1
|
Sternke-Hoffmann R, Pauly T, Norrild RK, Hansen J, Tucholski F, Høie MH, Marcatili P, Dupré M, Duchateau M, Rey M, Malosse C, Metzger S, Boquoi A, Platten F, Egelhaaf SU, Chamot-Rooke J, Fenk R, Nagel-Steger L, Haas R, Buell AK. Widespread amyloidogenicity potential of multiple myeloma patient-derived immunoglobulin light chains. BMC Biol 2023; 21:21. [PMID: 36737754 PMCID: PMC9898917 DOI: 10.1186/s12915-022-01506-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 12/15/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND In a range of human disorders such as multiple myeloma (MM), immunoglobulin light chains (IgLCs) can be produced at very high concentrations. This can lead to pathological aggregation and deposition of IgLCs in different tissues, which in turn leads to severe and potentially fatal organ damage. However, IgLCs can also be highly soluble and non-toxic. It is generally thought that the cause for this differential solubility behaviour is solely found within the IgLC amino acid sequences, and a variety of individual sequence-related biophysical properties (e.g. thermal stability, dimerisation) have been proposed in different studies as major determinants of the aggregation in vivo. Here, we investigate biophysical properties underlying IgLC amyloidogenicity. RESULTS We introduce a novel and systematic workflow, Thermodynamic and Aggregation Fingerprinting (ThAgg-Fip), for detailed biophysical characterisation, and apply it to nine different MM patient-derived IgLCs. Our set of pathogenic IgLCs spans the entire range of values in those parameters previously proposed to define in vivo amyloidogenicity; however, none actually forms amyloid in patients. Even more surprisingly, we were able to show that all our IgLCs are able to form amyloid fibrils readily in vitro under the influence of proteolytic cleavage by co-purified cathepsins. CONCLUSIONS We show that (I) in vivo aggregation behaviour is unlikely to be mechanistically linked to any single biophysical or biochemical parameter and (II) amyloidogenic potential is widespread in IgLC sequences and is not confined to those sequences that form amyloid fibrils in patients. Our findings suggest that protein sequence, environmental conditions and presence and action of proteases all determine the ability of light chains to form amyloid fibrils in patients.
Collapse
Affiliation(s)
- Rebecca Sternke-Hoffmann
- grid.411327.20000 0001 2176 9917Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany ,grid.5991.40000 0001 1090 7501Department of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland
| | - Thomas Pauly
- grid.411327.20000 0001 2176 9917Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany ,grid.8385.60000 0001 2297 375XForschungszentrum Jülich GmbH, IBI-7, Jülich, Germany
| | - Rasmus K. Norrild
- grid.5170.30000 0001 2181 8870Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Jan Hansen
- grid.411327.20000 0001 2176 9917Condensed Matter Physics Laboratory, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Florian Tucholski
- grid.411327.20000 0001 2176 9917Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Magnus Haraldson Høie
- grid.5170.30000 0001 2181 8870Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Paolo Marcatili
- grid.5170.30000 0001 2181 8870Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Mathieu Dupré
- grid.428999.70000 0001 2353 6535Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, 75015 Paris, France
| | - Magalie Duchateau
- grid.428999.70000 0001 2353 6535Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, 75015 Paris, France
| | - Martial Rey
- grid.428999.70000 0001 2353 6535Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, 75015 Paris, France
| | - Christian Malosse
- grid.428999.70000 0001 2353 6535Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, 75015 Paris, France
| | - Sabine Metzger
- grid.6190.e0000 0000 8580 3777Cologne Biocenter, Cluster of Excellence on Plant Sciences, Mass Spectrometry Platform, University of Cologne, Cologne, Germany
| | - Amelie Boquoi
- grid.411327.20000 0001 2176 9917Department of Hematology, Oncology and Clinical Oncology, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany
| | - Florian Platten
- grid.411327.20000 0001 2176 9917Condensed Matter Physics Laboratory, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany ,grid.8385.60000 0001 2297 375XForschungszentrum Jülich GmbH, IBI-4, Jülich, Germany
| | - Stefan U. Egelhaaf
- grid.411327.20000 0001 2176 9917Condensed Matter Physics Laboratory, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Julia Chamot-Rooke
- grid.428999.70000 0001 2353 6535Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, 75015 Paris, France
| | - Roland Fenk
- grid.411327.20000 0001 2176 9917Department of Hematology, Oncology and Clinical Oncology, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany
| | - Luitgard Nagel-Steger
- grid.411327.20000 0001 2176 9917Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany ,grid.8385.60000 0001 2297 375XForschungszentrum Jülich GmbH, IBI-7, Jülich, Germany
| | - Rainer Haas
- Department of Hematology, Oncology and Clinical Oncology, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany.
| | - Alexander K. Buell
- grid.411327.20000 0001 2176 9917Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany ,grid.5170.30000 0001 2181 8870Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| |
Collapse
|
2
|
Pauly T, Zhang T, Sternke-Hoffmann R, Nagel-Steger L, Willbold D. Differentiation of subnucleus-sized oligomers and nucleation-competent assemblies of the Aβ peptide. Biophys J 2023; 122:269-278. [PMID: 36529991 PMCID: PMC9892607 DOI: 10.1016/j.bpj.2022.12.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 11/16/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
A significant feature of Alzheimer's disease is the formation of amyloid deposits in the brain consisting mainly of misfolded derivatives of proteolytic cleavage products of the amyloid precursor protein amyloid-β (Aβ) peptide. While high-resolution structures already exist for both the monomer and the amyloid fibril of the Aβ peptide, the mechanism of amyloid formation itself still defies precise characterization. In this study, low and high molecular weight oligomers (LMWOs and HMWOs) were identified by sedimentation velocity analysis, and for the first time, the temporal evolution of oligomer size distributions was correlated with the kinetics of amyloid formation as determined by thioflavin T-binding studies. LMWOs of subnucleus size contain fewer than seven monomer units and exist alongside a heterogeneous group of HMWOs with 20-160 monomer units that represent potential centers of nucleus formation due to high local monomer concentrations. These HMWOs already have slightly increased β-strand content and appear structurally similar regardless of size, as shown by examination with a range of fluorescent dyes. Once fibril nuclei are formed, the monomer concentration begins to decrease, followed by a decrease in oligomer concentration, starting with LMWOs, which are the least stable species. The observed behavior classifies the two LMWOs as off pathway. In contrast, we consider HMWOs to be on-pathway, prefibrillar intermediates, representing structures in which nucleated conformational conversion is facilitated by high local concentrations. Aβ40 and Aβ42 M35ox take much longer to form nuclei and enter the growth phase than Aβ42 under identical reaction conditions, presumably because both the size and the concentration of HMWOs formed are much smaller.
Collapse
Affiliation(s)
- Thomas Pauly
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Research Center Jülich, Jülich, Germany
| | - Tao Zhang
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Research Center Jülich, Jülich, Germany
| | | | - Luitgard Nagel-Steger
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Research Center Jülich, Jülich, Germany.
| | - Dieter Willbold
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Research Center Jülich, Jülich, Germany
| |
Collapse
|
3
|
Pauly T, Bolakhrif N, Kaiser J, Nagel-Steger L, Gremer L, Gohlke H, Willbold D. Met/Val129 polymorphism of the full-length human prion protein dictates distinct pathways of amyloid formation. J Biol Chem 2022; 298:102430. [PMID: 36037966 PMCID: PMC9513279 DOI: 10.1016/j.jbc.2022.102430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 05/17/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 11/25/2022] Open
Abstract
Methionine/valine polymorphism at position 129 of the human prion protein, huPrP, is tightly associated with the pathogenic phenotype, disease progress, and age of onset of neurodegenerative diseases such as Creutzfeldt–Jakob disease or Fatal Familial Insomnia. This raises the question of whether and how the amino acid type at position 129 influences the structural properties of huPrP, affecting its folding, stability, and amyloid formation behavior. Here, our detailed biophysical characterization of the 129M and 129V variants of recombinant full-length huPrP(23–230) by amyloid formation kinetics, CD spectroscopy, molecular dynamics simulations, and sedimentation velocity analysis reveals differences in their aggregation propensity and oligomer content, leading to deviating pathways for the conversion into amyloid at acidic pH. We determined that the 129M variant exhibits less secondary structure content before amyloid formation and higher resistance to thermal denaturation compared to the 129V variant, whereas the amyloid conformation of both variants shows similar thermal stability. Additionally, our molecular dynamics simulations and rigidity analyses at the atomistic level identify intramolecular interactions responsible for the enhanced monomer stability of the 129M variant, involving more frequent minimum distances between E196 and R156, forming a salt bridge. Removal of the N-terminal half of the 129M full-length variant diminishes its differences compared to the 129V full-length variant and highlights the relevance of the flexible N terminus in huPrP. Taken together, our findings provide insight into structural properties of huPrP and the effects of the amino acid identity at position 129 on amyloid formation behavior.
Collapse
Affiliation(s)
- Thomas Pauly
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct: Jülich Center of Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Najoua Bolakhrif
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct: Jülich Center of Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Jesko Kaiser
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Luitgard Nagel-Steger
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct: Jülich Center of Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Lothar Gremer
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct: Jülich Center of Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany; Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; John von Neumann Institute for Computing (NIC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Dieter Willbold
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct: Jülich Center of Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.
| |
Collapse
|
4
|
Bovdilova A, Alexandre BM, Höppner A, Luís IM, Alvarez CE, Bickel D, Gohlke H, Decker C, Nagel-Steger L, Alseekh S, Fernie AR, Drincovich MF, Abreu IA, Maurino VG. Corrigendum to: Posttranslational Modification of the NADP-Malic Enzyme Involved in C4 Photosynthesis Modulates the Enzymatic Activity during the Day. Plant Cell 2022; 34:698-699. [PMID: 34718758 PMCID: PMC8981781 DOI: 10.1093/plcell/koab262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 10/21/2021] [Indexed: 06/13/2023]
|
5
|
Schmitz K, Cox J, Esser LM, Voss M, Sander K, Löffler A, Hillebrand F, Erkelenz S, Schaal H, Kähne T, Klinker S, Zhang T, Nagel-Steger L, Willbold D, Seggewiß S, Schlütermann D, Stork B, Grimmler M, Wesselborg S, Peter C. An essential role of the autophagy activating kinase ULK1 in snRNP biogenesis. Nucleic Acids Res 2021; 49:6437-6455. [PMID: 34096600 PMCID: PMC8216288 DOI: 10.1093/nar/gkab452] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 05/05/2021] [Accepted: 05/11/2021] [Indexed: 01/31/2023] Open
Abstract
The biogenesis of small uridine-rich nuclear ribonucleoproteins (UsnRNPs) depends on the methylation of Sm proteins catalyzed by the methylosome and the subsequent action of the SMN complex, which assembles the heptameric Sm protein ring onto small nuclear RNAs (snRNAs). In this sophisticated process, the methylosome subunit pICln (chloride conductance regulatory protein) is attributed to an exceptional key position as an ‘assembly chaperone’ by building up a stable precursor Sm protein ring structure. Here, we show that—apart from its autophagic role—the Ser/Thr kinase ULK1 (Uncoordinated [unc-51] Like Kinase 1) functions as a novel key regulator in UsnRNP biogenesis by phosphorylation of the C-terminus of pICln. As a consequence, phosphorylated pICln is no longer capable to hold up the precursor Sm ring structure. Consequently, inhibition of ULK1 results in a reduction of efficient UsnRNP core assembly. Thus ULK1, depending on its complex formation, exerts different functions in autophagy or snRNP biosynthesis.
Collapse
Affiliation(s)
- Katharina Schmitz
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jan Cox
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Lea Marie Esser
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Martin Voss
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Katja Sander
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Antje Löffler
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Frank Hillebrand
- Institute of Virology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Steffen Erkelenz
- Institute of Virology, University Hospital Düsseldorf, Düsseldorf, Germany.,Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Heiner Schaal
- Institute of Virology, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Thilo Kähne
- Insitute of Experimental Internal Medicine, Otto von Guericke University, Magdeburg, Germany
| | - Stefan Klinker
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Germany
| | - Tao Zhang
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Germany.,Institute of Biological Information Processing (Structural Biochemistry: IBI-7), Forschungszentrum Jülich, Jülich, Germany
| | - Luitgard Nagel-Steger
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Germany.,Institute of Biological Information Processing (Structural Biochemistry: IBI-7), Forschungszentrum Jülich, Jülich, Germany
| | - Dieter Willbold
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Germany.,Institute of Biological Information Processing (Structural Biochemistry: IBI-7), Forschungszentrum Jülich, Jülich, Germany
| | - Sabine Seggewiß
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - David Schlütermann
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Björn Stork
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Matthias Grimmler
- Hochschule Fresenius, Idstein, Germany.,DiaSys Diagnostic Systems GmbH, Alte Strasse 9, 65558 Holzheim, Germany
| | - Sebastian Wesselborg
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Christoph Peter
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| |
Collapse
|
6
|
Sindram J, Krüsmann M, Otten M, Pauly T, Nagel-Steger L, Karg M. Versatile Route toward Hydrophobically Polymer-Grafted Gold Nanoparticles from Aqueous Dispersions. J Phys Chem B 2021; 125:8225-8237. [PMID: 34260239 DOI: 10.1021/acs.jpcb.1c03772] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Stabilization of gold nanoparticles in organic solvents is a key challenge in making them available for a wider range of material applications. Polymers are often used as stabilizing ligands because they also allow for the introduction of new properties and functionalities. Many of the established synthesis protocols for gold nanoparticles are water-based. However, the insolubility of many synthetic polymers in water renders the direct functionalization of aqueous particle dispersions with these ligands difficult. Here, we report on an approach for the functionalization of gold nanoparticles, which were prepared by aqueous synthesis, with hydrophobic polymer ligands and their characterization in nonpolar, organic dispersions. Our method employs an auxiliary ligand to first transfer gold nanoparticles from an aqueous to an organic medium. In the organic phase, the auxiliary ligand is then displaced by thiolated polystyrene ligands to form a dense polymer brush on the particle surface. We characterize the structure of the ligand shell using electron microscopy, scattering techniques, and ultracentrifugation and analyze the influence of the molecular weight of the polystyrene ligands on the structure of the polymer brush. We further investigate the colloidal stability of polystyrene-functionalized gold nanoparticles in various organic solvents. Finally, we extend the use of our protocol from small, spherical gold nanoparticles to larger gold nanorods and nanocubes.
