MS(n) characterization of protonated cyclic peptides and metal complexes

Application of Combined Irradiation Mutagenesis Technique for Hyperproduction of Surfactin in Bacillus velezensis Strain AF_3B

The major challenge in large-scale industrial use of lipopeptide surfactin is the low yield by indigenous bacterial strains and the higher cost of its production that have been proved as a limiting factor in commercial applications. Therefore, there is an urgent demand for high-yielding strains that can be achieved through strain improvement. A first report on the use of a combination of UV and gamma-irradiation mutagenesis for the development of surfactin hyperproducing mutants of Bacillus spp. proved to be significant and resulted in a twofold enhancement in surfactin yield. The mutant was able to grow and produce surfactin on all the tested carbon and nitrogen sources, while 2% glycerol favored maximum surfactin yield (1.62 g/L) as compared to the wild-type strain that showed a maximum 0.85 g/L surfactin yield at 3% sucrose. Additionally, the mutant exhibited a good yield of pure surfactin, that is, 1.55 g/L as compared to the wild strain (0.411 g/L) by using corn steep liquor as the main component of the fermentation medium. The study concluded overall a threefold enhancement in the relative abundance of purified surfactin and its isoforms detected by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) analysis in mutant strain AF-UVγ2500.

Origin and characterization of cyclodepsipeptides: Comprehensive structural approaches with focus on mass spectrometry analysis of alkali-cationized molecular species

Cyclodepsipeptides (CDPs) represent a huge family of chemically and structurally diverse molecules with a wide ability for molecular interactions. CDPs are cyclic peptide-related natural products made up of both proteinogenic and nonproteinogenic amino acids linked by amide and ester bonds. The combined use of different analytical methods is required to accurately determine their integral structures including stereochemistry, thus allowing deeper insights into their often-intriguing bioactivities and their possible usefulness. Our goal is to present the various methods developed to accurately characterize CDPs. Presently, Marfey's method and NMR (nuclear magnetic resonance) are still considered the best for characterizing CDP configuration. Nevertheless, electrospray-high resolution tandem mass spectrometry (ESI-HRMS/MS) is of great value for efficiently resolving CDP's composition and sequences. For instance, recent data shows that the fragmentation of cationized CDPs (e.g., [M + Li]+ and [M + Na]+) leads to selective cleavage of ester bonds and specific cationized product ions (b series) useful to get unprecedented sequence information. Thus, after a brief presentation of their structure, biological functions, and biosynthesis, we also provide a historic overview of these various analytical approaches as well as their advantages and limitations with a special emphasis on the emergence of methods based on HRMS/MS through recent fundamental works and applications.

Exploring the Effects of Cyclosporin A to Isocyclosporin A Rearrangement on Ion Mobility Separation

Cyclosporin A (CycA) is a peptide secondary metabolite derived from fungi that plays a crucial role in transplantation surgery. Cyclic traveling wave ion mobility mass spectrometry (IM-MS) revealed an N → O peptidyl shift in singly protonated CycA to isocyclosporin A (isoA), whereas no such isomerization was observed for doubly protonated and sodiated molecules. CycA and isoA were able to be separated by considering doubly protonated precursors using a specific ion fragment. In parallel, sodium ion stabilization facilitated the simultaneous separation and quantitation of singly charged cyclosporin isomers with the limit of detection and coefficient of determination of 1.3% and 0.9908 for CycA in isoA and 1.0% and 0.9830 for isoA in CycA, respectively. Finally, 1H-13C gHSQC NMR experiments permitted parallel recording of up to 11 cyclosporin conformers. The ratios were determined by integrating the volume of cross-peaks of the upfield resonating hydrogen in the diastereotopic methylene group of sarcosine-3.

Lipopeptide production by Bacillus atrophaeus strain B44 and its biocontrol efficacy against cotton rhizoctoniosis

OBJECTIVES

An assay was conducted to show the comparisons the effects of nine metal ions on antagonistic metabolites (lipopeptides, siderophores and gibberellins) by Bacillus atrophaeus strain B44 using well-diffusion assays, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) analysis, chrome azurol S plus mannitol salt agar (CAS-MSA) tests, and reversed-phase high-performance liquid chromatography (RP-HPLC) analysis. This assay is also designed to demonstrate the biocontrol efficacy of B44 against cotton rhizoctoniosis using pot culture tests.

