TY - JOUR A1 - Zhang, Xiaorong A1 - Caserta, Giorgio A1 - Yarman, Aysu A1 - Supala, Eszter A1 - Tadjoung Waffo, Armel Franklin A1 - Wollenberger, Ulla A1 - Gyurcsanyi, Robert E. A1 - Zebger, Ingo A1 - Scheller, Frieder W. T1 - "Out of Pocket" protein binding BT - a dilemma of epitope imprinted polymers revealed for human hemoglobin JF - Chemosensors N2 - The epitope imprinting approach applies exposed peptides as templates to synthesize Molecularly Imprinted Polymers (MIPs) for the recognition of the parent protein. While generally the template protein binding to such MIPs is considered to occur via the epitope-shaped cavities, unspecific interactions of the analyte with non-imprinted polymer as well as the detection method used may add to the complexity and interpretation of the target rebinding. To get new insights on the effects governing the rebinding of analytes, we electrosynthesized two epitope-imprinted polymers using the N-terminal pentapeptide VHLTP-amide of human hemoglobin (HbA) as the template. MIPs were prepared either by single-step electrosynthesis of scopoletin/pentapeptide mixtures or electropolymerization was performed after chemisorption of the cysteine extended VHLTP peptide. Rebinding of the target peptide and the parent HbA protein to the MIP nanofilms was quantified by square wave voltammetry using a redox probe gating, surface enhanced infrared absorption spectroscopy, and atomic force microscopy. While binding of the pentapeptide shows large influence of the amino acid sequence, all three methods revealed strong non-specific binding of HbA to both polyscopoletin-based MIPs with even higher affinities than the target peptides. KW - Molecularly Imprinted Polymers KW - epitope imprinting KW - non-specific KW - binding KW - redox gating KW - SEIRA spectroelectrochemistry Y1 - 2021 U6 - https://doi.org/10.3390/chemosensors9060128 SN - 2227-9040 VL - 9 IS - 6 PB - MDPI CY - Basel ER - TY - JOUR A1 - Schrapers, Peer A1 - Hartmann, Tobias A1 - Kositzki, Ramona A1 - Dau, Holger A1 - Reschke, Stefan A1 - Schulzke, Carola A1 - Leimkühler, Silke A1 - Haumann, Michael T1 - 'Sulfido and Cysteine Ligation Changes at the Molybdenum Cofactor during Substrate Conversion by Formate Dehydrogenase (FDH) from Rhodobacter capsulatus JF - Inorganic chemistry N2 - Formate dehydrogenase (FDH) enzymes are attractive catalysts for potential carbon dioxide conversion applications. The FDH from Rhodobacter capsulatus (RcFDH) binds a bis-molybdopterin-guanine-dinucleotide (bis-MGD) cofactor, facilitating reversible formate (HCOO-) to CO2 oxidation. We characterized the molecular structure of the active site of wildtype RcFDH and protein variants using X-ray absorption spectroscopy (XAS) at the Mo K-edge. This approach has revealed concomitant binding of a sulfido ligand (Mo=S) and a conserved cysteine residue (S(Cys386)) to Mo(VI) in the active oxidized molybdenum cofactor (Moco), retention of such a coordination motif at Mo(V) in a chemically reduced enzyme, and replacement of only the S(Cys386) ligand by an oxygen of formate upon Mo(IV) formation. The lack of a Mo=S bond in RcFDH expressed in the absence of FdsC implies specific metal sulfuration by this bis-MGD binding chaperone. This process still functioned in the Cys386Ser variant, showing no Mo-S(Cys386) ligand, but retaining a Mo=S bond. The C386S variant and the protein expressed without FdsC were inactive in formate oxidation, supporting that both Moligands are essential for catalysis. Low-pH inhibition of RcFDH was attributed to protonation at the conserved His387, supported by the enhanced activity of the His387Met variant at low pH, whereas inactive cofactor species showed sulfido-to-oxo group exchange at the Mo ion. Our results support that the sulfido and S(Cys386) ligands at Mo and a hydrogen-bonded network including His387 are crucial for positioning, deprotonation, and oxidation of formate during the reaction cycle of RcFDH. Y1 - 2015 U6 - https://doi.org/10.1021/ic502880y SN - 0020-1669 SN - 1520-510X VL - 54 IS - 7 SP - 3260 EP - 3271 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Uhlig, Katja A1 - Madaboosi, Narayanan A1 - Schmidt, Stephan A1 - Jäger, Magnus S. A1 - Rose, Jürgen A1 - Duschl, Claus A1 - Volodkin, Dmitry V. T1 - 3d localization and diffusion of proteins in polyelectrolyte multilayers JF - Soft matter N2 - The interaction of diverse biomaterials with surfaces is more crucial than ever for biomedical applications to ensure efficiency and reproducibility. Very interesting surface materials