Collapse
Affiliation(s)
- Julian Sindram
- Institut für Physikalische Chemie I: Kolloide und Nanooptik, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Marcel Krüsmann
- Institut für Physikalische Chemie I: Kolloide und Nanooptik, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Marius Otten
- Institut für Physikalische Chemie I: Kolloide und Nanooptik, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Thomas Pauly
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany.,IBI-7, Structural Biochemistry, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Strasse, 52425 Jülich, Germany
| | - Luitgard Nagel-Steger
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany.,IBI-7, Structural Biochemistry, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Strasse, 52425 Jülich, Germany
| | - Matthias Karg
- Institut für Physikalische Chemie I: Kolloide und Nanooptik, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| |
Collapse
|
7
|
Zhang T, Gering I, Kutzsche J, Nagel-Steger L, Willbold D. Toward the Mode of Action of the Clinical Stage All-d-Enantiomeric Peptide RD2 on Aβ42 Aggregation. ACS Chem Neurosci 2019; 10:4800-4809. [PMID: 31710458 DOI: 10.1021/acschemneuro.9b00458] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The aggregation of amyloid-β (Aβ) into oligomers and fibrillary structures is critical for the pathogenesis of Alzheimer's disease (AD). Recently, research effort has been focused on developing novel agents that can preferentially suppress Aβ oligomer mediated toxicities, for example, by directly targeting these toxic assemblies. The compound RD2 has been developed and optimized for Aβ42 monomer binding and stabilization of the monomer in its native intrinsically disordered conformation. It has been demonstrated to improve and even reverse the cognitive and behavioral deficits in AD mouse models, while the detailed mechanism of action is not fully clarified. Here we focused on exploring the interaction between RD2 and Aβ42 monomers and its consequences for the fibrillation of Aβ42. RD2 binds to Aβ42 monomers with nanomolar affinities, according to microscale thermophoresis and surface plasmon resonance measurements. Complexes between RD2 and Aβ42 monomers are formed at 1:1 and other stoichiometries, as revealed by analytical ultracentrifugation. At substoichiometric levels, RD2 slows down the secondary structure conversion of Aβ42 and significantly delays the fibril formation. Our research provides experimental evidence in supporting that RD2 eliminates toxic Aβ assemblies by stabilizing Aβ monomers in their native intrinsically disordered conformation. The study further supports the promising application of RD2 in counteracting Aβ aggregation related pathologies.
Collapse
Affiliation(s)
- Tao Zhang
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Ian Gering
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Janine Kutzsche
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Luitgard Nagel-Steger
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Dieter Willbold
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| |
Collapse
|
8
|
Bovdilova A, Alexandre BM, Höppner A, Luís IM, Alvarez CE, Bickel D, Gohlke H, Decker C, Nagel-Steger L, Alseekh S, Fernie AR, Drincovich MF, Abreu IA, Maurino VG. Posttranslational Modification of the NADP-Malic Enzyme Involved in C 4 Photosynthesis Modulates the Enzymatic Activity during the Day. Plant Cell 2019; 31:2525-2539. [PMID: 31363039 PMCID: PMC6790091 DOI: 10.1105/tpc.19.00406] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/02/2019] [Accepted: 07/23/2019] [Indexed: 05/07/2023]
Abstract
Evolution of the C4 photosynthetic pathway involved in some cases recruitment of housekeeping proteins through gene duplication and their further neofunctionalization. NADP-malic enzyme (ME), the most widespread C4 decarboxylase, has increased its catalytic efficiency and acquired regulatory properties that allowed it to participate in the C4 pathway. Here, we show that regulation of maize (Zea mays) C4-NADP-ME activity is much more elaborate than previously thought. Using mass spectrometry, we identified phosphorylation of the Ser419 residue of C4-NADP-ME in protein extracts of maize leaves. The phosphorylation event increases in the light, with a peak at Zeitgeber time 2. Phosphorylation of ZmC4-NADP-ME drastically decreases its activity as shown by the low residual activity of the recombinant phosphomimetic mutant. Analysis of the crystal structure of C4-NADP-ME indicated that Ser419 is involved in the binding of NADP at the active site. Molecular dynamics simulations and effective binding energy computations indicate a less favorable binding of the cofactor NADP in the phosphomimetic and the phosphorylated variants. We propose that phosphorylation of ZmC4-NADP-ME at Ser419 during the first hours in the light is a cellular mechanism that fine tunes the enzymatic activity to coordinate the carbon concentration mechanism with the CO2 fixation rate, probably to avoid CO2 leakiness from bundle sheath cells.
Collapse
Affiliation(s)
- Anastasiia Bovdilova
- Institute of Developmental and Molecular Biology of Plants, Plant Molecular Physiology and Biotechnology Group, Heinrich Heine University Düsseldorf, Universitätsstraße 1, and Cluster of Excellence on Plant Sciences (CEPLAS), 40225 Düsseldorf, Germany
| | - Bruno M Alexandre
- Instituto de Biologia Experimental e Tecnológica, Avenida da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Astrid Höppner
- Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Inês Matias Luís
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Clarisa E Alvarez
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, University of Rosario, Suipacha 570, 2000 Rosario, Argentina
| | - David Bickel
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC) and Institute for Complex Systems-Structural Biochemistry (ICS 6), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Christina Decker
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Luitgard Nagel-Steger
- Institut für Physikalische Biologie, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Center for Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Maria F Drincovich
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, University of Rosario, Suipacha 570, 2000 Rosario, Argentina
| | - Isabel A Abreu
- Instituto de Biologia Experimental e Tecnológica, Avenida da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Veronica G Maurino
- Institute of Developmental and Molecular Biology of Plants, Plant Molecular Physiology and Biotechnology Group, Heinrich Heine University Düsseldorf, Universitätsstraße 1, and Cluster of Excellence on Plant Sciences (CEPLAS), 40225 Düsseldorf, Germany
| |
Collapse
|
9
|
Lorenz C, Ince S, Zhang T, Cousin A, Batra-Safferling R, Nagel-Steger L, Herrmann C, Stadler AM. Farnesylation of human guanylate-binding protein 1 as safety mechanism preventing structural rearrangements and uninduced dimerization. FEBS J 2019; 287:496-514. [PMID: 31330084 DOI: 10.1111/febs.15015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 06/25/2019] [Accepted: 07/19/2019] [Indexed: 01/03/2023]
Abstract
Human guanylate-binding protein 1 (hGBP1) belongs to the family of dynamin-like proteins and is activated by addition of nucleotides, leading to protein oligomerization and stimulated GTPase activity. In vivo, hGBP1 is post-translationally modified by attachment of a farnesyl group yielding farn-hGBP1. In this study, hydrodynamic differences in farn-hGBP1 and unmodified hGBP1 were investigated using dynamic light scattering (DLS), analytical ultracentrifugation (AUC) and analytical size-exclusion chromatography (SEC). In addition, we performed small-angle X-ray scattering (SAXS) experiments coupled with a SEC setup (SEC-SAXS) to investigate structural properties of nonmodified hGBP1 and farn-hGBP1 in solution. SEC-SAXS measurements revealed that farnesylation keeps hGBP1 in its inactive monomeric and crystal-like conformation in nucleotide-free solution, whereas unmodified hGBP1 forms a monomer-dimer equilibrium both in the inactive ground state in nucleotide-free solution as well as in the activated state that is trapped by addition of the nonhydrolysable GTP analogue GppNHp. Nonmodified hGBP1 is structurally perturbed as compared to farn-hGBP. In particular, GppNHp binding leads to large structural rearrangements and higher conformational flexibility of the monomer and the dimer. Structural changes observed in the nonmodified protein are prerequisites for further oligomer assemblies of farn-hGBP1 that occur in the presence of nucleotides. DATABASE: All SEC-SAXS data, corresponding fits to the data and structural models are deposited in the Small Angle Scattering Biological Data Bank [SASBDB (Nucleic Acids Res, 43, 2015, D357)] with project IDs: SASDEE8, SASDEF8, SASDEG8, SASDEH8, SASDEJ8, SASDEK8, SASDEL8 and SASDEM8.
Collapse
Affiliation(s)
- Charlotte Lorenz
- Jülich Centre for Neutron Science (JCNS-1) and Institute for Complex Systems (ICS-1), Forschungszentrum Jülich GmbH, Germany.,Institute of Physical Chemistry, RWTH Aachen University, Germany
| | - Semra Ince
- Physical Chemistry I, Faculty of Chemistry and Biochemistry, Ruhr-University, Bochum, Germany
| | - Tao Zhang
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Germany
| | - Anneliese Cousin
- Institute of Complex Systems (ICS-6), Structural Biochemistry, Forschungszentrum Jülich GmbH, Germany
| | - Renu Batra-Safferling
- Institute of Complex Systems (ICS-6), Structural Biochemistry, Forschungszentrum Jülich GmbH, Germany
| | | | - Christian Herrmann
- Physical Chemistry I, Faculty of Chemistry and Biochemistry, Ruhr-University, Bochum, Germany
| | - Andreas M Stadler
- Jülich Centre for Neutron Science (JCNS-1) and Institute for Complex Systems (ICS-1), Forschungszentrum Jülich GmbH, Germany.,Institute of Physical Chemistry, RWTH Aachen University, Germany
| |
Collapse
|
10
|
Alvarez CE, Bovdilova A, Höppner A, Wolff CC, Saigo M, Trajtenberg F, Zhang T, Buschiazzo A, Nagel-Steger L, Drincovich MF, Lercher MJ, Maurino VG. Molecular adaptations of NADP-malic enzyme for its function in C 4 photosynthesis in grasses. Nat Plants 2019; 5:755-765. [PMID: 31235877 DOI: 10.1038/s41477-019-0451-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 05/17/2019] [Indexed: 06/09/2023]
Abstract
In C4 grasses of agronomical interest, malate shuttled into the bundle sheath cells is decarboxylated mainly by nicotinamide adenine dinucleotide phosphate (NADP)-malic enzyme (C4-NADP-ME). The activity of C4-NADP-ME was optimized by natural selection to efficiently deliver CO2 to Rubisco. During its evolution from a plastidic non-photosynthetic NADP-ME, C4-NADP-ME acquired increased catalytic efficiency, tetrameric structure and pH-dependent inhibition by its substrate malate. Here, we identified specific amino acids important for these C4 adaptions based on strict differential conservation of amino acids, combined with solving the crystal structures of maize and sorghum C4-NADP-ME. Site-directed mutagenesis and structural analyses show that Q503, L544 and E339 are involved in catalytic efficiency; E339 confers pH-dependent regulation by malate, F140 is critical for the stabilization of the oligomeric structure and the N-terminal region is involved in tetramerization. Together, the identified molecular adaptations form the basis for the efficient catalysis and regulation of one of the central biochemical steps in C4 metabolism.
Collapse
Affiliation(s)
- Clarisa E Alvarez
- Centro de Estudios Fotosinteticos y Bioquimicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, University of Rosario, Rosario, Argentina
| | - Anastasiia Bovdilova
- Plant Molecular Physiology and Biotechnology Group, Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
| | - Astrid Höppner
- Center for Structural Studies, Hreinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Christian-Claus Wolff
- Plant Molecular Physiology and Biotechnology Group, Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
| | - Mariana Saigo
- Centro de Estudios Fotosinteticos y Bioquimicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, University of Rosario, Rosario, Argentina
| | - Felipe Trajtenberg
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Tao Zhang
- Institut für Physikalische Biologie, Heinrich Heine University, Düsseldorf, Germany
- Institut of Complex Systems, Structural Biochemistry (ICS-6), Jülich, Germany
| | - Alejandro Buschiazzo
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Integrative Microbiology of Zoonotic Agents, Department of Microbiology, Institut Pasteur, Paris, France
| | - Luitgard Nagel-Steger
- Institut für Physikalische Biologie, Heinrich Heine University, Düsseldorf, Germany
- Institut of Complex Systems, Structural Biochemistry (ICS-6), Jülich, Germany
| | - Maria F Drincovich
- Centro de Estudios Fotosinteticos y Bioquimicos (CEFOBI-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, University of Rosario, Rosario, Argentina
| | - Martin J Lercher
- Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
- Institute for Computer Science and Department of Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Veronica G Maurino
- Plant Molecular Physiology and Biotechnology Group, Institute of Developmental and Molecular Biology of Plants, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
- Cluster of Excellence on Plant Sciences, Düsseldorf, Germany.
| |
Collapse
|
11
|
Zhang T, Loschwitz J, Strodel B, Nagel-Steger L, Willbold D. Interference with Amyloid-β Nucleation by Transient Ligand Interaction. Molecules 2019; 24:E2129. [PMID: 31195746 PMCID: PMC6600523 DOI: 10.3390/molecules24112129] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 05/07/2019] [Revised: 06/02/2019] [Accepted: 06/04/2019] [Indexed: 12/20/2022] Open
Abstract
Amyloid-β peptide (Aβ) is an intrinsically disordered protein (IDP) associated with Alzheimer's disease. The structural flexibility and aggregation propensity of Aβ pose major challenges for elucidating the interaction between Aβ monomers and ligands. All-D-peptides consisting solely of D-enantiomeric amino acid residues are interesting drug candidates that combine high binding specificity with high metabolic stability. Here we characterized the interaction between the 12-residue all-D-peptide D3 and Aβ42 monomers, and how the interaction influences Aβ42 aggregation. We demonstrate for the first time that D3 binds to Aβ42 monomers with submicromolar affinities. These two highly unstructured molecules are able to form complexes with 1:1 and other stoichiometries. Further, D3 at substoichiometric concentrations effectively slows down the β-sheet formation and Aβ42 fibrillation by modulating the nucleation process. The study provides new insights into the molecular mechanism of how D3 affects Aβ assemblies and contributes to our knowledge on the interaction between two IDPs.
Collapse
Affiliation(s)
- Tao Zhang
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany.
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.
| | - Jennifer Loschwitz
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany.
- Institute of Theoretical and Computational Chemistry, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.
| | - Birgit Strodel
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany.
- Institute of Theoretical and Computational Chemistry, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.
| | - Luitgard Nagel-Steger
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany.
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.
| | - Dieter Willbold
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany.
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.
| |
Collapse
|
12
|
Kukuk L, Dingley AJ, Granzin J, Nagel-Steger L, Thiagarajan-Rosenkranz P, Ciupka D, Hänel K, Batra-Safferling R, Pacheco V, Stoldt M, Pfeffer K, Beer-Hammer S, Willbold D, Koenig BW. Structure of the SLy1 SAM homodimer reveals a new interface for SAM domain self-association. Sci Rep 2019; 9:54. [PMID: 30631134 PMCID: PMC6328559 DOI: 10.1038/s41598-018-37185-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 11/30/2018] [Indexed: 11/08/2022] Open
Abstract
Sterile alpha motif (SAM) domains are protein interaction modules that are involved in a diverse range of biological functions such as transcriptional and translational regulation, cellular signalling, and regulation of developmental processes. SH3 domain-containing protein expressed in lymphocytes 1 (SLy1) is involved in immune regulation and contains a SAM domain of unknown function. In this report, the structure of the SLy1 SAM domain was solved and revealed that this SAM domain forms a symmetric homodimer through a novel interface. The interface consists primarily of the two long C-terminal helices, α5 and α5', of the domains packing against each other. The dimerization is characterized by a dissociation constant in the lower micromolar range. A SLy1 SAM domain construct with an extended N-terminus containing five additional amino acids of the SLy1 sequence further increases the stability of the homodimer, making the SLy1 SAM dimer two orders of magnitude more stable than previously studied SAM homodimers, suggesting that the SLy1 SAM dimerization is of functional significance. The SLy1 SAM homodimer contains an exposed mid-loop surface on each monomer, which may provide a scaffold for mediating interactions with other SAM domain-containing proteins via a typical mid-loop-end-helix interface.
