1
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Göbl C, Morris VK, van Dam L, Visscher M, Polderman PE, Hartlmüller C, de Ruiter H, Hora M, Liesinger L, Birner-Gruenberger R, Vos HR, Reif B, Madl T, Dansen TB. Cysteine oxidation triggers amyloid fibril formation of the tumor suppressor p16 INK4A. Redox Biol 2020; 28:101316. [PMID: 31539802 PMCID: PMC6812003 DOI: 10.1016/j.redox.2019.101316] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 08/28/2019] [Accepted: 09/01/2019] [Indexed: 02/09/2023] Open
Abstract
The tumor suppressor p16INK4A induces cell cycle arrest and senescence in response to oncogenic transformation and is therefore frequently lost in cancer. p16INK4A is also known to accumulate under conditions of oxidative stress. Thus, we hypothesized it could potentially be regulated by reversible oxidation of cysteines (redox signaling). Here we report that oxidation of the single cysteine in p16INK4A in human cells occurs under relatively mild oxidizing conditions and leads to disulfide-dependent dimerization. p16INK4A is an all α-helical protein, but we find that upon cysteine-dependent dimerization, p16INK4A undergoes a dramatic structural rearrangement and forms aggregates that have the typical features of amyloid fibrils, including binding of diagnostic dyes, presence of cross-β sheet structure, and typical dimensions found in electron microscopy. p16INK4A amyloid formation abolishes its function as a Cyclin Dependent Kinase 4/6 inhibitor. Collectively, these observations mechanistically link the cellular redox state to the inactivation of p16INK4A through the formation of amyloid fibrils.
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Affiliation(s)
- Christoph Göbl
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry Technische Universität München, Lichtenbergstr. 4, 85747, Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Vanessa K Morris
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry Technische Universität München, Lichtenbergstr. 4, 85747, Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Loes van Dam
- Center for Molecular Medicine, Molecular Cancer Research, University Medical Center Utrecht, Universiteitsweg 100, 3584CG, Utrecht, The Netherlands
| | - Marieke Visscher
- Center for Molecular Medicine, Molecular Cancer Research, University Medical Center Utrecht, Universiteitsweg 100, 3584CG, Utrecht, The Netherlands
| | - Paulien E Polderman
- Center for Molecular Medicine, Molecular Cancer Research, University Medical Center Utrecht, Universiteitsweg 100, 3584CG, Utrecht, The Netherlands
| | - Christoph Hartlmüller
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry Technische Universität München, Lichtenbergstr. 4, 85747, Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Hesther de Ruiter
- Center for Molecular Medicine, Molecular Cancer Research, University Medical Center Utrecht, Universiteitsweg 100, 3584CG, Utrecht, The Netherlands
| | - Manuel Hora
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry Technische Universität München, Lichtenbergstr. 4, 85747, Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Laura Liesinger
- Omics Center Graz, BioTechMed-Graz, Graz, Austria; Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010, Graz, Austria
| | - Ruth Birner-Gruenberger
- Omics Center Graz, BioTechMed-Graz, Graz, Austria; Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010, Graz, Austria
| | - Harmjan R Vos
- Center for Molecular Medicine, Molecular Cancer Research, University Medical Center Utrecht, Universiteitsweg 100, 3584CG, Utrecht, The Netherlands
| | - Bernd Reif
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry Technische Universität München, Lichtenbergstr. 4, 85747, Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, 8010, Graz, Austria; BioTechMed-Graz, Austria.
| | - Tobias B Dansen
- Center for Molecular Medicine, Molecular Cancer Research, University Medical Center Utrecht, Universiteitsweg 100, 3584CG, Utrecht, The Netherlands.
