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Structure, Function and Folding of Membrane Proteins and their Complexes

English title Structure, Function and Folding of Membrane Proteins and their Complexes
Applicant Hiller Sebastian
Number 128419
Funding scheme SNSF Professorships
Research institution
Institution of higher education University of Basel - BS
Main discipline Molecular Biology
Start/End 01.08.2010 - 31.07.2014
Approved amount 1'516'305.00
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All Disciplines (2)

Discipline
Molecular Biology
Biophysics

Keywords (11)

Membrane Proteins; Protein Structure Determination; Protein Function; Protein Folding; Nuclear Magnetic Resonance (NMR); Transport across Membranes; Membrane Protein Biogenesis; Protein Dynamics; Mitochondria; Outer Membrane; Protein Complexes

Lay Summary (English)

Lead
Lay summary
All cells are surrounded by bilayers of lipid molecules, the cellular membranes. Embedded in these membranes are proteins that fulfill important functions. For example, some membrane proteins regulate the influx and outflow of nutrients, ions, vitamins and other molecules. Other membrane proteins are part of the defense mechanisms of the cell against viruses and diseases. It is a central goal for the life sciences to understand all these biological processes on the molecular level. Over the past fifty years tens of thousands structures of soluble proteins have brought tremendous biological insight, but we know only about 200 unique structures of membrane proteins and our knowledge on this class of proteins is thus still relatively sparse. The research of my group will contribute to understanding membrane proteins by studying the structures, functions and folding mechanisms of individual membrane proteins and their complexes at atomic resolution. We use solution nuclear magnetic resonance (NMR) spectroscopy as the main technique, but also complementary techniques, like solid state NMR and fluorescence spectroscopy to answer our biological and biophysical questions.NMR spectroscopy uses a strong magnetic field to polarize the nuclear spins in the protein and then electromagnetic waves to collect information about the local environment of each atom in the protein. By the analysis of many different NMR experiments we can deduce the atomic structure of membrane proteins. With additional experiments we obtain knowledge on their functions. For example, it is possible to determine the interface and the relative orientation, in which two membrane proteins interact with each other. In our projects, we work on selected membrane proteins of high biological relevance. One representative example is the voltage dependent anion channel, a protein from the human mitochondria, of which we have recently determined the three-dimensional structure and could thus understand which parts of the protein are involved in the voltage gating function. Along a second line of research, we investigate the biophysical principles of membrane protein folding. A detailed understanding of this process will help us understanding the biogenesis of cellular membranes and could also explain mechanisms of certain protein misfolding diseases. Additionally, we further improve and refine our experimental techniques so that bigger and more challenging systems can be studied in the future.
Direct link to Lay Summary Last update: 21.02.2013