Collapse
Affiliation(s)
- Laura Kukuk
- Institute of Complex Systems, Strukturbiochemie (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Andrew J Dingley
- Institute of Complex Systems, Strukturbiochemie (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Joachim Granzin
- Institute of Complex Systems, Strukturbiochemie (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Luitgard Nagel-Steger
- Institute of Complex Systems, Strukturbiochemie (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Pallavi Thiagarajan-Rosenkranz
- Institute of Complex Systems, Strukturbiochemie (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Daniel Ciupka
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Karen Hänel
- Institute of Complex Systems, Strukturbiochemie (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Renu Batra-Safferling
- Institute of Complex Systems, Strukturbiochemie (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Victor Pacheco
- Institute of Complex Systems, Strukturbiochemie (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
- Institut für Makromolekulare Chemie, Albert-Ludwigs-Universität Freiburg, Stefan-Meier-Straße 31, 79104, Freiburg, Germany
| | - Matthias Stoldt
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Klaus Pfeffer
- Institut für Medizinische Mikrobiologie und Krankenhaushygiene, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Sandra Beer-Hammer
- Institut für Medizinische Mikrobiologie und Krankenhaushygiene, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
- Institut für Experimentelle und Klinische Pharmakologie und Toxikologie, und Interfakultäres Zentrum für Pharmakogenomik und Arzneimittelforschung (ICePhA), Eberhard-Karls-Universität Tübingen, Wilhelmstraße 56, 72074, Tübingen, Germany
| | - Dieter Willbold
- Institute of Complex Systems, Strukturbiochemie (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany.
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany.
| | - Bernd W Koenig
- Institute of Complex Systems, Strukturbiochemie (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany.
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany.
| |
Collapse
|
13
|
Bhatia S, Diedrich D, Frieg B, Ahlert H, Stein S, Bopp B, Lang F, Zang T, Kröger T, Ernst T, Kögler G, Krieg A, Lüdeke S, Kunkel H, Rodrigues Moita AJ, Kassack MU, Marquardt V, Opitz FV, Oldenburg M, Remke M, Babor F, Grez M, Hochhaus A, Borkhardt A, Groth G, Nagel-Steger L, Jose J, Kurz T, Gohlke H, Hansen FK, Hauer J. Targeting HSP90 dimerization via the C terminus is effective in imatinib-resistant CML and lacks the heat shock response. Blood 2018; 132:307-320. [PMID: 29724897 PMCID: PMC6225350 DOI: 10.1182/blood-2017-10-810986] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 04/19/2018] [Indexed: 12/12/2022] Open
Abstract
Heat shock protein 90 (HSP90) stabilizes many client proteins, including the BCR-ABL1 oncoprotein. BCR-ABL1 is the hallmark of chronic myeloid leukemia (CML) in which treatment-free remission (TFR) is limited, with clinical and economic consequences. Thus, there is an urgent need for novel therapeutics that synergize with current treatment approaches. Several inhibitors targeting the N-terminal domain of HSP90 are under investigation, but side effects such as induction of the heat shock response (HSR) and toxicity have so far precluded their US Food and Drug Administration approval. We have developed a novel inhibitor (aminoxyrone [AX]) of HSP90 function by targeting HSP90 dimerization via the C-terminal domain. This was achieved by structure-based molecular design, chemical synthesis, and functional preclinical in vitro and in vivo validation using CML cell lines and patient-derived CML cells. AX is a promising potential candidate that induces apoptosis in the leukemic stem cell fraction (CD34+CD38-) as well as the leukemic bulk (CD34+CD38+) of primary CML and in tyrosine kinase inhibitor (TKI)-resistant cells. Furthermore, BCR-ABL1 oncoprotein and related pro-oncogenic cellular responses are downregulated, and targeting the HSP90 C terminus by AX does not induce the HSR in vitro and in vivo. We also probed the potential of AX in other therapy-refractory leukemias. Therefore, AX is the first peptidomimetic C-terminal HSP90 inhibitor with the potential to increase TFR in TKI-sensitive and refractory CML patients and also offers a novel therapeutic option for patients with other types of therapy-refractory leukemia because of its low toxicity profile and lack of HSR.
Collapse
MESH Headings
- Animals
- Antineoplastic Agents/chemistry
- Antineoplastic Agents/pharmacology
- Binding Sites
- Biomarkers, Tumor
- Cell Cycle/drug effects
- Cell Line, Tumor
- Cell Survival/drug effects
- Disease Models, Animal
- Drug Resistance, Neoplasm/drug effects
- Fusion Proteins, bcr-abl/antagonists & inhibitors
- Fusion Proteins, bcr-abl/chemistry
- HSP90 Heat-Shock Proteins/antagonists & inhibitors
- HSP90 Heat-Shock Proteins/chemistry
- HSP90 Heat-Shock Proteins/metabolism
- Heat-Shock Response/drug effects
- Humans
- Imatinib Mesylate/chemistry
- Imatinib Mesylate/pharmacology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Mice
- Models, Molecular
- Molecular Conformation
- Molecular Structure
- Protein Binding
- Protein Interaction Domains and Motifs
- Protein Kinase Inhibitors/chemistry
- Protein Kinase Inhibitors/pharmacology
- Protein Multimerization/drug effects
- Spectrum Analysis
- Structure-Activity Relationship
- Xenograft Model Antitumor Assays
Collapse
Affiliation(s)
- Sanil Bhatia
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, and
| | - Daniela Diedrich
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Benedikt Frieg
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- John von Neumann Institute for Computing, Jülich Supercomputing Centre, Institute for Complex Systems-Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Heinz Ahlert
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, and
| | - Stefan Stein
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt, Germany
| | - Bertan Bopp
- Institute for Pharmaceutical and Medicinal Chemistry, PharmaCampus, Westphalian Wilhelms University, Münster, Germany
| | - Franziska Lang
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, and
| | - Tao Zang
- Institute for Physical Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Tobias Kröger
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Thomas Ernst
- Hematology/Oncology, Internal Medicine II, Jena University Hospital, Jena, Germany
| | - Gesine Kögler
- Institute for Transplantation Diagnostics and Cell Therapeutics and
| | - Andreas Krieg
- Department of Surgery (A), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Steffen Lüdeke
- Institute of Pharmaceutical Sciences, University of Freiburg, Freiburg, Germany
| | - Hana Kunkel
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt, Germany
| | - Ana J Rodrigues Moita
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Matthias U Kassack
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Viktoria Marquardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, and
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute of Neuropathology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Division of Pediatric Neuro-Oncogenomics, German Cancer Consortium, partner site University Hospital Düsseldorf, Düsseldorf, Germany
| | - Friederike V Opitz
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, and
| | - Marina Oldenburg
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, and
| | - Marc Remke
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, and
- Institute of Neuropathology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Division of Pediatric Neuro-Oncogenomics, German Cancer Consortium, partner site University Hospital Düsseldorf, Düsseldorf, Germany
| | - Florian Babor
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, and
| | - Manuel Grez
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Frankfurt, Germany
| | - Andreas Hochhaus
- Hematology/Oncology, Internal Medicine II, Jena University Hospital, Jena, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, and
| | - Georg Groth
- Institute for Biochemical Plant Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany; and
| | - Luitgard Nagel-Steger
- Institute for Physical Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Joachim Jose
- Institute for Pharmaceutical and Medicinal Chemistry, PharmaCampus, Westphalian Wilhelms University, Münster, Germany
| | - Thomas Kurz
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- John von Neumann Institute for Computing, Jülich Supercomputing Centre, Institute for Complex Systems-Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Finn K Hansen
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Leipzig University, Leipzig, Germany
| | - Julia Hauer
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Medical Faculty, and
| |
Collapse
|
14
|
Zhang T, Pauly T, Nagel-Steger L. Stoichiometric Zn2+ interferes with the self-association of Aβ42: Insights from size distribution analysis. Int J Biol Macromol 2018; 113:631-639. [DOI: 10.1016/j.ijbiomac.2018.02.123] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 02/16/2018] [Accepted: 02/19/2018] [Indexed: 12/17/2022]
|
15
|
Cavini IA, Munte CE, Erlach MB, van Groen T, Kadish I, Zhang T, Ziehm T, Nagel-Steger L, Kutzsche J, Kremer W, Willbold D, Kalbitzer HR. Inhibition of amyloid Aβ aggregation by high pressures or specific d-enantiomeric peptides. Chem Commun (Camb) 2018. [PMID: 29537428 DOI: 10.1039/c8cc01458b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Pressure can shift the polymer-monomer equilibrium of Aβ, increasing pressure first leads to a release of Aβ-monomers, surprisingly at pressures higher than 180 MPa repolymerization is induced. By high pressure NMR spectroscopy, differences of partial molar volumes ΔV0 and compressibility factors Δβ' of polymerization were determined at different temperatures. The d-enantiomeric peptides RD2 and RD2D3 bind to monomeric Aβ with affinities substantially higher than those determined for fibril formation. By reducing the Aβ concentration below the critical concentration for polymerization they inhibit the formation of toxic oligomers. Chemical shift perturbation allows the identification of the binding sites. The d-peptides are candidates for drugs preventing Alzheimer's disease. We show that RD2D3 has a positive effect on the cognitive behaviour of transgenic (APPSwDI) mice prone to Alzheimer's disease. The heterodimer complexes have a smaller Stokes radius than Aβ alone indicating the recognition of a more compact conformation of Aβ identified by high pressure NMR before.
Collapse
Affiliation(s)
- Italo A Cavini
- Physics Institute of São Carlos, University of São Paulo, São Carlos, SP, Brazil
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
16
|
van Groen T, Schemmert S, Brener O, Gremer L, Ziehm T, Tusche M, Nagel-Steger L, Kadish I, Schartmann E, Elfgen A, Jürgens D, Willuweit A, Kutzsche J, Willbold D. The Aβ oligomer eliminating D-enantiomeric peptide RD2 improves cognition without changing plaque pathology. Sci Rep 2017; 7:16275. [PMID: 29176708 PMCID: PMC5701182 DOI: 10.1038/s41598-017-16565-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [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: 07/18/2017] [Accepted: 11/15/2017] [Indexed: 01/17/2023] Open
Abstract
While amyloid-β protein (Aβ) aggregation into insoluble plaques is one of the pathological hallmarks of Alzheimer’s disease (AD), soluble oligomeric Aβ has been hypothesized to be responsible for synapse damage, neurodegeneration, learning, and memory deficits in AD. Here, we investigate the in vitro and in vivo efficacy of the d-enantiomeric peptide RD2, a rationally designed derivative of the previously described lead compound D3, which has been developed to efficiently eliminate toxic Aβ42 oligomers as a promising treatment strategy for AD. Besides the detailed in vitro characterization of RD2, we also report the results of a treatment study of APP/PS1 mice with RD2. After 28 days of treatment we observed enhancement of cognition and learning behaviour. Analysis on brain plaque load did not reveal significant changes, but a significant reduction of insoluble Aβ42. Our findings demonstrate that RD2 was significantly more efficient in Aβ oligomer elimination in vitro compared to D3. Enhanced cognition without reduction of plaque pathology in parallel suggests that synaptic malfunction due to Aβ oligomers rather than plaque pathology is decisive for disease development and progression. Thus, Aβ oligomer elimination by RD2 treatment may be also beneficial for AD patients.
Collapse
Affiliation(s)
- Thomas van Groen
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
| | - Sarah Schemmert
- Institute of Complex Systems (ICS-6), Structural Biochemistry, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Oleksandr Brener
- Institute of Complex Systems (ICS-6), Structural Biochemistry, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Lothar Gremer
- Institute of Complex Systems (ICS-6), Structural Biochemistry, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Tamar Ziehm
- Institute of Complex Systems (ICS-6), Structural Biochemistry, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Markus Tusche
- Institute of Complex Systems (ICS-6), Structural Biochemistry, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Luitgard Nagel-Steger
- Institute of Complex Systems (ICS-6), Structural Biochemistry, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Inga Kadish
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Elena Schartmann
- Institute of Complex Systems (ICS-6), Structural Biochemistry, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Anne Elfgen
- Institute of Complex Systems (ICS-6), Structural Biochemistry, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Dagmar Jürgens
- Institute of Complex Systems (ICS-6), Structural Biochemistry, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Antje Willuweit
- Institute of Neuroscience and Medicine (INM-4), Medical Imaging Physics, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Janine Kutzsche
- Institute of Complex Systems (ICS-6), Structural Biochemistry, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Dieter Willbold
- Institute of Complex Systems (ICS-6), Structural Biochemistry, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany. .,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany.
| |
Collapse
|
17
|
Wolff M, Zhang-Haagen B, Decker C, Barz B, Schneider M, Biehl R, Radulescu A, Strodel B, Willbold D, Nagel-Steger L. Aβ42 pentamers/hexamers are the smallest detectable oligomers in solution. Sci Rep 2017; 7:2493. [PMID: 28559586 PMCID: PMC5449387 DOI: 10.1038/s41598-017-02370-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [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: 10/25/2016] [Accepted: 04/11/2017] [Indexed: 12/14/2022] Open
Abstract
Amyloid β (Aβ) oligomers may play a decisive role in Alzheimer's disease related neurodegeneration, but their structural properties are poorly understood. In this report, sedimentation velocity centrifugation, small angle neutron scattering (SANS) and molecular modelling were used to identify the small oligomeric species formed by the 42 amino acid residue long isoform of Aβ (Aβ42) in solution, characterized by a sedimentation coefficient of 2.56 S, and a radius of gyration between 2 and 4 nm. The measured sedimentation coefficient is in close agreement with the sedimentation coefficient calculated for Aβ42 hexamers using MD simulations at µM concentration. To the best of our knowledge this is the first report detailing the Aβ42 oligomeric species by SANS measurements. Our results demonstrate that the smallest detectable species in solution are penta- to hexamers. No evidences for the presence of dimers, trimers or tetramers were found, although the existence of those Aβ42 oligomers at measurable quantities had been reported frequently.
Collapse
Affiliation(s)
- Martin Wolff
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
- Physikalische Biochemie, University Potsdam, 14476, Golm, Germany
| | - Bo Zhang-Haagen
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
- Jülich Centre for Neutron Science & Institute of Complex Systems, Neutron Scattering (JCNS-1&ICS-1), Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Christina Decker
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Bogdan Barz
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Mario Schneider
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Ralf Biehl
- Jülich Centre for Neutron Science & Institute of Complex Systems, Neutron Scattering (JCNS-1&ICS-1), Forschungszentrum Jülich, 52425, Jülich, Germany
- Jülich Centre for Neutron Science, Outstation at MLZ (JCNS-MLZ), Forschungszentrum Jülich, 85747, Garching, Germany
| | - Aurel Radulescu
- Jülich Centre for Neutron Science, Outstation at MLZ (JCNS-MLZ), Forschungszentrum Jülich, 85747, Garching, Germany
| | - Birgit Strodel
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Dieter Willbold
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Luitgard Nagel-Steger
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany.
