the total urinary proteins were separated by 1-D and 2-D electrophoresis and then subsequently analyzed by Matrix Assisted Laser Desorption Ionization-Time of Flight and Mass Spectrometer (MALDI-TOF/MS). Furthermore, they were then fragmented with the aid of a Tandem Mass Spectrometer (TOF/TOF) and the identified sequences aligned and confirmed using similarity with the deduced primary structures of members of the lipocalin superfamily.Results: The SDS-PAGE protein profiles showed distinct proteins with molecular masses of 15, 22.4, 25, 28, 42, 50, 55, 68, and 91 kDa. Of these proteins, the 22.4 kDa protein was considered to be target candidate. When 2D electrophoresis was carried out, about similar to 50 spots were detected with different masses and various pI ranges. The 22.4 kDa protein was found to have a pI of about 4.9. This 22.4 kDa protein spot was digested and subjected to mass spectrometry; it was identified as rat MUP. The fragmented peptides from the rat MUP at 935, 1026, 1192, and 1303 m/z were further fragmented with the aid of MS/MS and generated de novo sequence and this confirmed this protein to be the MUP present in the urine of commensal rats.Conclusion: The present investigation confirms the presence of MUP with a molecular mass of 22.4 kDa in the urine of commensal rats. This protein may be involved in the binding of volatile molecules and opens up a discussion about how volatile and non-volatile molecules in the commensal rats' urine may contribute chemo-communication.

SEC-MALDI-TOF mass spectral characterization of a hyperbranched polyether prepared via melt transetherification

An AB(2) monomer, 1-(2-hydroxyethoxy)-3,5-bis-(methoxymethyl)-2,4,6-trimethylbenzene, was synthesized from mesitol and melt-polycondensed in the presence of an acid catalyst via a transetherification process at 145-150 degreesC to yield a soluble, moderately high molecular weight hyperbranched polyether. The degree of branching in the polymer was calculated to be 0.78 by a comparison of its NMR spectrum with that of an appropriately designed model compound. The weight-average molecular weight of the hyperbranched polymer was determined to be 64,600 (weight-average molecular weight/number-average molecular weight = 5.2) by size exclusion chromatography (SEC) in CHCl3, with polystyrene standards. The origin of the broad molecular weight distribution, which could either be intrinsic to such hyperbranched structures or be due to structural heterogeneity, was further probed by the fractionation of the samples by SEC and by the subjection of each fraction to matrix-assisted laser desorption/ionization time-of-flight mass spectral analysis. The mass spectral analysis suggested the presence of two primary types of species: one corresponding to the simple branched structure and the other to macrocyclics. Interestingly, from the relative intensities of the two peaks, it was apparent that cyclization became favorable at higher conversions in the melt transetherification process. (C) 2002 Wiley Periodicals, Inc.

Biodegradation of acrylamide by acrylamidase from Stenotrophomonas acidaminiphila MSU12 and analysis of degradation products by MALDI-TOF and HPLC

The present study examines an improved detoxification and rapid biological degradation of toxic pollutant acrylamide using a bacterium. The acrylamide degrading bacterium was isolated from the soil followed by its screening to know the acrylamide degrading capability. The minimal medium containing acrylamide (30 mM) served as a sole source of carbon and nitrogen for their active growth. The optimization of three different factors was analyzed by using Response Surface Methodology (RSM). The bacteria actively degraded the acrylamide at a temperature of 32 degrees C, with a maximum growth at 30 mM substrate (acrylamide) concentration at a pH of 7.2. The acrylamidase activity and degradation of acrylamide was determined by High Performance Liquid Chromatography (HPLC) and Matrix Assisted Laser Desorption and Ionization Time of Flight mass spectrometer (MALDI-TOF). Based on 168 rRNA analysis the selected strain was identified as Gram negative bacilli Stenotrophomonas acidaminiphila MSU12. The acrylamidase was isolated from bacterial extract and was purified by HPLC, whose mass spectrum showed a molecular mass of 38 kDa. (C) 2014 Elsevier Ltd. All rights reserved.

A sleep-inducing peptide from the venom of the Indian cone snail Conus araneosus

The marine snail Conus araneosus has unusual significance due to its confined distribution to coastal regions of southeast India and Sri Lanka. Due to its relative scarceness, this species has been poorly studied. In this work, we characterized the venom of C. araneosus to identify new venom peptides. We identified 14 novel compounds. We determined amino acid sequences from chemically-modified and unmodified crude venom using liquid chromatography-electrospray ionization mass spectrometry and matrix assisted laser desorption ionization time-of-flight mass spectrometry. Ten sequences showed six Cys residues arranged in a pattern that is most commonly associated with the M-superfamily of conotoxins. Four other sequences had four Cys residues in a pattern that is most commonly associated with the T-superfamily of conotoxins. The post-translationally modified residue (pyroglutamate) was determined at the N-terminus of two sequences, ar3h and ar3i respectively. In addition, two sequences, ar3g and ar3h were C-terminally amidated. At a dose of 2 nmol, peptide ar3j elicited sleep when injected intraperitoneally into mice. To our knowledge, this is the first report of a peptide from a molluscivorous cone snail with sleep-inducing effects in mice. The novel peptides characterized herein extend the repertoire of unique peptides derived from cone snails and may add value to the therapeutic promise of conotoxins. (C) 2015 Elsevier Ltd. All rights reserved.

