Proteome Factory AG

Berlin, Germany

Proteome Factory AG

Berlin, Germany
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Chen X.,University of Ulm | Chen X.,National University of Singapore | Muthoosamy K.,University of Ulm | Pfisterer A.,Max Planck Institute for Polymer Research | And 4 more authors.
Bioconjugate Chemistry | Year: 2012

The site-selective modification of the proteins RNase A, lysozyme C, and the peptide hormone somatostatin is presented via a kinetically controlled labeling approach. A single lysine residue on the surface of these biomolecules reacts with an activated biotinylation reagent at mild conditions, physiological pH, and at RT in a high yield of over 90%. In addition, fast reaction speed, quick and easy purification, as well as low reaction temperatures are particularly attractive for labeling sensitive peptides and proteins. Furthermore, the multifunctional bioorthogonal bioconjugation reagent (19) has been achieved allowing the site-selective incorporation of a single ethynyl group. The introduced ethynyl group is accessible for, e.g., click chemistry as demonstrated by the reaction of RNase A with azidocoumarin. The approach reported herein is fast, less labor-intensive and minimizes the risk for protein misfolding. Kinetically controlled labeling offers a high potential for addressing a broad range of native proteins and peptides in a site-selective fashion and complements the portfolio of recombinant techniques or chemoenzymatic approaches. © 2012 American Chemical Society.


PubMed | Complutense University of Madrid, BAM Federal Institute of Materials Research and Testing, Proteome Factory AG and Hospital General Universitario Gregorio Maranon
Type: Journal Article | Journal: Analytical and bioanalytical chemistry | Year: 2016

The study of the distribution of the cytostatic drugs cisplatin, carboplatin, and oxaliplatin along the kidney may help to understand their different nephrotoxic behavior. Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) allows the acquisition of trace element images in biological tissues. However, results obtained are affected by several variations concerning the sample matrix and instrumental drifts. In this work, an internal standardization method based on printing an Ir-spiked ink onto the surface of the sample has been developed to evaluate the different distributions and accumulation levels of the aforementioned drugs along the kidney of a rat model. A conventional ink-jet printer was used to print fresh sagittal kidney tissue slices of 4 m. A reproducible and homogenous deposition of the ink along the tissue was observed. The ink was partially absorbed on top of the tissue. Thus, this approach provides a pseudo-internal standardization, due to the fact that the ablation sample and internal standard take place subsequently and not simultaneously. A satisfactory normalization of LA-ICP-MS bioimages and therefore a reliable comparison of the kidney treated with different Pt-based drugs were achieved even for tissues analyzed on different days. Due to the complete ablation of the sample, the transport of the ablated internal standard and tissue to the inductively coupled plasma-mass spectrometry (ICP-MS) is practically taking place at the same time. Pt accumulation in the kidney was observed in accordance to the dosages administered for each drug. Although the accumulation rate of cisplatin and oxaliplatin is high in both cases, their Pt distributions differ. The strong nephrotoxicity observed for cisplatin and the absence of such side effect in the case of oxaliplatin could explain these distribution differences. The homogeneous distribution of oxaliplatin in the cortical and medullar areas could be related with its higher affinity for cellular transporters such as MATE2-k.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-IP | Phase: HEALTH.2013.2.2.1-4 | Award Amount: 13.02M | Year: 2013