RESULTS

Both the lipopeptide yield and the antimicrobial activity of B44 increase with the MnSO₄, MgSO₄, CaCO₃, and CuSO₄ treatments and either have no effect or decreased lipopeptide yield and antimicrobial activity with the FeSO₄, K₂HPO₄, KCl, KH₂PO₄ and ZnSO₄ treatments. The medium containing MgSO₄ has no significant effect on either the lipopeptide yield or antimicrobial activity. MALDI-TOF-MS analysis shows a broad range of m/z peaks, indicating that strain B44 produces a complex mixture of iturin, surfactin, and fengycin lipopeptides. Gibberellin production by strain B44 varies greatly depending on the culture medium, and the siderophore production is not significantly affected by the culture medium. Pot tests show that lipopeptide production affects the disease control efficacy of strain B44.

CONCLUSION

The biocontrol efficacy of B. atrophaeus strain B44 is related to the lipopeptide yield. Moreover, B. atrophaeus strain B44 significantly increases the size of cotton seedlings, which is related to the GA₃ concentration.

Combination of Isotope Labeling and Molecular Networking of Tandem Mass Spectrometry Data To Reveal 69 Unknown Metabolites Produced by Penicillium nordicum

The secondary metabolome of Penicillium nordicum is poorly documented despite its frequent detection on contaminated food and its capacity to produce toxic metabolites such as ochratoxin A. To characterize metabolites produced by this fungi, we combined a full stable isotopes labeling with the dereplication of tandem mass spectrometry (MS/MS) data by molecular networking. First, the untargeted metabolomic analysis by high-resolution mass spectrometry of a double stable isotope labeling of P. nordicum enabled the specific detection of its metabolites and the unambiguous determination of their elemental composition. Analyses showed that infection of substrate by P. nordicum lead to the production of at least 92 metabolites and that 69 of them were completely unknown. Then, curated molecular networks of MS/MS data were generated with GNPS and MetGem, specifically on the features of interest, which allowed highlighting 13 fungisporin-related metabolites that had not previously been identified in this fungus and 8 that had never been observed in any fungus. The structures of the unknown compounds, namely, a native fungisporin and seven linear peptides, were characterized by tandem mass spectrometry experiments. The analysis of P. nordicum growing on its natural substrates, i.e. pork ham, turkey ham, and cheese, demonstrated that 10 of the known fungisporin-related metabolites and three of the new metabolites were also synthesized. Thus, the curation of data for molecular networking using a specific detection of metabolites of interest with stable isotopes labeling allowed the discovery of new metabolites produced by the food contaminant P. nordicum.

Multifarious allelochemicals exhibiting antifungal activity from Bacillus subtilis MBCU5

A potential antagonist, designated strain Bacillus subtilis MBCU5 was previously isolated from vermicompost-amended soils of Gandhinagar, Gujarat, India. Crude allelochemicals from strain MBCU5 displayed strong antifungal activity against Macrophomina phaseolina as well as Rhizoctonia solani. These crude allelochemicals were tentatively identified as iturin, fengycin and surfactin through TLC and HPTLC analysis. Lipopeptides produced by MBCU5 were identified by MALDI-TOF-MS and LC-ESI-MS/MS analysis showed that iturin homologues (m/z 1020-1120), surfactin (m/z 1008.7 and m/z 1022.7), fengycin A and fengycin B (m/z 1400-1550) types of allelochemicals which are responsible for antifungal activity against pathogens. PCR analysis showed presence of genes (i.e. Iturin A synthetase KJ531680 and Surfactin synthetase KJ601726) involved in the biosynthesis of allelochemicals. Many reports showed lipopeptides from Bacillus species; this is the first report executed of multifarious allelochemicals from vermicompost-amended soil due to the presence of predominant Bacillus species.

Ion trap mass spectrometry of surfactins produced by Bacillus subtilis SZMC 6179J reveals novel fragmentation features of cyclic lipopeptides

RATIONALE

Surfactins are mixtures of cyclic lipopeptides consisting of variants of a heptapeptide and a linked β-hydroxy fatty acid with various chain lengths of 13-15 carbon atoms. A lactone bridge between the β-hydroxy functional group of the fatty acid and the carboxy terminal functional component of the peptide chain form their cyclic structures. Such lipopeptides, produced mainly by Bacillus species, possess several remarkable biological effects such as antitumor and antimicrobial activities, some of which are highly promising for utilization in plant disease biocontrol. The strain Bacillus subtilis SZMC 6179J was previously shown to exert significant antifungal properties against various phytopathogenic filamentous fungi; therefore, we characterized the structural features of the surfactins produced by this strain in order to explore the origin of the observed antagonistic effects of this potential biocontrol organism.

METHODS

Bacillus subtilis SZMC 6179J was used to produce surfactins, which were characterized by high-performance liquid chromatography/electrospray ionisation ion trap mass spectrometry (HPLC/ESI-ITMS) techniques after precipitation and extraction steps.