are micrometer-thick polyelectrolyte multilayers. Not only their surface but also the bulk can be loaded with biomaterials like proteins or DNA for various purposes. Therefore, we established a method to analyze the lateral and vertical distribution of fluorescently labelled proteins of various size and charge in polyelectrolyte films composed of poly(L-lysine) and hyaluronic acid by confocal laser scanning microscopy. This approach enables us to measure the diffusion coefficients of the proteins via fluorescence recovery after photobleaching as a function of their vertical position in the film and facilitates the understanding of molecular interactions in the film with a high resolution in both space and time. As a result, we confirm that protein loading in the film is driven by electrostatic interactions - uncharged dextran molecules of 10 and 500 kDa do not diffuse into the film. Proteins of different sizes (3-11 nm) can diffuse relatively fast (D = 2-4 mm(2) s(-1)) independent of their net charge, indicating complex interpolymer interactions. This approach is a new powerful experimental tool to design the polyelectrolyte multilayers for bio-applications by finding a relationship between intermolecular interactions and mobility and availability of biomolecules to biological samples (e.g. cells) or detection units (e.g. biosensors). Y1 - 2012 U6 - https://doi.org/10.1039/c2sm26500a SN - 1744-683X VL - 8 IS - 47 SP - 11786 EP - 11789 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Schwarzer, Christian A1 - Huamani, Fatima Cßceres A1 - Cano, Asunción A1 - La Torre, María I. La A1 - Weigend, Maximilian T1 - 400 years for long-distance dispersal and divergence in the northern atacama desert : insights from the Huaynaputina pumice slopes of Moquegua, Peru N2 - The Huaynaputina eruption (1600 AD, Moquegua, S Peru) in the northern Atacama Desert denuded the Ornate area of all vegetation and deposited deep pumice layers. Data on the flora, climate and soil characteristics of these slopes near Ornate at 1600-2600 m a.s.l. are provided. Fifty-nine angiosperm species established themselves on the pumice slopes in the past ca. 400 years, with the bulk of the small and herbaceous species and several species new records for Peru. Three Ornate sites were sampled in both a dry and a wet year and species numbers differed widely (14 versus 45 spp.). Among areas compared floristic composition is most similar to the Lomas de Tacna, and has less in common with geographically closer Lomas or Sierra formations. Nine species represent highly disjunct populations (200->700 km) from their nearest known living populations in central Peru, Chile, or Argentina/Bolivia and appear to have reached the area via long-distance dispersal. Abiotic conditions may have played an important role in limiting the establishment of species from the neighboring vegetation. Four taxa on the pumice slopes show clear morphological differences to populations elsewhere, two of them may represent neoendemics of the Ornate pumice, indicating rapid morphological divergence. (C) 2010 Elsevier Ltd. All rights reserved. Y1 - 2010 U6 - https://doi.org/10.1016/j.jaridenv.2010.05.034 SN - 0140-1963 ER - TY - JOUR A1 - Gruden, Kristina A1 - Hren, Matjaz A1 - Herman, Ana A1 - Blejec, Andrej A1 - Albrecht, Tanja A1 - Selbig, Joachim A1 - Bauer, Christian G. A1 - Schuchardt, Johannes A1 - Or-Guil, Michal A1 - Zupancic, Klemen A1 - Svajger, Urban A1 - Stabuc, Borut A1 - Ihan, Alojz A1 - Kopitar, Andreja Natasa A1 - Ravnikar, Maja A1 - Knezevic, Miomir A1 - Rozman, Primoz A1 - Jeras, Matjaz T1 - A "Crossomics" study analysing variability of different components in peripheral blood of healthy caucasoid individuals JF - PLoS one N2 - Background: Different immunotherapy approaches for the treatment of cancer and autoimmune diseases are being developed and tested in clinical studies worldwide. Their resulting complex experimental data should be properly evaluated, therefore reliable normal healthy control baseline values are indispensable. Methodology/Principal Findings: To assess intra- and inter-individual variability of various biomarkers, peripheral blood of 16 age and gender equilibrated healthy volunteers was sampled on 3 different days within a period of one month. Complex "crossomics'' analyses of plasma metabolite profiles, antibody concentrations and lymphocyte subset counts as well as whole genome expression profiling in CD4(+)T and NK cells were performed. Some of the observed age, gender and BMI dependences are in