SFB 803:  Functionality Controlled by Organisation in and between Membranes

• Subject Area: Chemistry ; Biology
• Term: from 2009 to 2020
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 55908123

• Final Report Year: 2021

Final Report Abstract

It was the aim of the Collaborative Research Center (CRC 803) to unravel the interactions between the large number of different lipids and specialized proteins in cellular membranes on the molecular level. We clarified how the spatial and temporal organization of membrane components influences their function. We have been able to elucidate how simple peptides and large transmembrane proteins, particularly pores and ion channels, organize in membranes and how they interact with their surrounding lipids. During this journey, new methods have been developed, and established ones have been further developed. To provide some examples: In case of simple transmembrane peptides, the synergy between bioorganic synthesis and EPR spectroscopy paved the way to new experiments to measure spin label orientations at high EPR frequencies. Relating the structure of an ion channel to its function was achieved in depth for the voltage dependent anion channel VDAC by a combination of NMR spectroscopic structural investigations, ion channel recordings, mathematical analysis and atomistic simulations. These results enabled us to draw molecular pictures of how peptides and proteins form structures that are responsible for transport processes across membranes. The CRC 803 contributed significantly to our current understanding of neuronal fusion mediated by soluble N-ethylmaleimide-sensitive-factor attachment receptors (SNAREs). We have been able to understand how physical mesoscopic parameters such as membrane curvature and lateral tension as well as molecular determinants such as particular lipids and the molecular structure of different SNAREs determine and influence the energy landscape along the fusion pathway. A combination of new experimental tools to analyze fusion intermediates, and new fusion assays combined with bioorganic synthetic approaches and simulation studies have led to a more molecular picture and the involved energetics that drive the merging of two membranes resulting in the release of neurotransmitters.

Publications

• (2010) Molecular recognition at the membrane−water interface: Controlling integral peptide helices by off-membrane nucleobase pairing. J. Am. Chem. Soc. 132, 8020–8028
  Schneggenburger, P. E., Müllar, S., Worbs, B., Steinem, C., Diederichsen, U.
  (See online at https://doi.org/10.1021/ja1006349)
• (2011) Membrane protein sequestering by ionic protein–lipid interactions. Nature 479, 552–555
  van den Bogaart, G., Meyenberg, K., Risselada, H. J., Amin, H., Willig, K. I., Hubrich, B. E., Dier, M., Hell, S. W., Grubmüller, H., Diederichsen, U., Jahn, R.
  (See online at https://doi.org/10.1038/nature10545)
• (2011) TOPP: A novel nitroxide-labeled amino acid for EPR distance measurements. Angew. Chem. Int. Ed. 50, 9743–9746
  Stoller, S., Sicoli, G., Baranova, T. Y., Bennati, M., Diederichsen, U.
  (See online at https://doi.org/10.1002/anie.201103315)
• (2011) Transmembrane domain peptide/peptide nucleic acid hybrid as a model of a SNARE protein in vesicle fusion. Angew. Chem. Int. Ed. 50, 8597–8601
  Lygina, A. S., Meyenberg, K., Jahn, R., Diederichsen, U.
  (See online at https://doi.org/10.1002/anie.201101951)
• (2012) Membrane fusion intermediates via directional and full assembly of the SNARE complex. Science 336, 1581-1584
  Hernandez, J. M., Stein, A., Behrmann, E., Riedel, D., Cypionka, A., Farsi, Z., Walla, P. J., Raunser, S., Jahn, R.
  (See online at https://doi.org/10.1126/science.1221976)
• (2012) Molecular driving forces defining lipid positions around aquaporin-0. Proc. Natl. Acad. Sci. U.S.A. 109, 9887–9892
  Aponte-Santamaria, C., Briones, R., Schenk, A. D., Walz, T., Groot, B. L. d.
  (See online at https://doi.org/10.1073/pnas.1121054109)
• (2012) Structure, hydration barrier and curvature of membrane hemifusion stalks with varying lipid composition obtained by x-ray diffraction. Proc. Natl. Acad. Sci. U.S.A. 109, 1609-1648
  Aeffner, S., Weinhausen, B., Reusch, T., Salditt, T.