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany.
| |
Collapse
|
18
|
Kroeger T, Frieg B, Zhang T, Hansen FK, Marmann A, Proksch P, Nagel-Steger L, Groth G, Smits SHJ, Gohlke H. EDTA aggregates induce SYPRO orange-based fluorescence in thermal shift assay. PLoS One 2017; 12:e0177024. [PMID: 28472107 PMCID: PMC5417642 DOI: 10.1371/journal.pone.0177024] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 03/29/2017] [Indexed: 12/16/2022] Open
Abstract
Ethylenediaminetetraacetic acid (EDTA) is widely used in the life sciences as chelating ligand of metal ions. However, formation of supramolecular EDTA aggregates at pH > 8 has been reported, which may lead to artifactual assay results. When applied as a buffer component at pH ≈ 10 in differential scanning fluorimetry (TSA) using SYPRO Orange as fluorescent dye, we observed a sharp change in fluorescence intensity about 20°C lower than expected for the investigated protein. We hypothesized that this change results from SYPRO Orange/EDTA interactions. TSA experiments in the presence of SYPRO Orange using solutions that contain EDTA-Na+ but no protein were performed. The TSA experiments provide evidence that suggests that at pH > 9, EDTA4- interacts with SYPRO Orange in a temperature-dependent manner, leading to a fluorescence signal yielding a "denaturation temperature" of ~68°C. Titrating Ca2+ to SYPRO Orange and EDTA solutions quenched fluorescence. Ethylene glycol tetraacetic acid (EGTA) behaved similarly to EDTA. Analytical ultracentrifugation corroborated the formation of EDTA aggregates. Molecular dynamics simulations of free diffusion of EDTA-Na+ and SYPRO Orange of in total 27 μs suggested the first structural model of EDTA aggregates in which U-shaped EDTA4- arrange in an inverse bilayer-like manner, exposing ethylene moieties to the solvent, with which SYPRO Orange interacts. We conclude that EDTA aggregates induce a SYPRO Orange-based fluorescence in TSA. These results make it relevant to ascertain that future TSA results are not influenced by interference between EDTA, or EDTA-related molecules, and the fluorescent dye.
Collapse
Affiliation(s)
- Tobias Kroeger
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Benedikt Frieg
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Tao Zhang
- Institute for Physical Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, Jülich, Germany
| | - Finn K. Hansen
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Andreas Marmann
- Institute for Pharmaceutical Biology and Biotechnology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Peter Proksch
- Institute for Pharmaceutical Biology and Biotechnology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Luitgard Nagel-Steger
- Institute for Physical Biology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, Jülich, Germany
| | - Georg Groth
- Institute for Biochemical Plant Physiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sander H. J. Smits
- Institute for Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| |
Collapse
|
19
|
Bradshaw NJ, Yerabham ASK, Marreiros R, Zhang T, Nagel-Steger L, Korth C. An unpredicted aggregation-critical region of the actin-polymerizing protein TRIOBP-1/Tara, determined by elucidation of its domain structure. J Biol Chem 2017; 292:9583-9598. [PMID: 28438837 DOI: 10.1074/jbc.m116.767939] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 04/20/2017] [Indexed: 12/22/2022] Open
Abstract
Aggregation of specific proteins in the brains of patients with chronic mental illness as a result of disruptions in proteostasis is an emerging theme in the study of schizophrenia in particular. Proteins including DISC1 (disrupted in schizophrenia 1) and dysbindin-1B are found in insoluble forms within brain homogenates from such patients. We recently identified TRIOBP-1 (Trio-binding protein 1, also known as Tara) to be another such protein through an epitope discovery and proteomics approach by comparing post-mortem brain material from schizophrenia patients and control individuals. We hypothesized that this was likely to occur as a result of a specific subcellular process and that it, therefore, should be possible to identify a region of the TRIOBP-1 protein that is essential for its aggregation to occur. Here, we probe the domain organization of TRIOBP-1, finding it to possess two distinct coiled-coil domains: the central and C-terminal domains. The central domain inhibits the depolymerization of F-actin and is also responsible for oligomerization of TRIOBP-1. Along with an N-terminal pleckstrin homology domain, the central domain affects neurite outgrowth. In neuroblastoma cells it was found that the aggregation propensity of TRIOBP-1 arises from its central domain, with a short "linker" region narrowed to within amino acids 324-348, between its first two coiled coils, as essential for the formation of TRIOBP-1 aggregates. TRIOBP-1 aggregation, therefore, appears to occur through one or more specific cellular mechanisms, which therefore have the potential to be of physiological relevance for the biological process underlying the development of chronic mental illness.
Collapse
Affiliation(s)
| | | | | | - Tao Zhang
- the Institute of Physical Biology, Heinrich Heine University, 40225 Düsseldorf, Germany and.,the Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Luitgard Nagel-Steger
- the Institute of Physical Biology, Heinrich Heine University, 40225 Düsseldorf, Germany and.,the Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | | |
Collapse
|
20
|
Yerabham ASK, Mas PJ, Decker C, Soares DC, Weiergräber OH, Nagel-Steger L, Willbold D, Hart DJ, Bradshaw NJ, Korth C. A structural organization for the Disrupted in Schizophrenia 1 protein, identified by high-throughput screening, reveals distinctly folded regions, which are bisected by mental illness-related mutations. J Biol Chem 2017; 292:6468-6477. [PMID: 28249940 DOI: 10.1074/jbc.m116.773903] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/22/2017] [Indexed: 11/06/2022] Open
Abstract
Disrupted in Schizophrenia 1 (DISC1) is a scaffolding protein of significant importance for neurodevelopment and a prominent candidate protein in the pathology of major mental illness. DISC1 modulates a number of critical neuronal signaling pathways through protein-protein interactions; however, the mechanism by which this occurs and how DISC1 causes mental illness is unclear, partly because knowledge of the structure of DISC1 is lacking. A lack of homology with known proteins has hindered attempts to define its domain composition. Here, we employed the high-throughput Expression of Soluble Proteins by Random Incremental Truncation (ESPRIT) technique to identify discretely folded regions of human DISC1 via solubility assessment of tens of thousands of fragments of recombinant DISC1. We identified four novel structured regions, named D, I, S, and C, at amino acids 257-383, 539-655, 635-738, and 691-836, respectively. One region (D) is located in a DISC1 section previously predicted to be unstructured. All regions encompass coiled-coil or α-helical structures, and three are involved in DISC1 oligomerization. Crucially, three of these domains would be lost or disrupted by a chromosomal translocation event after amino acid 597, which has been strongly linked to major mental illness. Furthermore, we observed that a known illness-related frameshift mutation after amino acid 807 causes the C region to form aberrantly multimeric and aggregated complexes with an unstable secondary structure. This newly revealed domain architecture of DISC1, therefore, provides a powerful framework for understanding the critical role of this protein in a variety of devastating mental illnesses.
Collapse
Affiliation(s)
| | - Philippe J Mas
- the Integrated Structural Biology Grenoble (ISBG) CNRS, CEA, Université Grenoble Alpes, EMBL, 38042 Grenoble, France
| | - Christina Decker
- the Institute of Physical Biology, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Dinesh C Soares
- the MRC Human Genetics Unit, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Oliver H Weiergräber
- the Institute of Complex Systems (ICS-6: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany, and
| | - Luitgard Nagel-Steger
- the Institute of Physical Biology, Heinrich Heine University, 40225 Düsseldorf, Germany.,the Institute of Complex Systems (ICS-6: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany, and
| | - Dieter Willbold
- the Institute of Physical Biology, Heinrich Heine University, 40225 Düsseldorf, Germany.,the Institute of Complex Systems (ICS-6: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany, and
| | - Darren J Hart
- the Institute of Complex Systems (ICS-6: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany, and
| | | | | |
Collapse
|
21
|
Michel M, Schwarten M, Decker C, Nagel-Steger L, Willbold D, Weiergräber OH. The mammalian autophagy initiator complex contains 2 HORMA domain proteins. Autophagy 2016; 11:2300-8. [PMID: 26236954 DOI: 10.1080/15548627.2015.1076605] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
ATG101 is an essential component of the ULK complex responsible for initiating cellular autophagy in mammalian cells; its 3-dimensional structure and molecular function, however, are currently unclear. Here we present the X-ray structure of human ATG101. The protein displays an open HORMA domain fold. Both structural properties and biophysical evidence indicate that ATG101 is locked in this conformation, in contrast to the prototypical HORMA domain protein MAD2. Moreover, we discuss a potential mode of dimerization with ATG13 as a fundamental aspect of ATG101 function.
Collapse
Affiliation(s)
- Max Michel
- a Institute of Complex Systems; ICS-6: Structural Biochemistry; Forschungszentrum Jülich; Jülich , Germany
| | - Melanie Schwarten
- a Institute of Complex Systems; ICS-6: Structural Biochemistry; Forschungszentrum Jülich; Jülich , Germany
| | - Christina Decker
- b Institut für Physikalische Biologie und BMFZ; Heinrich-Heine-Universität Düsseldorf ; Düsseldorf , Germany
| | - Luitgard Nagel-Steger
- b Institut für Physikalische Biologie und BMFZ; Heinrich-Heine-Universität Düsseldorf ; Düsseldorf , Germany
| | - Dieter Willbold
- a Institute of Complex Systems; ICS-6: Structural Biochemistry; Forschungszentrum Jülich; Jülich , Germany.,b Institut für Physikalische Biologie und BMFZ; Heinrich-Heine-Universität Düsseldorf ; Düsseldorf , Germany
| | - Oliver H Weiergräber
- a Institute of Complex Systems; ICS-6: Structural Biochemistry; Forschungszentrum Jülich; Jülich , Germany
| |
Collapse
|
22
|
Luczak SET, Smits SHJ, Decker C, Nagel-Steger L, Schmitt L, Hegemann JH. The Chlamydia pneumoniae Adhesin Pmp21 Forms Oligomers with Adhesive Properties. J Biol Chem 2016; 291:22806-22818. [PMID: 27551038 PMCID: PMC5077213 DOI: 10.1074/jbc.m116.728915] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 08/09/2016] [Indexed: 01/31/2023] Open
Abstract
Chlamydiae sp. are obligate intracellular pathogens that cause a variety of diseases in humans. The adhesion of Chlamydiae to the eukaryotic host cell is a pivotal step in pathogenesis. The adhesin family of polymorphic membrane proteins (Pmp) in Chlamydia pneumoniae consists of 21 members. Pmp21 binds to the epidermal growth factor receptor (EGFR). Pmps contain large numbers of FXXN (where X is any amino acid) and GGA(I/L/V) motifs. At least two of these motifs are crucial for adhesion by certain Pmp21 fragments. Here we describe how the two FXXN motifs in Pmp21-D (D-Wt), a domain of Pmp21, influence its self-interaction, folding, and adhesive capacities. Refolded D-Wt molecules form oligomers with high sedimentation values (8-85 S). These oligomers take the form of elongated protofibrils, which exhibit Thioflavin T fluorescence, like the amyloid protein fragment β42. A mutant version of Pmp21-D (D-Mt), with FXXN motifs replaced by SXXV, shows a markedly reduced capacity to form oligomers. Secondary-structure assays revealed that monomers of both variants exist predominantly as random coils, whereas the oligomers form predominantly β-sheets. Adhesion studies revealed that oligomers of D-Wt (D-Wt-O) mediate significantly enhanced binding to human epithelial cells relative to D-Mt-O and monomeric protein species. Moreover, D-Wt-O binds EGFR more efficiently than D-Wt monomers. Importantly, pretreatment of human cells with D-Wt-O reduces infectivity upon subsequent challenge with C. pneumoniae more effectively than all other protein species. Hence, the FXXN motif in D-Wt induces the formation of β-sheet-rich oligomeric protofibrils, which are important for adhesion to, and subsequent infection of human cells.
Collapse
Affiliation(s)
| | | | - Christina Decker
- Institute of Physical Biology, Heinrich-Heine-University, Universitaetsstrasse 1, 40225 Duesseldorf, Germany and
| | - Luitgard Nagel-Steger
- Institute of Physical Biology, Heinrich-Heine-University, Universitaetsstrasse 1, 40225 Duesseldorf, Germany and
- ICS-6 Research Center Juelich, 52425 Juelich, Germany
| | | | | |
Collapse
|
23
|
Streich C, Akkari L, Decker C, Bormann J, Rehbock C, Müller-Schiffmann A, Niemeyer FC, Nagel-Steger L, Willbold D, Sacca B, Korth C, Schrader T, Barcikowski S. Characterizing the Effect of Multivalent Conjugates Composed of Aβ-Specific Ligands and Metal Nanoparticles on Neurotoxic Fibrillar Aggregation. ACS Nano 2016; 10:7582-7597. [PMID: 27404114 DOI: 10.1021/acsnano.6b02627] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Therapeutically active small molecules represent promising nonimmunogenic alternatives to antibodies for specifically targeting disease-relevant receptors. However, a potential drawback compared to antibody-antigen interactions may be the lower affinity of small molecules toward receptors. Here, we overcome this low-affinity problem by coating the surface of nanoparticles (NPs) with multiple ligands. Specifically, we explored the use of gold and platinum nanoparticles to increase the binding affinity of Aβ-specific small molecules to inhibit Aβ peptide aggregation into fibrils in vitro. The interactions of bare NPs, free ligands, and NP-bound ligands with Aβ are comprehensively studied via physicochemical methods (spectroscopy, microscopy, immunologic tests) and cell assays. Reduction of thioflavin T fluorescence, as an indicator for β-sheet content, and inhibition of cellular Aβ excretion are even more effective with NP-bound ligands than with the free ligands. The results from this study may have implications in the development of therapeutics for treating Alzheimer's disease.
