FMP Publications

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

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References
Structural Biology outside the box-inside the cell
Plitzko(*), J. M., Schuler(*), B.; Selenko, P.
Curr Opin Struct Biol, 46:110-121
(2017)

Tags: In-Cell NMR (Selenko)

Abstract: Recent developments in cellular cryo-electron tomography, in-cell single-molecule Forster resonance energy transfer-spectroscopy, nuclear magnetic resonance-spectroscopy and electron paramagnetic resonance-spectroscopy delivered unprecedented insights into the inner workings of cells. Here, we review complementary aspects of these methods and provide an outlook toward joint applications in the future.

Membrane-traversing mechanism of thyroid hormone transport by monocarboxylate transporter 8
Protze, J., Braun(*), D., Hinz, K. M., Bayer-Kusch(*), D., Schweizer(*), U.; Krause, G.
Cellular and molecular life sciences : CMLS,
(2017)

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

Abstract: Monocarboxylate transporter 8 (MCT8) mediates thyroid hormone (TH) transport across the plasma membrane in many cell types. In order to better understand its mechanism, we have generated three new MCT8 homology models based on sugar transporters XylE in the intracellular opened (PDB ID: 4aj4) and the extracellular partly occluded (PDB ID: 4gby) conformations as well as FucP (PDB ID: 3o7q) and GLUT3 (PDB ID: 4zwc) in the fully extracellular opened conformation. T3-docking studies from both sides revealed interactions with His192, His415, Arg445 and Asp498 as previously identified. Selected mutations revealed further transport-sensitive positions mainly at the discontinuous transmembrane helices TMH7 and 10. Lys418 is potentially involved in neutralising the charge of the TH substrate because it can be replaced by charged, but not by uncharged, amino acids. The side chain of Thr503 was hypothesised to stabilise a helix break at TMH10 that undergoes a prominent local shift during the transport cycle. A T503V mutation accordingly affected transport. The aromatic Tyr419, the polar Ser313 and Ser314 as well as the charged Glu422 and Glu423 lining the transport channel have been studied. Based on related sugar transporters, we suggest an alternating access mechanism for MCT8 involving a series of amino acid positions previously and newly identified as critical for transport.

Regulation of body weight and energy homeostasis by neuronal cell adhesion molecule 1
Rathjen(*), T., Yan(*), X., Kononenko, N. L., Ku(*), M. C., Song(*), K., Ferrarese(*), L., Tarallo(*), V., Puchkov, D., Kochlamazashvili, G., Brachs(*), S., Varela(*), L., Szigeti-Buck(*), K., Yi(*), C. X., Schriever(*), S. C., Tattikota(*), S. G., Carlo(*), A. S., Moroni(*), M., Siemens(*), J., Heuser(*), A., van der Weyden(*), L., Birkenfeld(*), A. L., Niendorf(*), T., Poulet(*), J. F. A., Horvath(*), T. L., Tschop(*), M. H., Heinig(*), M., Trajkovski(*), M., Haucke, V.; Poy(*), M. N.
Nat Neurosci,
(2017)

Tags: Molecular Pharmacology and Cell Biology (Haucke), Cellular Imaging (Wiesner, Puchkov)

Abstract: Susceptibility to obesity is linked to genes regulating neurotransmission, pancreatic beta-cell function and energy homeostasis. Genome-wide association studies have identified associations between body mass index and two loci near cell adhesion molecule 1 (CADM1) and cell adhesion molecule 2 (CADM2), which encode membrane proteins that mediate synaptic assembly. We found that these respective risk variants associate with increased CADM1 and CADM2 expression in the hypothalamus of human subjects. Expression of both genes was elevated in obese mice, and induction of Cadm1 in excitatory neurons facilitated weight gain while exacerbating energy expenditure. Loss of Cadm1 protected mice from obesity, and tract-tracing analysis revealed Cadm1-positive innervation of POMC neurons via afferent projections originating from beyond the arcuate nucleus. Reducing Cadm1 expression in the hypothalamus and hippocampus promoted a negative energy balance and weight loss. These data identify essential roles for Cadm1-mediated neuronal input in weight regulation and provide insight into the central pathways contributing to human obesity.

