A serum proteome signature to predict mortality in severe COVID-19 patients

Here, we recorded serum proteome profiles of 33 severe COVID-19 patients admitted to respiratory and intensive care units because of respiratory failure. We received, for most patients, blood samples just after admission and at two more later time points. With the aim to predict treatment outcome, we focused on serum proteins different in abundance between the group of survivors and non-survivors. We observed that a small panel of about a dozen proteins were significantly different in abundance between these two groups. The four structurally and functionally related type-3 cystatins AHSG, FETUB, histidine-rich glycoprotein, and KNG1 were all more abundant in the survivors. The family of inter-α-trypsin inhibitors, ITIH1, ITIH2, ITIH3, and ITIH4, were all found to be differentially abundant in between survivors and non-survivors, whereby ITIH1 and ITIH2 were more abundant in the survivor group and ITIH3 and ITIH4 more abundant in the non-survivors. ITIH1/ITIH2 and ITIH3/ITIH4 also showed opposite trends in protein abundance during disease progression. We defined an optimal panel of nine proteins for mortality risk assessment. The prediction power of this mortality risk panel was evaluated against two recent COVID-19 serum proteomics studies on independent cohorts measured in other laboratories in different countries and observed to perform very well in predicting mortality also in these cohorts. This panel may not be unique for COVID-19 as some of the proteins in the panel have previously been annotated as mortality markers in aging and in other diseases caused by different pathogens, including bacteria.

TREM-1 multimerization is essential for its activation on monocytes and neutrophils

The triggering receptor expressed on myeloid cells-1 (TREM-1) is a receptor expressed on innate immune cells. By promoting the amplification of inflammatory signals that are initially triggered by Toll-like receptors (TLRs), TREM-1 has been characterized as a major player in the pathophysiology of acute and chronic inflammatory diseases, such as septic shock, myocardial infarction, atherosclerosis, and inflammatory bowel diseases. However, the molecular events leading to the activation of TREM-1 in innate immune cells remain unknown. Here, we show that TREM-1 is activated by multimerization and that the levels of intracellular Ca²⁺ release, reactive oxygen species, and cytokine production correlate with the degree of TREM-1 aggregation. TREM-1 activation on primary human monocytes by LPS required a two-step process consisting of upregulation followed by clustering of TREM-1 at the cell surface, in contrast to primary human neutrophils, where LPS induced a rapid cell membrane reorganization of TREM-1, which confirmed that TREM-1 is regulated differently in primary human neutrophils and monocytes. In addition, we show that the ectodomain of TREM-1 is able to homooligomerize in a concentration-dependent manner, which suggests that the clustering of TREM-1 on the membrane promotes its oligomerization. We further show that the adapter protein DAP12 stabilizes TREM-1 surface expression and multimerization. TREM-1 multimerization at the cell surface is also mediated by its endogenous ligand, a conclusion supported by the ability of the TREM-1 inhibitor LR12 to limit TREM-1 multimerization. These results provide evidence for ligand-induced, receptor-mediated dimerization of TREM-1. Collectively, our findings uncover the mechanisms necessary for TREM-1 activation in monocytes and neutrophils.

Kinesin-4 KIF21B is a potent microtubule pausing factor

Microtubules are dynamic polymers that in cells can grow, shrink or pause, but the factors that promote pausing are poorly understood. Here, we show that the mammalian kinesin-4 KIF21B is a processive motor that can accumulate at microtubule plus ends and induce pausing. A few KIF21B molecules are sufficient to induce strong growth inhibition of a microtubule plus end in vitro. This property depends on non-motor microtubule-binding domains located in the stalk region and the C-terminal WD40 domain. The WD40-containing KIF21B tail displays preference for a GTP-type over a GDP-type microtubule lattice and contributes to the interaction of KIF21B with microtubule plus ends. KIF21B also contains a motor-inhibiting domain that does not fully block the interaction of the protein with microtubules, but rather enhances its pause-inducing activity by preventing KIF21B detachment from microtubule tips. Thus, KIF21B combines microtubule-binding and regulatory activities that together constitute an autonomous microtubule pausing factor.

DOI:http://dx.doi.org/10.7554/eLife.24746.001

Microtubules are tiny tubes that cells use as rails to move various cell compartments and structures to different locations within the cell. They are made of building blocks called tubulin and form extensive networks across the cell. Depending on the cell’s needs, microtubule networks can be rapidly assembled and disassembled by adding or removing tubulin subunits at the ends of individual microtubules. While a lot is known about how cells regulate the growth and shrinkage of microtubules, much less is known about the factors that can pause these processes and thus stabilize a microtubule.

Proteins belonging to the kinesin family are molecular motors that can walk along microtubules and control how microtubules grow and shrink. A kinesin known as KIF21B is found in several types of cells including neurons and immune cells and genetic alterations in this protein have been linked with several neurodegenerative diseases. KIF21B is made up of three regions: a motor domain, a stalk and a tail domain that binds to microtubules. Recent studies have suggested that this kinesin affects the ability of one end of microtubules (known as the plus end) to grow.