RESULTS

The 26 isoforms separated and identified represent three types of known surfactin variants and a fourth, previously unknown group characterised by the replacement of the leucine residue by valine in position 2. The relative amounts of this newly identified surfactin group were below 1%, and their cyclic structures were closed by C13-C15 hydroxy fatty acids. The structural assessment of the isoforms by MS(2) measurements led to the characterisation and description of a new fragmentation mechanism of surfactins.

CONCLUSIONS

The detected new natural lipoheptapeptide compounds with modified structures have significant potential for biotechnological and biocontrol applications. The complementary ITMS(2) data as well as the described internal fragmentation mechanism obtained from the sodiated surfactin molecules may further facilitate the structural elucidation of cyclic lipopeptides in the future. Copyright © 2016 John Wiley & Sons, Ltd.

Systematic comparison of the functional physico-chemical characteristics and biocidal activity of microbial derived biosurfactants on blood-derived and breast cancer cells

HYPOTHESIS

The cytotoxicity of biosurfactants on cell membranes may be influenced by composition of their hydrophilic head and hydrophobic tails. It is hypothesised that they form mixed micelles which exert a detergent-like effect that disrupts the plasma membrane. The functional physico-chemical and biocidal characteristics of four biosurfactants were concurrently investigated to determine which of their structural characteristics may be tuned for greater efficacy.

EXPERIMENTS

Rhamnolipid-95, rhamnolipid-90, surfactin and sophorolipid were characterised using FTIR, LC-MS, HPLC, surface tension and critical micelle concentration. Their biocidal activity against HEK 293, MCF-7 and THP-1 cell lines were investigated by MTT assay, using doxorubicin as cytotoxic control. Growth curves were established for all cell lines using trypan blue (TB) and MTT assays, corresponding doubling time (DT) and growth rate were obtained and compared.

FINDINGS

HEK 293 cell-line had the highest growth rate amongst the three cell lines. For TB assay, growth of HEK 293>THP-1 and for MTT, HEK 293>MCF-7 while the DT was in the order of THP-1>MCF-7>HEK 293. Sophorolipid showed anti-proliferative activity comparable to doxorubicin on THP-1>MCF-7>HEK 293. THP-1 showed high sensitivity to sophorolipid with IC50 of 10.50, 25.58 and 6.78(μg/ml) after 24, 48 and 72h respectively. However, sophorolipid was cytotoxic from 24 to 72h on HEK 293 cell lines with IC50 of 21.53, 40.57 and 27.53μg/ml respectively. Although, doxorubicin showed higher anti-proliferative activity than all biosurfactants, it had poorer selectivity index for the same time durations compared to the biosurfactants. This indicates that biosurfactants were more effective for slowing the growth of the tested cancer cell lines and hence may be potential candidates for use in human cancer therapy. Physico-chemical characteristics of the biosurfactants suggest that their mechanism of action may be due to activity on the cell membrane.

Exploitation of the Ornithine Effect Enhances Characterization of Stapled and Cyclic Peptides

A method to facilitate the characterization of stapled or cyclic peptides is reported via an arginine-selective derivatization strategy coupled with MS/MS analysis. Arginine residues are converted to ornithine residues through a deguanidination reaction that installs a highly selectively cleavable site in peptides. Upon activation by CID or UVPD, the ornithine residue cyclizes to promote cleavage of the adjacent amide bond. This Arg-specific process offers a unique strategy for site-selective ring opening of stapled and cyclic peptides. Upon activation of each derivatized peptide, site-specific backbone cleavage at the ornithine residue results in two complementary products: the lactam ring-containing portion of the peptide and the amine-containing portion. The deguanidination process not only provides a specific marker site that initiates fragmentation of the peptide but also offers a means to unlock the staple and differentiate isobaric stapled peptides.

Twisted amide electrophiles enable cyclic peptide sequencing

There is an ever-increasing interest in synthetic methods that not only enable peptide macrocyclization, but also facilitate downstream application of the synthesized molecules. We have found that aziridine amides are stereoelectronically attenuated in a macrocyclic environment such that non-specific interactions with biological nucleophiles are reduced or even shut down. The electrophilic reactivity, revealed at high pH, enables peptide sequencing by mass spectrometry, which will further broaden the utility of aziridine amide-containing libraries of macrocycles.

Selective complexation of alkaline earth metal ions with nanotubular cyclopeptides: DFT theoretical study

The interaction of alkaline earth metal cations including Be²⁺, Mg²⁺, Ca²⁺, Sr²⁺ and Ba²⁺ with cyclic peptides containing 3 or 4 (S) alanine molecules (CyAla3 and CyAla4) was investigated by density functional theory (DFT-CAM-B3LYP and DFT-B3LYP).