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2
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Hartlmüller C, Spreitzer E, Göbl C, Falsone F, Madl T. NMR characterization of solvent accessibility and transient structure in intrinsically disordered proteins. J Biomol NMR 2019; 73:305-317. [PMID: 31297688 PMCID: PMC6692294 DOI: 10.1007/s10858-019-00248-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 04/11/2019] [Indexed: 05/12/2023]
Abstract
In order to understand the conformational behavior of intrinsically disordered proteins (IDPs) and their biological interaction networks, the detection of residual structure and long-range interactions is required. However, the large number of degrees of conformational freedom of disordered proteins require the integration of extensive sets of experimental data, which are difficult to obtain. Here, we provide a straightforward approach for the detection of residual structure and long-range interactions in IDPs under near-native conditions using solvent paramagnetic relaxation enhancement (sPRE). Our data indicate that for the general case of an unfolded chain, with a local flexibility described by the overwhelming majority of available combinations, sPREs of non-exchangeable protons can be accurately predicted through an ensemble-based fragment approach. We show for the disordered protein α-synuclein and disordered regions of the proteins FOXO4 and p53 that deviation from random coil behavior can be interpreted in terms of intrinsic propensity to populate local structure in interaction sites of these proteins and to adopt transient long-range structure. The presented modification-free approach promises to be applicable to study conformational dynamics of IDPs and other dynamic biomolecules in an integrative approach.
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Affiliation(s)
- Christoph Hartlmüller
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 87548, Garching, Germany
| | - Emil Spreitzer
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Institute of Molecular Biology & Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010, Graz, Austria
| | - Christoph Göbl
- The Campbell Family Institute for Breast Cancer Research at Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Fabio Falsone
- Institute of Pharmaceutical Sciences, University of Graz, Schubertstrasse 1, 8010, Graz, Austria
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Institute of Molecular Biology & Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010, Graz, Austria.
- BioTechMed-Graz, Graz, Austria.
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3
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Merle DA, Witternigg A, Tam-Amersdorfer C, Hartlmüller C, Spreitzer E, Schrank E, Wagner-Lichtenegger S, Werzer O, Zangger K, Kungl AJ, Madl T, Meyer NH, Falsone SF. Increased Aggregation Tendency of Alpha-Synuclein in a Fully Disordered Protein Complex. J Mol Biol 2019; 431:2581-2598. [PMID: 31034892 DOI: 10.1016/j.jmb.2019.04.031] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 04/17/2019] [Accepted: 04/18/2019] [Indexed: 01/17/2023]
Abstract
The recent discovery of biologically active fully disordered, so called random fuzzy protein-protein interactions leads to the question of how the high flexibility of these protein complexes correlates to aggregation and pathologic misfolding. We identify the structural mechanism by which a random fuzzy protein complex composed of the intrinsically disordered proteins alpha-Synuclein and SERF1a is able to potentiate cytotoxic aggregation. A structural model derived from an integrated NMR/SAXS analysis of the reconstituted aSyn:SERF1a complex enabled us to observe the partial deprotection of one precise aSyn amyloid nucleation element in the fully unstructured ensemble. This minimal exposure was sufficient to increase the amyloidogenic tendency of SERF1a-bound aSyn. Our findings provide a structural explanation of the previously observed pro-amyloid activity of SERF1a. They further demonstrate that random fuzziness can trigger a structurally organized disease-associated reaction such as amyloid polymerization.
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Affiliation(s)
- David A Merle
- Institute of Chemistry, University of Graz, Heinrichstr. 28, 8010 Graz, Austria
| | - Anja Witternigg
- Institute of Chemistry, University of Graz, Heinrichstr. 28, 8010 Graz, Austria
| | - Carmen Tam-Amersdorfer
- Otto Loewi Research Center for Vascular Biology, Immunology and Inflammation, Institute of Pathophysiology and Immunology, Medical University of Graz, Heinrichstr, 31, 8010 Graz, Austria
| | - Christoph Hartlmüller
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry Technische Universität München, Lichtenbergstr. 4, 87548, Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Emil Spreitzer
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Institute of Molecular Biology & Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Evelyne Schrank
- Institute of Chemistry, University of Graz, Heinrichstr. 28, 8010 Graz, Austria
| | - Sabine Wagner-Lichtenegger
- Diagnostic & Research Center for Molecular BioMedicine, Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Neue Stiftingtalstraße 2, 8010 Graz, Austria
| | - Oliver Werzer
- Institute of Pharmaceutical Sciences, University of Graz, Schubertstr. 1, 8010 Graz, Austria
| | - Klaus Zangger
- Institute of Chemistry, University of Graz, Heinrichstr. 28, 8010 Graz, Austria
| | - Andreas J Kungl
- Institute of Pharmaceutical Sciences, University of Graz, Schubertstr. 1, 8010 Graz, Austria
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Institute of Molecular Biology & Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria.