Detection of alpha(2u)-globulin and its bound putative pheromones in the preputial gland of the Indian commensal rat (Rattus rattus) using mass spectrometry

The role of pheromones and pheromone-binding proteins in the laboratory rat has been extensively investigated. However, we have previously reported that the preputial gland of the Indian commensal rat produces a variety of pheromonal molecules and preputial glands would seem to be the predominant source for pheromonal communication. The presence of pheromone-binding proteins has not yet been identified in the preputial gland of the Indian commensal rat; therefore, the experiments were designed to unravel the alpha(2u)-globulin (alpha 2u) and its bound volatiles in the commensal rat. Total preputial glandular proteins were first fractionated by sodium dodecyl sulfate/polyacrylamide gel electrophoresis (SDS-PAGE) and subsequently analyzed by mass spectrometry. Further, we purified alpha 2u and screened for the presence of bound pheromonal molecules with the aid of gas chromatography/mass spectrometry (GC/MS). A novel alpha 2u was identified with a high score and this protein has not been previously described as present in the preputial gland of Indian commensal rats.This novel alpha 2u was then characterized by tandem mass spectrometry (MS/MS). Peptides with m/z values of 969, 1192, 1303 and 1876 were further fragmented with the aid of MS/MS and generated de novo sequences which provided additional evidence for the presence of alpha 2u in the preputial gland. Finally, we identified the presence of farnesol 1 and 2 bound to alpha 2u. The present investigation confirms the presence of alpha 2u (18.54 kDa) in the preputial gland of the Indian commensal rat and identifies farnesol 1 and 2 as probably involved in chemo-communication by the Indian commensal rat.Copyright (C) 2010 John Wiley & Sons, Ltd.

Reactive Pulsed Laser Deposition of titanium nitride thin film: Optimization of process parameters using Secondary Ion Mass Spectrometry

Reactive Pulsed Laser Deposition is a single step process wherein the ablated elemental metal reacts with a low pressure ambient gas to form a compound. We report here a Secondary Ion Mass Spectrometry based analytical methodology to conduct minimum number of experiments to arrive at optimal process parameters to obtain high quality TiN thin film. Quality of these films was confirmed by electron microscopic analysis. This methodology can be extended for optimization of other process parameters and materials. (C) 2009 Elsevier B.V. All rights reserved.

Matrix-Assisted Refolding, Purification and Activity Assessment Using a `Form Invariant' Assay for Matrix Metalloproteinase 2 (MMP2)

Matrix metalloproteinases expression is used as biomarker for various cancers and associated malignancies. Since these proteinases can cleave many intracellular proteins, overexpression tends to be toxic; hence, a challenge to purify them. To overcome these limitations, we designed a protocol where full length pro-MMP2 enzyme was overexpressed in E. coli as inclusion bodies and purified using 6xHis affinity chromatography under denaturing conditions. In one step, the enzyme was purified and refolded directly on the affinity matrix under redox conditions to obtain a bioactive protein. The pro-MMP2 protein was characterized by mass spectrometry, CD spectroscopy, zymography and activity analysis using a simple in-house developed `form invariant' assay, which reports the total MMP2 activity independent of its various forms. The methodology yielded higher yields of bioactive protein compared to other strategies reported till date, and we anticipate that using the protocol, other toxic proteins can also be overexpressed and purified from E. coli and subsequently refolded into active form using a one step renaturation protocol.

Thermal degradation products of poly(styrenesulfides) investigated by direct pyrolysis�mass spectrometry and flash pyrolysis�gas chromatography/mass spectrometry

The thermal degradation products of two sulfur polymers, poly(styrenedisulfide) (PSD) and poly(styrenetetrasulfide) (PST), were investigated in parallel by direct pyrolysis-mass spectrometry (DPMS) and by flash pyrolysis-GC/MS (Py-GC/MS). The time-scale of the two pyrolysis techniques is quite different, and therefore they were able to detect significantly different products in the pyrolysis of PSD and PST because of the thermal lability of sulfur-containing compounds. However, the results obtained are not contradictory, and satisfactory mechanisms for the thermal degradation of PSD and PST have been derived from the overall evidence available. Pyrolysis compounds containing sulfur, styrene, and a number of cyclic styrene sulfides and diphenyldithianes have been observed by DPMS. However, in flash pyrolysis-GC/MS, styrene, sulfur, only one cyclic styrene sulfide, and two isomers of diphenylthiophene have been detected. These thiophene derivatives were indeed absent among the compounds obtained by DPMS because they were the terminal (most thermally stable) species arising from further decomposition of the cyclic styrene sulfides formed in the primary thermal degradation processes of PSD and PST.

