SFB 807:  Transport and Communication across Biological Membrans

• Subject Area: Biology ; Chemistry
• Term: from 2008 to 2020
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 57566863

• Final Report Year: 2020

Final Report Abstract

The aim of the CRC 807 was to elucidate the structure, function, and mechanism of membrane proteins involved in transport processes across cell membranes. The research focus ranged from small transporter and receptor units to large, dynamic multi-subunit membrane complexes in subcellular compartments. Applied methods included X-ray crystallography, cryogenic electron microscopy, solid-state and solution NMR, pulsed EPR, time-resolved spectroscopy, single-molecule techniques, super-resolution microscopy, native mass spectrometry, theoretical biophysics, optogenetics and electrophysiology. The CRC 807 was based on a well-balanced combination of enthralling topics, highly topical biological questions, and new approaches in membrane protein research. Five subtopics were covered: (i) secondary active transporters, (ii) ATP-binding cassette (ABC) transporters, (iii) 7TM receptors and retinal proteins, (iv) ATP synthases, and (v) large membrane protein complexes. During the 12-year funding period, the CRC 807 took on ever more challenging topics and mastered a steady increase in system complexity by applying the most advanced methods. In the end, our CRC provided fundamental knowledge about a wide range of membrane proteins, documented by highly regarded and cited publications. Over the last 12 years, the CRC has been part of a transformation. Starting with a sparsely populated database, more than 1,000 unique membrane protein structures have since been deposited. At the beginning, the CRC 807 combined structural genomics, in which sequence-related targets were funneled into structures, with physiological and functional assays. Independently, researchers within the CRC already recognized the power of integrative approaches, taking on central cellular machineries and applying diverse techniques to answer specific biological questions or to pursue important hypotheses. As a consequence, an unprecedented spectrum of emerging topics and techniques has been successfully integrated in our CRC 807, which fostered Frankfurt’s prime position in the membrane protein research. As a major contribution to the research on membrane proteins, the CRC elucidated the mechanistic basis of transport and regulation by transporters, exemplified by BetP and other secondary active transporters. Frankfurt’s longstanding track record in resolving macromolecular complexes of the respiratory chain was continued by setting the focus on deciphering the structural, supramolecular organization of rotary ATPases. Within the large protein family of primary active transporters, the CRC 807 catalyzed the first cryo-EM structure of a membrane transporter, followed by a series of high-resolution structural snapshots of ABC-type machines under turnover conditions. Furthermore, the CRC 807 has been at the forefront of the development of optogenetic tools based on channelrhodopsin and other retinal proteins, which can be applied to control and monitor the activity of neuronal networks in live animals. A major breakthrough was the elucidation of transient MHC I chaperone and peptide-loading complexes, which are of vital importance in mounting an immune response against infectious diseases and tumor development. These outstanding contributions, which attracted worldwide attention, have already found their way into textbooks and catalyzed front cover stories and editorials in Nature, Science, etc.

Publications

• (2009) An ER-resident membrane protein complex regulates nicotinic acetylcholine receptor subunit composition at the synapse. EMBO J 28, 2636-49
  Almedom RB, Liewald JF, Hernando G, Schultheis C, Rayes D, Pan J, Schedletzky T, Hutter H, Bouzat C, Gottschalk A
  
• (2009) Channelrhodopsin-2 is a leaky proton pump. Proc Natl Acad Sci USA 106, 12317-22
  Feldbauer K, Zimmermann D, Pintschovius V, Spitz J, Bamann C, Bamberg E
  
• (2009) High-resolution structure of the rotor ring of a proton-dependent ATP synthase. Nat Struct Mol Biol 16, 1068-73
  Pogoryelov D, Yildiz Ö, Faraldo-Gómez JD, Meier T
  
• (2009) Molecular basis of transport and regulation in the Na+/betaine symporter BetP. Nature 458, 47-52
  Ressl S, Terwisscha van Scheltinga AC, Vonrhein C, Ott V, Ziegler C
  
• (2009) Pulsed Electron-Electron Double-Resonance Determination of Spin-Label Distances and Orientations on the Tetrameric Potassium Ion Channel KcsA. J Am Chem Soc 131, 15246-50
  Endeward B, Butterwick JA, MacKinnon R, Prisner TF
  
• (2009) Structural arrangement of the transmission interface in the antigen ABC transport complex TAP. Proc Natl Acad Sci USA 106, 5551-6
  Oancea G, O'Mara ML, Bennett WF, Tieleman DP, Abele R, Tampé R
  
• (2010) Structural basis of Na+-independent and cooperative substrate/product antiport in CaiT. Nature 467, 233-36
  Schulze S, Koster S, Geldmacher U, Terwisscha van Scheltinga AC, Kühlbrandt W
  
