Standardisation of the C:N ratio in ileal digesta changes relationships among fermentation end-products during in vitro hindgut fermentation in pigs.

Undigested proteins that become available for the microbiota in the hindgut can be used as building blocks for bacterial cells, or can enter various catabolic pathways. Degradation via protein fermentation pathways is least preferred, as several fermentation end-products released can be toxic for the host. Directing microbial protein metabolism towards protein synthesis or degradative pathways that result in less toxic end-products, for example through nutritional interventions, is an interesting strategy for improving health. We studied variation in protein fermentation patterns, resulting from variation in substrate composition. Ileal digesta, obtained from cannulated pigs fed different protein sources, were subjected to fermentation in vitro under different conditions; (1) ileal digesta were fermented as-is, (2) ileal digesta were fermented after standardisation to a constant high C:N ratio, by addition of high fermentable carbohydrates and (3) ileal digesta samples were incubated under limiting N concentrations. Gas production was monitored as an indirect measure of microbial activity, and fermentation end-products at different points in time were analysed by gas chromatography and high resolution mass spectrometry. Using principal component analysis, we identified patterns in protein fermentation end-products and related them to the composition of ileal digesta. Protein-associated fermentation end-product concentrations of e.g. isovaleric-, isobutyric-, phenylacetic acid and p-cresol were negatively affected by the available amount of high fermentable carbohydrates combined with a high C:N ratio. The aforementioned fermentation end-products positively correlated with NH3 concentrations and negatively with short-chain fatty acid (SCFA) concentrations. Standardisation to a constant high C:N ratio changed their relationship; isovaleric-, isobutyric-, phenylacetic acid and p-cresol lost their correlation with NH3 concentrations, became positively correlated with SCFA concentrations, and now showed a positive correlation with available amounts of high fermentable carbohydrates. Our observations demonstrate an important role of the C:N ratio in the relationship between fermentation end-products. At constant C:N, protein fermentation end-products correlate with end-products of carbohydrate fermentation and NH3, often considered as a proxy for protein fermentation, loses its predictive power.

Psoromic acid is a selective and covalent Rab-prenylation inhibitor targeting autoinhibited RabGGTase.

Post-translational attachment of geranylgeranyl isoprenoids to Rab GTPases, the key organizers of intracellular vesicular transport, is essential for their function. Rab geranylgeranyl transferase (RabGGTase) is responsible for prenylation of Rab proteins. Recently, RabGGTase inhibitors have been proposed to be potential therapeutics for treatment of cancer and osteoporosis. However, the development of RabGGTase selective inhibitors is complicated by its structural and functional similarity to other protein prenyltransferases. Herein we report identification of the natural product psoromic acid (PA) that potently and selectively inhibits RabGGTase with an IC(50) of 1.3 µM. Structure-activity relationship analysis suggested a minimal structure involving the depsidone core with a 3-hydroxyl and 4-aldehyde motif for binding to RabGGTase. Analysis of the crystal structure of the RabGGTase:PA complex revealed that PA forms largely hydrophobic interactions with the isoprenoid binding site of RabGGTase and that it attaches covalently to the N-terminus of the α subunit. We found that in contrast to other protein prenyltransferases, RabGGTase is autoinhibited through N-terminal (α)His2 coordination with the catalytic zinc ion. Mutation of (α)His dramatically enhances the reaction rate, indicating that the activity of RabGGTase is likely regulated in vivo. The covalent binding of PA to the N-terminus of the RabGGTase α subunit seems to potentiate its interaction with the active site and explains the selectivity of PA for RabGGTase. Therefore, psoromic acid provides a new starting point for the development of selective RabGGTase inhibitors.

Fatty Acid and Carnitine Metabolism Are Dysregulated in Systemic Sclerosis Patients.

Systemic sclerosis (SSc) is a rare chronic disease of unknown pathogenesis characterized by fibrosis of the skin and internal organs, vascular alteration, and dysregulation of the immune system. In order to better understand the immune system and its perturbations leading to diseases, the study of the mechanisms regulating cellular metabolism has gained a widespread interest. Here, we have assessed the metabolic status of plasma and dendritic cells (DCs) in patients with SSc. We identified a dysregulated metabolomic signature in carnitine in circulation (plasma) and intracellularly in DCs of SSc patients. In addition, we confirmed carnitine alteration in the circulation of SSc patients in three independent plasma measurements from two different cohorts and identified dysregulation of fatty acids. We hypothesized that fatty acid and carnitine alterations contribute to potentiation of inflammation in SSc. Incubation of healthy and SSc dendritic cells with etoposide, a carnitine transporter inhibitor, inhibited the production of pro-inflammatory cytokines such as IL-6 through inhibition of fatty acid oxidation. These findings shed light on the altered metabolic status of the immune system in SSc patients and opens up for potential novel avenues to reduce inflammation.