Thermal degradation processes in polysulfide copolymers investigated by direct pyrolysis mass spectrometry and flash pyrolysis-gas chromatography/mass spectrometry

This is the first report on the analysis of random block polysulfide copolymers containing different amounts of repeating units in the copolymer backbone, which has been studied by direct pyrolysis mass spectrometry (DPMS) and by pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS). The homopolymers such as poly(ethylene sulfide) (PES), poly(styrene sulfide) (PSS), and two random copolymers, viz., poly(ethylene sulfide(x)-co-styrene sulfide(y)) [copolymer I (x = y = 0.5) and copolymer II (x = 0.74, y = 0.26)] were investigated by both DPMS and Py-GC/MS (except copolymer II) techniques. In the case of copolymer I, the thermal degradation products of SE1, SE2, S-2, and S2E (S = styrene sulfide, E = ethylene sulfide) were detected in DPMS, whereas the formation of SE1 and SE2 were observed by Py-GC/MS technique. However, for copolymer II, SE3 was also found along with SE1, SE2, S-2, and S2E in DPMS. The formation of additional product (SE3) observed in copolymer II could be due to an increase in the block length formed during copolymerization. Further, a comparative study on thermal degradation of PES, poly(ethylene disulfide) (PEDS), and poly(ethylene tetrasulfide) (PETS) were investigated by Py-GC/MS. The pyrolysis products detected by both DPMS and Py-GC/MS indicates that the thermal decomposition of these polymers yield cyclic sulfides through an intramolecular exchange or by backbiting processes. The linear products with thiol and vinyl groups were also observed by Py-GC/MS along with the cyclic products via carbon hydrogen transfer reaction.

Sensitive Liquid Chromatography-Tandem Mass Spectrometry Method for the Determination of Olanzapine in Human Urine

A sensitive and selective liquid chromatographic-tandem mass spectrometric (LC-MS-MS) method was developed to determine olanzapine (OLZ) in human urine. After solid-phase extraction with SPE cartridge, the urine sample was analysed on a C-18 column (Symmetry 3.5 mu m, 50 x 4.6 mm i.d) interfaced with a triple quadrupole tandem mass spectrometer. Positive electrospray ionization was employed as the ionization source. The mobile phase consisted of ammonium acetate (pH 7.8)-acetonitrile (10:90, v/v). The method was linear over a concentration range of 1-100 ngml(-1). The lower limit of quantitation was 1 ngml(-1). The intra-day and inter-day relative standard deviation across three validation runs over the entire concentration range was < 11.5 %. The accuracy determined at three concentrations (8.0, 50.0 and 85.0 ngml(-1) OLZ) was within +/- 1.21 % in terms of relative errors.

High precision Mg isotope measurements of meteoritic samples by secondary ion mass spectrometry

The possibility of establishing an accurate relative chronology of the early solar system events based on the decay of short-lived Al-26 to Mg-26 (half-life of 0.72 Myr) depends on the level of homogeneity (or heterogeneity) of Al-26 and Mg isotopes. However, this level is difficult. to constrain precisely because of the very high precision needed for the determination of isotopic ratios, typically of +/- 5 ppm. In this study, we report for the first time a detailed analytical protocol developed for high precision in situ Mg isotopic measurements ((25)mg/(24)mg and (26)mg/Mg-24 ratios, as well as Mg-26 excess) by MC-SIMS. As the data reduction process is critical for both accuracy and precision of the final isotopic results, factors such as the Faraday cup (FC) background drift and matrix effects on instrumental fractionation have been investigated. Indeed these instrumental effects impacting the measured Mg-isotope ratios can be as large or larger than the variations we are looking for to constrain the initial distribution of Al-26 and Mg isotopes in the early solar system. Our results show that they definitely are limiting factors regarding the precision of Mg isotopic compositions, and that an under- or over-correction of both FC background instabilities and instrumental isotopic fractionation leads to important bias on delta Mg-25, delta(26)mg and Delta Mg-26 values (for example, olivines not corrected for FC background drifts display Delta Mg-26 values that can differ by as much as 10 ppm from the truly corrected value). The new data reduction process described here can then be applied to meteoritic samples (components of chondritic meteorites for instance) to accurately establish their relative chronology of formation.