Here, van Riel, Rai, Bianchi et al. used a biochemical approach to investigate the activity of KIF21B. The experiments show that KIF21B can walk to the plus end of microtubules and efficiently pause growth. Small numbers of KIF21B molecules are enough to inhibit microtubule growth and this activity depends on the motor domain and the tail domain of KIF21B working together. These experiments were performed a cell-free system and so the next challenge is to investigate how KIF21B works in living cells, including neurons and immune cells.

DOI:http://dx.doi.org/10.7554/eLife.24746.002

The diverse and expanding role of mass spectrometry in structural and molecular biology

The emergence of proteomics has led to major technological advances in mass spectrometry (MS). These advancements not only benefitted MS-based high-throughput proteomics but also increased the impact of mass spectrometry on the field of structural and molecular biology. Here, we review how state-of-the-art MS methods, including native MS, top-down protein sequencing, cross-linking-MS, and hydrogen-deuterium exchange-MS, nowadays enable the characterization of biomolecular structures, functions, and interactions. In particular, we focus on the role of mass spectrometry in integrated structural and molecular biology investigations of biological macromolecular complexes and cellular machineries, highlighting work on CRISPR-Cas systems and eukaryotic transcription complexes.

Talin-KANK1 interaction controls the recruitment of cortical microtubule stabilizing complexes to focal adhesions

The cross-talk between dynamic microtubules and integrin-based adhesions to the extracellular matrix plays a crucial role in cell polarity and migration. Microtubules regulate the turnover of adhesion sites, and, in turn, focal adhesions promote the cortical microtubule capture and stabilization in their vicinity, but the underlying mechanism is unknown. Here, we show that cortical microtubule stabilization sites containing CLASPs, KIF21A, LL5β and liprins are recruited to focal adhesions by the adaptor protein KANK1, which directly interacts with the major adhesion component, talin. Structural studies showed that the conserved KN domain in KANK1 binds to the talin rod domain R7. Perturbation of this interaction, including a single point mutation in talin, which disrupts KANK1 binding but not the talin function in adhesion, abrogates the association of microtubule-stabilizing complexes with focal adhesions. We propose that the talin-KANK1 interaction links the two macromolecular assemblies that control cortical attachment of actin fibers and microtubules.

DOI:http://dx.doi.org/10.7554/eLife.18124.001

Animal cells are organized into tissues and organs. A scaffold-like framework outside of the cells called the extracellular matrix provides support to the cells and helps to hold them in place. Cells attach to the extracellular matrix via structures called focal adhesions on the cell surface; these structures contain a protein called talin.

For a cell to be able to move, the existing focal adhesions must be broken down and new adhesions allowed to form. This process is regulated by the delivery and removal of different materials along fibers called microtubules. Microtubules can usually grow and shrink rapidly, but near focal adhesions they are captured at the surface of the cell and become more stable. However, it is not clear how focal adhesions promote microtubule capture and stability.

Bouchet et al. found that a protein called KANK1 binds to the focal adhesion protein talin in human cells grown in a culture dish. This allows KANK1 to recruit microtubules to the cell surface around the focal adhesions by binding to particular proteins that are associated with microtubules. Disrupting the interaction between KANK1 and talin by making small alterations in these two proteins blocked the ability of focal adhesions to capture surrounding microtubules. The next step following on from this work will be to find out whether this process also takes place in the cells within an animal’s body, such as a fly or a mouse.

DOI:http://dx.doi.org/10.7554/eLife.18124.002

Reconciling proteomics with next generation sequencing

Both genomics and proteomics technologies have matured in the last decade to a level where they are able to deliver system-wide data on the qualitative and quantitative abundance of their respective molecular entities, that is DNA/RNA and proteins. A next logical step is the collective use of these technologies, ideally gathering data on matching samples. The first large scale so-called proteogenomics studies are emerging, and display the benefits each of these layers of analysis has on the other layers to together generate more meaningful insight into the connection between the phenotype/physiology and genotype of the system under study. Here we review a selected number of these studies, highlighting what they can uniquely deliver. We also discuss the future potential and remaining challenges, from a somewhat proteome biased perspective.

Quantitative mass spectrometry of TATA binding protein-containing complexes and subunit phosphorylations during the cell cycle

BACKGROUND

Progression through the cell cycle is accompanied by tightly controlled regulation of transcription. On one hand, a subset of genes is expressed in a cell cycle-dependent manner. On the other hand, a general inhibition of transcription occurs during mitosis. Genetic and genome-wide studies suggest cell cycle regulation at the level of transcription initiation by protein complexes containing the common DNA-binding subunit TATA binding protein (TBP). TBP is a key player in regulating transcription by all three nuclear RNA polymerases. It forms at least four distinct protein complexes with TBP-associated factors (TAFs): SL1, B-TFIID, TFIID, and TFIIIB. Some TAFs are known to remain associated with TBP during the cell cycle. Here we analyze all TAFs and their phosphorylation status during the cell cycle using a quantitative mass spectrometry approach.