On the response of a label-free interferon-gamma immunosensor utilizing electrochemical impedance spectroscopy.

The research on our flow-injection, label-free, non-faradaic impedimetric immunosensor for interferon-gamma (IFN-gamma) has been extended. The sensor is prepared by immobilization of anti-IFN-gamma antibodies on a self-assembled monolayer (SAM) of acetylcysteine, deposited on polycrystalline gold. A multi-frequency impedance method is described, which allows time-resolved measurement of Nyquist plots. To these plots, an equivalent circuit was fitted, which is discussed in terms of a two-layer structure (inner and outer layer) of the interfacial region. Because binding of IFN-gamma mainly causes a decrease of Q (a constant-phase element), this element is considered as the outer layer. Several aspects of the impedimetric sensor response are studied, including the dependence on detection frequency, target concentration and applied dc potential. For quantitative detection of IFN-gamma, an optimum of the signal-to-noise (S/N) ratio of the out-of-phase impedance component (Z'') was found at about 100 Hz. At a dc-potential of +0.2 V versus a saturated calomel reference electrode, the sensor response is higher than at 0.0 V. Logarithmic dose-response curves of IFN-gamma in the concentration range of 10(-18) to 10(-9) M were obtained using two procedures: by successive injections over a single electrode, and by using freshly prepared electrodes for each measurement. Using the latter method, the repeatability is impaired. The need for in situ complementary techniques for a correct interpretation of the studied parameters is discussed.

An improved coating for the isolation and quantitation of interferon-gamma in spiked plasma using surface plasmon resonance (SPR).

A study was initiated to investigate the use of surface plasmon resonance (SPR) for the detection in plasma of a high pI model protein, recombinant human interferon-gamma (IFN-gamma). Initially a number of self-assembled monolayers (SAMs) and hydrogel-derivatised SAM-coatings were characterised for the adsorptive and desorptive properties of plasma components. Next a monoclonal anti-IFN-gamma antibody, MD-2, was covalently attached to dextran-modified mercaptoundecanoic acid surfaces that performed best. On coatings consisting of carboxyl-modified dextran (CMD) a difference in interaction behaviour was observed when IFN-gamma was injected in either buffer or diluted plasma. During the injection of IFN-gamma in buffer, an acceleration of the interaction process was observed and the signal continued to increase after the injection plug had passed. Upon injection of diluted plasma spiked with IFN-gamma, the response increased without acceleration of the binding process. After the injection was finished, some of the bound material desorbed as expected, resulting in a signal decrease. On non-charged dextrans, the interaction between the antibody-modified surface and IFN-gamma in either plasma or buffer was similar. During sample injection the response increased with a binding rate depending on the concentration of IFN-gamma present in solution. When the injection was finished, some of the bound material was washed away from the surface and only a minor contribution of non-specific adsorbed plasma components was noticeable. From the coatings tested, the non-modified dextran-coated SPR sensor disks prove to be best suited for the detection of IFN-gamma in complex matrices like plasma. The interaction of IFN-gamma in both diluted plasma and buffer is comparable and concentrations of IFN-gamma of 250 ng ml-1 and higher can be detected in both buffer and 100x-diluted plasma. The non-specific adsorption of plasma components is low, whereas the specific IFN-gamma response is relatively high.

Antiprogestins and iatrogenic glucocorticoid resistance.

The antiglucocorticoid action of the antiprogestin RU 38486 has interfered with its successful clinical application in long-term treatment. Several new antiprogestins (Org 31710, Org 31806 and ZK 98299) have recently been developed with the aim to eliminate this side-effect. We have used a human lymphocyte proliferation assay to estimate the antiglucocorticoid potency of RU 38486 and the newer antiprogestins. In this assay 100 nmol/L RU 38486 shifted the dexamethasone inhibition curve by at least one order of magnitude. The other antiprogestins showed no effect at 100 nmol/L. RU 38486 (30 nmol/L) was able to antagonize 1000 nmol/L dexamethasone. The other antiprogestins showed only slight effects even at 1000 nmol/L. We conclude that the new antiprogestins have antiglucocorticoid effects that are one to two orders of magnitude lower than that of RU 38486. This may make them more suitable than RU 38486 for application in long-term antiprogestin treatment.

Development of selective, potent RabGGTase inhibitors.