| | - N Helge Meyer
- Division of Experimental Allergology and Immunodermatology, Department of Human Medicine, University of Oldenburg, Carl-von-Ossietzky-Straße 9-11, 26129 Oldenburg, Germany.
| | - S Fabio Falsone
- Institute of Pharmaceutical Sciences, University of Graz, Schubertstr. 1, 8010 Graz, Austria.
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4
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Tants JN, Fesser S, Kern T, Stehle R, Geerlof A, Wunderlich C, Juen M, Hartlmüller C, Böttcher R, Kunzelmann S, Lange O, Kreutz C, Förstemann K, Sattler M. Molecular basis for asymmetry sensing of siRNAs by the Drosophila Loqs-PD/Dcr-2 complex in RNA interference. Nucleic Acids Res 2017; 45:12536-12550. [PMID: 29040648 PMCID: PMC5716069 DOI: 10.1093/nar/gkx886] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 09/22/2017] [Accepted: 09/22/2017] [Indexed: 12/26/2022] Open
Abstract
RNA interference defends against RNA viruses and retro-elements within an organism's genome. It is triggered by duplex siRNAs, of which one strand is selected to confer sequence-specificity to the RNA induced silencing complex (RISC). In Drosophila, Dicer-2 (Dcr-2) and the double-stranded RNA binding domain (dsRBD) protein R2D2 form the RISC loading complex (RLC) and select one strand of exogenous siRNAs according to the relative thermodynamic stability of base-pairing at either end. Through genome editing we demonstrate that Loqs-PD, the Drosophila homolog of human TAR RNA binding protein (TRBP) and a paralog of R2D2, forms an alternative RLC with Dcr-2 that is required for strand choice of endogenous siRNAs in S2 cells. Two canonical dsRBDs in Loqs-PD bind to siRNAs with enhanced affinity compared to miRNA/miRNA* duplexes. Structural analysis, NMR and biophysical experiments indicate that the Loqs-PD dsRBDs can slide along the RNA duplex to the ends of the siRNA. A moderate but notable binding preference for the thermodynamically more stable siRNA end by Loqs-PD alone is greatly amplified in complex with Dcr-2 to initiate strand discrimination by asymmetry sensing in the RLC.
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Affiliation(s)
- Jan-Niklas Tants
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, 85748 Garching, Germany
| | - Stephanie Fesser
- Genzentrum & Department Biochemie, Ludwig-Maximilians-Universität, 81377 München, Germany
| | - Thomas Kern
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, 85748 Garching, Germany
| | - Ralf Stehle
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, 85748 Garching, Germany
| | - Arie Geerlof
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Christoph Wunderlich
- Institute of Organic Chemistry and Center for Molecular Biosciences CMBI, Universität Innsbruck, 6020 Innsbruck, Austria
| | - Michael Juen
- Institute of Organic Chemistry and Center for Molecular Biosciences CMBI, Universität Innsbruck, 6020 Innsbruck, Austria
| | - Christoph Hartlmüller
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, 85748 Garching, Germany
| | - Romy Böttcher
- Genzentrum & Department Biochemie, Ludwig-Maximilians-Universität, 81377 München, Germany
| | - Stefan Kunzelmann
- Genzentrum & Department Biochemie, Ludwig-Maximilians-Universität, 81377 München, Germany
| | - Oliver Lange
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, 85748 Garching, Germany
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences CMBI, Universität Innsbruck, 6020 Innsbruck, Austria
| | - Klaus Förstemann
- Genzentrum & Department Biochemie, Ludwig-Maximilians-Universität, 81377 München, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Center for Integrated Protein Science Munich at Chair of Biomolecular NMR Spectroscopy, Department Chemie, Technische Universität München, 85748 Garching, Germany
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5
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Öster C, Kosol S, Hartlmüller C, Lamley JM, Iuga D, Oss A, Org ML, Vanatalu K, Samoson A, Madl T, Lewandowski JR. Characterization of Protein-Protein Interfaces in Large Complexes by Solid-State NMR Solvent Paramagnetic Relaxation Enhancements. J Am Chem Soc 2017; 139:12165-12174. [PMID: 28780861 PMCID: PMC5590091 DOI: 10.1021/jacs.7b03875] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Solid-state NMR is becoming a viable
alternative for obtaining
information about structures and dynamics of large biomolecular complexes,
including ones that are not accessible to other high-resolution biophysical
techniques. In this context, methods for probing protein–protein
interfaces at atomic resolution are highly desirable. Solvent paramagnetic
relaxation enhancements (sPREs) proved to be a powerful method for