  (See online at https://doi.org/10.1016/j.bpj.2012.03.069)
• (2012) β-Barrel mobility underlies closure of the voltage-dependent anion channel. Structure 20, 1540-1549
  Zachariae, U., Schneider, R., Briones, R., Gattin, Z., Demers, J. P., Giller, K., Maier, E., Zweckstetter, M., Griesinger, C., Becker, S., Benz, R., de Groot, B. L., Lange, A.
  (See online at https://doi.org/10.1016/j.str.2012.06.015)
• (2013) Idealizing ion channel recordings by a jump segmentation multiresolution filter. IEEE Transact. NanoBiosci. 12, 376–386
  Hotz, T., Schütte, O. M., Sieling, H., Polupanow, T., Diederichsen, U., Steinem, C., Munk, A.
  (See online at https://doi.org/10.1109/tnb.2013.2284063)
• (2013) Quantifying the diffusion of membrane proteins and peptides in black lipid membranes with 2- focus fluorescence correlation spectroscopy. Biophys. J. 105, 455–462
  Weiß, K., Neef, A., Van, Q., Kramer, S., Gregor, I., Enderlein, J.
  (See online at https://doi.org/10.1016/j.bpj.2013.06.004)
• (2014) Control of membrane gaps by synaptotagmin-Ca2+ measured with a novel membrane distance ruler. Nat. Commun. 5, 6859
  Lin, C. C., Seikowski, J., Perez-Lara, A., Jahn, R., Höbartner, C., Walla, P. J.
  (See online at https://doi.org/10.1038/ncomms6859)
• (2014) Expansion of the fusion stalk and its implication for biological membrane fusion. Proc. Natl. Acad. Sci. U.S.A. 111, 11043–11048
  Risselada, H. J., Bubnis, G., Grubmüller, H.
  (See online at https://doi.org/10.1073/pnas.1323221111)
• (2014) Fluorescence nanoscopy by polarization modulation and polarization angle narrowing. Nat. Methods 11, 579-584
  Hafi, N., Grunwald, M., van den Heuvel, L. S., Aspelmeier, T., Chen, J. H., Zagrebelsky, M., Schütte, O. M., Steinem, C., Korte, M., Munk, A., Walla, P. J.
  (See online at https://doi.org/10.1038/nmeth.2919)
• (2014) Influence of Gb3 glycosphingolipids differing in their fatty acid chain on the phase behaviour of solid supported membranes: chemical syntheses and impact of Shiga toxin binding. Chem. Sci. 5, 3104
  Schütte, O. M., Ries, A., Orth, A., Patalag, L. J., Römer, W., Steinem, C., Werz, D. B.
  (See online at https://doi.org/10.1039/C4SC01290A)
• (2014) Structure of the mitochondrial translocator protein in complex with a diagnostic ligand. Science 343, 1363–1366
  Jaremko, L., Jaremko, M., Giller, K., Becker, S., Zweckstetter, M.
  (See online at https://doi.org/10.1126/science.1248725)
• (2015) Synaptotagmin-1 binds to PIP2-containing membrane but not to SNAREs at physiological ionic strength. Nat. Struct. Mol. Biol. 22, 815-823
  Park, Y., Seo, J. B., Fraind, A., Perez-Lara, A., Yavuz, H., Han, K., Jung, S. R., Kattan, I., Walla, P. J., Choi, M., Cafiso, D. S., Koh, D. S., Jahn, R.
  (See online at https://doi.org/10.1038/nsmb.3097)
• (2016) Epsin N-terminal homology domain (ENTH) activity as a function of membrane tension. J. Biol. Chem. 291, 19953-19961
  Gleisner, M., Kroppen, B., Fricke, C., Teske, N., Kliesch, T. T., Janshoff, A., Meinecke, M., Steinem, C.
  (See online at https://doi.org/10.1074/jbc.m116.731612)
• (2016) Pulse EPR measurements of intramolecular distances in a TOPP-labeled transmembrane peptide in lipids. Biophys. J. 111, 2345–2348
  Halbmair, K., Wegner, J., Diederichsen, U., Bennati, M.