RESULTS

TBP protein complexes present in human cells at the G2/M and G1/S transitions were analyzed by combining affinity purification with quantitative mass spectrometry using stable isotope labeling with amino acids in cell culture (SILAC). Phosphorylations were mapped and quantified after enrichment of tryptic peptides by titanium dioxide. This revealed that subunit stoichiometries of TBP complexes remained intact, but their relative abundances in nuclear extracts changed during the cell cycle. Several novel phosphorylations were detected on subunits of the TBP complexes TFIID and SL1. G2/M-specific phosphorylations were detected on TAF1, TAF4, TAF7, and TAFI41/TAF1D, and G1/S-specific dephosphorylations were detected on TAF3. Many phosphorylated residues were evolutionary conserved from human to zebrafish and/or drosophila, and were present in conserved regions suggesting important regulatory functions.

CONCLUSIONS

This study provides the first quantitative proteomic analysis of human TBP containing protein complexes at the G2/M and G1/S transitions, and identifies new cell cycle-dependent phosphorylations on TAFs present in their protein complex. We speculate that phosphorylation of complex-specific subunits may be involved in regulating the activities of TBP protein complexes during the cell cycle.

Oxidation of recombinant human interleukin-2 by potassium peroxodisulfate

PURPOSE

The oxidation of recombinant human interleukin-2 (rhlL-2) by potassium peroxodisulfate (KPS) with or without N,N,N',N'-tetramethylethylenediamine (TEMED), which are used for the preparation of dextran-based hydrogels, was investigated.

METHODS

The oxidation of (derivatives of) methionine. tryptophan, histidine and tyrosine, as well as rhlL-2 was investigated. Both the oxidation kinetics (RP-HPLC) and the nature of the oxidation products (mass spectrometry) were studied as a function of the KPS and TEMED concentration, and the presence of a competitive antioxidant, methionine.

RESULTS

Under conditions relevant for the preparation of rhIL-2 loaded hydrogels, only methionine and tryptophan derivatives were susceptible to oxidation by KPS. The oxidation of these compounds was inhibited once TEMED was present, suggesting that the peroxodisulfate anion, rather than the radicals formed in the presence of TEMED, is the oxidative species. KPS only induced oxidation of the four methionines present in rhIL-2, whereas the tryptophan residue remained unaffected. The radicals, formed after KPS decomposition by TEMED, induced some dimerization of rhIL-2. The oxidation of rhIL-2 could be substantially reduced by the addition of methionine, or by pre-incubation of KPS with TEMED.

CONCLUSIONS

Only the methionine residues in rhlL-2 are oxidized by KPS. The extent of oxidation can be minimized by a proper selection of the reaction conditions.

Interfacial positioning and stability of transmembrane peptides in lipid bilayers studied by combining hydrogen/deuterium exchange and mass spectrometry

Nano-electrospray ionization mass spectrometry (ESI-MS) was used to analyze hydrogen/deuterium (H/D) exchange properties of transmembrane peptides with varying length and composition. Synthetic transmembrane peptides were used with a general acetyl-GW(2)(LA)(n)LW(2)A-ethanolamine sequence. These peptides were incorporated in large unilamellar vesicles of 1,2-dimyristoyl-sn-glycero-3-phosphocholine. The vesicles were diluted in buffered deuterium oxide, and the H/D exchange after different incubation times was directly analyzed by means of ESI-MS. First, the influence of the length of the hydrophobic Leu-Ala sequence on exchange behavior was investigated. It was shown that longer peptide analogs are more protected from H/D exchange than expected on the basis of their length with respect to bilayer thickness. This is explained by an increased protection from the bilayer environment, because of stretching of the lipid acyl chains and/or tilting of the longer peptides. Next, the role of the flanking tryptophan residues was investigated. The length of the transmembrane part that shows very slow H/D exchange was found to depend on the exact position of the tryptophans in the peptide sequence, suggesting that tryptophan acts as a strong determinant for positioning of proteins at the membrane/water interface. Finally, the influence of putative helix breakers was studied. It was shown that the presence of Pro in the transmembrane segment results in much higher exchange rates as compared with Gly or Leu, suggesting a destabilization of the alpha-helix. Tandem MS measurements suggested that the increased exchange takes place over the entire transmembrane segment. The results show that ESI-MS is a convenient technique to gain detailed insight into properties of peptides in lipid bilayers by monitoring H/D exchange kinetics.

Capillary electrophoretic bioanalysis of therapeutically active peptides with UV and mass spectrometric detection after on-capillary preconcentration

An earlier developed capillary electrophoresis (CE) system with an on-capillary adsorptive phase is investigated for its suitability to quantitate low concentrations of angiotensin II and gonadorelin in plasma. An off-line solid-phase extraction is used for sample preparation. The on-line preconcentration CE system allows multiple capillary volumes of sample solution to be injected, increasing the concentration sensitivity of CE with 3-4 orders of magnitude. Furthermore, possible influence of matrix salts can be ruled out by employing a rinsing step after sample application. Using short-wavelength UV detection, reproducibility and linearity in the low nanomolar range were satisfactory. The capillary could be efficiently regenerated using a programmed between-run rinsing procedure, allowing 20-30 large injections of sample extracts. Coating of the capillary improved the robustness of the method. Mass spectrometric detection via a previously reported sheathless interface increased the selectivity and sensitivity substantially. Recommendations are provided for the sample preparation process, the most critical part of the system. Further purification of the sample is required to allow the loading of larger sample volumes and to optimize the system's robustness.