Collapse
Affiliation(s)
- Carmen Streich
- Technical Chemistry I and Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen , 45141 Essen, Germany
| | - Laura Akkari
- Institute for Organic Chemistry, University of Duisburg-Essen , 45117 Essen, Germany
| | - Christina Decker
- Institut für Physikalische Biologie, Heinrich-Heine-University Düsseldorf , 40225 Düsseldorf, Germany
| | - Jenny Bormann
- Chemical Biology, Zentrum für Medizinische Biotechnologie (ZMB), Fakultät für Biologie, Universtität Duisburg-Essen , 45117 Essen, Germany
| | - Christoph Rehbock
- Technical Chemistry I and Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen , 45141 Essen, Germany
| | | | | | - Luitgard Nagel-Steger
- Institut für Physikalische Biologie, Heinrich-Heine-University Düsseldorf , 40225 Düsseldorf, Germany
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Centre Jülich , 52425 Jülich, Germany
| | - Dieter Willbold
- Institut für Physikalische Biologie, Heinrich-Heine-University Düsseldorf , 40225 Düsseldorf, Germany
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Centre Jülich , 52425 Jülich, Germany
| | - Barbara Sacca
- Bionanotechnology, Zentrum für Medizinische Biotechnologie (ZMB), Fakultät für Biologie, University of Duisburg-Essen , 45117 Essen, Germany
| | - Carsten Korth
- Department Neuropathology, University of Düsseldorf Medical School , 40225 Düsseldorf, Germany
| | - Thomas Schrader
- Institute for Organic Chemistry, University of Duisburg-Essen , 45117 Essen, Germany
| | - Stephan Barcikowski
- Technical Chemistry I and Center for Nanointegration Duisburg-Essen (CENIDE), University of Duisburg-Essen , 45141 Essen, Germany
| |
Collapse
|
24
|
Ziehm T, Brener O, van Groen T, Kadish I, Frenzel D, Tusche M, Kutzsche J, Reiß K, Gremer L, Nagel-Steger L, Willbold D. Increase of Positive Net Charge and Conformational Rigidity Enhances the Efficacy of d-Enantiomeric Peptides Designed to Eliminate Cytotoxic Aβ Species. ACS Chem Neurosci 2016; 7:1088-96. [PMID: 27240424 DOI: 10.1021/acschemneuro.6b00047] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder and the most common type of dementia. Until now, there is no curative therapy available. Previously, we selected the amyloid-beta (Aβ) targeting peptide D3 consisting of 12 d-enantiomeric amino acid residues by mirror image phage display as a potential drug candidate for the treatment of AD. In the current approach, we investigated the optimization potential of linear D3 with free C-terminus (D3COOH) by chemical modifications. First, the impact of the net charge was investigated and second, cyclization was introduced which is a well-known tool for the optimization of peptides for enhanced target affinity. Following this strategy, three D3 derivatives in addition to D3COOH were designed: C-terminally amidated linear D3 (D3CONH2), cyclic D3 (cD3), and cyclic D3 with an additional arginine residue (cD3r) to maintain the net charge of linear D3CONH2. These four compounds were compared to each other according to their binding affinities to Aβ(1-42), their efficacy to eliminate cytotoxic oligomers, and consequently their potency to neutralize Aβ(1-42) oligomer induced neurotoxicity. D3CONH2 and cD3r versions with equally increased net charge showed superior properties over D3COOH and cD3, respectively. The cyclic versions showed superior properties compared to their linear version with equal net charge, suggesting cD3r to be the most efficient compound among these four. Indeed, treatment of the transgenic AD mouse model Tg-SwDI with cD3r significantly enhanced spatial memory and cognition of these animals as revealed by water maze performance. Therefore, charge increase and cyclization imply suitable modification steps for an optimization approach of the Aβ targeting compound D3.
Collapse
Affiliation(s)
- Tamar Ziehm
- Institute of Complex
Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Oleksandr Brener
- Institute of Complex
Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Thomas van Groen
- Department of Cell, Developmental and Integrative
Biology, University of Alabama at Birmingham (UAB), Birmingham, Alabama 35233, United States
| | - Inga Kadish
- Department of Cell, Developmental and Integrative
Biology, University of Alabama at Birmingham (UAB), Birmingham, Alabama 35233, United States
| | - Daniel Frenzel
- Institute of Complex
Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Markus Tusche
- Institute of Complex
Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Janine Kutzsche
- Institute of Complex
Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Kerstin Reiß
- Institute of Complex
Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Lothar Gremer
- Institute of Complex
Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Luitgard Nagel-Steger
- Institute of Complex
Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Dieter Willbold
- Institute of Complex
Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| |
Collapse
|
25
|
Nagel-Steger L, Owen MC, Strodel B. An Account of Amyloid Oligomers: Facts and Figures Obtained from Experiments and Simulations. Chembiochem 2016; 17:657-76. [PMID: 26910367 DOI: 10.1002/cbic.201500623] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Indexed: 12/27/2022]
Abstract
The deposition of amyloid in brain tissue in the context of neurodegenerative diseases involves the formation of intermediate species-termed oligomers-of lower molecular mass and with structures that deviate from those of mature amyloid fibrils. Because these oligomers are thought to be primarily responsible for the subsequent disease pathogenesis, the elucidation of their structure is of enormous interest. Nevertheless, because of the high aggregation propensity and the polydispersity of oligomeric species formed by the proteins or peptides in question, the preparation of appropriate samples for high-resolution structural methods has proven to be rather difficult. This is why theoretical approaches have been of particular importance in gaining insights into possible oligomeric structures for some time. Only recently has it been possible to achieve some progress with regard to the experimentally based structural characterization of defined oligomeric species. Here we discuss how theory and experiment are used to determine oligomer structures and what can be done to improve the integration of the two disciplines.
Collapse
Affiliation(s)
- Luitgard Nagel-Steger
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätstrasse 1, 40225, Düsseldorf, Germany
| | - Michael C Owen
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425, Jülich, Germany. .,Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitätstrasse 1, 40225, Düsseldorf, Germany.
| |
Collapse
|
26
|
Zhang-Haagen B, Biehl R, Nagel-Steger L, Radulescu A, Richter D, Willbold D. Monomeric Amyloid Beta Peptide in Hexafluoroisopropanol Detected by Small Angle Neutron Scattering. PLoS One 2016; 11:e0150267. [PMID: 26919121 PMCID: PMC4769228 DOI: 10.1371/journal.pone.0150267] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [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: 12/22/2015] [Accepted: 02/11/2016] [Indexed: 01/17/2023] Open
Abstract
Small proteins like amyloid beta (Aβ) monomers are related to neurodegenerative disorders by aggregation to insoluble fibrils. Small angle neutron scattering (SANS) is a nondestructive method to observe the aggregation process in solution. We show that SANS is able to resolve monomers of small molecular weight like Aβ for aggregation studies. We examine Aβ monomers after prolonged storing in d-hexafluoroisopropanol (dHFIP) by using SANS and dynamic light scattering (DLS). We determined the radius of gyration from SANS as 1.0±0.1 nm for Aβ1–40 and 1.6±0.1 nm for Aβ1–42 in agreement with 3D NMR structures in similar solvents suggesting a solvent surface layer with 5% increased density. After initial dissolution in dHFIP Aβ aggregates sediment with a major component of pure monomers showing a hydrodynamic radius of 1.8±0.3 nm for Aβ1–40 and 3.2±0.4 nm for Aβ1–42 including a surface layer of dHFIP solvent molecules.
Collapse
Affiliation(s)
- Bo Zhang-Haagen
- Jülich Centre for Neutron Science & Institute of Complex Systems, Neutron Scattering (JCNS-1&ICS-1), Research Centre Jülich, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Ralf Biehl
- Jülich Centre for Neutron Science & Institute of Complex Systems, Neutron Scattering (JCNS-1&ICS-1), Research Centre Jülich, Jülich, Germany
- * E-mail:
| | - Luitgard Nagel-Steger
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Centre Jülich, Jülich, Germany
| | - Aurel Radulescu
- Jülich Centre for Neutron Science, Outstation at MLZ (JCNS-MLZ), Research Centre Jülich, Garching, Germany
| | - Dieter Richter
- Jülich Centre for Neutron Science & Institute of Complex Systems, Neutron Scattering (JCNS-1&ICS-1), Research Centre Jülich, Jülich, Germany
| | - Dieter Willbold
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Centre Jülich, Jülich, Germany
| |
Collapse
|
27
|
Brener O, Dunkelmann T, Gremer L, van Groen T, Mirecka EA, Kadish I, Willuweit A, Kutzsche J, Jürgens D, Rudolph S, Tusche M, Bongen P, Pietruszka J, Oesterhelt F, Langen KJ, Demuth HU, Janssen A, Hoyer W, Funke SA, Nagel-Steger L, Willbold D. QIAD assay for quantitating a compound's efficacy in elimination of toxic Aβ oligomers. Sci Rep 2015; 5:13222. [PMID: 26394756 PMCID: PMC4585794 DOI: 10.1038/srep13222] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [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: 05/07/2015] [Accepted: 07/21/2015] [Indexed: 02/07/2023] Open
Abstract
Strong evidence exists for a central role of amyloid β-protein (Aβ) oligomers in the pathogenesis of Alzheimer’s disease. We have developed a fast, reliable and robust in vitro assay, termed QIAD, to quantify the effect of any compound on the Aβ aggregate size distribution. Applying QIAD, we studied the effect of homotaurine, scyllo-inositol, EGCG, the benzofuran derivative KMS88009, ZAβ3W, the D-enantiomeric peptide D3 and its tandem version D3D3 on Aβ aggregation. The predictive power of the assay for in vivo efficacy is demonstrated by comparing the oligomer elimination efficiency of D3 and D3D3 with their treatment effects in animal models of Alzheimer´s disease.
Collapse
Affiliation(s)
- Oleksandr Brener
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Centre Jülich, 52425 Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Tina Dunkelmann
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Centre Jülich, 52425 Jülich, Germany
| | - Lothar Gremer
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Centre Jülich, 52425 Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Thomas van Groen
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ewa A Mirecka
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Inga Kadish
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Antje Willuweit
- Institute of Neuroscience and Medicine (INM-4), Research Centre Jülich (FZJ), 52425 Jülich, Germany
| | - Janine Kutzsche
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Centre Jülich, 52425 Jülich, Germany
| | - Dagmar Jürgens
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Centre Jülich, 52425 Jülich, Germany
| | - Stephan Rudolph
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Centre Jülich, 52425 Jülich, Germany
| | - Markus Tusche
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Centre Jülich, 52425 Jülich, Germany
| | - Patrick Bongen
- Institute for Bioorganic Chemistry, Heinrich-Heine-Universität Düsseldorf, 52426 Jülich, Germany
| | - Jörg Pietruszka
- Institute for Bioorganic Chemistry, Heinrich-Heine-Universität Düsseldorf, 52426 Jülich, Germany.,Institut für Bio- und Geowissenschaften: Biotechnologie (IBG-1), Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Filipp Oesterhelt
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Karl-Josef Langen
- Institute of Neuroscience and Medicine (INM-4), Research Centre Jülich (FZJ), 52425 Jülich, Germany
| | - Hans-Ulrich Demuth
- Fraunhofer Institute for Cell Therapy and Immunology, Dep. Molecular Drug Biochemistry and Therapy, 06120 Halle, Germany
| | - Arnold Janssen
- Institute of Mathematics, Lehrstuhl für Statistik und Wahrscheinlichkeitstheorie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Wolfgang Hoyer
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Centre Jülich, 52425 Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Susanne A Funke
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Centre Jülich, 52425 Jülich, Germany.,Bioanalytik, Hochschule für Angewandte Wissenschaften, Coburg, Germany
| | - Luitgard Nagel-Steger
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Centre Jülich, 52425 Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Dieter Willbold
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Research Centre Jülich, 52425 Jülich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| |
Collapse
|
28
|
Zhao H, Ghirlando R, Alfonso C, Arisaka F, Attali I, Bain DL, Bakhtina MM, Becker DF, Bedwell GJ, Bekdemir A, Besong TMD, Birck C, Brautigam CA, Brennerman W, Byron O, Bzowska A, Chaires JB, Chaton CT, Cölfen H, Connaghan KD, Crowley KA, Curth U, Daviter T, Dean WL, Díez AI, Ebel C, Eckert DM, Eisele LE, Eisenstein E, England P, Escalante C, Fagan JA, Fairman R, Finn RM, Fischle W, de la Torre JG, Gor J, Gustafsson H, Hall D, Harding SE, Cifre JGH, Herr AB, Howell EE, Isaac RS, Jao SC, Jose D, Kim SJ, Kokona B, Kornblatt JA, Kosek D, Krayukhina E, Krzizike D, Kusznir EA, Kwon H, Larson A, Laue TM, Le Roy A, Leech AP, Lilie H, Luger K, Luque-Ortega JR, Ma J, May CA, Maynard EL, Modrak-Wojcik A, Mok YF, Mücke N, Nagel-Steger L, Narlikar GJ, Noda M, Nourse A, Obsil T, Park CK, Park JK, Pawelek PD, Perdue EE, Perkins SJ, Perugini MA, Peterson CL, Peverelli MG, Piszczek G, Prag G, Prevelige PE, Raynal BDE, Rezabkova L, Richter K, Ringel AE, Rosenberg R, Rowe AJ, Rufer AC, Scott DJ, Seravalli JG, Solovyova AS, Song R, Staunton D, Stoddard C, Stott K, Strauss HM, Streicher WW, Sumida JP, Swygert SG, Szczepanowski RH, Tessmer I, Toth RT, Tripathy A, Uchiyama S, Uebel SFW, Unzai S, Gruber AV, von Hippel PH, Wandrey C, Wang SH, Weitzel SE, Wielgus-Kutrowska B, Wolberger C, Wolff M, Wright E, Wu YS, Wubben JM, Schuck P. A multilaboratory comparison of calibration accuracy and the performance of external references in analytical ultracentrifugation. PLoS One 2015; 10:e0126420. [PMID: 25997164 PMCID: PMC4440767 DOI: 10.1371/journal.pone.0126420] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 04/02/2015] [Indexed: 12/21/2022] Open
Abstract
Analytical ultracentrifugation (AUC) is a first principles based method to determine absolute sedimentation coefficients and buoyant molar masses of macromolecules and their complexes, reporting on their size and shape in free solution. The purpose of this multi-laboratory study was to establish the precision and accuracy of basic data dimensions in AUC and validate previously proposed calibration techniques. Three kits of AUC cell assemblies containing radial and temperature calibration tools and a bovine serum albumin (BSA) reference sample were shared among 67 laboratories, generating 129 comprehensive data sets. These allowed for an assessment of many parameters of instrument performance, including accuracy of the reported scan time after the start of centrifugation, the accuracy of the temperature calibration, and the accuracy of the radial magnification. The range of sedimentation coefficients obtained for BSA monomer in different instruments and using different optical systems was from 3.655 S to 4.949 S, with a mean and standard deviation of (4.304 ± 0.188) S (4.4%). After the combined application of correction factors derived from the external calibration references for elapsed time, scan velocity, temperature, and radial magnification, the range of s-values was reduced 7-fold with a mean of 4.325 S and a 6-fold reduced standard deviation of ± 0.030 S (0.7%). In addition, the large data set provided an opportunity to determine the instrument-to-instrument variation of the absolute radial positions reported in the scan files, the precision of photometric or refractometric signal magnitudes, and the precision of the calculated apparent molar mass of BSA monomer and the fraction of BSA dimers. These results highlight the necessity and effectiveness of independent calibration of basic AUC data dimensions for reliable quantitative studies.
