FMP Publications

Our publications are recorded in a searchable database since 2010, updates will be added regularly.

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References
Proteotoxic stress and ageing triggers the loss of redox homeostasis across cellular compartments
Kirstein, J., Morito(*), D., Kakihana(*), T., Sugihara(*), M., Minnen(*), A., Hipp(*), M. S., Nussbaum-Krammer(*), C., Kasturi(*), P., Hartl(*), F. U., Nagata(*), K.; Morimoto(*), R. I.
EMBO J, 34:2334-2349
(2015)

Tags: Proteostasis in Aging and Disease (Kirstein)

Abstract: The cellular proteostasis network integrates the protein folding and clearance machineries in multiple sub-cellular compartments of the eukaryotic cell. The endoplasmic reticulum (ER) is the site of synthesis and folding of membrane and secretory proteins. A distinctive feature of the ER is its tightly controlled redox homeostasis necessary for the formation of inter- and intra-molecular disulphide bonds. Employing genetically encoded in vivo sensors reporting on the redox state in an organelle-specific manner, we show in the nematode Caenorhabditis elegans that the redox state of the ER is subject to profound changes during worm lifetime. In young animals, the ER is oxidizing and this shifts towards reducing conditions during ageing, whereas in the cytosol the redox state becomes more oxidizing with age. Likewise, the redox state in the cytosol and the ER change in an opposing manner in response to proteotoxic challenges in C. elegans and in HeLa cells revealing conservation of redox homeostasis. Moreover, we show that organelle redox homeostasis is regulated across tissues within C. elegans providing a new measure for organismal fitness.

Defining a conformational consensus motif in cotransin-sensitive signal sequences: a proteomic and site-directed mutagenesis study
Klein, W., Westendorf, C., Schmidt, A., Conill-Cortes, M., Rutz, C., Blohs, M., Beyermann, M., Protze, J., Krause, G., Krause, E.; Schülein, R.
Plos One, 10:e0120886
(2015)

Tags: Protein Trafficking (Schülein), Mass Spectrometry (Krause, E.), Structural Bioinformatics and Protein Design (Krause, G.), Peptide Chemistry (Beyermann)

Abstract: The cyclodepsipeptide cotransin was described to inhibit the biosynthesis of a small subset of proteins by a signal sequence-discriminatory mechanism at the Sec61 protein-conducting channel. However, it was not clear how selective cotransin is, i.e. how many proteins are sensitive. Moreover, a consensus motif in signal sequences mediating cotransin sensitivity has yet not been described. To address these questions, we performed a proteomic study using cotransin-treated human hepatocellular carcinoma cells and the stable isotope labelling by amino acids in cell culture technique in combination with quantitative mass spectrometry. We used a saturating concentration of cotransin (30 micromolar) to identify also less-sensitive proteins and to discriminate the latter from completely resistant proteins. We found that the biosynthesis of almost all secreted proteins was cotransin-sensitive under these conditions. In contrast, biosynthesis of the majority of the integral membrane proteins was cotransin-resistant. Cotransin sensitivity of signal sequences was neither related to their length nor to their hydrophobicity. Instead, in the case of signal anchor sequences, we identified for the first time a conformational consensus motif mediating cotransin sensitivity.

Analysis of phosphorylation-dependent protein-protein interactions of histone h3
Klingberg(*), R., Jost(*), J. O., Schümann, M., Gelato(*), K. A., Fischle(*), W., Krause, E.; Schwarzer(*), D.
ACS Chem Biol, 10:138-145
(2015)

Tags: Mass Spectrometry (Krause, E.)

Abstract: Multiple posttranslational modifications (PTMs) of histone proteins including site-specific phosphorylation of serine and threonine residues govern the accessibility of chromatin. According to the histone code theory, PTMs recruit regulatory proteins or block their access to chromatin. Here, we report a general strategy for simultaneous analysis of both of these effects based on a SILAC MS scheme. We applied this approach for studying the biochemical role of phosphorylated S10 of histone H3. Differential pull-down experiments with H3-tails synthesized from l- and d-amino acids uncovered that histone acetyltransferase 1 (HAT1) and retinoblastoma-binding protein 7 (RBBP7) are part of the protein network, which interacts with the unmodified H3-tail. An additional H3-derived bait containing the nonhydrolyzable phospho-serine mimic phosphonomethylen-alanine (Pma) at S10 recruited several isoforms of the 14-3-3 family and blocked the recruitment of HAT1 and RBBP7 to the unmodified H3-tail. Our observations provide new insights into the many functions of H3S10 phosphorylation. In addition, the outlined methodology is generally applicable for studying specific binding partners of unmodified histone tails.