The bacterial lipopeptide iturins induce Verticillium dahliae cell death by affecting fungal signalling pathways and mediate plant defence responses involved in pathogen-associated molecular pattern-triggered immunity

Verticillium wilt in cotton caused by Verticillium dahliae is one of the most serious plant diseases worldwide. Because no known fungicides or cotton cultivars provide sufficient protection against this pathogen, V. dahliae causes major crop yield losses. Here, an isolated cotton endophytic bacterium, designated Bacillus amyloliquefaciens 41B-1, exhibited greater than 50% biocontrol efficacy against V. dahliae in cotton plants under greenhouse conditions. Through high-performance liquid chromatography and mass analysis of the filtrate, we found that the antifungal compounds present in the strain 41B-1 culture filtrate were a series of isoforms of iturins. The purified iturins suppressed V. dahliae microsclerotial germination in the absence or presence of cotton. Treatment with the iturins induced reactive oxygen species bursts, Hog1 mitogen-activated protein kinase (MAPK) activation and defects in cell wall integrity. The oxidative stress response and high-osmolarity glycerol pathway contribute to iturins resistance in V. dahliae. In contrast, the Slt2 MAPK pathway may be involved in iturins sensitivity in this fungus. In addition to antagonism, iturins could induce plant defence responses as activators and mediate pathogen-associated molecular pattern-triggered immunity. These findings suggest that iturins may affect fungal signalling pathways and mediate plant defence responses against V. dahliae.

Negative charge induced dissociation: fragmentation of deprotonated N-benzylidene-2-hydroxylanilines in electrospray ionization mass spectrometry

Unimolecular reactivities of different N-benzylidene-2-hydroxylaniline anions were investigated in gas phase by electrospray ionization tandem mass spectrometry. All the collision-induced dissociation spectra of N-benzylidene-2-hydroxylaniline anions show similar ions at phenyl anions, neutral loss of benzonitrile and benzoxazole anions, respectively. The possible fragmentation pathway was probed through deuterium labeling and various group substituents experiments. Computational results were applied to shed light on the mechanism of fragmentation patterns. The proton in the CH=N is reactive in the formation of the concerned ions. Its direct transfer to the oxygen results in 2-hydroxyphenyl anion. Proton abstraction between benzoxazole and phenyl anion leads to the formation of benzene and benzoxazole anion.

Identification of surfactins and iturins produced by potent fungal antagonist, Bacillus subtilis K1 isolated from aerial roots of banyan (Ficus benghalensis) tree using mass spectrometry

The banyan endophyte, Bacillus subtilis K1, produces a complex mixture of lipopeptides exhibiting potent antifungal activity. These lipopeptides were purified by high-performance liquid chromatography and analyzed using MALDI-TOF-MS as well as liquid chromatography coupled with ESI-MS. A heterogenous mixture of lipopeptides belonging to three different families of cyclic lipopeptides, viz., fengycins, iturins and surfactins, was detected in the cell-free extracellular extract of B. subtilis K1. The detailed mass spectrometric characterization revealed the presence of four variants of iturin A and three variants of iturin C varying in the β-amino fatty acid chain length from C₁₃ to C₁₇. The MS/MS of monovalent alkali metal ion adducts (Na and K) of iturin suggested the Glu⁴ as a binding site for metal ion. The LC-ESI-MS/MS analysis of surfactins enabled the identification of seven surfactin variants with the variations in Val/Ile/Leu at position 4 and C₁₃–C₁₇ β-hydroxy fatty acids. This study demonstrates the application of tandem mass spectrometry in identification of closely related lipopeptides from a heterogenous mixture obtained from a natural source. Furthermore, this is the first report of an endophytic bacillus strain co-producing so many variants of surfactins and iturins.

Differentiation of cyclosporin A from isocyclosporin A by liquid chromatography/electrospray ionization mass spectrometry with post-column addition of divalent metal salt

RATIONALE

Cyclosporin A (CsA) rearranges to its isomer isocyclosporin A (isoCsA) upon acid hydrolysis and also during ionization in the ion source of the mass spectrometer. It has been reported that both compounds could not be differentiated by tandem mass spectrometry (MS/MS) using atmospheric pressure ionization (API) sources and ambiguously differentiated by using other sources. In order to analyze these compounds which are common fungal metabolites, it is relevant to develop a simple method for their differentiation.

METHODS

CsA and isoCsA were analyzed by liquid chromatography/mass spectrometry (LC/MS) with post-column addition of metal ion solutions in a quadrupole time-of-flight instrument equipped with an electrospray ionization (ESI) source.

RESULTS

Mass spectra of CsA obtained upon post-column addition of solutions of Ca(II), Cu(II) and Zn(II) showed complexes between cyclosporin and the metal, including [2CsA + Me](2+) and [CsA-H + Me](+). These complexes were not observed in the spectra of isoCsA. The same results were observed at different metal concentrations.