Robust and cost-effective capillary electrophoresis-mass spectrometry interfaces suitable for combination with on-line analyte preconcentration

This paper describes several successful cost-effective attempts to couple capillary electrophoresis (CE) and mass spectrometry (MS) without make-up flow or nebulizing gas. An in-depth analysis of several interfaces using conductive spray tips was performed as well as an easy-to-prepare T-junction with direct electrode contact, the latter being the most robust interface. No coating is necessary and the spray voltage is applied through a gold wire positioned at the gap between the separation and spray capillaries. The T-junction interface is made by puncturing a small piece of transparent rubber. The on-line preconcentration CE-MS system allows immunoassay sensitivity, as is demonstrated by a calibration plot in the picomolar range for angiotensin II and gonadorelin. It also shows good reproducibility and has the ability of excellent automation. The secure electrical contact gives a constant spray quality, even with 100% aqueous separation buffers. The described setup has a wide applicability as is demonstrated by the analysis of larger peptides, such as insulin and cytochrome c. Detailed information is given on critical factors in the preparation of the described interfaces.

Modification and inhibition of vancomycin group antibiotics by formaldehyde and acetaldehyde

It is shown that several vancomycin group antibiotics (vancomycin, eremomycin, and avoparcin) undergo spontaneous chemical modifications when kept at room temperature at neutral pH in aqueous solutions containing traces of formaldehyde or acetaldehyde. This chemical modification predominantly results in a mass increase of 12 Da in the reaction with formaldehyde and 26 Da in the case of acetaldehyde. By using tandem mass spectrometry the modification can unambiguously be identified as originating from the formation of a ring-closed 4-imidazolidinone moiety at the N-terminus of the glycopeptide antibiotics, that is, near the receptor binding pocket of the glycopeptide antibiotics. Bioaffinity mass spectrometry shows that this ring-closure results in a dramatically decreased affinity for the peptidoglycan-mimicking D-alanyl-D-alanine receptor. Additionally, in vitro inhibition measurements on two different strains of bacteria have revealed that the modified antibiotics display reduced antibacterial activity. The ring-closure is also shown to have a dissociative effect on the dimerization of the vancomycin-analogue eremomycin. The spontaneous reaction of vancomycin with formaldehyde or acetaldehyde may have implications not only for the clinical use of this class of antibiotics, but also for the effectiveness of these antibiotics when they are used in chiral separation chromatography or capillary electrophoresis.

Metastable ion formation and disparate charge separation in the gas-phase dissection of protein assemblies studied by orthogonal time-of-flight mass spectrometry

The dissection of specific and nonspecific protein complexes in the gas phase is studied by collisionally activated decomposition. In particular, the gas phase dissection of multiple protonated homodimeric Human Galectin I, E. Coli Glyoxalase I, horse heart cytochrome c, and Hen egg Lysozyme have been investigated. Both the Human Galectin I and E. Coli Glyoxalase I enzymes are biologically active as a dimer, exhibiting molecular weights of approximately 30 kDa. Cytochrome c and Lysozyme are monomers, but may aggregate to some extent at high protein concentrations. The gas phase dissociation of these multiple protonated dimer assemblies does lead to the formation of monomers. The charge distribution over the two concomitant monomers following the dissociation of these multiple protonated dimers is found to be highly dissimilar. There is no evident correlation between the solution phase stability of the dimeric proteins and their gas-phase dissociation pattern. Additionally, in the collisionally activated decomposition spectra diffuse ion signals are observed, which are attributed to monomer ions formed via slow decay of the collisionally activated dimer ions inside the reflectron time-of-flight. Although, the formation of these diffuse metastable ions may complicate the interpretation of collisionally activated decomposition mass spectra, especially when studying noncovalent protein complexes, a simple mathematical equation may be used to reveal their origin and pathway of formation.

Formation and efficacy of vancomycin group glycopeptide antibiotic stereoisomers studied by capillary electrophoresis and bioaffinity mass spectrometry

The conformational stability of vancomycin group antibiotics (i.e., vancomycin and avoparcin) in aqueous solution has been studied. These complex glycopeptide antibiotics contain many chiral centers allowing the potential formation of stereoisomers. Using capillary electrophoresis these stereoisomers could be separated and detected by UV and/or mass spectrometry. Fresh aqueous samples of both vancomycin and avoparcin already contained a plethora of stereoisomers. Thermal degradation of the antibiotics was studied as well. For vancomycin thermal degradation led primarily to the formation of CDP-I and aglycons. In the case of avoparcin thermal degradation led mainly to the interconversion between stereoisomers. These antibiotic stereoisomers may exhibit different antibacterial efficacy. Solution-phase association constants of fresh and heated samples of these antibiotics and their bacterial cell wall mimicking receptors were determined by bioaffinity mass spectrometry and revealed that the heated samples exhibited, in general, a lower affinity. Minimum inhibitory concentrations (Micrococcus flavus) were determined and confirmed the decrease in antibacterial efficacy upon heating.