Despite a great progress in the management of epilepsy, still one third of patients is refractory to available medications. The incidence of epilepsy is highest in infancy and 50% of children experience epilepsy-related comorbidities, such as developmental delay and autism. The development of epilepsy (epileptogenesis), extensively studied in animals, is barely studied in humans, as patients usually present AFTER the seizure onset. EPISTOP is the first prospective study of epileptogenesis in humans, beginning BEFORE seizures and continuing through age 2\ years, permitting detailed analysis of the onset, drug-resistance, and comorbidities of epilepsy. To maximize information derived from the study we have chosen homogenous group of patients with prenatal or early infantile diagnosis of Tuberous Sclerosis Complex (TSC). A clinical randomized study of pre-seizure treatment in TSC infants is a part of the project. The aim of EPISTOP is to examine the risk factors and biomarkers of epilepsy and to identify possible new therapeutic targets to block or otherwise modify epileptogenesis in humans. Biomarker analysis will be performed by a multidisciplinary, systematic approach in three clinical settings: 1/ prospective study of epilepsy development in infants with TSC, including analysis of clinical, neuroimaging, and molecular, blood-derived biomarkers at predefined time points: before the onset of seizures, at the onset of epileptiform discharges on EEG, at seizure onset and at the age of 24 months 2/ prospective study of blood-based biomarkers in infants with TSC treated with antiepileptic drugs prior to seizure onset in comparison to children treated only after clinical seizures appearance. 3/ analysis of biomarkers of epileptogenesis and drug-resistant epilepsy in brain specimens obtained from TSC patients who have had epilepsy surgery and TSC autopsy cases. EPISTOP will be carried out by a consortium of 14 partners from 9 countries, including 2 SMEs.


Schwab K.,Charité - Medical University of Berlin | Stein R.,I and B Informatics and Biology | Scheler C.,Proteome Factory AG | Theuring F.,Charité - Medical University of Berlin
Electrophoresis | Year: 2012

There is evidence that isoflavones, such as genistein, can directly or indirectly improve lipid profile and lower blood pressure and hence exert cardiovascular protection. It is further believed, that genistein attenuates vascular contraction and thus vascular tone and blood pressure through altering the phosphorylation of the regulatory myosin light chain (MLC) probably via the myosin light chain kinase (MLCK) or the RhoA pathway. However, the direct role of genistein in the myocardium is poorly reviewed. In this study, we investigated the impact of genistein on the cardiac proteome in ovariectomized female mice using a 2DE-MS approach. Dietary genistein intake considerably changed the abundance of several cytoskeletal and contractile proteins and enhanced the phosphorylation of MLC. The MLC phosphorylation was mediated through increased abundance of MLCK and inhibition of myosin light chain phosphatase latest known to be inversely regulated by RhoA. Contrary to others, in our model genistein did neither inhibit the cardiac MLCK, nor the cardiac RhoA pathway in vivo. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Schwab K.,Charité - Medical University of Berlin | Neumann B.,Charité - Medical University of Berlin | Neumann B.,Proteome Factory AG | Scheler C.,Proteome Factory AG | And 2 more authors.
Amino Acids | Year: 2011

Disturbed energy metabolism with impaired fatty acid oxidation, ATP synthesis and changing levels of contractile proteins has been observed during the development and manifestation of cardiovascular diseases, with the latter showing sexual differences in terms of onset, manifestation and progress. Estrogenic compounds, such as estrogens and phytoestrogens, are known to exert beneficial effects on several cardiovascular parameters. However, global studies implying the normal, non-failing myocardium are rare. Thus, identifying and characterizing protein patterns involved in the maintenance of normal heart physiology at the protein species level will help understanding disease conditions. In this study, we performed an adapted 2-DE/MS approach in order to identify and characterize post-translational modified and truncated protein species from murine heart. Female and male animals of different age were receiving the phytoestrogen genistein and comparative analyses were performed to identify sex and genistein treatment-related effects. Selected 2-DE spots that exposed varying abundance between animal groups and identified as identical proteins were subject to multi-protease cleavage to generate an elevated sequence coverage enabling characterization of post-translational modifications and truncation loci via high-resolution MS. Several truncated, phosphorylated and acetylated species were identified for mitochondrial ATP synthase, malate dehydrogenase and trifunctional enzyme subunit alpha. However, confirmation of several of these modifications by manual spectra interpretation failed. Thus, our results warrant caution for the blind trust in software output. For the regulatory light chain of myosin, we identified an N-terminal processed species, which so far has been related to ischemic conditions only. We tried to unravel the information content of protein species separated by high-resolution 2-DE as an alternative to high-throughput proteomics, which mainly is interested in lists of protein names, ignoring the protein species identity. © 2010 Springer-Verlag.