• (2011) Angew Chem Int Ed Engl 50, 11942-6
  Reckel S, Gottstein D, Stehle J, Löhr F, Verhoefen MK, Takeda M, Silvers R, Kainosho M, Glaubitz C, Wachtveitl J, Bernhard F, Schwalbe H, Güntert P, Dötsch V
  
• (2011) Chloroplast Omp85 proteins change orientation during evolution. Proc Natl Acad Sci USA 108, 13841-6
  Sommer MS, Daum B, Gross LE, Weis BL, Mirus O, Abram L, Maier UG, Kühlbrandt W, Schleiff E
  
• (2011) Conformation of peptides bound to the transporter associated with antigen processing (TAP). Proc Natl Acad Sci USA 108, 1349-54
  Herget M, Baldauf C, Schölz C, Parcej D, Wiesmüller KH, Tampé R, Abele R, Bordignon E
  
• (2011) Ultra lightsensitve and fast neuronal activation with the Ca2+-permeable channelrhodopsin CatCh. Nat Neurosci 14, 513-8
  Kleinlogel S, Feldbauer K, Dempski RE, Fotis H, Wood PG, Bamann C, Bamberg E
  
• (2012) Alternating-access mechanism observed in conformationally asymmetric trimers of the betaine transporter BetP. Nature 490, 126-30
  Perez C, Koshy C, Yildiz O, Ziegler C
  
• (2012) Investigation of the sodium-binding sites in the sodium-coupled betaine transporter BetP. Proc Natl Acad Sci USA 109, E3035-44
  Khafizov K, Perez C, Koshy Cm, Quick M, Fendler K, Ziegler C, Forrest LR
  
• (2012) Promiscuous archaeal ATP synthase concurrently coupled to Na+ and H+ translocation. Proc Natl Acad Sci USA 109, 947-52
  Schlegel K, Leone V, Faraldo-Gomez JD, Müller V
  
• (2012) Stochastic sensing of proteins with receptor-modified solid-state nanopores. Nat Nanotech 7, 257-63
  Wei RS, Gatterdam V, Wieneke R, Tampé R, Rant U
  
• (2012) Structural study on the architecture of the bacterial ATP synthase Fo motor. Proc Natl Acad Sci USA 109, E2050-6
  Hakulinen JK, Klyszejiko AL Hoffmann J, Eckhardt-Strelau L, Brutschy B, Vonck J, Meier T
  
• (2012) Transport of drugs by the multidrug transporter AcrB involves an access and a deep binding pocket that are separated by a switch-loop. Proc Natl Acad Sci USA 109, 5687-9
  Eicher T, Cha H, Seeger MA, Brandstätter L, El-Delik J, Bohnert JA, Kern WV, Verrey F, Grütter MG, Diederichs K, Pos KM
  
• (2013) Structural evidence for functional lipid interactions in the betaine transporter BetP. EMBO J 32, 3096-105
  Koshy C, Schweikhard ES, Gärtner RM, Perez C, Yildiz O, Ziegler C
  
• (2013) The cring stoichiometry of ATP synthase is adapted to cell physiological requirements of alkaliphilic Bacillus pseudofirmus OF4. Proc Natl Acad Sci USA 110, 7875-9
  Preiss L, Klyszejko AL, Hicks DB, Liu J, Fackelmayer OJ, Yildiz O, Krulwich TA, Meier T
  
• (2013) Ultrafast infrared spectroscopy on channelrhodopsin-2 reveals efficient energy transfer from the retinal chromophore to the protein. J Am Chem Soc 135, 6968-76
  Neumann-Verhoefen MK, Neumann K, Bamann C, Radu I, Heberle J, Bamberg E, Wachtveitl J
  
• (2014) Coupling of remote alternating-access transport mechanisms for protons and substrates in the multidrug efflux pump AcrB. eLife 3, e03145
  Eicher T, Seeger MA, Anselmi C, Zhou WC, Brandstätter L, Verrey F, Diederichs K, Faraldo-Gomez JD, Pos KM
  
• (2014) Structural basis of the green-blue color switching in proteorhodopsin as determined by NMR spectroscopy. J Am Chem Soc 136, 17578-90
  Mao JF, Do NN, Scholz F, Reggie L, Mehler M, Lakatos A, Ong YS, Ullrich SJ, Brown LJ, Brown RCD, Becker-Baldus J, Wachtveitl J, Glaubitz C
  
• (2015) Enlightening the photoactive site of channelrhodopsin-2 by DNP-enhanced solid-state NMR spectroscopy. Proc Natl Acad Sci USA 112, 9898-901
  Becker-Baldus J, Bamann C, Saxena K, Gustmann H, Brown LJ, Brown RCD, Reiter C, Bamberg E, Wachtveitl J, Schwalbe H, Glaubitz C
  