Stable Positioning of Unc13 Restricts Synaptic Vesicle Fusion to Defined Release Sites to Promote Synchronous Neurotransmission
Reddy-Alla(*), S., Böhme, M. A., Reynolds(*), E., Beis(*), C., Grasskamp, A. T., Mampell(*), M. M., Maglione, M., Jusyte, M., Rey(*), U., Babikir(*), H., McCarthy, A. W., Quentin(*), C., Matkovic(*), T., Bergeron(*), D. D., Mushtaq, Z., Goettfert(*), F., Owald(*), D., Mielke(*), T., Hell(*), S. W., Sigrist(*), S. J.; Walter, A. M.
Neuron,
(2017)

Tags: Molecular and Theoretical Neuroscience (Walter)

Abstract: Neural information processing depends on precisely timed, Ca2+-activated synaptic vesicle exocytosis from release sites within active zones (AZs), but molecular details are unknown. Here, we identify that the (M)Unc13-family member Unc13A generates release sites and show the physiological relevance of their restrictive AZ targeting. Super-resolution and intravital imaging of Drosophila neuromuscular junctions revealed that (unlike the other release factors Unc18 and Syntaxin-1A) Unc13A was stably and precisely positioned at AZs. Local Unc13A levels predicted single AZ activity. Different Unc13A portions selectively affected release site number, position, and functionality. An N-terminal fragment stably localized to AZs, displaced endogenous Unc13A, and reduced the number of release sites, while a C-terminal fragment generated excessive sites at atypical locations, resulting in reduced and delayed evoked transmission that displayed excessive facilitation. Thus, release site generation by the Unc13A C terminus and their specific AZ localization via the N terminus ensure efficient transmission and prevent ectopic, temporally imprecise release.

Tag-Free Semi-Synthesis of the Tau Protein
Reimann, O., Smet-Nocca(*), C.; Hackenberger, C. P.
Methods Mol Biol, 1523:215-235
(2017)

Tags: Chemical Biology II (Hackenberger)

Abstract: Expressed protein ligation (EPL) is a valuable tool to study site-specific functionalities on proteins such as posttranslational modifications. The purification of such ligation products from EPL mixtures can be cumbersome due to a small size difference between the expressed protein portion and the desired ligated protein. Therefore, affinity tags are often required, which remain on the protein after purification. Herein, we present an efficient protocol to install a photocleavable biotin building block on synthetic C-terminal tau[390-441] and describe its use for purification of full-length semi-synthetic tau[1-441].

Control of AMPA receptor activity by the extracellular loops of auxiliary proteins
Riva, I., Eibl, C., Volkmer, R., Carbone, A. L.; Plested, A. J.
Elife, 6
(2017)

Tags: Molecular Neuroscience and Biophysics (Plested)

Abstract: At synapses throughout the mammalian brain, AMPA receptors form complexes with auxiliary proteins, including TARPs. However, how TARPs modulate AMPA receptor gating remains poorly understood. We built structural models of TARP-AMPA receptor complexes for TARPs gamma2 and gamma8, combining recent structural studies and de novo structure predictions. These models, combined with peptide binding assays, provide evidence for multiple interactions between GluA2 and variable extracellular loops of TARPs. Substitutions and deletions of these loops had surprisingly rich effects on the kinetics of glutamate-activated currents, without any effect on assembly. Critically, by altering the two interacting loops of gamma2 and gamma8, we could entirely remove all allosteric modulation of GluA2, without affecting formation of AMPA receptor-TARP complexes. Likewise, substitutions in the linker domains of GluA2 completely removed any effect of gamma2 on receptor kinetics, indicating a dominant role for this previously overlooked site proximal to the AMPA receptor channel gate.

Mechanism of partial agonism in AMPA-type glutamate receptors
Salazar, H., Eibl, C., Chebli, M.; Plested, A.
Nat Commun, 8:14327
(2017)

Tags: Molecular Neuroscience and Biophysics (Plested)

Abstract: Neurotransmitters trigger synaptic currents by activating ligand-gated ion channel receptors. Whereas most neurotransmitters are efficacious agonists, molecules that activate receptors more weakly-partial agonists-also exist. Whether these partial agonists have weak activity because they stabilize less active forms, sustain active states for a lesser fraction of the time or both, remains an open question. Here we describe the crystal structure of an alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionate receptor (AMPAR) ligand binding domain (LBD) tetramer in complex with the partial agonist 5-fluorowillardiine (FW). We validate this structure, and others of different geometry, using engineered intersubunit bridges. We establish an inverse relation between the efficacy of an agonist and its promiscuity to drive the LBD layer into different conformations. These results suggest that partial agonists of the AMPAR are weak activators of the receptor because they stabilize multiple non-conducting conformations, indicating that agonism is a function of both the space and time domains.