Members of the Ras superfamily of small GTPases are frequently mutated in cancer. Therefore, inhibitors have been developed to address the acitivity of these GTPases by inhibiting their prenylating enzymes FTase, GGTase I, and RabGGTase. In contrast to FTase and GGTase I, only a handful of RabGGTase inhibitors have been developed. The most active RabGGTase inhibitor known until recently was an FTase inhibitor which hit RabGGTase as an off-target. We recently reported our efforts to tune the selectivity of these inhibitors toward RabGGTase. Here we describe an extended set of selective inhibitors. The requirements for selective RabGGTase inhibitors are described in detail, guided by multiple crystal structures. In order to relate in vitro and cellular activity, a high-throughput assay system to detect the attachment of [(3)H]geranylgeranyl groups to Rab was used. Selective RabGGTase inhibition allows the establishment of novel drug discovery programs aimed at the development of anticancer therapeutics.

Development of an on-line SPR-digestion-nanoLC-MS/MS system for the quantification and identification of interferon-gamma in plasma.

An automated, on-line system for protein quantification and identification, employing Surface Plasmon Resonance (SPR), enzymatic protein digestion, nanoLC and tandem-MS (MS/MS), has been developed. For the experiments recombinant human interferon-gamma (rhIFN-gamma) in buffer or diluted bovine plasma was used as a model protein. Upon injecting 90muL of a 1mugmL(-1) solution of rhIFN-gamma in diluted plasma at a flow rate of 10muLmin(-1), 320fmol of protein was reproducibly bound to the sensor surface. After desorption of the isolated protein from the SPR surface using 10mM glycine pH 1.3, on-line digestion, nanoLC and MS/MS analysis, rhIFN-gamma could be identified on basis of peptide masses and MS/MS fragmentation data. A sequence recovery of 66% was found when a pepsin micro reactor was used. For a trypsin micro reactor the sequence recovery was 50%. In the latter case, the desorbed protein solution was pH-tuned with a TRIS buffer for optimal enzyme activity. With the identified trypsin- and pepsin-produced peptides and because parts of their amino acid sequences overlap, the protein sequence can be largely elucidated showing the potential for the analysis of unknown proteins. The SPR-digestion-nanoLC-MS/MS platform provides unattended analysis of a sample within 60min.

Pepsin immobilized in dextran-modified fused-silica capillaries for on-line protein digestion and peptide mapping.

On-line digestion of proteins under acidic conditions was studied using micro-reactors consisting of dextran-modified fused-silica capillaries with covalently immobilized pepsin. The proteins used in this study differed in molecular weight, isoelectric point and sample composition. The injected protein samples were completely digested in 3 min and the digest was analyzed with micro-high performance liquid chromatography (HPLC) and tandem mass spectrometry (MS/MS). The different proteins present in the samples could be identified with a Mascot database search on the basis of auto-MS/MS data. It proved also to be possible to digest and analyze protein mixtures with a sequence coverage of 55% and 97% for the haemoglobin beta- and alpha-chain, respectively, and 35-55% for the various casein variants. Protease auto-digestion, sample carry-over and loss of signal due to adsorption of the injected proteins were not observed. The backpressure of the reactor is low which makes coupling to systems such as Surface Plasmon Resonance biosensors, which do not tolerate too high pressure, possible. The reactor was stable for at least 40 days when used continuously.

Development of an open-tubular trypsin reactor for on-line digestion of proteins.

A study was initiated to construct a micro-reactor for protein digestion based on trypsin-coated fused-silica capillaries. Initially, surface plasmon resonance was used both for optimization of the surface chemistry applied in the preparation and for monitoring the amount of enzyme that was immobilized. The highest amount of trypsin was immobilized on dextran-coated SPR surfaces which allowed the covalent coupling of 11 ng mm(-2) trypsin. Fused-silica capillaries were modified in a similar manner and the resulting open-tubular trypsin-reactors having a pH optimum of pH 8.5, display a high activity when operated at 37 degrees C and are stable for at least two weeks when used continuously. Trypsin auto-digestion fragments, sample carry-over, and loss of signal due to adsorption of the protein were not observed. On-line digestion without prior protein denaturation, followed by micro-LC separation and photodiode array detection, was tested with horse-heart cytochrome C and horse skeletal-muscle myoglobin. The complete digestion of 20 pmol microL(-1) horse cytochrome C was observed when the average residence time of the protein sample in a 140 cm x 50 microm capillary immobilized enzyme reactor (IMER) was 165 s. Mass spectrometric identification of the injected protein on the basis of the tryptic peptides proved possible. Protein digestion was favorable with respect to reaction time and fragments formed when compared with other on-line and off-line procedures. These results and the easy preparation of this micro-reactor provide possibilities for miniaturized enzyme-reactors for on-line peptide mapping and inhibitor screening.