Collapse
Affiliation(s)
- Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
| | - Carlos Alfonso
- Analytical Ultracentrifugacion and Light Scattering Facility, Centro de Investigaciones Biológicas, CSIC, Madrid, 28040, Spain
| | - Fumio Arisaka
- Life Science Research Center, Nihon University, College of Bioresource Science, Fujisawa, 252–0880, Japan
| | - Ilan Attali
- Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, 69978, Israel
| | - David L. Bain
- Department of Pharmaceutical Sciences, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado, 80045, United States of America
| | - Marina M. Bakhtina
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, Ohio, 43210, United States of America
| | - Donald F. Becker
- Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States of America
| | - Gregory J. Bedwell
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, 35294, United States of America
| | - Ahmet Bekdemir
- Supramolecular Nanomaterials and Interfaces Laboratory, Institute of Materials, École Polytechnique Fédérale de Lausanne, Lausanne, CH-1015, Switzerland
| | - Tabot M. D. Besong
- National Centre for Macromolecular Hydrodynamics, University of Nottingham, School of Biosciences, Sutton Bonington, LE12 5RD, United Kingdom
| | | | - Chad A. Brautigam
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, Texas, 75390, United States of America
| | - William Brennerman
- Beckman Coulter, Inc., Life Science Division, Indianapolis, Indiana, 46268, United States of America
| | - Olwyn Byron
- School of Life Sciences, University of Glasgow, Glasgow, G37TT, United Kingdom
| | - Agnieszka Bzowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, 02–089, Poland
| | - Jonathan B. Chaires
- JG Brown Cancer Center, University of Louisville, Louisville, Kentucky, 40202, United States of America
| | - Catherine T. Chaton
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45267, United States of America
| | - Helmut Cölfen
- Physical Chemistry, University of Konstanz, 78457, Konstanz, Germany
| | - Keith D. Connaghan
- Department of Pharmaceutical Sciences, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado, 80045, United States of America
| | - Kimberly A. Crowley
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, 01605, United States of America
| | - Ute Curth
- Institute for Biophysical Chemistry, Hannover Medical School, 30625, Hannover, Germany
| | - Tina Daviter
- Institute of Structural and Molecular Biology Biophysics Centre, Birkbeck, University of London and University College London, London, WC1E 7HX, United Kingdom
| | - William L. Dean
- JG Brown Cancer Center, University of Louisville, Louisville, Kentucky, 40202, United States of America
| | - Ana I. Díez
- Department of Physical Chemistry, University of Murcia, Murcia, 30071, Spain
| | - Christine Ebel
- Univ. Grenoble Alpes, IBS, F-38044, Grenoble, France
- CNRS, IBS, F-38044, Grenoble, France
- CEA, IBS, F-38044, Grenoble, France
| | - Debra M. Eckert
- Protein Interactions Core, Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, 84112, United States of America
| | - Leslie E. Eisele
- Wadsworth Center, New York State Department of Health, Albany, New York, 12208, United States of America
| | - Edward Eisenstein
- Institute for Bioscience and Biotechnology Research, Fischell Department of Bioengineering, University of Maryland, Rockville, Maryland, 20850, United States of America
| | - Patrick England
- Institut Pasteur, Centre of Biophysics of Macromolecules and Their Interactions, Paris, 75724, France
| | - Carlos Escalante
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, 23220, United States of America
| | - Jeffrey A. Fagan
- Materials Science and Engineering Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland, 20899, United States of America
| | - Robert Fairman
- Department of Biology, Haverford College, Haverford, Pennsylvania, 19041, United States of America
| | - Ron M. Finn
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Wolfgang Fischle
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | | | - Jayesh Gor
- Department of Structural and Molecular Biology, Darwin Building, University College London, London, WC1E 6BT, United Kingdom
| | | | - Damien Hall
- Research School of Chemistry, Section on Biological Chemistry, The Australian National University, Acton, ACT 0200, Australia
| | - Stephen E. Harding
- National Centre for Macromolecular Hydrodynamics, University of Nottingham, School of Biosciences, Sutton Bonington, LE12 5RD, United Kingdom
| | | | - Andrew B. Herr
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45267, United States of America
| | - Elizabeth E. Howell
- Biochemistry, Cell and Molecular Biology Department, University of Tennessee, Knoxville, Tennessee, 37996–0840, United States of America
| | - Richard S. Isaac
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, 94158, United States of America
- Tetrad Graduate Program, University of California San Francisco, San Francisco, California, 94158, United States of America
| | - Shu-Chuan Jao
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
- Biophysics Core Facility, Scientific Instrument Center, Academia Sinica, Taipei, 115, Taiwan
| | - Davis Jose
- Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, 97403, United States of America
| | - Soon-Jong Kim
- Department of Chemistry, Mokpo National University, Muan, 534–729, Korea
| | - Bashkim Kokona
- Department of Biology, Haverford College, Haverford, Pennsylvania, 19041, United States of America
| | - Jack A. Kornblatt
- Enzyme Research Group, Concordia University, Montreal, Quebec, H4B 1R6, Canada
| | - Dalibor Kosek
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Prague, 12843, Czech Republic
| | - Elena Krayukhina
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, 565–0871, Japan
| | - Daniel Krzizike
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, United States of America
| | - Eric A. Kusznir
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-LaRoche Ltd., Basel, 4070, Switzerland
| | - Hyewon Kwon
- Analytical Biopharmacy Core, University of Washington, Seattle, Washington, 98195, United States of America
| | - Adam Larson
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, 94158, United States of America
- Tetrad Graduate Program, University of California San Francisco, San Francisco, California, 94158, United States of America
| | - Thomas M. Laue
- Department of Biochemistry, University of New Hampshire, Durham, New Hampshire, 03824, United States of America
| | - Aline Le Roy
- Univ. Grenoble Alpes, IBS, F-38044, Grenoble, France
- CNRS, IBS, F-38044, Grenoble, France
- CEA, IBS, F-38044, Grenoble, France
| | - Andrew P. Leech
- Technology Facility, Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Hauke Lilie
- Institute of Biochemistry and Biotechnology, Martin-Luther University Halle-Wittenberg, 06120, Halle, Germany
| | - Karolin Luger
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, United States of America
| | - Juan R. Luque-Ortega
- Analytical Ultracentrifugacion and Light Scattering Facility, Centro de Investigaciones Biológicas, CSIC, Madrid, 28040, Spain
| | - Jia Ma
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
| | - Carrie A. May
- Department of Biochemistry, University of New Hampshire, Durham, New Hampshire, 03824, United States of America
| | - Ernest L. Maynard
- Department of Biochemistry, Uniformed Services University of the Health Sciences, Bethesda, Maryland, 20814, United States of America
| | - Anna Modrak-Wojcik
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, 02–089, Poland
| | - Yee-Foong Mok
- Department of Biochemistry and Molecular Biology, Bio21 Instute of Molecular Science and Biotechnology, University of Melbourne, Parkville, 3010, Victoria, Australia
| | - Norbert Mücke
- Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, 69120, Germany
| | | | - Geeta J. Narlikar
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, 94158, United States of America
| | - Masanori Noda
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, 565–0871, Japan
| | - Amanda Nourse
- Molecular Interaction Analysis Shared Resource, St. Jude Children’s Research Hospital, Memphis, Tennessee, 38105, United States of America
| | - Tomas Obsil
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Prague, 12843, Czech Republic
| | - Chad K. Park
- Analytical Biophysics & Materials Characterization, Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, 85721, United States of America
| | - Jin-Ku Park
- Central Instrument Center, Mokpo National University, Muan, 534–729, Korea
| | - Peter D. Pawelek
- Department of Chemistry and Biochemistry, Concordia University, Montreal, Quebec, H4B 1R6, Canada
| | - Erby E. Perdue
- Beckman Coulter, Inc., Life Science Division, Indianapolis, Indiana, 46268, United States of America
| | - Stephen J. Perkins
- Department of Structural and Molecular Biology, Darwin Building, University College London, London, WC1E 6BT, United Kingdom
| | - Matthew A. Perugini
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Craig L. Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, 01605, United States of America
| | - Martin G. Peverelli
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Grzegorz Piszczek
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
| | - Gali Prag
- Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Peter E. Prevelige
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, 35294, United States of America
| | - Bertrand D. E. Raynal
- Institut Pasteur, Centre of Biophysics of Macromolecules and Their Interactions, Paris, 75724, France
| | - Lenka Rezabkova
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232, Villigen PSI, Switzerland
| | - Klaus Richter
- Department of Chemistry and Center for Integrated Protein Science, Technische Universität München, 85748, Garching, Germany
| | - Alison E. Ringel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, United States of America
| | - Rose Rosenberg
- Physical Chemistry, University of Konstanz, 78457, Konstanz, Germany
| | - Arthur J. Rowe
- National Centre for Macromolecular Hydrodynamics, University of Nottingham, School of Biosciences, Sutton Bonington, LE12 5RD, United Kingdom
| | - Arne C. Rufer
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-LaRoche Ltd., Basel, 4070, Switzerland
| | - David J. Scott
- Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire, OX11 0FA, United Kingdom
| | - Javier G. Seravalli
- Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States of America
| | - Alexandra S. Solovyova
- Proteome and Protein Analysis, University of Newcastle, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Renjie Song
- Wadsworth Center, New York State Department of Health, Albany, New York, 12208, United States of America
| | - David Staunton
- Molecular Biophysics Suite, Department of Biochemistry, Oxford, Oxon, OX1 3QU, United Kingdom
| | - Caitlin Stoddard
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, 94158, United States of America
- Tetrad Graduate Program, University of California San Francisco, San Francisco, California, 94158, United States of America
| | - Katherine Stott
- Biochemistry Department, University of Cambridge, Cambridge, CB2 1GA, United Kingdom
| | | | - Werner W. Streicher
- Protein Function and Interactions, Novo Nordisk Foundation Center for Protein Research, Copenhagen, 2200, Denmark
| | - John P. Sumida
- Analytical Biopharmacy Core, University of Washington, Seattle, Washington, 98195, United States of America
| | - Sarah G. Swygert
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, 01605, United States of America
| | - Roman H. Szczepanowski
- Core Facility, International Institute of Molecular and Cell Biology, Warsaw, 02–109, Poland
| | - Ingrid Tessmer
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97080, Würzburg, Germany
| | - Ronald T. Toth
- Macromolecule and Vaccine Stabilization Center, University of Kansas, Lawrence, Kansas, 66047, United States of America
| | - Ashutosh Tripathy
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, United States of America
| | - Susumu Uchiyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, 565–0871, Japan
| | - Stephan F. W. Uebel
- Biochemistry Core Facility, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Satoru Unzai
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, 230–0045, Japan
| | - Anna Vitlin Gruber
- Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Peter H. von Hippel
- Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, 97403, United States of America
| | - Christine Wandrey
- Laboratoire de Médecine Régénérative et de Pharmacobiologie, Ecole Polytechnique Fédérale de Lausanne, Lausanne, CH-1015, Switzerland
| | - Szu-Huan Wang
- Biophysics Core Facility, Scientific Instrument Center, Academia Sinica, Taipei, 115, Taiwan
| | - Steven E. Weitzel
- Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, 97403, United States of America
| | - Beata Wielgus-Kutrowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, 02–089, Poland
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, United States of America
| | - Martin Wolff
- ICS-6, Structural Biochemistry, Research Center Juelich, 52428, Juelich, Germany
| | - Edward Wright
- Biochemistry, Cell and Molecular Biology Department, University of Tennessee, Knoxville, Tennessee, 37996–0840, United States of America
| | - Yu-Sung Wu
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, Delaware, 19716, United States of America
| | - Jacinta M. Wubben
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
- * E-mail:
| |
Collapse
|
29
|
Olubiyi O, Frenzel D, Bartnik D, Gluck J, Brener O, Nagel-Steger L, Funke S, Willbold D, Strodel B. Amyloid Aggregation Inhibitory Mechanism of Arginine-rich D-peptides. Curr Med Chem 2014; 21:1448-57. [DOI: 10.2174/0929867321666131129122247] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 11/11/2013] [Accepted: 11/20/2013] [Indexed: 11/22/2022]
|
30
|
Kötter S, Unger A, Hamdani N, Lang P, Vorgerd M, Nagel-Steger L, Linke WA. Human myocytes are protected from titin aggregation-induced stiffening by small heat shock proteins. J Gen Physiol 2014. [DOI: 10.1085/jgp.1432oia1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
31
|
Thakur HC, Singh M, Nagel-Steger L, Prumbaum D, Fansa EK, Gremer L, Ezzahoini H, Abts A, Schmitt L, Raunser S, Ahmadian MR, Piekorz RP. Role of centrosomal adaptor proteins of the TACC family in the regulation of microtubule dynamics during mitotic cell division. Biol Chem 2014; 394:1411-23. [PMID: 23787465 DOI: 10.1515/hsz-2013-0184] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 06/18/2013] [Indexed: 02/04/2023]
Abstract
During the mitotic division cycle, cells pass through an extensive microtubule rearrangement process where microtubules forming the mitotic spindle apparatus are dynamically instable. Several centrosomal- and microtubule-associated proteins are involved in the regulation of microtubule dynamics and stability during mitosis. Here, we focus on members of the transforming acidic coiled coil (TACC) family of centrosomal adaptor proteins, in particular TACC3, in which their subcellular localization at the mitotic spindle apparatus is controlled by Aurora-A kinase-mediated phosphorylation. At the effector level, several TACC-binding partners have been identified and characterized in greater detail, in particular, the microtubule polymerase XMAP215/ch-TOG/CKAP5 and clathrin heavy chain (CHC). We summarize the recent progress in the molecular understanding of these TACC3 protein complexes, which are crucial for proper mitotic spindle assembly and dynamics to prevent faulty cell division and aneuploidy. In this regard, the (patho)biological role of TACC3 in development and cancer will be discussed.
Collapse
|
32
|
Amin E, Dubey BN, Zhang SC, Gremer L, Dvorsky R, Moll JM, Taha MS, Nagel-Steger L, Piekorz RP, Somlyo AV, Ahmadian MR. Rho-kinase: regulation, (dys)function, and inhibition. Biol Chem 2014; 394:1399-410. [PMID: 23950574 DOI: 10.1515/hsz-2013-0181] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 08/09/2013] [Indexed: 01/08/2023]
Abstract
In a variety of normal and pathological cell types, Rho-kinases I and II (ROCKI/II) play a pivotal role in the organization of the nonmuscle and smooth muscle cytoskeleton and adhesion plaques as well as in the regulation of transcription factors. Thus, ROCKI/II activity regulates cellular contraction, motility, morphology, polarity, cell division, and gene expression. Emerging evidence suggests that dysregulation of the Rho-ROCK pathways at different stages is linked to cardiovascular, metabolic, and neurodegenerative diseases as well as cancer. This review focuses on the current status of understanding the multiple functions of Rho-ROCK signaling pathways and various modes of regulation of Rho-ROCK activity, thereby orchestrating a concerted functional response.