Welter S.,Leibniz Institute of Vegetable and Ornamental Crops | Dolle S.,Charité - Medical University of Berlin | Lehmann K.,Proteome Factory AG | Schwarz D.,Leibniz Institute of Vegetable and Ornamental Crops | And 3 more authors.
PLoS ONE | Year: 2013

The plant pathogen Pepino mosaic virus (PepMV) is a major disease of greenhouse tomato crops worldwide. Plant pathogens can induce expression of defence- or pathogenesis-related proteins, including identified allergens. Therefore we hypothesised that PepMV infection results in the expression of allergens leading to a higher allergenic potential of tomato fruits. Transcript level analyses showed differential expression of 17 known and putative tomato fruit allergen encoding genes at early and late time points after PepMV inoculation, but no general induction was detected. Immunoblot analyses were conducted and IgEs from a serum pool of tomato allergic subjects reacted with 20 proteins, of which ten have not yet been described. In parallel, skin prick tests with a group of tomato allergic subjects did not show a general difference between PepMV infected and non-infected tomato fruits and basophil activation tests confirmed these results. In summary, PepMV infection of tomato plants can lead to long-lasting up-regulation of particular allergens in fruits, but the hypothesis that this results in a higher allergenic potential of the fruits proved invalid. © 2013 Welter et al.


Schulz I.,Probiodrug | Engel C.,Probiodrug | Niestroj A.J.,Probiodrug | Kehlen A.,Probiodrug | And 8 more authors.
Biochimica et Biophysica Acta - Molecular Cell Research | Year: 2014

Interleukin-6 is one of the most prominent triggers of inflammatory processes. We have shown recently that heteroarylketones (HAKs) interfere with stimulated interleukin-6 expression in astrocytes by suppression of STAT3 phosphorylation at serine 727. Surprisingly, this effect is not based on the inhibition of STAT3-relevant kinases. Therefore, we here used the structurally modified HAK compound biotin-HAK-3 in a reverse chemical approach to identify the relevant molecular target in UV-mediated cross-linking experiments. Employing streptavidin-specific 2D-immunoblotting followed by mass spectrometry we identified nine proteins putatively interacting with biotin-HAK-3. After co-immunoprecipitation, co-immunofluorescence, surface plasmon resonance analyses and RNAi-mediated knock-down, the eukaryotic elongation factor 1A1 (eEF1A1) was verified as the relevant target of HAK bioactivity. eEF1A1 forms complexes with STAT3 and PKCδ, which are crucial for STAT3S727 phosphorylation and for NF-κB/STAT3-enhanced interleukin-6 expression. Furthermore, the intracellular HAK accumulation is strongly dependent on eEF1A1 expression. Taken together, the results reveal a novel molecular mechanism for a non-canonical role of eEF1A1 in signal transduction via direct modulation of kinase-dependent phosphorylation events. © 2014 Elsevier B.V.


Meganathan K.,Institute of Neurophysiology | Jagtap S.,Institute of Neurophysiology | Wagh V.,Institute of Neurophysiology | Winkler J.,Institute of Neurophysiology | And 7 more authors.
PLoS ONE | Year: 2012

Embryonic development can be partially recapitulated in vitro by differentiating human embryonic stem cells (hESCs). Thalidomide is a developmental toxicant in vivo and acts in a species-dependent manner. Besides its therapeutic value, thalidomide also serves as a prototypical model to study teratogenecity. Although many in vivo and in vitro platforms have demonstrated its toxicity, only a few test systems accurately reflect human physiology. We used global gene expression and proteomics profiling (two dimensional electrophoresis (2DE) coupled with Tandem Mass spectrometry) to demonstrate hESC differentiation and thalidomide embryotoxicity/teratogenecity with clinically relevant dose(s). Proteome analysis showed loss of POU5F1 regulatory proteins PKM2 and RBM14 and an over expression of proteins involved in neuronal development (such as PAK2, PAFAH1B2 and PAFAH1B3) after 14 days of differentiation. The genomic and proteomic expression pattern demonstrated differential expression of limb, heart and embryonic development related transcription factors and biological processes. Moreover, this study uncovered novel possible mechanisms, such as the inhibition of RANBP1, that participate in the nucleocytoplasmic trafficking of proteins and inhibition of glutathione transferases (GSTA1, GSTA2), that protect the cell from secondary oxidative stress. As a proof of principle, we demonstrated that a combination of transcriptomics and proteomics, along with consistent differentiation of hESCs, enabled the detection of canonical and novel teratogenic intracellular mechanisms of thalidomide. © 2012 Meganathan et al.