The effect of the source pressure on the abundance of ions of noncovalent protein assemblies in an electrospray ionization orthogonal time-of-flight instrument

The effect of elevating the pressure in the interface region of an electrospray ionization orthogonal time-of-flight mass spectrometer on the ion intensity of different noncovalent protein assemblies has been investigated. Elevating the pressure in the interface region generally led to an enhanced detection of high m/z ions. The optimum pressure was found to be dependent on the m/z value of the ions. This pressure effect should be carefully addressed when relating ion abundance in the mass spectra to solution phase abundance of noncovalent protein assemblies.

The early glycation products of the Maillard reaction: mass spectrometric characterization of novel imidazolidinones derived from an opioid pentapeptide and glucose

Glucose-substituted imidazolidinones related to the endogenous opioid peptide leucine-enkephalin have been investigated using fast atom bombardment tandem mass spectrometry (FAB-MS/MS) and electrospray ionization tandem mass spectrometry (ESI-MS/MS). In addition to Amadori compounds, the studied imidazolidinones represent a novel type of the early glycation products formed in the Maillard reaction. To obtain insight into the fragmentation behavior of these carbohydrate-peptide adducts, we also studied synthetic precursors of the glucose-substituted imidazolidinones as well as the corresponding isopropylidene derivatives. The collision-induced dissociation (CID) spectra of [M + H](+) ions of all these imidazolidinones have been compared. Detailed analysis showed that fragmentation of each compound generates two ions at m/z 566 and m/z 598 which are characteristic and undoubtedly confirm the imidazolidinone-type structure. These two significant ions were identified as the M + 10 and M + 42 modifications of the N-terminus of the parent opioid pentapeptide effected by the carbohydrate moiety. Furthermore, the ion at m/z 178 is identified as the M + 42 modification of the immonium ion of the N-terminal amino acid (tyrosine) also effected by the carbohydrate moiety. They can be used as diagnostic ions for imidazolidinone-type compounds in studying the Maillard reaction. Thus, we have demonstrated the utility of FAB-MS/MS and ESI-MS/MS in the structural determination and identification of such novel peptide-carbohydrate adducts, useful in understanding the details of the mechanism of non-enzymatic glycation in vivo.

Characterization of glyoxalase I (E. coli)-inhibitor interactions by electrospray time-of-flight mass spectrometry and enzyme kinetic analysis

Potential inhibitors of the enzyme glyoxalase I from Escherichia coli have been evaluated using a combination of electrospray mass spectrometry and conventional kinetic analysis. An 11-membered library of potential inhibitors included a glutathione analogue resembling the transition-state intermediate in the glyoxalase I catalysis, several alkyl-glutathione, and one flavonoid. The E. coli glyoxalase I quaternary structure was found to be predominantly dimeric, as is the homologous human glyoxalase I. Binding studies by electrospray revealed that inhibitors bind exclusively to the dimeric form of glyoxalase I. Two specific binding sites were observed per dimer. The transition-state analogue was found to have the highest binding affinity, followed by a newly identified inhibitor; S-(2-[3-(hexyloxy)benzoyl]-vinyl)glutathione. Kinetic analysis confirmed that the order of affinity established by mass spectrometry could be correlated to inhibitory effects on the enzymatic reaction. This study shows that selective inhibitors may exist for the E. coli homologue of the glyoxalase I enzyme.

Stability of thioTEPA and its metabolites, TEPA, monochloroTEPA and thioTEPA-mercapturate, in plasma and urine

The degradation of N,N',N"-triethylenethiophosphoramide (thioTEPA) and its metabolites N,N',N"-triethylenephosphoramide (TEPA), N, N'-diethylene,N"-2-chloroethylphosphoramide (monochloroTEPA) and thioTEPA-mercapturate in plasma and urine has been investigated. ThioTEPA, TEPA and monochloroTEPA were analyzed using a gas chromatographic (GC) system with selective nitrogen/phosphorous detection; thioTEPA-mercapturate was analyzed on a liquid chromatography-mass spectrometric (LC-MS) system. The influences of pH and temperature on the stability of thioTEPA and its metabolites were studied. An increase in degradation rate was observed with decreasing pH as measured for all studied metabolites. In urine the rate of degradation at 37 degrees C was approximately 2.5+/-1 times higher than at 22 degrees C. At 37 degrees C thioTEPA and TEPA were more stable in plasma than in urine, with half lives ranging from 9-20 h for urine and 13-34 h for plasma at pH 6. Mono- and dichloro derivatives of thioTEPA were formed in urine and the monochloro derivative was found in plasma. Degradation of TEPA in plasma and urine resulted in the formation of monochloroTEPA. During the degradation of TEPA in plasma also the methoxy derivative of TEPA was formed as a consequence of the applied procedure. The monochloro derivative of thioTEPA-mercapturate was formed in urine, whereas for monochloroTEPA no degradation products could be detected.