CONCLUSIONS

Differentiation via metal complexation in positive ion mode LC/ESI-MS was performed to simultaneously distinguish CsA and its isomer isoCsA.

Structural characterization of cyclosporin A, C and microbial bio-transformed cyclosporin A analog AM6 using HPLC-ESI-ion trap-mass spectrometry

Cyclosporin A (CyA), a cyclic undecapeptide produced by a number of fungi, contains 11 unusual amino acids, and has been one of the most commonly prescribed immunosuppressive drugs. To date, there are over sixty different analogs reported as congeners and analogs resulting from precursor-directed biosynthesis, human CYP-mediated metabolites, or microbial bio-transformed analogs. However, there is still a need for more structurally diverse CyA analogs in order to discover new biological potentials and/or improve the physicochemical properties of the existing cyclosporins. As a result of the complexity of the resulting mass spectrometric (MS) data caused by its unusual amino acid composition and its cyclic nature, structural characterization of these cyclic peptides based on fragmentation patterns using multiple tandem MS analyses is challenging task. Here, we describe, an efficient HPLC-ESI-ion trap MS(n) (up to MS(8)) was developed for the identification of CyA and CyC, a (Thr(2))CyA congener in which L-aminobutyric acid (Abu) is replaced by L-threonine (Thr). In addition, we examined the fragmentation patterns of a CyA analog obtained from the cultivation of a recombinant Streptomyces venezuelae strain fed with CyA, assigning this analog as (γ-hydroxy-MeLeu(6))CyA (otherwise, known as an human CYP metabolite AM6). This is the first report on both the MS(n)-aided identification of CyC and the structural characterization of a CyA analog by employing HPLC-ESI-ion trap MS(n) analysis.

Locating Pb2+ and Zn2+ in zinc finger-like peptides using mass spectrometry

The binding preferences of Pb(2+)and Zn(2+) in doubly charged complexes with zinc finger-like 12-residue peptides (Pep), [Mn(Pep-2(n-1)H)](2+) have been explored using tandem mass spectrometry. The peptides were synthesized strategically by blocking the N-terminus with an acetyl group and with four cysteine and/or histidine residues in positions 2, 5, 8, and 11, arranged in different motifs: CCHH, CHCH, and CCCC. The MS(2) spectra of the Pb(2+) and Zn(2+) complexes show multiple losses of water and a single methane loss and these provide a sensitive method for locating the metal dication and so elucidating its coordination. The elimination of a methane molecule indicated the position of the metal at the Cys2 residue. Whereas lead was observed to preferentially bind to cysteine residues, zinc was found to primarily bind to histidine residues and secondarily to cysteine residues. Preferential binding of lead to cysteine is preserved in the complexes with more than one Pb(2+). Key to the mechanism of the loss of water and methane is the metal dication withdrawing electrons from the proximal amidic nitrogen. This acidic nitrogen loses its hydrogen to an amidic oxygen situated four atoms away leading to formation of a five-member ring and the elimination of water.

Imaging mass spectrometry of a coral microbe interaction with fungi

Fungal infections are increasing worldwide, including in the aquatic environment. Microbiota that coexist with marine life can provide protection against fungal infections by secretion of metabolites with antifungal properties. Our laboratory has developed mass spectrometric methodologies with the goal of improving our functional understanding of microbial metabolites and guiding the discovery process of anti-infective agents from natural sources. GA40, a Bacillus amyloliquefaciens strain isolated from an octocoral in Panama, displayed antifungal activity against various terrestrial and marine fungal strains. Using matrix-assisted laser desorption/ionization-imaging mass spectrometry (MALDI-IMS), the molecular species produced by this microbe were visualized in a side-by-side interaction with two representative fungal strains, Aspergillus fumigatus and Aspergillus niger. The visualization was performed directly on the agar without the need for extraction. By evaluating the spatial distributions, relative intensities and m/z values of GA40 secreted metabolites in the fungal interactions and singly grown control colonies, we obtained insight into the antifungal activity of secreted metabolites. Annotation of GA40 metabolites observed in MALDI-IMS was facilitated by MS/MS networking analysis, a mass spectrometric technique that clusters metabolites with similar MS/MS fragmentation patterns. This analysis established that the predominant GA40 metabolites belong to the iturin family. In a fungal inhibition assay of A. fumigatus, the GA40 iturin metabolites were found to be responsible for the antifungal properties of this Bacillus strain.