Collapse
|
33
|
Kötter S, Unger A, Hamdani N, Lang P, Vorgerd M, Nagel-Steger L, Linke WA. Human myocytes are protected from titin aggregation-induced stiffening by small heat shock proteins. ACTA ACUST UNITED AC 2014; 204:187-202. [PMID: 24421331 PMCID: PMC3897184 DOI: 10.1083/jcb.201306077] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [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: 12/26/2022]
Abstract
Small heat shock proteins translocate to unfolded titin Ig domains under stress conditions to prevent titin aggregation and myocyte stiffening. In myocytes, small heat shock proteins (sHSPs) are preferentially translocated under stress to the sarcomeres. The functional implications of this translocation are poorly understood. We show here that HSP27 and αB-crystallin associated with immunoglobulin-like (Ig) domain-containing regions, but not the disordered PEVK domain (titin region rich in proline, glutamate, valine, and lysine), of the titin springs. In sarcomeres, sHSP binding to titin was actin filament independent and promoted by factors that increased titin Ig unfolding, including sarcomere stretch and the expression of stiff titin isoforms. Titin spring elements behaved predominantly as monomers in vitro. However, unfolded Ig segments aggregated, preferentially under acidic conditions, and αB-crystallin prevented this aggregation. Disordered regions did not aggregate. Promoting titin Ig unfolding in cardiomyocytes caused elevated stiffness under acidic stress, but HSP27 or αB-crystallin suppressed this stiffening. In diseased human muscle and heart, both sHSPs associated with the titin springs, in contrast to the cytosolic/Z-disk localization seen in healthy muscle/heart. We conclude that aggregation of unfolded titin Ig domains stiffens myocytes and that sHSPs translocate to these domains to prevent this aggregation.
Collapse
Affiliation(s)
- Sebastian Kötter
- Department of Cardiovascular Physiology and 2 Neurological University Clinic Bergmannsheil, Ruhr University Bochum, 44780 Bochum, Germany
| | | | | | | | | | | | | |
Collapse
|
34
|
Kötter S, Unger A, Hamdani N, Nagel-Steger L, Linke WA. Small Heat Shock Proteins Prevent Titin Aggregation-Induced Stiffening in Human Myocytes. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
|
35
|
Thakur HC, Singh M, Nagel-Steger L, Kremer J, Prumbaum D, Fansa EK, Ezzahoini H, Nouri K, Gremer L, Abts A, Schmitt L, Raunser S, Ahmadian MR, Piekorz RP. The centrosomal adaptor TACC3 and the microtubule polymerase chTOG interact via defined C-terminal subdomains in an Aurora-A kinase-independent manner. J Biol Chem 2013; 289:74-88. [PMID: 24273164 DOI: 10.1074/jbc.m113.532333] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The cancer-associated, centrosomal adaptor protein TACC3 (transforming acidic coiled-coil 3) and its direct effector, the microtubule polymerase chTOG (colonic and hepatic tumor overexpressed gene), play a crucial function in centrosome-driven mitotic spindle assembly. It is unclear how TACC3 interacts with chTOG. Here, we show that the C-terminal TACC domain of TACC3 and a C-terminal fragment adjacent to the TOG domains of chTOG mediate the interaction between these two proteins. Interestingly, the TACC domain consists of two functionally distinct subdomains, CC1 (amino acids (aa) 414-530) and CC2 (aa 530-630). Whereas CC1 is responsible for the interaction with chTOG, CC2 performs an intradomain interaction with the central repeat region of TACC3, thereby masking the TACC domain before effector binding. Contrary to previous findings, our data clearly demonstrate that Aurora-A kinase does not regulate TACC3-chTOG complex formation, indicating that Aurora-A solely functions as a recruitment factor for the TACC3-chTOG complex to centrosomes and proximal mitotic spindles. We identified with CC1 and CC2, two functionally diverse modules within the TACC domain of TACC3 that modulate and mediate, respectively, TACC3 interaction with chTOG required for spindle assembly and microtubule dynamics during mitotic cell division.
Collapse
Affiliation(s)
- Harish C Thakur
- From the Institut für Biochemie und Molekularbiologie II, Medizinische Fakultät der Heinrich-Heine-Universität, D-40225 Düsseldorf, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Grüning CSR, Klinker S, Wolff M, Schneider M, Toksöz K, Klein AN, Nagel-Steger L, Willbold D, Hoyer W. The off-rate of monomers dissociating from amyloid-β protofibrils. J Biol Chem 2013; 288:37104-11. [PMID: 24247242 DOI: 10.1074/jbc.m113.513432] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The interconversion of monomers, oligomers, and amyloid fibrils of the amyloid-β peptide (Aβ) has been implicated in the pathogenesis of Alzheimer disease. The determination of the kinetics of the individual association and dissociation reactions is hampered by the fact that forward and reverse reactions to/from different aggregation states occur simultaneously. Here, we report the kinetics of dissociation of Aβ monomers from protofibrils, prefibrillar high molecular weight oligomers previously shown to possess pronounced neurotoxicity. An engineered binding protein sequestering specifically monomeric Aβ was employed to follow protofibril dissociation by tryptophan fluorescence, precluding confounding effects of reverse or competing reactions. Aβ protofibril dissociation into monomers follows exponential decay kinetics with a time constant of ∼2 h at 25 °C and an activation energy of 80 kJ/mol, values typical for high affinity biomolecular interactions. This study demonstrates the high kinetic stability of Aβ protofibrils toward dissociation into monomers and supports the delineation of the Aβ folding and assembly energy landscape.
Collapse
Affiliation(s)
- Clara S R Grüning
- From the Institute of Physical Biology, Heinrich-Heine-Universität, 40204 Düsseldorf and
| | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Luers L, Bannach O, Stöhr J, Wördehoff MM, Wolff M, Nagel-Steger L, Riesner D, Willbold D, Birkmann E. Seeded fibrillation as molecular basis of the species barrier in human prion diseases. PLoS One 2013; 8:e72623. [PMID: 23977331 PMCID: PMC3748051 DOI: 10.1371/journal.pone.0072623] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [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: 03/26/2013] [Accepted: 07/11/2013] [Indexed: 12/04/2022] Open
Abstract
Prion diseases are transmissible spongiform encephalopathies in humans and animals, including scrapie in sheep, bovine spongiform encephalopathy (BSE) in cattle, chronic wasting disease (CWD) in deer, and Creutzfeldt-Jakob disease (CJD) in humans. The hallmark of prion diseases is the conversion of the host-encoded prion protein (PrPC) to its pathological isoform PrPSc, which is accompanied by PrP fibrillation. Transmission is not restricted within one species, but can also occur between species. In some cases a species barrier can be observed that results in limited or unsuccessful transmission. The mechanism behind interspecies transmissibility or species barriers is not completely understood. To analyse this process at a molecular level, we previously established an in vitro fibrillation assay, in which recombinant PrP (recPrP) as substrate can be specifically seeded by PrPSc as seed. Seeding with purified components, with no additional cellular components, is a direct consequence of the “prion-protein-only” hypothesis. We therefore hypothesise, that the species barrier is based on the interaction of PrPC and PrPSc. Whereas in our earlier studies, the interspecies transmission in animal systems was analysed, the focus of this study lies on the transmission from animals to humans. We therefore combined seeds from species cattle, sheep and deer (BSE, scrapie, CWD) with human recPrP. Homologous seeding served as a control. Our results are consistent with epidemiology, other in vitro aggregation studies, and bioassays investigating the transmission between humans, cattle, sheep, and deer. In contrast to CJD and BSE seeds, which show a seeding activity we can demonstrate a species barrier for seeds from scrapie and CWD in vitro. We could show that the seeding activity and therewith the molecular interaction of PrP as substrate and PrPSc as seed is sufficient to explain the phenomenon of species barriers. Therefore our data supports the hypothesis that CWD is not transmissible to humans.
Collapse
Affiliation(s)
- Lars Luers
- Institute of Physical Biology, Heinrich-Heine University, Düsseldorf, Germany
| | - Oliver Bannach
- Institute of Physical Biology, Heinrich-Heine University, Düsseldorf, Germany
| | - Jan Stöhr
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, California, United States of America
| | | | - Martin Wolff
- Institute of Physical Biology, Heinrich-Heine University, Düsseldorf, Germany
- Institute of Complex Systems (ICS-6), Research Centre Juelich, Juelich, Germany
| | - Luitgard Nagel-Steger
- Institute of Physical Biology, Heinrich-Heine University, Düsseldorf, Germany
- Institute of Complex Systems (ICS-6), Research Centre Juelich, Juelich, Germany
| | - Detlev Riesner
- Institute of Physical Biology, Heinrich-Heine University, Düsseldorf, Germany
| | - Dieter Willbold
- Institute of Physical Biology, Heinrich-Heine University, Düsseldorf, Germany
- Institute of Complex Systems (ICS-6), Research Centre Juelich, Juelich, Germany
| | - Eva Birkmann
- Institute of Physical Biology, Heinrich-Heine University, Düsseldorf, Germany
- Institute of Complex Systems (ICS-6), Research Centre Juelich, Juelich, Germany
- * E-mail:
| |
Collapse
|
38
|
Arslan Z, Wurm R, Brener O, Ellinger P, Nagel-Steger L, Oesterhelt F, Schmitt L, Willbold D, Wagner R, Gohlke H, Smits SHJ, Pul U. Double-strand DNA end-binding and sliding of the toroidal CRISPR-associated protein Csn2. Nucleic Acids Res 2013; 41:6347-59. [PMID: 23625968 PMCID: PMC3695520 DOI: 10.1093/nar/gkt315] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [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: 12/26/2022] Open
Abstract
The adaptive immunity of bacteria against foreign nucleic acids, mediated by CRISPR (clustered regularly interspaced short palindromic repeats), relies on the specific incorporation of short pieces of the invading foreign DNA into a special genomic locus, termed CRISPR array. The stored sequences (spacers) are subsequently used in the form of small RNAs (crRNAs) to interfere with the target nucleic acid. We explored the DNA-binding mechanism of the immunization protein Csn2 from the human pathogen Streptococcus agalactiae using different biochemical techniques, atomic force microscopic imaging and molecular dynamics simulations. The results demonstrate that the ring-shaped Csn2 tetramer binds DNA ends through its central hole and slides inward, likely by a screw motion along the helical path of the enclosed DNA. The presented data indicate an accessory function of Csn2 during integration of exogenous DNA by end-joining.
Collapse
Affiliation(s)
- Zihni Arslan
- Institut für Physikalische Biologie, Heinrich-Heine-Universität, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Funke SA, Liu H, Sehl T, Bartnik D, Brener O, Nagel-Steger L, Wiesehan K, Willbold D. Identification and characterization of an aβ oligomer precipitating peptide that may be useful to explore gene therapeutic approaches to Alzheimer disease. Rejuvenation Res 2012; 15:144-7. [PMID: 22533419 DOI: 10.1089/rej.2011.1262] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A key feature of Alzheimer disease (AD) is the pathologic self-association of the amyloid-β (Aβ) peptide, leading to the formation of diffusible toxic Aβ oligomers and extracellular amyloid plaques. Next to extracellular Aβ, intraneuronal Aβ has important pathological functions in AD. Agents that specifically interfere with the oligomerization processes either outside or inside of neurons are highly desired for the elucidation of the pathologic mechanisms of AD and might even pave the way for new AD gene therapeutic approaches. Here, we characterize the Aβ binding peptide L3 and its influence on Aβ oligomerization in vitro. Preliminary studies in cell culture demonstrate that stably expressed L3 reduces cell toxicity of externally added Aβ in neuroblastoma cells.
Collapse
|
40
|
Kroth H, Ansaloni A, Varisco Y, Jan A, Sreenivasachary N, Rezaei-Ghaleh N, Giriens V, Lohmann S, López-Deber MP, Adolfsson O, Pihlgren M, Paganetti P, Froestl W, Nagel-Steger L, Willbold D, Schrader T, Zweckstetter M, Pfeifer A, Lashuel HA, Muhs A. Discovery and structure activity relationship of small molecule inhibitors of toxic β-amyloid-42 fibril formation. J Biol Chem 2012; 287:34786-800. [PMID: 22891248 DOI: 10.1074/jbc.m112.357665] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Increasing evidence implicates Aβ peptides self-assembly and fibril formation as crucial events in the pathogenesis of Alzheimer disease. Thus, inhibiting Aβ aggregation, among others, has emerged as a potential therapeutic intervention for this disorder. Herein, we employed 3-aminopyrazole as a key fragment in our design of non-dye compounds capable of interacting with Aβ42 via a donor-acceptor-donor hydrogen bond pattern complementary to that of the β-sheet conformation of Aβ42. The initial design of the compounds was based on connecting two 3-aminopyrazole moieties via a linker to identify suitable scaffold molecules. Additional aryl substitutions on the two 3-aminopyrazole moieties were also explored to enhance π-π stacking/hydrophobic interactions with amino acids of Aβ42. The efficacy of these compounds on inhibiting Aβ fibril formation and toxicity in vitro was assessed using a combination of biophysical techniques and viability assays. Using structure activity relationship data from the in vitro assays, we identified compounds capable of preventing pathological self-assembly of Aβ42 leading to decreased cell toxicity.
Collapse
Affiliation(s)
- Heiko Kroth
- AC Immune SA, PSE Building B, Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Kötter S, Nagel-Steger L, Lang P, Linke WA. Small Heat Shock Proteins Associate under Stress Conditions with Elastic Titin Filaments and Provide Protection from Aggregation. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.1964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
|
42
|
Hochdörffer K, März-Berberich J, Nagel-Steger L, Epple M, Meyer-Zaika W, Horn AHC, Sticht H, Sinha S, Bitan G, Schrader T. Rational design of β-sheet ligands against Aβ42-induced toxicity. J Am Chem Soc 2011; 133:4348-58. [PMID: 21381732 DOI: 10.1021/ja107675n] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
A β-sheet-binding scaffold was equipped with long-range chemical groups for tertiary contacts toward specific regions of the Alzheimer's Aβ fibril. The new constructs contain a trimeric aminopyrazole carboxylic acid, elongated with a C-terminal binding site, whose influence on the aggregation behavior of the Aβ(42) peptide was studied. MD simulations after trimer docking to the anchor point (F19/F20) suggest distinct groups of complex structures each of which featured additional specific interactions with characteristic Aβ regions. Members of each group also displayed a characteristic pattern in their antiaggregational behavior toward Aβ. Specifically, remote lipophilic moieties such as a dodecyl, cyclohexyl, or LPFFD fragment can form dispersive interactions with the nonpolar cluster of amino acids between I31 and V36. They were shown to strongly reduce Thioflavine T (ThT) fluorescence and protect cells from Aβ lesions (MTT viability assays). Surprisingly, very thick fibrils and a high β-sheet content were detected in transmission electron microscopy (TEM) and CD spectroscopic experiments. On the other hand, distant single or multiple lysines which interact with the ladder of stacked E22 residues found in Aβ fibrils completely dissolve existing β-sheets (ThT, CD) and lead to unstructured, nontoxic material (TEM, MTT). Finally, the triethyleneglycol spacer between heterocyclic β-sheet ligand and appendix was found to play an active role in destabilizing the turn of the U-shaped protofilament. Fluorescence correlation spectroscopy (FCS) and sedimentation velocity analysis (SVA) provided experimental evidence for some smaller benign aggregates of very thin, delicate structure (TEM, MTT). A detailed investigation by dynamic light scattering (DLS) and other methods proved that none of the new ligands acts as a colloid. The evolving picture for the disaggregation mechanism by these new hybrid ligands implies transformation of well-ordered fibrils into less structured aggregates with a high molecular weight. In the few cases where fibrillar components remain, these display a significantly altered morphology and have lost their acute cellular toxicity.