Pharmaceutical development of a parenteral lyophilized formulation of the novel antitumor agent aplidine

Aplidine is a naturally occurring cyclic depsipeptide isolated from the Mediterranean tunicate Aplidium albicans. Aplidine displays promising in vitro and in vivo antitumor activities against various solid human tumor xenografts and is therefore developed now for clinical testing. The aim of this study was to develop a stable parenteral pharmaceutical dosage form for clinical Phase I testing. Aplidine raw material was characterized by using several chromatographic and spectrometric techniques. These experiments showed that aplidine exists as two isomers. A stability-indicating HPLC assay was developed. Solubility testing showed that aplidine exhibits very poor aqueous solubility. Because solubilized aplidine showed substantial degradation under heat and light stress testing conditions, it was decided to develop a lyophilized dosage form. Freeze-drying was carried out with a 500 micrograms/mL solution of aplidine in 40% (v/v) tert-butanol in Water for Injection (WfI) containing 25 mg/mL D-mannitol as a bulking agent. Differential scanning calorimetry was applied to determine the optimal freeze-drying cycle parameters. The prototype, containing 500 micrograms aplidine and 25 mg D-mannitol per vial, was found to be the optimal formulation in terms of solubility, length of lyophilization cycle, and dosage requirements in the forthcoming Phase I clinical studies. Quality control of the freeze-dried formulation demonstrates that the manufacturing process does not affect the integrity of aplidine. The optimal reconstitution solution was found to be 15/15/70% (v/v/v) Cremophor EL/ethanol/WfI (CEW). Both reconstituted product and dilutions of the reconstituted product with normal saline (up to 1:100 v/v) appeared to be stable for at least 24 hours after preparation. Shelf-life data, available thus far, show that the lyophilized formulation is stable for at least 1 year when stored at +2-8 degrees C in the dark.

Electrospray ionization mass spectrometry as a tool to analyze hydrogen/deuterium exchange kinetics of transmembrane peptides in lipid bilayers

A method is described to study the precise positioning of transmembrane peptides in a phospholipid bilayer combining hydrogen/deuterium (H/D) exchange and nanoelectrospray ionization mass spectrometry. The method was tested by using model systems consisting of designed alpha-helical transmembrane peptides [acetylGW(2)(LA)(5)W(2)Aethanolamine (WALP16) and acetyl-(GA)(3)W(2)(LA)(5)W(2)(AG)(3)ethanolamine (WALP16(+10))] incorporated in large unilamellar vesicles of 1, 2-dimyristoyl-sn-glycero-3-phosphocholine. Both peptides consist of an alternating leucine/alanine hydrophobic core sequence flanked by tryptophan residues as interfacial anchor residues. In the case of WALP16(+10), this sequence is extended at both ends by 5-aa glycine/alanine tails extending into the aqueous phase surrounding the bilayer. H/D exchange of labile hydrogens in these peptides was monitored in time after dilution of the vesicles in buffered deuterium oxide. It was found that the peptides can be measured by direct introduction of the proteoliposome suspension into the mass spectrometer. Several distinct H/D exchange rates were observed (corresponding to half-life values varying from </=2 to approximately 2 x 10(4) min). Fast exchange rates were assigned to the water-exposed tails of WALP16(+10). For both WALP16 and WALP16(+10), intermediate exchange rates were assigned to the residues close to the membrane/water interface, and the slow exchange rates to the membrane-embedded hydrophobic core. These assignments were confirmed by results from collision-induced dissociation tandem mass spectrometry experiments, which allowed analysis of exchange of individual peptide amide linkages. This proteoliposome nanoelectrospray ionization mass spectrometry technique is shown to be an extremely sensitive and powerful tool for revealing site-specific information on peptide-membrane interactions.

Detection of intact megaDalton protein assemblies of vanillyl-alcohol oxidase by mass spectrometry

Well-resolved ion signals of intact large protein assemblies, with molecular masses extending above one million Dalton, have been detected and mass analyzed using electrospray ionization mass spectrometry, with an uncertainty in mass of <0.2%. The mass spectral data seem to reflect known solution-phase behavior of the studied protein assembly and have therefore been directly used to probe the protein assembly topology and stability as a function of ionic strength and pH.

The formation of heterodimers by vancomycin group antibiotics

The formation of heterodimers in mixtures of glycopeptide antibiotics has been detected by electrospray ionization mass spectrometry (ESI-MS), and dimerization constants have been determined. By using NMR spectroscopy, it has been shown that these heterodimers indeed exist in aqueous solution. The dimerization constants obtained by NMR spectroscopy are in good agreement with those determined by ESI-MS. Structural information on the heterodimer interface of some of the heterodimers is obtained by using two-dimensional NMR techniques and reveals that these heterodimers are similar in structure to the homodimers.