Molecular mechanisms of presynaptic membrane retrieval and synaptic vesicle reformation
Kononenko, N. L.; Haucke, V.
Neuron, 85:484-496
(2015)

Tags: Molecular Pharmacology and Cell Biology (Haucke)

Abstract: The function of the nervous system depends on the exocytotic release of neurotransmitter from synaptic vesicles (SVs). To sustain neurotransmission, SV membranes need to be retrieved, and SVs have to be reformed locally within presynaptic nerve terminals. In spite of more than 40 years of research, the mechanisms underlying presynaptic membrane retrieval and SV recycling remain controversial. Here, we review the current state of knowledge in the field, focusing on the molecular mechanism involved in presynaptic membrane retrieval and SV reformation. We discuss the challenges associated with studying these pathways and present perspectives for future research.

Vesicular Synaptobrevin/VAMP2 Levels Guarded by AP180 Control Efficient Neurotransmission
Koo, S. J., Kochlamazashvili, G., Rost(*), B., Puchkov, D., Gimber, N., Lehmann, M., Tadeus, G., Schmoranzer, J., Rosenmund(*), C., Haucke, V.; Maritzen, T.
Neuron, 88:330-344
(2015)

Tags: Membrane Traffic and Cell Motility (Maritzen), Molecular Pharmacology and Cell Biology (Haucke)

Abstract: Neurotransmission depends on synaptic vesicle (SV) exocytosis driven by soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex formation of vesicular synaptobrevin/VAMP2 (Syb2). Exocytic fusion is followed by endocytic SV membrane retrieval and the high-fidelity reformation of SVs. Syb2 is the most abundant SV protein with 70 copies per SV, yet, one to three Syb2 molecules appear to be sufficient for basal exocytosis. Here we demonstrate that loss of the Syb2-specific endocytic adaptor AP180 causes a moderate activity-dependent reduction of vesicular Syb2 levels, defects in SV reformation, and a corresponding impairment of neurotransmission that lead to excitatory/inhibitory imbalance, epileptic seizures, and premature death. Further reduction of Syb2 levels in AP180(-/-)/Syb2(+/-) mice results in perinatal lethality, whereas Syb2(+/-) mice partially phenocopy loss of AP180, indicating that reduced vesicular Syb2 levels underlie the observed defects in neurotransmission. Thus, a large vesicular Syb2 pool maintained by AP180 is crucial to sustain efficient neurotransmission and SV reformation.

Peptide-polymer ligands for a tandem WW-domain, an adaptive multivalent protein-protein interaction: lessons on the thermodynamic fitness of flexible ligands
Koschek, K., Durmaz(*), V., Krylova, O., Wieczorek, M., Gupta(*), S., Richter, M., Bujotzek(*), A., Fischer(*), C., Haag(*), R., Freund, C., Weber(*), M.; Rademann, J.
Beilstein J Org Chem, 11:837-847
(2015)

Tags: Medicinal Chemistry (Rademann), Protein Engineering (Freund), Peptide-Lipid-Interaction/ Peptide Transport (Dathe)

Abstract: Three polymers, poly(N-(2-hydroxypropyl)methacrylamide) (pHPMA), hyperbranched polyglycerol (hPG), and dextran were investigated as carriers for multivalent ligands targeting the adaptive tandem WW-domain of formin-binding protein (FBP21). Polymer carriers were conjugated with 3-9 copies of the proline-rich decapeptide GPPPRGPPPR-NH2 (P1). Binding of the obtained peptide-polymer conjugates to the tandem WW-domain was investigated employing isothermal titration calorimetry (ITC) to determine the binding affinity, the enthalpic and entropic contributions to free binding energy, and the stoichiometry of binding for all peptide-polymer conjugates. Binding affinities of all multivalent ligands were in the microM range, strongly amplified compared to the monovalent ligand P1 with a K D > 1 mM. In addition, concise differences were observed, pHPMA and hPG carriers showed moderate affinity and bound 2.3-2.8 peptides per protein binding site resulting in the formation of aggregates. Dextran-based conjugates displayed affinities down to 1.2 microM, forming complexes with low stoichiometry, and no precipitation. Experimental results were compared with parameters obtained from molecular dynamics simulations in order to understand the observed differences between the three carrier materials. In summary, the more rigid and condensed peptide-polymer conjugates based on the dextran scaffold seem to be superior to induce multivalent binding and to increase affinity, while the more flexible and dendritic polymers, pHPMA and hPG are suitable to induce crosslinking upon binding.