probing protein–protein interfaces in large complexes in solution
but have not been employed toward this goal in the solid state. We
demonstrate that 1H and 15N relaxation-based
sPREs provide a powerful tool for characterizing intermolecular interactions
in large assemblies in the solid state. We present approaches for
measuring sPREs in practically the entire range of magic angle spinning
frequencies used for biomolecular studies and discuss their benefits
and limitations. We validate the approach on crystalline GB1, with
our experimental results in good agreement with theoretical predictions.
Finally, we use sPREs to characterize protein–protein interfaces
in the GB1 complex with immunoglobulin G (IgG). Our results suggest
the potential existence of an additional binding site and provide
new insights into GB1:IgG complex structure that amend and revise
the current model available from studies with IgG fragments. We demonstrate
sPREs as a practical, widely applicable, robust, and very sensitive
technique for determining intermolecular interaction interfaces in
large biomolecular complexes in the solid state.
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Affiliation(s)
- Carl Öster
- Department of Chemistry, University of Warwick , Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Simone Kosol
- Department of Chemistry, University of Warwick , Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Christoph Hartlmüller
- Center for Integrated Protein Science, Department of Chemistry, Munich Technische Universität München , Lichtenbergstrasse 4, 85748 Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München , Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Jonathan M Lamley
- Department of Chemistry, University of Warwick , Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Dinu Iuga
- Department of Physics, University of Warwick , Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Andres Oss
- Institute of Health Technologies, Tallinn University of Technology , Akadeemia tee 15a, 19086 Tallinn, Estonia
| | - Mai-Liis Org
- Institute of Health Technologies, Tallinn University of Technology , Akadeemia tee 15a, 19086 Tallinn, Estonia
| | - Kalju Vanatalu
- Institute of Health Technologies, Tallinn University of Technology , Akadeemia tee 15a, 19086 Tallinn, Estonia
| | - Ago Samoson
- Institute of Health Technologies, Tallinn University of Technology , Akadeemia tee 15a, 19086 Tallinn, Estonia
| | - Tobias Madl
- Center for Integrated Protein Science, Department of Chemistry, Munich Technische Universität München , Lichtenbergstrasse 4, 85748 Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München , Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.,Institute of Molecular Biology and Biochemistry, Center of Molecular Medicine, Medical University of Graz , Harrachgasse 21, 8010 Graz, Austria
| | - Józef R Lewandowski
- Department of Chemistry, University of Warwick , Gibbet Hill Road, Coventry CV4 7AL, U.K
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6
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Rodriguez Camargo DC, Tripsianes K, Buday K, Franko A, Göbl C, Hartlmüller C, Sarkar R, Aichler M, Mettenleiter G, Schulz M, Böddrich A, Erck C, Martens H, Walch AK, Madl T, Wanker EE, Conrad M, de Angelis MH, Reif B. The redox environment triggers conformational changes and aggregation of hIAPP in Type II Diabetes. Sci Rep 2017; 7:44041. [PMID: 28287098 PMCID: PMC5347123 DOI: 10.1038/srep44041] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 02/03/2017] [Indexed: 12/22/2022] Open
Abstract
Type II diabetes (T2D) is characterized by diminished insulin production and resistance of cells to insulin. Among others, endoplasmic reticulum (ER) stress is a principal factor contributing to T2D and induces a shift towards a more reducing cellular environment. At the same time, peripheral insulin resistance triggers the over-production of regulatory hormones such as insulin and human islet amyloid polypeptide (hIAPP). We show that the differential aggregation of reduced and oxidized hIAPP assists to maintain the redox equilibrium by restoring redox equivalents. Aggregation thus induces redox balancing which can assist initially to counteract ER stress. Failure of the protein degradation machinery might finally result in β-cell disruption and cell death. We further present a structural characterization of hIAPP in solution, demonstrating that the N-terminus of the oxidized peptide has a high propensity to form an α-helical structure which is lacking in the reduced state of hIAPP. In healthy cells, this residual structure prevents the conversion into amyloidogenic aggregates.