Sapofectosid - Ensuring non-toxic and effective DNA and RNA delivery
Sama(*), S., Jerz(*), G., Schmieder, P., Woith(*), E., Melzig(*), M. F.; Weng(*), A.
International journal of pharmaceutics, 534:195-205
(2017)

Tags: Solution NMR (Schmieder)

Abstract: Different methods are being deployed for non-viral DNA/RNA delivery. However non-viral formulations for DNA/RNA-delivery are often accompanied by severe toxicity and thus low efficiency. Particular costly cell culture media are required as well. Here we introduce sapofection as a valuable enhancing method for non-viral DNA/RNA delivery. Sapofection is based on the application of DNA/RNA nanoplexes and sapofectosid, a plant derived natural transfection reagent. Sapofectosid was produced from plant raw material by chromatographic methods and characterized by tandem mass spectrometry and intensive one and two dimensional NMR-spectroscopy. Sapofectosid did enhance the transfection efficiency of different DNA- and RNA-nanoplexes formulated with liposomes, polyethylenimine (PEI) or targeted and non-targeted oligo-lysine peptides. All nanoplexes were characterized physicochemically and the influence of sapofectosid on the nanoplex integrity was determined by DNA complexation assays. The nanoplexes and sapofectosid were administered to a variety of cancer cell lines and the transfection efficiency was investigated by flow cytometry and confocal microscopy. Dependent on the cell line the transfection efficiencies varied from 6 to 76%. The saponin- and receptor-mediated endocytosis of nanoplexes was investigated by flow cytometry. As demonstrated by impedance based live cell imaging sapofection was non-toxic. The findings show the great potential of sapofection to be used as an effective and non-toxic transfection enhancing method.

Emerin self-assembly mechanism: role of the LEM domain
Samson(*), C., Celli(*), F., Hendriks, K., Zinke, M., Essawy(*), N., Herrada(*), I., Arteni(*), A. A., Theillet(*), F. X., Alpha-Bazin(*), B., Armengaud(*), J., Coirault(*), C., Lange, A.; Zinn-Justin(*), S.
Febs J, 284:338-352
(2017)

Tags: Molecular Biophysics (Lange, A.)

Abstract: At the nuclear envelope, the inner nuclear membrane protein emerin contributes to the interface between the nucleoskeleton and the chromatin. Emerin is an essential actor of the nuclear response to a mechanical signal. Genetic defects in emerin cause Emery-Dreifuss muscular dystrophy. It was proposed that emerin oligomerization regulates nucleoskeleton binding, and impaired oligomerization contributes to the loss of function of emerin disease-causing mutants. We here report the first structural characterization of emerin oligomers. We identified an N-terminal emerin region from amino acid 1 to amino acid 132 that is necessary and sufficient for formation of long curvilinear filaments. In emerin monomer, this region contains a globular LEM domain and a fragment that is intrinsically disordered. Solid-state nuclear magnetic resonance analysis identifies the LEM beta-fragment as part of the oligomeric structural core. However, the LEM domain alone does not self-assemble into filaments. Additional residues forming a beta-structure are observed within the filaments that could correspond to the unstructured region in emerin monomer. We show that the delK37 mutation causing muscular dystrophy triggers LEM domain unfolding and increases emerin self-assembly rate. Similarly, inserting a disulfide bridge that stabilizes the LEM folded state impairs emerin N-terminal region self-assembly, whereas reducing this disulfide bridge triggers self-assembly. We conclude that the LEM domain, responsible for binding to the chromatin protein BAF, undergoes a conformational change during self-assembly of emerin N-terminal region. The consequences of these structural rearrangement and self-assembly events on emerin binding properties are discussed.

Measurement of Cell Membrane Fluidity by Laurdan GP: Fluorescence Spectroscopy and Microscopy
Scheinpflug, K., Krylova, O.; Strahl(*), H.
Methods Mol Biol, 1520:159-174
(2017)

Tags: Peptide-Lipid-Interaction/ Peptide Transport (Dathe)

Abstract: Membrane fluidity is a critical parameter of cellular membranes which cells continuously strive to maintain within a viable range. An interference with the correct membrane fluidity state can strongly inhibit cell function. Triggered changes in membrane fluidity have been postulated to contribute to the mechanism of action of membrane targeting antimicrobials, but the corresponding analyses have been hampered by the absence of readily available analytical tools. Here, we provide detailed protocols that allow straightforward measurement of antibiotic compound-triggered changes in membrane fluidity both in vivo and in vitro.

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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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