• (2015) Single liposome analysis of peptide translocation by the ABC transporter TAPL. Proc Natl Acad Sci USA 112, 2046-51
  Zollmann T, Moiset G, Tumulka F, Tampé R, Poolman B, Abele R
  
• (2015) Subnanometre-resolution electron cryo-microscopy structure of a heterodimeric ABC exporter. Nature 517, 396-400
  Kim JM, Wu, S, Tomasiak T, Mergel C, Winter MN, Stiller S, Robles-Colmanares Y, Stroud RM, Tampé R, Craik CS, Cheng Y
  
• (2016) A eukaryotic sensor for membrane lipid saturation. Mol Cell 63, 49-5
  Covino R, Ballweg S, Stordeur C, Michaelis JB, Puth K, Wernig F, Bahrami A, Ernst AM, Hummer G, Ernst R
  
• (2016) Molecular basis for inhibition of AcrB multidrug efflux pump by novel and powerful pyranopyridine derivatives. Proc Natl Acad Sci USA 113, 3509-14
  Sjuts H, Vargiu AV, Kwasny SM, Nguyen ST, Kim H-S, Ding X, Ornik AR, Ruggerone P, Bowlin T, Nikaido H, Pos KM, Opperman TJ
  
• (2017) Activation of the unfolded protein response by lipid bilayer stress. Mol Cell 67, 673-84
  Halbleib K, Pesek K, Covino R, Hofbauer HF, Wunnicke D, Hänelt I, Hummer G, Ernst R
  
• (2017) Analyzing native membrane protein assembly in nanodiscs by combined non-covalent mass spectrometry and synthetic biology. eLife 6, e20954
  Henrich E, Peetz O, Hein C, Laguerre A, Hoffmann B, Hoffmann J, Dötsch V, Bernhard, F, Morgner N
  
• (2017) Crystal structure and mechanistic basis of a functional homolog of the antigen transporter TAP. Proc Natl Acad Sci USA 114, E438-47
  Nöll A, Thomas C, Herbring V, Zollmann T, Barth K, Mehdipour AR, Tomasiak TM, Brüchert S, Joseph B, Abele R, Oliéric V, Wang M, Diederichs K, Hummer G, Stroud RM, Pos KM, Tampé R
  
• (2017) Helical jackknives control the gates of the double-pore K+ uptake system KtrAB. eLife 6, e24303
  Diskowski M, Mehdipour AR, Wunnicke D, Mills D, Mikusevic V, Bärland N, Hoffmann J, Morgner N, Steinhoff HJ, Hummer G, Vonck J, Hänelt I
  
• (2017) Structural insights into ion conduction by channelrhodopsin 2. Science 358, eaan8862
  Volkov O, Kovalev K, Polovinkin V, Borshchevskiy V, Bamann C, Astashkin R, Marin E, Popov A, Balandin T, Willbold D, Büldt G, Bamberg E, Gordeliy V
  
• (2017) Structure of the human MHC I peptide-loading complex. Nature 551, 525-8
  Blees A, Januliene D, Hofmann T, Koller N, Schmidt C, Trowitzsch S, Moeller A, Tampé R
  
• (2017) Structure of the TAPBPR-MHC I complex defines the mechanism of peptide loading and editing. Science 358, 1060-4
  Thomas C, Tampé R
  
• (2018) Conformational coupling and trans-inhibition in the human antigen transporter ortholog TmrAB resolved with dipolar EPR spectroscopy. J Am Chem Soc 140, 4527-33
  Barth K, Hank S, Spindler PE, Prisner TF, Tampè R, Joseph B
  
• (2018) Functionally asymmetric motor neurons contribute to coordinating locomotion of Caenorhabditis elegans. eLife 7, e34997
  Tolstenkov O, van der Auwera P, Costa WS, Bashanova O, Gemeinhardt TM, Bergs ACF, Gottschalk A
  
• (2018) Structure, mechanism, and regulation of the chloroplast ATP synthase. Science 360, eaat4318
  Hahn A, Vonck J, Mills DJ, Meier T, Kühlbrandt W
  
• (2019) Conformation space of a heterodimeric ABC exporter under turnover conditions. Nature 571, 580-3
  Hofmann S, Januliene D, Mehdipour AR, Thomas C, Stefan E, Brüchert S, Kuhn BT, Geertsma ER, Hummer G, Tampé R , Moeller A
  
• (2019) Photocycle-dependent conformational changes in the proteorhodopsin cross-protomer Asp-His-Trp triad revealed by DNP-enhanced MAS-NMR. Proc Natl Acad Sci USA 116, 8342-9
  Maciejko J, Kaur J, Becker-Baldus J, Glaubitz C
  
• (2019) Rotary substates of mitochondrial ATP synthase reveal the basis of flexible F1-Fo coupling. Science 364, eaaw9128
  Murphy BJ, Klusch N, Langer J, Mills DJ, Yildiz O, Kühlbrandt W