Interactions of alpha- and beta-avoparcin with bacterial cell-wall receptor-mimicking peptides studied by electrospray ionization mass spectrometry

Solution phase affinity constants of the glycopeptide antibiotic alpha- and beta-avoparcin, with a range of bacterial cell-wall receptor-mimicking model peptides, were determined by a relatively new method: affinity electrospray ionization mass spectrometry (ESI-MS). This method is relatively efficient and allows the parallel determination of several affinity constants in mixtures of antibiotics and receptors. The determined binding constants for alpha- and beta-avoparcin were compared with those of the related glycopeptide antibiotic vancomycin. The solution phase binding affinities of alpha- and beta-avoparcin on one hand, and vancomycin on the other, were found to be in the same order, at least for the range of receptor-mimicking peptides studied. However, beta-avoparcin displayed slightly higher binding affinities than alpha-avoparcin, particularly for strong binding receptor-mimicking peptides. The evidence that alpha- and beta-avoparcin and vancomycin are structurally similar, combined with the present data revealing their similar affinity for bacterial cell-wall receptor-mimicking peptides, supports the hypothesis that the appearance of vancomycin-resistant enterococci (VRE) might be linked to the widespread use of avoparcin.

A search for new metabolites of N,N',N''-triethylenethiophosphoramide

An attempt was made to unravel the metabolic profile of the alkylating agent N,N',N''-triethylenethiophosphoramide (thioTEPA). thioTEPA and its metabolite N,N',N-triethylenephosphoramide (TEPA) were quantified in urine of treated patients by gas chromatography with selective nitrogen/phosphorous detection. Total alkylating activity was assessed by p-nitrobenzylpyridine reactivity. The total alkylating activity exceeded the amount of thioTEPA and TEPA, indicating the presence of other alkylating metabolites. Solid-phase extraction and liquid-liquid extractions followed by gas chromatography-mass spectrometry analysis revealed the conversion of an aziridinyl function of TEPA into a beta-chloroethyl moiety. This metabolite, N,N'-diethylene-N''-2-chloroethylphosphoramide, was quantified by gas chromatography with selective nitrogen/phosphorous detection and accounted for only 0.69% of the administered dose. Large volumes of urine were concentrated with solid-phase extraction and fractionated with high-performance liquid chromatography. Alkylating activity was determined for each 2-ml fraction and showed the presence of an alkylating compound eluting between 8 and 12 ml. The fractions with alkylating activity were collected, evaporated under a stream of nitrogen at room temperature to dryness, reconstituted in methanol, and subjected to fast atom bombardment-mass spectrometry and fast atom bombardment-tandem mass spectrometry. A new metabolite was found with a molecular mass of 352 Da, the same as that of thioTEPA-mercapturate. thioTEPA-mercapturate is likely the result of glutathione conjugation, after which the glutathione adduct loses two amino acid residues in separate stages. The fragmentation pattern and chromatographic properties of this new metabolite were identical to those of the reference, thioTEPA-mercapturate, which was obtained by incubation of thioTEPA with N-acetylcysteine at pH 11 and 95 degrees C for 30 min. Quantification of thioTEPA-mercapturate was carried out by liquid chromatography-mass spectrometry. The thioTEPA-mercapturate levels in urine accounted for 12.3% of the administered dose and exceeded the amount of TEPA, which was previously assumed to be the main metabolite of thioTEPA. The total excreted amount of thioTEPA and its metabolites accounts for 54-100% of the total alkylating activity, indicating the presence of still other alkylating metabolites.

Covalent and non-covalent dissociations of gas-phase complexes of avoparcin and bacterial receptor mimicking precursor peptides studied by collisionally activated decomposition mass spectrometry

The gas-phase stability and reactivity of non-covalent complexes of avoparcin and bacterial receptor mimicking precursor peptides were probed by electrospray ionization mass spectrometry combined with collisionally activated decomposition (CAD) studies. The order of the gas-phase stabilities of these non-covalent complexes is different from the order of the stabilities of the same complexes in solution. The specific stereoselectivity observed in non-covalent binding in solution is not retained in the gas phase. The presence of a lysine residue in the bacterial receptor mimicking precursor peptides appears to promote the gas-phase stabilities of the antibiotic-peptide complexes. Complexes of avoparcin with receptor peptides containing a lysine residue are stabilized in the gas phase to such an extent that CAD of these non-covalent complexes proceeds through a competition between non-covalent and covalent fragmentation pathways. These results indicate clearly that the use of CAD mass spectra for the quantitative characterization of the stability of non-covalent complexes in solution should be applied with extreme caution.

Copper and iron interactions with angiotensin-converting enzyme inhibitors. A study by fast-atom bombardment tandem mass spectrometry

Fast atom bombardment, combined with high-energy collision-induced tandem mass spectrometry, has been used to investigate gas-phase metal-ion interactions with captopril, enalaprilat and lisinopril, all angiotensin-converting enzyme inhibitors.Suggestions for the location of metal-binding sites are presented. For captopril, metal binding occurs most likely at both the sulphur and the nitrogen atom. For enalaprilat and lisinopril, binding preferably occurs at the amine nitrogen. Copyright 1999 John Wiley & Sons, Ltd.