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Affiliation(s)
- Diana C Rodriguez Camargo
- Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg 85764, Germany.,Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Germany
| | - Konstantinos Tripsianes
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno 62500, Czech Republic
| | - Katalin Buday
- Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg 85764, Germany
| | - Andras Franko
- Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg 85764, Germany.,German Center for Diabetes Research (DZD e.V.), Neuherberg 85764, Germany
| | - Christoph Göbl
- Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg 85764, Germany.,Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Germany
| | - Christoph Hartlmüller
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Germany
| | - Riddhiman Sarkar
- Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg 85764, Germany.,Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Germany
| | - Michaela Aichler
- Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg 85764, Germany
| | | | - Michael Schulz
- Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg 85764, Germany
| | - Annett Böddrich
- Max-Delbrück-Center Berlin (MDC), Robert-Rössle-Str. 10, Berlin 13125, Germany
| | - Christian Erck
- Synaptic Systems GmbH, Rudolf-Wissell-Straße 28, Göttingen, 37079, Germany
| | - Henrik Martens
- Synaptic Systems GmbH, Rudolf-Wissell-Straße 28, Göttingen, 37079, Germany
| | - Axel Karl Walch
- Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg 85764, Germany
| | - Tobias Madl
- Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg 85764, Germany.,Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Germany.,Institute of Molecular Biology &Biochemistry, Center of Molecular Medicine, Medical University of Graz, Austria
| | - Erich E Wanker
- Max-Delbrück-Center Berlin (MDC), Robert-Rössle-Str. 10, Berlin 13125, Germany
| | - Marcus Conrad
- Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg 85764, Germany
| | - Martin Hrabě de Angelis
- Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg 85764, Germany.,German Center for Diabetes Research (DZD e.V.), Neuherberg 85764, Germany.,Technische Universität München, Center of Life and Food Sciences Weihenstephan, Freising 85354, Germany
| | - Bernd Reif
- Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg 85764, Germany.,Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Germany
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7
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Göbl C, Resch M, Strickland M, Hartlmüller C, Viertler M, Tjandra N, Madl T. Verbesserung der Dispersion der chemischen Verschiebungen von unstrukturierten Proteinen durch einen kovalent gebundenen Lanthanoidkomplex. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201607261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Christoph Göbl
- Center for Integrated Protein Science Munich; Technische Universität München; Fakultät für Chemie; Lichtenbergstraße 4 85748 Garching Deutschland
- Institut für Strukturbiologie; Helmholtz Zentrum München; Ingolstädter Landstr. 1 85764 Neuherberg Deutschland
| | - Moritz Resch
- Center for Integrated Protein Science Munich; Technische Universität München; Fakultät für Chemie; Lichtenbergstraße 4 85748 Garching Deutschland
- Institut für Strukturbiologie; Helmholtz Zentrum München; Ingolstädter Landstr. 1 85764 Neuherberg Deutschland
| | - Madeleine Strickland
- Laboratory of Structural Biophysics Biochemistry and Biophysics Center; National Heart, Lung, and Blood Institute; National Institutes of Health; Building 50 Bethesda MD 20814 USA
| | - Christoph Hartlmüller
- Center for Integrated Protein Science Munich; Technische Universität München; Fakultät für Chemie; Lichtenbergstraße 4 85748 Garching Deutschland
- Institut für Strukturbiologie; Helmholtz Zentrum München; Ingolstädter Landstr. 1 85764 Neuherberg Deutschland
| | - Martin Viertler
- Institut für Strukturbiologie; Helmholtz Zentrum München; Ingolstädter Landstr. 1 85764 Neuherberg Deutschland
| | - Nico Tjandra
- Laboratory of Structural Biophysics Biochemistry and Biophysics Center; National Heart, Lung, and Blood Institute; National Institutes of Health; Building 50 Bethesda MD 20814 USA
| | - Tobias Madl
- Center for Integrated Protein Science Munich; Technische Universität München; Fakultät für Chemie; Lichtenbergstraße 4 85748 Garching Deutschland
- Institut für Strukturbiologie; Helmholtz Zentrum München; Ingolstädter Landstr. 1 85764 Neuherberg Deutschland
- Institut für Molekularbiologie & Biochemie; Zentrum für Medizinische Forschung; Medizinische Universität Graz; 8010 Graz Österreich