  (See online at https://doi.org/10.1016/j.bpj.2016.10.022)
• (2016) Simulations of pore formation in lipid membranes: Reaction coordinates, convergence, hysteresis, and finite-size effects. J. Chem. Theory Comput. 12, 3261–3269
  Awasthi, N., Hub, J. S.
  (See online at https://doi.org/10.1021/acs.jctc.6b00369)
• (2016) SNARE-mediated membrane fusion trajectories derived from force-clamp experiments. Proc. Natl. Acad. Sci. U.S.A. 113, 13051–13056
  Oelkers, M., Witt, H., Halder, P., Jahn, R., Janshoff, A.
  (See online at https://doi.org/10.1073/pnas.1615885113)
• (2016) Super-resolution optical fluctuation bio-imaging with dual-color carbon nanodots. Nano Lett. 16, 237-242
  Chizhik, A. M., Stein, S., Dekaliuk, M. O., Battle, C., Li, W. X., Huss, A., Platen, M., Schaap, I. A. T., Gregor, I., Demchenko, A. P., Schmidt, C. F., Enderlein, J., Chizhik, A. I.
  (See online at https://doi.org/10.1021/acs.nanolett.5b03609)
• (2016) Voltage dependence of conformational dynamics and subconducting states of VDAC-1. Biophys. J. 111, 1223–1234
  Briones, R., Weichbrodt, C., Paltrinieri, L., Mey, I., Villinger, S., Giller, K., Lange, A., Zweckstetter, M., Griesinger, C., Becker, S., de Groot, B. L., Steinem, C.
  (See online at https://doi.org/10.1016/j.bpj.2016.08.007)
• (2016) β-Glutamine-mediated selfassociation of transmembrane β-peptides within lipid bilayers. Chem. Sci. 7, 5900–5907
  Rost, U., Steinem, C., Diederichsen, U.
  (See online at https://doi.org/10.1039/c6sc01147k)
• (2017) Cholesterol-mediated allosteric regulation of the mitochondrial translocator protein structure. Nat. Commun. 8, 14893
  Jaipuria, G., Leonov, A., Giller, K., Vasa, S. K., Jaremko, Ł., Jaremko, M., Linser, R., Becker, S., Zweckstetter, M.
  (See online at https://doi.org/10.1038/ncomms14893)
• (2017) SNARE-mediated single-vesicle fusion events with supported and freestanding lipid membranes. Biophys. J. 113, 2573–2574
  Kuhlmann, J. W., Junius, M., Diederichsen, U., Steinem, C.
  (See online at https://doi.org/10.1016/j.bpj.2017.10.039)
• (2018) Insights into cholesterol/membrane protein interactions using paramagnetic solid-state NMR. Chem. Eur. J. 24, 17606–17611
  Jaipuria, G., Giller, K., Leonov, A., Becker, S., Zweckstetter, M.
  (See online at https://doi.org/10.1002/chem.201804550)
• (2018) Mechanism of mechanosensitive gating of the TREK-2 potassium channel. Biophys. J. 114, 1336–1343
  Brennecke, J. T., Groot, B. L. d.
  (See online at https://doi.org/10.1016/j.bpj.2018.01.030)
• (2018) Metastable prepores in tensionfree lipid bilayers. Phys. Rev. Lett. 120, 128103
  Ting, C. L., Awasthi, N., Müller, M., Hub, J. S.
  (See online at https://doi.org/10.1103/physrevlett.120.128103)
• (2018) PNA hybrid sequences as recognition units in SNARE‐ protein‐mimicking peptides. Angew. Chem. Int. Ed. 57, 14932-14936
  Hubrich, B. E., Kumar, P., Neitz, H., Grunwald, M., Grothe, T., Walla, P. J., Jahn, R., Diederichsen, U.
  (See online at https://doi.org/10.1002/anie.201805752)
• (2018) Vesicle adhesion and fusion studied by small-angle X-ray scattering. Biophys. J. 114, 1908–1920
  Komorowski, K., Salditt, A., Xu, Y., Yavuz, H., Brennich, M., Jahn, R., Salditt, T.