Collapse
Affiliation(s)
- Katrin Hochdörffer
- Universität Duisburg-Essen, Fachbereich Chemie, Universitätstrasse 5, 45117 Essen, Germany
| | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Hickman DT, López-Deber MP, Ndao DM, Silva AB, Nand D, Pihlgren M, Giriens V, Madani R, St-Pierre A, Karastaneva H, Nagel-Steger L, Willbold D, Riesner D, Nicolau C, Baldus M, Pfeifer A, Muhs A. Sequence-independent control of peptide conformation in liposomal vaccines for targeting protein misfolding diseases. J Biol Chem 2011; 286:13966-76. [PMID: 21343310 DOI: 10.1074/jbc.m110.186338] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Synthetic peptide immunogens that mimic the conformation of a target epitope of pathological relevance offer the possibility to precisely control the immune response specificity. Here, we performed conformational analyses using a panel of peptides in order to investigate the key parameters controlling their conformation upon integration into liposomal bilayers. These revealed that the peptide lipidation pattern, the lipid anchor chain length, and the liposome surface charge all significantly alter peptide conformation. Peptide aggregation could also be modulated post-liposome assembly by the addition of distinct small molecule β-sheet breakers. Immunization of both mice and monkeys with a model liposomal vaccine containing β-sheet aggregated lipopeptide (Palm1-15) induced polyclonal IgG antibodies that specifically recognized β-sheet multimers over monomer or non-pathological native protein. The rational design of liposome-bound peptide immunogens with defined conformation opens up the possibility to generate vaccines against a range of protein misfolding diseases, such as Alzheimer disease.
Collapse
|
44
|
Panza G, Luers L, Stöhr J, Nagel-Steger L, Weiβ J, Riesner D, Willbold D, Birkmann E. Molecular interactions between prions as seeds and recombinant prion proteins as substrates resemble the biological interspecies barrier in vitro. PLoS One 2010; 5:e14283. [PMID: 21151607 PMCID: PMC3000319 DOI: 10.1371/journal.pone.0014283] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [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: 11/12/2009] [Accepted: 09/26/2010] [Indexed: 02/04/2023] Open
Abstract
Prion diseases like Creutzfeldt-Jakob disease in humans, Scrapie in sheep or bovine spongiform encephalopathy are fatal neurodegenerative diseases, which can be of sporadic, genetic, or infectious origin. Prion diseases are transmissible between different species, however, with a variable species barrier. The key event of prion amplification is the conversion of the cellular isoform of the prion protein (PrPC) into the pathogenic isoform (PrPSc). We developed a sodiumdodecylsulfate-based PrP conversion system that induces amyloid fibril formation from soluble α-helical structured recombinant PrP (recPrP). This approach was extended applying pre-purified PrPSc as seeds which accelerate fibrillization of recPrP. In the present study we investigated the interspecies coherence of prion disease. Therefore we used PrPSc from different species like Syrian hamster, cattle, mouse and sheep and seeded fibrillization of recPrP from the same or other species to mimic in vitro the natural species barrier. We could show that the in vitro system of seeded fibrillization is in accordance with what is known from the naturally occurring species barriers.
Collapse
Affiliation(s)
- Giannantonio Panza
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Lars Luers
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Jan Stöhr
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Luitgard Nagel-Steger
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Jürgen Weiβ
- Institut für klinische Biochemie und Pathobiochemie, Deutsches Diabetes-Zentrum, Düsseldorf, Germany
| | - Detlev Riesner
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Dieter Willbold
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
- Institut für Strukturbiologie und Biophysik 3, Forschungszentrum Jülich, Jülich, Germany
| | - Eva Birkmann
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
- Institut für Strukturbiologie und Biophysik 3, Forschungszentrum Jülich, Jülich, Germany
- * E-mail:
| |
Collapse
|
45
|
Funke SA, van Groen T, Kadish I, Bartnik D, Nagel-Steger L, Brener O, Sehl T, Batra-Safferling R, Moriscot C, Schoehn G, Horn AHC, Müller-Schiffmann A, Korth C, Sticht H, Willbold D. Oral treatment with the d-enantiomeric peptide D3 improves the pathology and behavior of Alzheimer's Disease transgenic mice. ACS Chem Neurosci 2010; 1:639-48. [PMID: 22778851 DOI: 10.1021/cn100057j] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Accepted: 07/21/2010] [Indexed: 11/28/2022] Open
Abstract
Several lines of evidence suggest that the amyloid-β-peptide (Aβ) plays a central role in the pathogenesis of Alzheimer's disease (AD). Not only Aβ fibrils but also small soluble Aβ oligomers in particular are suspected to be the major toxic species responsible for disease development and progression. The present study reports on in vitro and in vivo properties of the Aβ targeting d-enantiomeric amino acid peptide D3. We show that next to plaque load and inflammation reduction, oral application of the peptide improved the cognitive performance of AD transgenic mice. In addition, we provide in vitro data elucidating the potential mechanism underlying the observed in vivo activity of D3. These data suggest that D3 precipitates toxic Aβ species and converts them into nonamyloidogenic, nonfibrillar, and nontoxic aggregates without increasing the concentration of monomeric Aβ. Thus, D3 exerts an interesting and novel mechanism of action that abolishes toxic Aβ oligomers and thereby supports their decisive role in AD development and progression.
Collapse
Affiliation(s)
| | - Thomas van Groen
- Department of Cell Biology, University of Alabama at Birmingham, Birmingham, Alabama 35294
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Inga Kadish
- Department of Cell Biology, University of Alabama at Birmingham, Birmingham, Alabama 35294
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Dirk Bartnik
- Heinrich-Heine-Universität Düsseldorf, Institut für Physikalische Biologie and BMFZ, 40225 Düsseldorf, Germany
| | - Luitgard Nagel-Steger
- Heinrich-Heine-Universität Düsseldorf, Institut für Physikalische Biologie and BMFZ, 40225 Düsseldorf, Germany
| | - Oleksandr Brener
- Heinrich-Heine-Universität Düsseldorf, Institut für Physikalische Biologie and BMFZ, 40225 Düsseldorf, Germany
| | - Torsten Sehl
- Heinrich-Heine-Universität Düsseldorf, Institut für Physikalische Biologie and BMFZ, 40225 Düsseldorf, Germany
| | | | - Christine Moriscot
- CEA
- CNRS
- Université Joseph Fourier
- Unit for Virus Host Cell Interactions, 6, rue Jules Horowitz BP 181, F38042 Grenoble, France
| | - Guy Schoehn
- CEA
- CNRS
- Université Joseph Fourier
- Unit for Virus Host Cell Interactions, 6, rue Jules Horowitz BP 181, F38042 Grenoble, France
| | - Anselm H. C. Horn
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Institut für Biochemie, 91054 Erlangen, Germany
| | | | - Carsten Korth
- Heinrich-Heine-Universität Düsseldorf, Institut für Neuropathologie, 40225 Düsseldorf, Germany
| | - Heinrich Sticht
- Friedrich-Alexander-Universität Erlangen-Nürnberg, Institut für Biochemie, 91054 Erlangen, Germany
| | - Dieter Willbold
- Forschungszentrum Jülich, ISB-3, 52425 Jülich, Germany
- Heinrich-Heine-Universität Düsseldorf, Institut für Physikalische Biologie and BMFZ, 40225 Düsseldorf, Germany
- CEA
| |
Collapse
|
46
|
Nagel-Steger L, Demeler B, Meyer-Zaika W, Hochdörffer K, Schrader T, Willbold D. Modulation of aggregate size- and shape-distributions of the amyloid-beta peptide by a designed beta-sheet breaker. Eur Biophys J 2009; 39:415-22. [PMID: 19238376 DOI: 10.1007/s00249-009-0416-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2008] [Revised: 01/26/2009] [Accepted: 02/02/2009] [Indexed: 11/28/2022]
Abstract
A peptide with 42 amino acid residues (Abeta42) plays a key role in the pathogenesis of the Alzheimer's disease. It is highly prone to self aggregation leading to the formation of fibrils which are deposited in amyloid plaques in the brain of diseased individuals. In our study we established a method to analyze the aggregation behavior of the Abeta peptide with a combination of sedimentation velocity centrifugation and enhanced data evaluation software as implemented in the software package UltraScan. Important information which becomes accessible by this methodology is the s-value distribution and concomitantly also the shape-distribution of the Abeta peptide aggregates generated by self-association. With this method we characterized the aggregation modifying effect of a designed beta-sheet breaker molecule. This compound is built from three head-to-tail connected aminopyrazole moieties and represents a derivative of the already described Tripyrazole. By addition of this compound to a solution of the Abeta42 peptide the maximum of the s-value distribution was clearly shifted to smaller s-values as compared to solutions where only the vehicle DMSO was added. This shift to smaller s-values was stable for at least 7 days. The information about size- and shape-distributions present in aggregated Abeta42 solutions was confirmed by transmission electron microscopy and by measurement of amyloid formation by thioflavin T fluorescence.
Collapse
Affiliation(s)
- Luitgard Nagel-Steger
- Institute for Physical Biology, Geb.26.12.U1, Heinrich-Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany.
| | | | | | | | | | | |
Collapse
|
47
|
van Groen T, Wiesehan K, Funke SA, Kadish I, Nagel-Steger L, Willbold D. Reduction of Alzheimer's disease amyloid plaque load in transgenic mice by D3, A D-enantiomeric peptide identified by mirror image phage display. ChemMedChem 2009; 3:1848-52. [PMID: 19016284 DOI: 10.1002/cmdc.200800273] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Thomas van Groen
- Dept. Cell Biology, University of Alabama at Birmingham, AL 35294, USA
| | | | | | | | | | | |
Collapse
|
48
|
Demeler B, Brookes E, Nagel-Steger L. Analysis of heterogeneity in molecular weight and shape by analytical ultracentrifugation using parallel distributed computing. Methods Enzymol 2009; 454:87-113. [PMID: 19216924 DOI: 10.1016/s0076-6879(08)03804-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
A computational approach for fitting sedimentation velocity experiments from an analytical ultracentrifuge in a model-independent fashion is presented. This chapter offers a recipe for obtaining high-resolution information for both the shape and the molecular weight distributions of complex mixtures that are heterogeneous in shape and molecular weight and provides suggestions for experimental design to optimize information content. A combination of three methods is used to find the solution most parsimonious in parameters and to verify the statistical confidence intervals of the determined parameters. A supercomputer implementation with a MySQL database back end is integrated into the UltraScan analysis software. The UltraScan LIMS Web portal is used to perform the calculations through a Web interface. The performance and limitations of the method when employed for the analysis of complex mixtures are demonstrated using both simulated data and experimental data characterizing amyloid aggregation.
Collapse
Affiliation(s)
- Borries Demeler
- Department of Biochemistry, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | | | | |
Collapse
|
49
|
Wiesehan K, Stohr J, Nagel-Steger L, van Groen T, Riesner D, Willbold D. Inhibition of cytotoxicity and amyloid fibril formation by a D-amino acid peptide that specifically binds to Alzheimer's disease amyloid peptide. Protein Eng Des Sel 2008; 21:241-6. [DOI: 10.1093/protein/gzm054] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
50
|
Muhs A, Hickman DT, Pihlgren M, Chuard N, Giriens V, Meerschman C, van der Auwera I, van Leuven F, Sugawara M, Weingertner MC, Bechinger B, Greferath R, Kolonko N, Nagel-Steger L, Riesner D, Brady RO, Pfeifer A, Nicolau C. Liposomal vaccines with conformation-specific amyloid peptide antigens define immune response and efficacy in APP transgenic mice. Proc Natl Acad Sci U S A 2007; 104:9810-5. [PMID: 17517595 PMCID: PMC1887581 DOI: 10.1073/pnas.0703137104] [Citation(s) in RCA: 128] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We investigated the therapeutic effects of two different versions of Abeta(1-15 (16)) liposome-based vaccines. Inoculation of APP-V717IxPS-1 (APPxPS-1) double-transgenic mice with tetra-palmitoylated amyloid 1-15 peptide (palmAbeta(1-15)), or with amyloid 1-16 peptide (PEG-Abeta(1-16)) linked to a polyethyleneglycol spacer at each end, and embedded within a liposome membrane, elicited fast immune responses with identical binding epitopes. PalmAbeta(1-15) liposomal vaccine elicited an immune response that restored the memory defect of the mice, whereas that of PEG-Abeta(1-16) had no such effect. Immunoglobulins that were generated were predominantly of the IgG class with palmAbeta(1-15), whereas those elicited by PEG-Abeta(1-16) were primarily of the IgM class. The IgG subclasses of the antibodies generated by both vaccines were mostly IgG2b indicating noninflammatory Th2 isotype. CD and NMR revealed predominantly beta-sheet conformation of palmAbeta(1-15) and random coil of PEG-Abeta(1-16). We conclude that the association with liposomes induced a variation of the immunogenic structures and thereby different immunogenicities. This finding supports the hypothesis that Alzheimer's disease is a "conformational" disease, implying that antibodies against amyloid sequences in the beta-sheet conformation are preferred as potential therapeutic agents.
Collapse
Affiliation(s)
- Andreas Muhs
- *AC Immune, PSE-B, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - David T. Hickman
- *AC Immune, PSE-B, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Maria Pihlgren
- *AC Immune, PSE-B, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Nathalie Chuard
- *AC Immune, PSE-B, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Valérie Giriens
- *AC Immune, PSE-B, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Carine Meerschman
- *AC Immune, PSE-B, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | | | - Fred van Leuven
- Experimental Genetics Group, KULeuven, B-3000 Leuven, Belgium
| | - Masae Sugawara
- Institut de Science et d'Ingénierie Supramoléculaires, Université Louis Pasteur, F-67083 Strasbourg, France
| | | | - Burkhard Bechinger
- Institut de Science et d'Ingénierie Supramoléculaires, Université Louis Pasteur, F-67083 Strasbourg, France
| | - Ruth Greferath
- *AC Immune, PSE-B, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Nadine Kolonko
- *AC Immune, PSE-B, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Luitgard Nagel-Steger
- Institut für Biophysikalische Chemie, Heinrich-Heine Universität, 40225 Düsseldorf, Germany
| | - Detlev Riesner
- Institut für Biophysikalische Chemie, Heinrich-Heine Universität, 40225 Düsseldorf, Germany
| | - Roscoe O. Brady
- Developmental and Metabolic Neurology Branch, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20892; and
- **To whom correspondence may be addressed. E-mail: or
| | - Andrea Pfeifer
- *AC Immune, PSE-B, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Claude Nicolau
- *AC Immune, PSE-B, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA 02111
- **To whom correspondence may be addressed. E-mail: or
| |
Collapse
|