Assembly and function of claudins: Structure-function relationships based on homology models and crystal structures
Krause, G., Protze, J.; Piontek(*), J.
Semin Cell Dev Biol, 42:3-12
(2015)

Tags: Structural Bioinformatics and Protein Design (Krause, G.)

Abstract: The tetra-span transmembrane proteins of the claudin family are critical components of formation and function of tight junctions (TJ). Homo- and heterophilic side-by-side (cis) and intercellular head-to-head (trans) interactions of 27 claudin-subtypes regulate tissue-specifically the paracellular permeability and/or tightness between epithelial or endothelial cells. This review highlights the functional impact that has been identified for particular claudin residues by relating them to structural features and architectural characteristics in the light of structural advances, which have been contributed by homology models, cryo-electron microscopy and crystal structures. The differing contributions to the TJ functionalities by claudins are dissected for the transmembrane region, the first and the second extracellular loop of claudins separately. Their particular impact to oligomerisation and TJ strand- and pore-formation is surveyed. Detailed knowledge about structure-function relationships about claudins helps to reveal the molecular mechanisms of TJ assembly and regulation of paracellular permeability, which is yet not fully understood.

A grab to move on: ER-endosome contacts in membrane protrusion formation and neurite outgrowth
Krauss, M.; Haucke, V.
EMBO J, 34:1442-1444
(2015)

Tags: Molecular Pharmacology and Cell Biology (Haucke)

Cysteine-Functional Polymers via Thiol-ene Conjugation
Kuhlmann(*), M., Reimann, O., Hackenberger, C. P. R.; Groll(*), J.
Macromol Rapid Comm, 36:472-476
(2015)

Tags: Chemical Biology II (Hackenberger)

Abstract: A thiofunctional thiazolidine is introduced as a new low-molar-mass building block for the introduction of cysteine residues via a thiol-ene reaction. Allyl-functional polyglycidol (PG) is used as a model polymer to demonstrate polymer-analogue functionalization through reaction with the unsaturated side-chains. A modified trinitrobenzenesulfonic acid (TNBSA) assay is used for the redox-insensitive quantification and a precise final cysteine content can be predetermined at the polymerization stage. Native chemical ligation at cysteine-functional PG is performed as a model reaction for a chemoselective peptide modification of this polymer. The three-step synthesis of the thiofunctional thiazolidine reactant, together with the standard thiol-ene coupling and the robust quantification assay, broadens the toolbox for thiol-ene chemistry and offers a generic and straight-forward approach to cysteine-functional materials.

Identification, classification, and signal amplification capabilities of high-turnover gas binding hosts in ultra-sensitive NMR
Kunth, M., Witte, C., Hennig(*), A.; Schröder, L.
Chem Sci, 6:6069-6075
(2015)

Tags: Molecular Imaging (Schröder)

Abstract: Nuclear Magnetic Resonance (NMR) can be a powerful tool for investigating exchange kinetics of host-guest interactions in solution. Beyond conventional direct NMR detection, radiofrequency (RF) saturation transfer can be used to enhance the study of such chemical exchange or to enable signal amplification from a dilute host. However, systems that are both dilute and labile (fast dissociation/re-association) impose specific challenges to direct as well as saturation transfer detection. Here we investigate host-guest systems under previously inaccessible conditions using saturation transfer techniques in combination with hyperpolarized nuclei and quantitative evaluation under different RF exposure. We further use that information to illustrate the consequences for signal amplification capabilities and correct interpretation of observed signal contrast from comparative exchange data of different types of hosts. In particular, we compare binding of xenon (Xe) to cucurbit[6]uril (CB6) with binding to cryptophane-A monoacid (CrA) in water as two different model systems. The Xe complexation with CB6 is extremely difficult to access by conventional NMR due to its low water solubility. We successfully quantified the exchange kinetics of this system and found that the absence of Xe signals related to encapsulated Xe in conventional hyperpolarized Xe-129 NMR is due to line broadening and not due to low binding. By introducing a measure for the gas turnover during constant association-dissociation, we demonstrate that the signal amplification from a dilute pool of CB6 can turn this host into a very powerful contrast agent for Xe MRI applications (100-fold more efficient than cryptophane). However, labile systems only provide improved signal amplification for suitable saturation conditions and otherwise become disadvantageous. The method is applicable to many hosts where Xe is a suitable spy nucleus to probe for non-covalent interactions and should foster reinvestigation of several systems to delineate true absence of interaction from labile complex formation.

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Leibniz-Forschungsinstitut für Molekulare Pharmakologie im Forschungsverbund Berlin e.V. (FMP)
Campus Berlin-Buch
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13125 Berlin, Germany
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info(at)fmp-berlin.de

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