Responsible applicant and co-applicants

Employees

Publications

Publication
Monitoring Backbone Hydrogen-Bond Formation in β-Barrel Membrane Protein Folding.
Raschle Thomas, Rios Flores Perla, Opitz Christian, Müller Daniel J, Hiller Sebastian (2016), Monitoring Backbone Hydrogen-Bond Formation in β-Barrel Membrane Protein Folding., in Angewandte Chemie (International ed. in English), 55(20), 5952-5.
Chaperones and chaperone-substrate complexes: Dynamic playgrounds for NMR spectroscopists.
Burmann Björn M, Hiller Sebastian (2015), Chaperones and chaperone-substrate complexes: Dynamic playgrounds for NMR spectroscopists., in Progress in nuclear magnetic resonance spectroscopy, 86-87, 41-64.
Characterization of the insertase BamA in three different membrane mimetics by solution NMR spectroscopy.
Morgado Leonor, Zeth Kornelius, Burmann Björn M, Maier Timm, Hiller Sebastian (2015), Characterization of the insertase BamA in three different membrane mimetics by solution NMR spectroscopy., in Journal of biomolecular NMR, 61(3-4), 333-45.
Conserved Omp85 lid-lock structure and substrate recognition in FhaC.
Maier Timm, Clantin Bernard, Gruss Fabian, Dewitte Frédérique, Delattre Anne-Sophie, Jacob-Dubuisson Françoise, Hiller Sebastian, Villeret Vincent (2015), Conserved Omp85 lid-lock structure and substrate recognition in FhaC., in Nature communications, 6, 7452-7452.
Impact of holdase chaperones Skp and SurA on the folding of β-barrel outer-membrane proteins.
Thoma Johannes, Burmann Björn M, Hiller Sebastian, Müller Daniel J (2015), Impact of holdase chaperones Skp and SurA on the folding of β-barrel outer-membrane proteins., in Nature structural & molecular biology, 22(10), 795-802.
Purification and Bicelle Crystallization for Structure Determination of the E. coli Outer Membrane Protein TamA.
Gruss Fabian, Hiller Sebastian, Maier Timm (2015), Purification and Bicelle Crystallization for Structure Determination of the E. coli Outer Membrane Protein TamA., in Buchanan S Noinaj N (ed.), Springer, New York, 259-70.
Revisiting the interaction between the chaperone Skp and lipopolysaccharide.
Burmann Björn M, Holdbrook Daniel A, Callon Morgane, Bond Peter J, Hiller Sebastian (2015), Revisiting the interaction between the chaperone Skp and lipopolysaccharide., in Biophysical journal, 108(6), 1516-26.
Structural mapping of a chaperone-substrate interaction surface.
Callon Morgane, Burmann Björn M, Hiller Sebastian (2014), Structural mapping of a chaperone-substrate interaction surface., in Angew. Chem. Int. Engl., 53(20), 5069-72.
Trypanosomal TAC40 constitutes a novel subclass of mitochondrial β-barrel proteins specialized in mitochondrial genome inheritance.
Schnarwiler Felix, Niemann Moritz, Doiron Nicholas, Harsman Anke, Käser Sandro, Mani Jan, Chanfon Astrid, Dewar Caroline E, Oeljeklaus Silke, Jackson Christopher B, Pusnik Mascha, Schmidt Oliver, Meisinger Chris, Hiller Sebastian, Warscheid Bettina, Schnaufer Achim C, Ochsenreiter Torsten, Schneider André (2014), Trypanosomal TAC40 constitutes a novel subclass of mitochondrial β-barrel proteins specialized in mitochondrial genome inheritance., in Proc. Natl. Acad. Sci. USA, 111(21), 7624-9.
Conformation and dynamics of the periplasmic membrane-protein-chaperone complexes OmpX-Skp and tOmpA-Skp.
Burmann Björn M, Wang Congwei, Hiller Sebastian (2013), Conformation and dynamics of the periplasmic membrane-protein-chaperone complexes OmpX-Skp and tOmpA-Skp., in Nat. Struct. Mol. Biol., 20(11), 1265-72.
The functional heart of the M2 channel.
Hiller Sebastian (2013), The functional heart of the M2 channel., in Biophysical journal, 104(8), 1639-40.
The structural basis of autotransporter translocation by TamA.
Gruss Fabian, Zähringer Franziska, Jakob Roman P, Burmann Björn M, Hiller Sebastian, Maier Timm (2013), The structural basis of autotransporter translocation by TamA., in Nat. Struct. Mol. Biol., 20(11), 1318-20.
4D solid-state NMR for protein structure determination.
Huber Matthias, Böckmann Anja, Hiller Sebastian, Meier Beat H (2012), 4D solid-state NMR for protein structure determination., in Physical chemistry chemical physics : PCCP, 14(15), 5239-46.
Bacterial Origin of a Mitochondrial Outer Membrane Protein Translocase
Harsman Anke, Niemann Moritz, Pusnik Mascha, Schmidt Oliver, Burmann Björn M, Hiller Sebastian, Meisinger Chris, Schneider André, Wagner Richard (2012), Bacterial Origin of a Mitochondrial Outer Membrane Protein Translocase, in J. Biol. Chem., 287(37), 31437-45.
Solution NMR spectroscopic characterization of human VDAC-2 in detergent micelles and lipid bilayer nanodiscs.
Yu Tsyr-Yan, Raschle Thomas, Hiller Sebastian, Wagner Gerhard (2012), Solution NMR spectroscopic characterization of human VDAC-2 in detergent micelles and lipid bilayer nanodiscs., in Biochimica et biophysica acta, 1818(6), 1562-9.
Solution NMR Spectroscopy of Integral Membrane Proteins
Hiller Sebastian, Wagner Gerhard (2012), Solution NMR Spectroscopy of Integral Membrane Proteins, in Egelman E. (ed.), Elsevier, New York, 120-138.
Solution NMR studies of membrane-protein-chaperone complexes.
Burmann Björn M, Hiller Sebastian (2012), Solution NMR studies of membrane-protein-chaperone complexes., in Chimia, 66(10), 759-63.
4D APSY-HBCB(CG)CDHD experiment for automated assignment of aromatic amino acid side chains in proteins.
Krähenbühl Barbara, Hiller Sebastian, Wider Gerhard (2011), 4D APSY-HBCB(CG)CDHD experiment for automated assignment of aromatic amino acid side chains in proteins., in Journal of biomolecular NMR, 51(3), 313-8.
Automated NMR Resonance Assignment of Large Proteins for Protein-Ligand Interaction Studies.
Gossert Alvar D, Hiller Sebastian, Fernandez Cesar (2010), Automated NMR Resonance Assignment of Large Proteins for Protein-Ligand Interaction Studies., in Journal of the American Chemical Society, 133, 210-213.
How Amphipols Embed Membrane Proteins: Global Solvent Accessibility and Interaction with a Flexible Protein Terminus.
Etzkorn Manuel, Zoonens Manuela, Catoire Laurent J, Popot Jean-Luc, Hiller Sebastian, How Amphipols Embed Membrane Proteins: Global Solvent Accessibility and Interaction with a Flexible Protein Terminus., in J. Membr. Biol..
Perspectives of solution NMR spectroscopy for structural and functional studies of integral membrane proteins
Reckel Sina, Hiller Sebastian, Perspectives of solution NMR spectroscopy for structural and functional studies of integral membrane proteins, in Molecular Physics.