Gas phase chemistry of Li+ with amides: the observation of LiOH loss in mass spectrometry

Collision-induced dissociation (CID) of Li(+) adducts of three sets of compounds that contains an amide bond, including 2-(4, 6-dimethoxypyrimidin-2-ylsulfanyl)-N-phenylbenzamide, its derivatives and simpler structures was investigated by electrospray ionization tandem mass spectrometry (ESI-MS/MS). Observed fragment ions include those that reflect loss of LiOH. Other product ions result from the Smiles rearrangement and direct C-S bond cleavage. MS/MS of H/D exchange products demonstrated occurrence of a 1,3-H shift from the amide nitrogen atom to the phenyl ring of these compounds. The LiOH loss from Li(+) adducts of amides was further examined by CID of [M + Li](+) ions of N-phenylbenzamide and N-phenylcinnamide. Loss of LiOH was essentially the sole fragmentation reaction observed for the former. For the latter, both losses of LiOH and H(2)O were discovered. The presence of electron-donating substituents of the phenyl ring of these compounds was found to facilitate elimination of LiOH, while that loss was retarded by electron-withdrawing substituents. Proposed fragment ion structures were supported by elemental compositions deduced from ultrahigh resolution Fourier transform ion cyclotron resonance tandem mass spectrometry (FTICR-MS/MS) m/z value determinations. Density functional theory-based (DFT) calculations were performed to evaluate potential mechanisms for these reactions.

Effect of ester chemical structure and peptide bond conformation in fragmentation pathways of differently metal cationized cyclodepsipeptides

Fragmentation behavior of two classes of cyclodepsipeptides, isariins and isaridins, obtained from the fungus Isaria, was investigated in the presence of different metal ions using multistage tandem mass spectrometry (MS(n)) with collision induced dissociation (CID) and validated by NMR spectroscopy. During MS(n) process, both protonated and metal-cationized isariins generated product ions belonging to the identical 'b-ion' series, exhibiting initial backbone cleavage explicitly at the β-ester bond. Fragmentation behavior for the protonated and metal-cationized acyclic methyl ester derivative of isariins was very similar. On the contrary, isaridins during fragmentation produced ions belonging to the 'b' or/and the 'y' ion series depending on the nature of interacting metal ions, due to initial backbone cleavages at the α-ester linkage or/and at a specific amide linkage. Interestingly, independent of the nature of the interacting metal ions, the product ions formed from the acyclic methyl ester derivative of isaridins belonged only to the 'y-type'. Complementary NMR data showed that, while all metal ions were located around the β-ester group of isariins, the metal ion interacting sites varied across the backbone for isaridins. Combined MS and NMR data suggest that the different behavior in sequence specific charge-driven fragmentation of isariins and isaridins is predetermined because of the constituent β-hydroxy acid residue in isariins and the cis peptide bond in isaridins.

Histone deacetylase inhibitors as a tool to up-regulate new fungal biosynthetic products: isolation of EGM-556, a cyclodepsipeptide, from Microascus sp

The histone deacetylase (HDAC) inhibitor suberoylanilide hydroxamic acid (SAHA) was used to turn on the biosynthesis of EGM-556, a new cyclodepsipeptide of hybrid biosynthetic origin, isolated from the Floridian marine sediment-derived fungus Microascus sp. The absolute configurations of three chiral centers were determined by Marfey's derivatization. EGM-556 represents one of the few examples in which silent biosynthetic genes, encoding a new secondary metabolite, were activated by means of epigenetic manipulation of the fungal metabolome.

The effects of chromium(III) coordination on the dissociation of acidic peptides

The complexes formed between chromium(III) and synthetic acidic peptides were studied by sustained off-resonance irradiation collision-induced dissociation (SORI-CID) in a Fourier transform ion-cyclotron resonance (FT-ICR) mass spectrometer equipped with electrospray ionization (ESI). Neutral peptides and peptides containing one, two, and multiple acidic residues were studied. Formation of [M + Cr-2H]+ occurred for all peptides. Three noteworthy features were found in the CID spectra of [M + Cr-2H]+. The first is that fewer fragment ions were produced from [M + Cr-2H]+ than from [M + H]+. The reason may be that multiple coordination between chromium(III) and carboxylate or carbonyl groups hinders the production of fragment ions by continuing to bind pieces of the peptide to chromium(III) after cleavage of bonds within the peptide. The second feature is loss of CO from [M + Cr-2H]+ and [y(n) + Cr-H]+. A mechanism involving coordination of chromium(III) with carboxylate groups is proposed to rationalize elimination of CO. The third feature is that chromium(III) is retained in all fragment ions, indicating strong binding of the metal ion to the peptides. The complex [M + 2Cr-5H]+ is formed as the peptide chain length and number of acidic residues increases. Longer peptides have more sites to coordinate with chromium(III) and more conformational flexibility. In addition, formation of [M + Cr-2H]+ from AGGAAAA-OCH(3), which has no carboxylic acid groups, suggests that chromium(III) can coordinate with sites on the peptide backbone, albeit in low abundance. In the negative mode, [M + Cr-4H](-) was only found for peptides containing four or more carboxylic acid groups. This is consistent with deprotonated carboxylic acid groups being involved in chromium(III) coordination and with chromium existing in the 3 + state in the gas-phase ions.