  (See online at https://doi.org/10.1016/j.bpj.2018.02.040)
• (2019) Graphene-based metal-induced energy transfer for sub-nanometre optical localization. Nat. Photonics 13, 860–865
  Ghosh, A., Sharma, A., Chizhik, A. I., Isbaner, S., Ruhlandt, D., Tsukanov, R., Gregor, I., Karedla, N., Enderlein, J.
  (See online at https://doi.org/10.1038/s41566-019-0510-7)
• (2019) Semi-rigid nitroxide spin label for long-range EPR distance measurements of lipid bilayer embedded β-peptides. Chem. Eur. J. 25, 2203–2207
  Wegner, J., Valora, G., Halbmair, K., Kehl, A., Worbs, B., Bennati, M., Diederichsen, U.
  (See online at https://doi.org/10.1002/chem.201805880)
• (2019) Synthesis of Gb3 glycosphingolipids with labeled head groups: Distribution in phase‐separated giant unilamellar vesicles. Angew. Chem. Int. Ed. 58, 17805–17813
  Sibold, J., Kettelhoit, K., Vuong, L., Liu, F., Werz, D. B., Steinem, C.
  (See online at https://doi.org/10.1002/anie.201910148)
• (2019) Thermodynamically reversible paths of the first fusion intermediate reveal an important role for membrane anchors of fusion proteins. Proc. Natl. Acad. Sci. U.S.A. 116, 2571–2576
  Smirnova, Y. G., Risselada, H. J., Müller, M.
  (See online at https://doi.org/10.1073/pnas.1818200116)
• (2020) A β-barrel for oil transport through lipid membranes: Dynamic NMR structures of AlkL. Proc. Natl. Acad. Sci. U.S.A. 117, 21014-21021
  Schubeis, T., Le Marchand, T., Daday, C., Kopec, W., Movellan, K. T., Stanek, J., Schwarzer, T. S., Castiglione, K., de Groot, B. L., Pintacuda, G., Andreas, L. B.
  (See online at https://doi.org/10.1073/pnas.2002598117)
• (2020) Fusion pore formation observed during SNARE-mediated vesicle fusion with pore-spanning membranes. Biophys. J. 119, 151-161
  Mühlenbrock, P., Herwig, K., Vuong, L., Mey, I., Steinem, C.
  (See online at https://doi.org/10.1016/j.bpj.2020.05.023)
• (2020) Sequential water and headgroup merger: Membrane poration paths and energetics from MD simulations. Biophys. J. 119, 2418-2430
  Bubnis, G., Grubmüller, H.
  (See online at https://dx.doi.org/10.1016/j.bpj.2020.10.037)
• (2021) Cooperativity of membrane-protein and protein-protein interactions control membrane remodeling by epsin 1 and affects clathrin-mediated endocytosis. Cell. Mol. Life Sci. 78, 2355-2370
  Kroppen, B., Teske, N., Yambire, K. F., Denkert, N., Mukherjee, I., Tarasenko, D., Jaipuria, G., Zweckstetter, M., Milosevic, I., Steinem, C., Meinecke, M.
  (See online at https://doi.org/10.1007/s00018-020-03647-z)
• (2021) Insights into the molecular mechanism of amyloid filament formation: segmental folding of αsynuclein on lipid membranes: Molecular mechanism of αS filament folding on membrane. Sci. Adv. 7, eabg2174
  Antonschmidt, L., Dervisoglu, R., Sant, V., Tekwani Movellan, K., Mey, I., Riedel, D., Steinem, C., Becker, S., Andreas, L. B., Griesinger, C.
  (See online at https://doi.org/10.1126/sciadv.abg2174)
• (2021) The effect of polydispersity, shape fluctuations and curvature on small unilamellar vesicle smallangle X-ray scattering curves. J. Appl. Crystal. 54, 557–568
  Chappa, V., Smirnova, Y., Komorowski, K., Müller, M., Salditt, T.
  (See online at https://doi.org/10.1107/s1600576721001461)