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Structural Studies of Aggregates and Membrane Proteins

English title Structural Studies of Aggregates and Membrane Proteins
Applicant Riek Roland
Number 163284
Funding scheme Project funding
Research institution Laboratorium für Physikalische Chemie D-CHAB ETH Zürich
Institution of higher education ETH Zurich - ETHZ
Main discipline Physical Chemistry
Start/End 01.01.2016 - 31.12.2018
Approved amount 850'000.00
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All Disciplines (2)

Discipline
Physical Chemistry
Biophysics

Keywords (1)

3D structure, NMR, membrane protein, aggregation

Lay Summary (German)

Lead
Das Wissen der dreidimensionalen Gestalt von Proteinen ist essentiell für das Verstehen Ihrer Aktivität im kranken als auch im gesunden Körper. Die Bestimmung der drei dimensionalen Struktur von Proteinaggregaten assoziiert mit neurodegenerativen Erkrankungen als auch von Protein-Lipid Komplexen involviert im Cholesteroltransport im Blut sind das Haupt-Ziel dieser Forschungsarbeit.
Lay summary

Proteinaggregation ist ein Prozess, bei dem identische Eiweisse verklumpen. Dabei verklumpen sie in einer bestimmten Art und Weise und formen sogenannte Beta-Blatt Strukturen, die Amyloide genannt werden. Bei der Alzheimerkrankheit findet man diese Amyloide bestehend aus dem Eiweiss Aβ(1-42) als Ablagerungen im Hirn und man glaubt, dass diese Amyloide für die Uebertragung der Krankheit von einer Zelle zur anderen wichtig sind. Es ist das Ziel dieser Forschungsarbeit, die drei dimensionale Gestalt dieses physiologisch relevanten Amyloids zu bestimmen. Dabei werden verschiedene Techniken angewendet insbesondere auch die Festkörper Kernspin Resonanz Spektroskopie (NMR).

Membranproteine sind Eiweisse, die viele wichtige Funktionen in unserem Körper ausüben. Obwohl etwa 20% von den 25’000 Proteine Membranprotein sind, kennen wir nur von ein paar Dutzend deren drei dimensionale Gestalt. Es ist das Ziel dieser Forschungsarbeit, die drei dimensionale Struktur eines solchen Membranproteins des sogenannten high density lipoportein particles (HDL) mit Hilfe von NMR und Elektronen paramagnetische Resonanz Spektroskopie (EPR) zu bestimmen. Die Bestimmung dieser Struktur wird Einsichten geben, wieso HDL das sogenanntes „gute Cholesterol“ in unserem Körper ist.

Direct link to Lay Summary Last update: 08.12.2015

Responsible applicant and co-applicants

Employees

Publications

Publication
Fast NMR-Based Determination of the 3D Structure of the Binding Site of Protein-Ligand Complexes with Weak Affinity Binders
Wälti Marielle A., Riek Roland, Orts Julien (2017), Fast NMR-Based Determination of the 3D Structure of the Binding Site of Protein-Ligand Complexes with Weak Affinity Binders, in Angewandte Chemie International Edition, 56(19), 5208-5211.
Solution structure of discoidal high-density lipoprotein particles with a shortened apolipoprotein A-I
Bibow Stefan, Polyhach Yevhen, Eichmann Cédric, Chi Celestine N, Kowal Julia, Albiez Stefan, McLeod Robert A, Stahlberg Henning, Jeschke Gunnar, Güntert Peter, Riek Roland (2017), Solution structure of discoidal high-density lipoprotein particles with a shortened apolipoprotein A-I, in Nature Structural & Molecular Biology, 24(2), 187-193.
α-Synuclein lipoprotein nanoparticles
Eichmann Cédric, Bibow Stefan, Riek Roland (2017), α-Synuclein lipoprotein nanoparticles, in Nanotechnology Reviews, 6(1), 105-110.
Solid-state NMR sequential assignment of an Amyloid-β(1–42) fibril polymorph
Ravotti Francesco, Wälti Marielle Aulikki, Güntert Peter, Riek Roland, Böckmann Anja, Meier Beat H. (2016), Solid-state NMR sequential assignment of an Amyloid-β(1–42) fibril polymorph, in Biomolecular NMR Assignments, 10(2), 269-276.
Solid-state NMR sequential assignment of the β-endorphin peptide in its amyloid form
Seuring Carolin, Gath Julia, Verasdonck Joeri, Cadalbert Riccardo, Rivier Jean, Böckmann Anja, Meier Beat H., Riek Roland (2016), Solid-state NMR sequential assignment of the β-endorphin peptide in its amyloid form, in Biomolecular NMR Assignments, 10(2), 259-268.
Atomic-resolution structure of a disease-relevant Aβ(1–42) amyloid fibril
Wälti Marielle Aulikki, Ravotti Francesco, Arai Hiromi, Glabe Charles G., Wall Joseph S., Böckmann Anja, Güntert Peter, Meier Beat H., Riek Roland (2016), Atomic-resolution structure of a disease-relevant Aβ(1–42) amyloid fibril, in Proceedings of the National Academy of Sciences, 113(34), E4976-E4984.
S-Sulfhydration of the Catalytic Cysteine in the Rhodanese Domain of YgaP is Complex Dynamic Process
Eichmann Cédric, Tzitzilonis Christos, Kwiatkowski Witek, Riek Roland (2016), S-Sulfhydration of the Catalytic Cysteine in the Rhodanese Domain of YgaP is Complex Dynamic Process, in Matters (Zürich), y(c), 0-0.
Dynamic Assembly and Disassembly of Functional β-Endorphin Amyloid Fibrils
Nespovitaya Nadezhda, Gath Julia, Barylyuk Konstantin, Seuring Carolin, Meier Beat H., Riek Roland (2016), Dynamic Assembly and Disassembly of Functional β-Endorphin Amyloid Fibrils, in Journal of the American Chemical Society, 138(3), 846-856.