Collaboration

Group / person Country
Types of collaboration
Chris Meisinger, University of Freiburg Germany (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Paul Gooley, University of Melbourne Australia (Oceania)
- in-depth/constructive exchanges on approaches, methods or results
Gerhard Wagner, Harvard Medical School United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
André Schneider, University of Bern Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Beat Meier, ETH Zurich Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
- Exchange of personnel
Timm Maier, University of Basel Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
- Exchange of personnel
Daniel Müller, ETH Zurich Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Research Infrastructure
- Exchange of personnel

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
FASEB conference “Protein folding in the cell” Talk given at a conference Molecular mechanisms in outer membrane protein biogenesis 25.07.2014 Saxtons River VT, United States of America Hiller Sebastian;
Biochemistry lecture series Individual talk Molecular mechanisms in outer membrane protein biogenesis 10.07.2014 University of Tübingen, Germany Hiller Sebastian;
15th Rhône Alpes NMR meeting Talk given at a conference Molecular mechanisms in outer membrane protein biogenesis 13.06.2014 IBS Grenoble, France Hiller Sebastian;
Application seminar Individual talk Molecular mechanisms in outer membrane protein biogenesis 12.06.2014 University of Regensburg, Germany Hiller Sebastian;
Gordon research conference "Protein transport across membranes" Talk given at a conference Skp and TamA: Molecular mechanisms in outer membrane protein biogenesis 12.03.2014 Galveston TX, United States of America Hiller Sebastian;
Structural Biology Lecture Series Individual talk Molecular mechanisms in outer membrane protein biogenesis 20.02.2014 CEITEC Brno, Czech Republic Hiller Sebastian;
Biochemistry Lecture Series, University Zurich Individual talk Molecular mechanisms in outer membrane protein biogenesis 12.12.2013 Zurich, Switzerland Hiller Sebastian;
NMR Symposium, ETH Zurich Individual talk Molecular mechanisms in outer membrane protein biogenesis 20.11.2013 Zurich, Switzerland Hiller Sebastian;
International Symposium of the German Society for Biochemistry and Molecular Biology (GBM) Talk given at a conference Mechanism of membrane protein transport by a periplasmic chaperone 04.10.2013 Frankfurt, Germany Hiller Sebastian;
9th European Magnetic Resonance Meeting Poster Moelcular mechanisms in outer membrane protein biogenesis 30.06.2013 Hersonissos, Greece Hiller Sebastian;
1st International Conference on Membrane Protein Folding Talk given at a conference Mechanism of membrane protein transport by a periplasmic chaperone 19.05.2013 Seoul, Korean Republic (South Korea) Hiller Sebastian;
17th European Bioenergetics Conference Talk given at a conference The dynamic, compacted state of outer membrane proteins bound to the chaperone Skp 16.09.2012 Freiburg, Germany Hiller Sebastian;
25th International Conference on Magnetic Resonance in Biological Systems Talk given at a conference The dynamic, compacted state of outer membrane proteins bound to the chaperone Skp 23.08.2012 Lyon, France Hiller Sebastian;
3rd MitoNet Conference: Mitochondrial Medicine Talk given at a conference Structural and functional studies of VDAC by solution NMR spectroscopy 12.07.2012 Bern, Switzerland Hiller Sebastian;
1st Indo-Swiss symposium: Recent Trends in NMR of Biomolecules and Advanced Materials Talk given at a conference Membrane protein structure and folding studied by NMR 24.01.2012 Pune, India Hiller Sebastian;
Towards structural studies of membrane proteins: a BioNMR symposium Talk given at a conference Membrane protein structure and folding studied by NMR 18.01.2012 Zurich, Switzerland Hiller Sebastian;
3rd CCPN European Conference Talk given at a conference Preparation of membrane protein samples for solution NMR studies 30.09.2011 Lisbon, Portugal Hiller Sebastian;
Advanced course on new methods of data acquisition and analysis in biomolecular NMR Talk given at a conference Automated projection spectroscopy (APSY): applications to proteins 21.09.2010 Gothenburg, Sweden Hiller Sebastian;