Bergmann U.,Humboldt University of Berlin | Bergmann U.,Proteome Factory AG | Ahrends R.,Humboldt University of Berlin | Neumann B.,Proteome Factory AG | And 2 more authors.
Analytical Chemistry | Year: 2012

As the quantification of peptides and proteins extends from comparative analyses to the determination of actual amounts, methodologies for absolute protein quantification are desirable. Metal-coded affinity tags (MeCAT) are chemical labels for peptides and proteins with a lanthanide-bearing chelator as a core. This modification of analytes with non-naturally occurring heteroelements adds the analytical possibilities of inductively coupled plasma mass spectrometry (ICPMS) to quantitative proteomics. We here present the absolute quantification of recombinantly expressed aprotinin out of its host cell protein background using two independent MeCAT methodologies. A bottom-up strategy employs labeling of primary amino groups on peptide level. Synthetic peptides with a MeCAT label which are externally quantified by flow injection analysis (FIA)-ICPMS serve as internal standard in nanoHPLC-ESI-MS/MS. In the top-down approach, protein is labeled on cysteine residues and separated by two-dimensional gel electrophoresis. Flow injection analysis of dissolved gel spots by ICPMS yields the individual protein amount via its lanthanide label content. The enzymatic determination of the fusion protein via its β-galactosidase activity found 8.3 and 9.8 ng/μg (nanogram fusion protein per microgram sample) for batches 1 and 2, respectively. Using MeCAT values of 4.0 and 5.4 ng/μg are obtained for top-down analysis, while 14.5 and 15.9 ng/μg were found in the bottom-up analysis. © 2012 American Chemical Society.


Esteban-Fernandez D.,Humboldt University of Berlin | Scheler C.,Proteome Factory AG | Linscheid M.W.,Humboldt University of Berlin
Analytical and Bioanalytical Chemistry | Year: 2011

Nowadays, the most common strategies used in quantitative proteomics are based on isotope-coded labeling followed by specific molecule mass spectrometry. The implementation of inductively coupled plasma mass spectrometry (ICP-MS) for quantitative purposes can solve important drawbacks such as lack of sensitivity, structure-dependent responses, or difficulties in absolute quantification. Recently, lanthanide-containing labels as metal-coded affinity tag (MeCAT) reagents have been introduced, increasing the interest and scope of elemental mass spectrometry techniques for quantitative proteomics. In this work one of the first methodologies for absolute quantification of peptides and proteins using MeCAT labeling is presented. Liquid chromatography (LC) interfaced to ICP-MS has been used to separate and quantify labeled peptides while LC coupled to electrospray ionization mass spectrometry served for identification tasks. Synthetic-labeled peptides were used as standards to calibrate the response of the detector with compounds as close as possible to the target species. External calibration was employed as a quantification technique. The first step to apply this approach was MeCAT-Eu labeling and quantification by isotope dilution ICP-MS of the selected peptides. The standards were mixed in different concentrations and subjected to reverse-phase chromatography before ICP-MS detection to consider the column effect over the peptides. Thus, the prepared multi-peptide mix allowed a calibration curve to be obtained in a single chromatographic run, correcting possible non-quantitative elutions of the peptides from the column. The quantification strategy was successfully applied to other labeled peptides and to standard proteins such as digested lysozyme and bovine serum albumin. [Figure not available: see fulltext.] © 2011 Springer-Verlag.

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