Evaluation of metal-mediated DNA binding of benzoxazole ligands by electrospray ionization mass spectrometry

The binding of a series of benzoxazole analogs with different amide- and ester-linked side chains to duplex DNA in the absence and presence of divalent metal cations is examined. All ligands were found to form complexes with Ni2+, Cu2+, and Zn2+, with 2:1 ligand/metal cation binding stoichiometries dominating for ligands containing shorter side chains (2, 6, 7, and 8), while 1:1 complexes were the most abundant for ligands with long side chains (9, 10, and 11). Ligand binding with duplex DNA in the absence of metal cations was assessed, and the long side-chain ligands were found to form low abundance complexes with 1:1 ligand/DNA binding stoichiometries. The ligands with the shorter side chains only formed DNA complexes in the presence of metal cations, most notably for 7 and 8 binding to DNA in the presence of Cu2+. The binding of long side-chain ligands was enhanced by Cu2+ and to a lesser degree by Ni2+ and Zn2+. The cytotoxicities of all of the ligands against the A549 lung cancer and MCF7 breast cancer cell lines were also examined. The ligands exhibiting the most dramatic metal-enhanced DNA binding also demonstrated the greatest cytotoxic activity. Both 7 and 8 were found to be the most cytotoxic against the A549 lung cancer cell line and 8 demonstrated moderate cytotoxicity against MCF7 breast cancer cells. Metal ions also enhanced the DNA binding of the ligands with the long side chains, especially for 9, which also exhibited the highest level of cytotoxicity of the long side-chain compounds.

Thermochemistry, bonding, and reactivity of Ni+ and Ni2+ in the gas phase

In this review, we present a general overview on the studies carried out on Ni(+-)- and Ni(2+)-containing systems in the gas phase since 1996. We have focused our attention in the determination of binding energies in parallel with an analysis of the structure and bonding of the complexes formed by the interaction of Ni(+) with one ligand, or in clusters where this metal ion binds several identical or different ligands. Solvation of Ni(2+) by different ligands is also discussed, together with the theoretical information available of doubly charged Ni-containing species. The final section of this review is devoted to an analysis of the gas-phase uni- and bimolecular reactivity of Ni(+) and Ni(2+) complexes.

Cyclization reaction of peptide fragment ions during multistage collisionally activated decomposition: an inducement to lose internal amino-acid residues

During characterization of some peptides (linear precursors of the cyclic peptides showing potential to be anticancer drugs) in an ion trap, it was noted that many internal amino acid residues could be lost from singly charged b ions. The phenomenon was not obvious at the first stage of collisionally activated decomposition (CAD), but was apparent at multiple stages of CAD. The unique fragmentation consisting of multiple steps is induced by a cyclization reaction of b ions, the mechanism of which has been probed by experiments of N-acetylation, MS(n), rearranged-ion design, and activation-time adjustment. The fragmentation of synthetic cyclic peptides demonstrates that a cyclic peptide intermediate (CPI) formed by b ion cyclization exhibits the same fragmentation pattern as a protonated cyclic peptide. Although no rules for the cyclization reaction were discerned in the experiments of peptide modification, the fragmentations of a number of b ions indicate that the "Pro and Asn/Gln effects" can influence ring openings of CPIs. In addition, large-scale losses of internal residues from different positions of a-type ions have been observed when pure helium was used as collision gas. The fragmentation is initiated by a cyclization reaction forming an a-type ion CPI. This CPI with a fixed-charge structure cannot be influenced by the "Pro effect", causing a selective ring opening at the amide bond Pro-Xxx rather than Xxx-Pro. With the knowledge of the unique fragmentations leading to internal residue losses, the misidentification of fragments and sequences of peptides may be avoided.

Tandem mass spectrometry of kahalalides: identification of two new cyclic depsipeptides, kahalalide R and S from Elysia grandifolia