agreement with the existing knowledge, like negative correlation between sex hormone levels and age or BMI related increase in lipids and soluble sugars. Thus we can assume that the distribution of all 39.743 analysed markers is well representing the normal Caucasoid population. All lymphocyte subsets, 20% of metabolites and less than 10% of genes, were identified as highly variable in our dataset. Conclusions/Significance: Our study shows that the intra- individual variability was at least two-fold lower compared to the inter-individual one at all investigated levels, showing the importance of personalised medicine approach from yet another perspective. Y1 - 2012 U6 - https://doi.org/10.1371/journal.pone.0028761 SN - 1932-6203 VL - 7 IS - 1 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Leong, Jia Xuan A1 - Raffeiner, Margot A1 - Spinti, Daniela A1 - Langin, Gautier A1 - Franz-Wachtel, Mirita A1 - Guzman, Andrew R. A1 - Kim, Jung-Gun A1 - Pandey, Pooja A1 - Minina, Alyona E. A1 - Macek, Boris A1 - Hafren, Anders A1 - Bozkurt, Tolga O. A1 - Mudgett, Mary Beth A1 - Börnke, Frederik A1 - Hofius, Daniel A1 - Uestuen, Suayib T1 - A bacterial effector counteracts host autophagy by promoting degradation of an autophagy component JF - The EMBO journal N2 - Beyond its role in cellular homeostasis, autophagy plays anti- and promicrobial roles in host-microbe interactions, both in animals and plants. One prominent role of antimicrobial autophagy is to degrade intracellular pathogens or microbial molecules, in a process termed xenophagy. Consequently, microbes evolved mechanisms to hijack or modulate autophagy to escape elimination. Although well-described in animals, the extent to which xenophagy contributes to plant-bacteria interactions remains unknown. Here, we provide evidence that Xanthomonas campestris pv. vesicatoria (Xcv) suppresses host autophagy by utilizing type-III effector XopL. XopL interacts with and degrades the autophagy component SH3P2 via its E3 ligase activity to promote infection. Intriguingly, XopL is targeted for degradation by defense-related selective autophagy mediated by NBR1/Joka2, revealing a complex antagonistic interplay between XopL and the host autophagy machinery. Our results implicate plant antimicrobial autophagy in the depletion of a bacterial virulence factor and unravel an unprecedented pathogen strategy to counteract defense-related autophagy in plant-bacteria interactions. KW - autophagy KW - effectors KW - immunity KW - ubiquitination KW - xenophagy Y1 - 2022 U6 - https://doi.org/10.15252/embj.2021110352 SN - 0261-4189 SN - 1460-2075 VL - 41 IS - 13 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Ruzanski, Christian A1 - Smirnova, Julia A1 - Rejzek, Martin A1 - Cockburn, Darrell A1 - Pedersen, Henriette L. A1 - Pike, Marilyn A1 - Willats, William G. T. A1 - Svensson, Birte A1 - Steup, Martin A1 - Ebenhöh, Oliver A1 - Smith, Alison M. A1 - Field, Robert A. T1 - A bacterial glucanotransferase can replace the complex maltose metabolism required for starch to sucrose conversion in leaves at night JF - The journal of biological chemistry N2 - Controlled conversion of leaf starch to sucrose at night is essential for the normal growth of Arabidopsis. The conversion involves the cytosolic metabolism of maltose to hexose phosphates via an unusual, multidomain protein with 4-glucanotransferase activity, DPE2, believed to transfer glucosyl moieties to a complex heteroglycan prior to their conversion to hexose phosphate via a cytosolic phosphorylase. The significance of this complex pathway is unclear; conversion of maltose to hexose phosphate in bacteria proceeds via a more typical 4-glucanotransferase that does not require a heteroglycan acceptor. It has recently been suggested that DPE2 generates a heterogeneous series of terminal glucan chains on the heteroglycan that acts as a glucosyl buffer to ensure a constant rate of sucrose synthesis in the leaf at night. Alternatively, DPE2 and/or the heteroglycan may have specific properties important for their function in the plant. To distinguish between these ideas, we compared the properties of DPE2 with those of the Escherichia coli glucanotransferase MalQ. We found that MalQ cannot use the plant heteroglycan as an acceptor for glucosyl transfer. However, experimental and modeling approaches suggested that it can potentially generate a glucosyl buffer between maltose and hexose phosphate because, unlike DPE2, it can generate polydisperse malto-oligosaccharides from maltose. Consistent with this