Self-organised

Title Date Place
20th Swiss NMR sypmosium 21.01.2014 University of Basel, Switzerland
Frontiers in Structural Biology and Biophysics 22.03.2013 Basel, Switzerland

Associated projects

Number Title Start Funding scheme
145023 Advanced Imaging System for Biomolecular Crystallization Screening 01.12.2012 R'EQUIP
150814 Purchase of a 900 MHz high-resolution NMR instrument 01.12.2013 R'EQUIP
152989 Structure, Function and Folding of Membrane Proteins and their Complexes 01.08.2014 SNSF Professorships

Abstract

One of the key goals in the current era of life sciences is the understanding of all cellular processes on a molecular level. Membrane proteins, which comprise about a third of typical proteomes, are responsible for a wide range of vital cellular functions, including signal transduction, catalysis, respiration, and transport. The function of a protein is dependent on its three-dimensional structure and whereas tens of thousands of high-resolution structures of soluble proteins have brought us tremendous biological insight over the past fifty years, with only 200 unique structures our knowledge of membrane proteins is still relatively sparse.The research of my group will contribute to our understanding of membrane proteins by studying the structures, functions and folding mechanisms of selected membrane proteins and their complexes at atomic resolution. We will mainly use solution nuclear magnetic resonance (NMR) spectroscopy, but also complementary techniques to answer our biological and biophysical questions. I propose three projects:A. One project is the structural biology of the translocase of the outer mitochondrial membrane (Tom), a multiprotein channel through which proteins are transported into the mitochondria. A large body of biochemical and biophysical data is available in the literature, including electron micrographs, but high-resolution three-dimensional structures of the Tom complex are unknown. We will determine the structure of Tom40, the core unit of the Tom complex by solution NMR spectroscopy. Then, we will study the structures of the transmembrane domains of the other Tom complex members and map their interaction sites with Tom40. The ultimate goal is a full biophysical model of the Tom complex and its substrate recognition mechanism. B. A second line of research aims at understanding fundamental biophysical principles of beta-barrel membrane protein folding. These proteins fold by a complex cooperative mechanism, which involves both a hydrophilic and a hydrophobic external phase. Using solution NMR spectroscopy with proton/deuterium exchange labeling, we want to characterize the in vitro folding mechanism of beta-barrel membrane proteins resolved for individual atomic sites. We also want to relate our studies to kinetic data on the single molecule level. Further, we will study mechanistic details of the chaperone assisted in vivo folding process and address the role of hydrophobic clusters in the unfolded states of soluble and membrane proteins. Our ultimate goal is to come up with a comprehensive description of the in vivo and in vitro folding mechanism of the beta-barrel integral membrane protein OmpX and related proteins.C. The development of groundbreaking NMR technology for structural and functional studies of proteins will be an integral part of the above projects. Such techniques will be applicable to membrane proteins but also stimulate NMR research on other proteins and their complexes. We will develop and improve isotope labeling schemes, NMR pulse sequences and high-resolution non-uniform sampling and processing schemes.
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