Spectra obtained using electrospray ionization mass spectrometry (ESI-MS) of the mollusk Elysia grandifolia showed a cluster of molecular ion peaks centered at a molecular mass of 1478 Da (kahalalide F, an anticancer agent). Two new molecules, kahalalide R (m/z 1464) and S (m/z 1492) were characterized using tandem mass spectrometry. The mass differences of 14 Da suggest that they are homologous molecules. In addition, previously identified kahalalide D and kahalalide G are also reported. However, the ESI-MS of the mollusk's algal diet Bryopsis plumosa showed the presence of only kahalalide F. The amino acid sequences of kahalalide R and S are proposed using collision-induced dissociation (CID) experiments of singly and doubly charged molecular ions and by comparison with the amino acid sequence of kahalalide F. The pathway is presented for the loss of amino acid residues in kahalalide F. It is observed that there is sequential loss of amino acids in the linear peptide chain, but in the cyclic part the ring opens at the amide bond rather than at the lactone linkage, and the loss of amino acid residues is not sequential. The CID experiment of the alkali-metal-cationized molecular ions shows that the sodium and potassium ions coordinate to the amide nitrogen/oxygen in the linear peptide chain of the molecule and not to the lactone oxygen of the lactone. In the case of kahalalide D, CID of the protonated peptide opens the depsipeptide ring to form a linear peptide with acylium ion, and fragment ion signals indicate losses of amino acids in sequential order. In this study, tandem mass spectrometry has provided the detailed information required to fully characterize the new peptides.

Structure elucidation of cyclic pyoverdins and examination of rearrangement reactions in MS/MS experiments by determination of exact product ion masses

Structure elucidation of naturally occurring linear and cyclic peptidic compounds can be complicated by rearrangement reactions induced upon collision activation (CA) when parts of the molecule migrate, suggesting incorrect substitution patterns. Such complex rearrangements are examined and discussed for two iron complexing compounds produced by the bacterial genus Pseudomonas (so-called pyoverdins). Various MS2- and MS3-product ion experiments were performed using a quadrupole-ion trap (QIT) at low resolution and a FT-ICR at high resolution allowing accurate mass determinations. The results of the multidimensional study confirm the proposed processes. On the basis of the series of tandem-MS experiments the structure of a new pyoverdin from a P. fluorescens strain [PVD(D47)] is deduced.

Sequencing peptides by electrospray ion-trap mass spectrometry: A useful tool in synthesis of Axinastatin 3

Axinastatin 3 as a potential anticancer agent was synthesized by chemical methods. In an electrospray ion-trap mass spectrometer, using one stage of tandem mass spectrometry (MS/MS), the linear peptide intermediate was sequenced via the complementarities of y and b ions. Then, using multistep MS/MS (to MS6), the cyclic peptide was sequenced through sequentially removing one amino acid residue in each stage of MS/MS. The difference of the fragmentation mechanisms and the sequencing approaches between them is discussed.

Multi-stage collisionally-activated decomposition in an ion trap for identification of sequences, structures and bn --> bn-1 fragmentation pathways of protonated cyclic peptides

Cyclic penta-, hexa- and heptapeptides have been designed, synthesized and their fragmentations induced by multistage tandem mass spectrometry have been studied. Under low-energy collisionally activated decomposition (CAD), the protonated cyclic peptides mainly dissociate via ring opening pathways and the corresponding bn --> bn-1 pathways to form several sets of b ions as oxazolone rings (and b1 ions as aziridinone rings). Through repeated observation of these b ions in multistep CAD experiments, accurate sequencing and head-to-tail ring structure of cyclic peptides can be determined. The mistaken assignments of these b ions can be avoided by this sequencing method. Semiempirical molecular orbital calculations have been utilized to provide insight into the proposed dissociation mechanism. In addition, for cyclic peptides that include an Asn residue, the nitrogen of the Asn side chain is observed to be preferentially protonated, which can induce a unique ring-opening pathway with a loss of ammonia that competes with the conventional ring opening pathway.

Speciation of cyclo(Pro-Gly)3 and its divalent metal-ion complexes by electrospray ionization mass spectrometry

Electrospray ionization mass spectrometry (ESI-MS) was used to study the binding of selected group II and divalent transition-metal ions by cyclo(Pro-Gly)3 (CPG3), a model ion carrier peptide. Metal salts (CatXn) were combined with the peptide (M) at a molar ratio of 1:10 M/Cat in aqueous solvents containing 50% vol/vol acetonitrile or methanol and 1 or 10 mM ammonium acetate (NH4Ac). Species detected include [M+H]+, [M+Cat-H]+, [M2+Cat]2+, [M+Cat+Ac]+, and [M+Cat+X]+. The relative stabilities of complexes formed with different cations (Mg2+, Ca2+, Sr2+, Mn2+, Co2+, Ni2+, Cu2+, and Zn2+) were determined from the abundance of 1:1 and 2:1 M/Cat species relative to that of the unbound peptide. The largest metal ions (Ca2+, Sr2+, and Mn2+) formed the most stable complexes. Reducing the buffer concentration increased the overall extent of metal binding. Results show that the binding specificity of CPG3 depends upon the size of the metal ion and its propensity for electrostatic interaction with oxygen atoms. Product ion tandem mass spectrometry of [M+H]+ and [M+Cu-H]+ confirmed the cyclic structure of the peptide, although the initial site(s) of metal attachment could not be determined.