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8
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Göbl C, Resch M, Strickland M, Hartlmüller C, Viertler M, Tjandra N, Madl T. Increasing the Chemical-Shift Dispersion of Unstructured Proteins with a Covalent Lanthanide Shift Reagent. Angew Chem Int Ed Engl 2016; 55:14847-14851. [PMID: 27763708 PMCID: PMC5146990 DOI: 10.1002/anie.201607261] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/16/2016] [Indexed: 01/19/2023]
Abstract
The study of intrinsically disordered proteins (IDPs) by NMR often suffers from highly overlapped resonances that prevent unambiguous chemical-shift assignments, and data analysis that relies on well-separated resonances. We present a covalent paramagnetic lanthanide-binding tag (LBT) for increasing the chemical-shift dispersion and facilitating the chemical-shift assignment of challenging, repeat-containing IDPs. Linkage of the DOTA-based LBT to a cysteine residue induces pseudo-contact shifts (PCS) for resonances more than 20 residues from the spin-labeling site. This leads to increased chemical-shift dispersion and decreased signal overlap, thereby greatly facilitating chemical-shift assignment. This approach is applicable to IDPs of varying sizes and complexity, and is particularly helpful for repeat-containing IDPs and low-complexity regions. This results in improved efficiency for IDP analysis and binding studies.
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Affiliation(s)
- Christoph Göbl
- Center for Integrated Protein Science Munich, Technische Universität München, Department of Chemistry, Lichtenbergstraße 4, 85748, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Moritz Resch
- Center for Integrated Protein Science Munich, Technische Universität München, Department of Chemistry, Lichtenbergstraße 4, 85748, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Madeleine Strickland
- Laboratory of Structural Biophysics Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Building 50, Bethesda, MD, 20814, USA
| | - Christoph Hartlmüller
- Center for Integrated Protein Science Munich, Technische Universität München, Department of Chemistry, Lichtenbergstraße 4, 85748, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Martin Viertler
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Nico Tjandra
- Laboratory of Structural Biophysics Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Building 50, Bethesda, MD, 20814, USA
| | - Tobias Madl
- Center for Integrated Protein Science Munich, Technische Universität München, Department of Chemistry, Lichtenbergstraße 4, 85748, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.,Institute of Molecular Biology & Biochemistry, Center of Molecular Medicine, Medical University of Graz, 8010, Graz, Austria
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9
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Affiliation(s)
- Christoph Hartlmüller
- Center for Integrated Protein Science Munich Technische Universität München Department of Chemistry Lichtenbergstrasse 4 85748 Garching Germany
- Institute of Structural Biology Helmholtz Zentrum München Ingolstädter Landstrasse 1 85764 Neuherberg Germany
| | - Christoph Göbl
- Center for Integrated Protein Science Munich Technische Universität München Department of Chemistry Lichtenbergstrasse 4 85748 Garching Germany
- Institute of Structural Biology Helmholtz Zentrum München Ingolstädter Landstrasse 1 85764 Neuherberg Germany
| | - Tobias Madl
- Center for Integrated Protein Science Munich Technische Universität München Department of Chemistry Lichtenbergstrasse 4 85748 Garching Germany
- Institute of Structural Biology Helmholtz Zentrum München Ingolstädter Landstrasse 1 85764 Neuherberg Germany
- Institute of Molecular Biology & Biochemistry Center of Molecular Medicine Medical University of Graz 8010 Graz Austria
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10
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Abstract
An approach to the de novo structure prediction of proteins is described that relies on surface accessibility data from NMR paramagnetic relaxation enhancements by a soluble paramagnetic compound (sPRE). This method exploits the distance-to-surface information encoded in the sPRE data in the chemical shift-based CS-Rosetta de novo structure prediction framework to generate reliable structural models. For several proteins, it is demonstrated that surface accessibility data is an excellent measure of the correct protein fold in the early stages of the computational folding algorithm and significantly improves accuracy and convergence of the standard Rosetta structure prediction approach.