Collaboration

Group / person Country
Types of collaboration
The Meier group/ETH Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
The Jeschke group/ETH Zürich Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
The Stahlberg group/ Biozentrum Basel Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results

Associated projects

Number Title Start Funding scheme
144444 Structural Studies of Aggregates and Membrane Proteins 01.01.2013 Project funding
182800 Structural Studies of Aggregates and Membrane Proteins 01.01.2019 Project funding

Abstract

The presented proposal covers both main scientific projects of the Riek group. Project A: Structural Studies of Protein AggregatesProtein aggregation is a process in which identical proteins self-associate into imperfectly ordered macroscopic entities. Protein aggregates are in generally composed of a ß-sheet-rich entity termed cross-ß-sheet structure. These highly ordered cross-ß-sheet containing aggregates, termed amyloids, are the pathological hallmarks of several diseases including Alzheimer’s, and Parkinson’s disease, but are also associated with functional states such as hormone storage in secretory granules in mammals. It is the aim of this continuing proposal to study protein aggregation from a structural point of view with a particular focus on the structural and mechanistic comparison between functional and disease-associated amyloid systems. Aim 1 is the 3D structure determination of Aß(1-42) fibrils associated with Alzheimer’s disease: While the mechanism of toxicity of Aß(1-42) is unknown, Aß(1-42) amyloid fibrils are a pathological hallmark of Alzheimer’s disease and appear to play a role in cell-to-cell transmission. It is the goal to elucidate a 3D structure of a physiological relevant Aß(1-42) amyloid amongst other techniques by quenched H/D exchange Nuclear Magnetic Resonance Spectroscopy (NMR) and solid state NMR (in collaboration with B. Meier, ETH). Aim 2 is the study of the phase-space of Aß(1-42): Aß(1-42) is able to from many structural polymorphs. It is the goal to study structurally the phase-space of Aß(1-42) aggregation by covering diverse physiological buffers with various biological additives, followed by the analysis of the potential polymorphs by structural techniques including solid state NMR (in collaboration with B. Meier) and quenched H/D exchange NMR.Aim 3 is the structure-activity relationship of hormone amyloids: In striking contrast to the disease-associated amyloids, there are also amyloids with native biological activities including hormones storage in secretory granules. It is the aim to investigate the 3D structures of amyloids of the hormone ß-endorphin and somatostatin by quenched H/D exchange and solid state NMR (in collaboration with B. Meier) and establish a relationship between amyloid structure and secretory granule formation and hormone release by biophysical studies in vitro.Aim 4 is the structural studies of a-synuclein nanodiscs: a-synuclein associated with Parkinson’s disease is able to form a lipid-bilayer filled nanodisc. It is the goal to study this eventually biologically relevant entity structurally by electron microscopy in collaboration with H. Stahlberg (Biozentrum, Basel), NMR, multi-angle light scattering, etc.Project B: Structural Studies of Membrane ProteinsIntegral membrane proteins constitute more than 20% of all the proteins in mammalian organisms. However, membrane protein structure determination is still a challenge attributed to the two main bottlenecks: protein preparation and structure determination. It is the attempt to solve the 3D structure of an engineered nanodisc, and the study of the ion dynamics in the prototypical potassium channel KcsA.Aim 5 is the 3D structure determination of a nanodisc: Lipid-bilayer filled nanodiscs are an appreciated tool to study membrane proteins in a well-defined lipid bilayer. It is the goal to determine the 3D structure of an engineered nanodisc by solution NMR and EPR (in collaboration with G. Jeschke, ETH).Aim 6 is the study of the ion kinetics of the potassium channel KcsA: There are 4 K+ binding sites in the filter of KcsA. It has been proposed that only two are occupied per time during action. By replacing the K+ ion by the ammonium ion, the ion kinetics can be studied eventually site-resolved by solution state NMR.
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