suggestion, MalQ is capable of restoring an essentially wild-type phenotype when expressed in mutant Arabidopsis plants lacking DPE2. In light of these findings, we discuss the possible evolutionary origins of the complex DPE2-heteroglycan pathway. KW - Carbohydrate Metabolism KW - Computer Modeling KW - Metabolic Regulation KW - Oligosaccharide KW - Plant Biochemistry KW - Glucanotransferase KW - Leaf Cell KW - Maltose Metabolism KW - Starch Degradation Y1 - 2013 U6 - https://doi.org/10.1074/jbc.M113.497867 SN - 0021-9258 SN - 1083-351X VL - 288 IS - 40 SP - 28581 EP - 28598 PB - American Society for Biochemistry and Molecular Biology CY - Bethesda ER - TY - JOUR A1 - Wolff, Martin A1 - Zhang-Haagen, Bo A1 - Decker, Christina A1 - Barz, Bogdan A1 - Schneider, Mario A1 - Biehl, Ralf A1 - Radulescu, Aurel A1 - Strodel, Birgit A1 - Willbold, Dieter A1 - Nagel-Steger, Luitgard T1 - A beta 42 pentamers/hexamers are the smallest detectable oligomers in solution JF - Scientific reports Y1 - 2017 U6 - https://doi.org/10.1038/s41598-017-02370-3 SN - 2045-2322 VL - 7 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Klauschies, Toni A1 - Coutinho, Renato Mendes A1 - Gaedke, Ursula T1 - A beta distribution-based moment closure enhances the reliability of trait-based aggregate models for natural populations and communities JF - Ecological modelling : international journal on ecological modelling and engineering and systems ecolog N2 - Ecological communities are complex adaptive systems that exhibit remarkable feedbacks between their biomass and trait dynamics. Trait-based aggregate models cope with this complexity by focusing on the temporal development of the community’s aggregate properties such as its total biomass, mean trait and trait variance. They are based on particular assumptions about the shape of the underlying trait distribution, which is commonly assumed to be normal. However, ecologically important traits are usually restricted to a finite range, and empirical trait distributions are often skewed or multimodal. As a result, normal distribution-based aggregate models may fail to adequately represent the biomass and trait dynamics of natural communities. We resolve this mismatch by developing a new moment closure approach assuming the trait values to be beta-distributed. We show that the beta distribution captures important shape properties of both observed and simulated trait distributions, which cannot be captured by a Gaussian. We further demonstrate that a beta distribution-based moment closure can strongly enhance the reliability of trait-based aggregate models. We compare the biomass, mean trait and variance dynamics of a full trait distribution (FD) model to the ones of beta (BA) and normal (NA) distribution-based aggregate models, under different selection regimes. This way, we demonstrate under which general conditions (stabilizing, fluctuating or disruptive selection) different aggregate models are reliable tools. All three models predicted very similar biomass and trait dynamics under stabilizing selection yielding unimodal trait distributions with small standing trait variation. We also obtained an almost perfect match between the results of the FD and BA models under fluctuating selection, promoting skewed trait distributions and ongoing oscillations in the biomass and trait dynamics. In contrast, the NA model showed unrealistic trait dynamics and exhibited different alternative stable states, and thus a high sensitivity to initial conditions under fluctuating selection. Under disruptive selection, both aggregate models failed to reproduce the results of the FD model with the mean trait values remaining within their ecologically feasible ranges in the BA model but not in the NA model. Overall, a beta distribution-based moment closure strongly improved the realism of trait-based aggregate models. KW - Moment closure KW - Normal and beta distribution KW - Skewed and peaked trait distributions KW - Fitness landscape and frequency-dependent selection KW - Eco-evolutionary dynamics KW - Modelling functional diversity Y1 - 2018 U6 - https://doi.org/10.1016/j.ecolmodel.2018.02.001 SN - 0304-3800 SN - 1872-7026 VL - 381 SP - 46 EP - 77 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Huang, T. A1 - Warsinke, Axel A1 - Koroljova-Skorobogatko, O. V. A1 - Makower, Alexander A1 - Kuwana, T. A1 - Scheller, Frieder W. T1 - A bienzyme carbon paste electrode for the sensitive detection of NADPH and the measurement of glucose-6- phosphate dehydrogenase Y1 - 1999 ER -