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Affiliation(s)
- Christoph Hartlmüller
- Center for Integrated Protein Science Munich, Technische Universität München, Department of Chemistry, Lichtenbergstrasse 4, 85748, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Christoph Göbl
- Center for Integrated Protein Science Munich, Technische Universität München, Department of Chemistry, Lichtenbergstrasse 4, 85748, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Tobias Madl
- Center for Integrated Protein Science Munich, Technische Universität München, Department of Chemistry, Lichtenbergstrasse 4, 85748, Garching, Germany. .,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany. .,Institute of Molecular Biology & Biochemistry, Center of Molecular Medicine, Medical University of Graz, 8010, Graz, Austria.
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Weber J, Bao H, Hartlmüller C, Wang Z, Windhager A, Janowski R, Madl T, Jin P, Niessing D. Structural basis of nucleic-acid recognition and double-strand unwinding by the essential neuronal protein Pur-alpha. eLife 2016; 5:e11297. [PMID: 26744780 PMCID: PMC4764581 DOI: 10.7554/elife.11297] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 01/07/2016] [Indexed: 01/01/2023] Open
Abstract
The neuronal DNA-/RNA-binding protein Pur-alpha is a transcription regulator and core factor for mRNA localization. Pur-alpha-deficient mice die after birth with pleiotropic neuronal defects. Here, we report the crystal structure of the DNA-/RNA-binding domain of Pur-alpha in complex with ssDNA. It reveals base-specific recognition and offers a molecular explanation for the effect of point mutations in the 5q31.3 microdeletion syndrome. Consistent with the crystal structure, biochemical and NMR data indicate that Pur-alpha binds DNA and RNA in the same way, suggesting binding modes for tri- and hexanucleotide-repeat RNAs in two neurodegenerative RNAopathies. Additionally, structure-based in vitro experiments resolved the molecular mechanism of Pur-alpha's unwindase activity. Complementing in vivo analyses in Drosophila demonstrated the importance of a highly conserved phenylalanine for Pur-alpha's unwinding and neuroprotective function. By uncovering the molecular mechanisms of nucleic-acid binding, this study contributes to understanding the cellular role of Pur-alpha and its implications in neurodegenerative diseases.
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Affiliation(s)
- Janine Weber
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Han Bao
- Department of Human Genetics, Emory University, Atlanta, United States
| | - Christoph Hartlmüller
- Center for Integrated Protein Science Munich, Department of Chemistry, Technische Universität München, Munich, Germany
| | - Zhiqin Wang
- Department of Human Genetics, Emory University, Atlanta, United States
| | - Almut Windhager
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Robert Janowski
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Tobias Madl
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Center for Integrated Protein Science Munich, Department of Chemistry, Technische Universität München, Munich, Germany
- Institute of Molecular Biology & Biochemistry, Center of Molecular Medicine, Medical University of Graz, Graz, Austria
- Omics Center Graz, BioTechMed Graz, Graz, Austria
| | - Peng Jin
- Department of Human Genetics, Emory University, Atlanta, United States
| | - Dierk Niessing
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Department Cell Biology, Biomedical Center of the Ludwig-Maximilians-University München, Planegg-Martinsried, Germany
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