Evidence of noncovalent dimerization of calmodulin

Calcium-binding proteins, such as S-100, dimerize readily, and this phenomenon plays an important role in their regulation of target enzymes [Krebs, J., Quadroni, M. & Van Eldik, L.J. (1995) Nat. Struct. Biol. 2, 711-714; Kilby, P.M., Van Eldik, L.J. & Roberts, G. C. (1996) Structure 4, 1041-1052]. We have investigated by Fourier-transform ion cyclotron resonance (FTICR) MS the conformational states of the calcium-binding protein calmodulin, and present clear evidence for a calmodulin dimer formed as a result of noncovalent interactions between folded monomers. Ultra-high-resolution electrospray ionization (ESI) mass spectra for calmodulin, obtained with a 9.4 T FTICR mass spectrometer, are presented. With the use of denaturing solutions (1 : 1 acetonitrile/water + 1% formic acid), relatively high charge states (20 < z < 10) of monomeric calmodulin ions were detected, whereas when calmodulin was electrosprayed from buffer, monomers ions with only 5-10 charges were detected. CD measurements for calmodulin in buffered solution revealed that its alpha-helical content was significantly higher than that for calmodulin in acetonitrile/water solutions, consistent with a proposition that changes in charge state distributions observed in the MS experiments reflect differing states of calmodulin folding. Under buffered conditions, noncovalently bound calmodulin dimers were observed by ESI FTICR MS. Analytical ultracentrifugation experiments carried out in the same solution conditions as those used in the MS experiments were consistent with the proposed calmodulin dimer-monomer equilibrium. The ultra-high mass resolution achieved with the 9.4 T FTICR mass spectrometer allowed unequivocal identification of the noncovalent, as opposed to covalent, character of the calmodulin dimer.

Analysis of nisin A and some of its variants using Fourier transform ion cyclotron resonance mass spectrometry

The lantibiotic nisin and some of its variants and degradation products have been characterized, using a 9.4-T Fourier transform ion cyclotron resonance mass spectrometer and electrospray ionization. The abundances of all products in the sample (i.e., major component, variants, degradation products, and adducts) have been measured quantitatively. The mass resolution obtained in the electrospray ionisation mass spectra was approximately 100,000 over the measured range. The resulting mass accuracy, better than 0.7 ppm (or within 0.001 Da) allowed the molecular masses and in many cases chemical formulae of most components in the mixture to be identified unambiguously. Additionally, amino acid sequence information on nisin and a variant [nisin + 18 Da] was obtained using sustained off-resonance irradiation collisional activated decomposition (SORI-CAD) of mass-selected precursor ions. Even after introducing collision gas into the mass analyser for the SORI-CAD experiments, the mass accuracy in the fragment ion mass spectra was approximately 5 ppm. It was established that the [nisin + 18 Da] molecule, present as a minor component in the mixture, was a species formed predominantly via hydration of nisin at position 33, i.e., [Ser33]nisin, with a small contribution due to hydration at position 5,[2-hydroxy-Ala5]nisin.

Gas phase bimolecular chemistry of isomeric C3H 6Br (+) cations

The gas phase chemistry of C3H6Br(+) cations generated via low energy electron impact on various dibromopropanes has been studied by using Fourier transform ion cyclotron resonance mass spectrometry. Neutral substrate molecules that have been selected to probe the bimolecular reactivity of the C3H6Br(+) isomers are ammonia, methylamine, trimethylamine, cis-butene, and 2, 3-dimethyl-2-butene. At least three different isomers are characterized on the basis of their different reactivity toward the various substrate molecules. It is suggested that these isomers have (a) the 2-bromo-2-propyl cation structure, (b) the propylenebromomum ion structure, and (c) the cyclic four-membered trimethylenebromonium ion structure. The 2-bromo-2-propyl cations react predominantely via proton transfer. This reaction is hampered for the propylenebromonium ions, which react mainly as electrophiles or bromanyl cation donors. Cyclic trimethylenebromoruum ions react predominantly via adduct formation, even under low pressure conditions, which implies that tturd body collisions are not the only stabilization mechanism.

On the structure of protonated methane

Results of a Fourier transform-ion cyclotron resonance study are reported concerning the reactivity of protonated perdeuteromethane and deuteronated methane, generated under varying pressure conditions in an external chemical ionization ion source, toward ammonia. The competition between proton and deuteron transfer from both protonated perdeuteromethane and deuteronated methane to ammonia exhibits chemically distinguishable hydrogens. The chemical behavior of protonated methane appears to be compatible with the theoretically predicted stable structure with Cs symmetry, involving a three-center two-electron bond associating two hydrogens and the carbon atom. Interconversion of this structure due to exchange between one of these hydrogens and one of the three remaining hydrogens appears to be a fast process that is induced by interactions with the chemical ionization gas.