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Thacker D, Willas A, Dear AJ, Linse S. Role of Hydrophobicity at the N-Terminal Region of Aβ42 in Secondary Nucleation. ACS Chem Neurosci 2022; 13:3477-3487. [PMID: 36411082 PMCID: PMC9732875 DOI: 10.1021/acschemneuro.2c00504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/19/2022] [Indexed: 11/23/2022] Open
Abstract
The self-assembly of the amyloid β 42 (Aβ42) peptide is linked to Alzheimer's disease, and oligomeric intermediates are linked to neuronal cell death during the pathology of the disease. These oligomers are produced prolifically during secondary nucleation, by which the aggregation of monomers is catalyzed on fibril surfaces. Significant progress has been made in understanding the aggregation mechanism of Aβ42; still, a detailed molecular-level understanding of secondary nucleation is lacking. Here, we explore the role of four hydrophobic residues on the unstructured N-terminal region of Aβ42 in secondary nucleation. We create eight mutants with single substitutions at one of the four positions─Ala2, Phe4, Tyr10, and Val12─to decrease the hydrophobicity at respective positions (A2T, A2S, F4A, F4S, Y10A, Y10S, V12A, and V12S) and one mutant (Y10F) to remove the polar nature of Tyr10. Kinetic analyses of aggregation data reveal that the hydrophobicity at the N-terminal region of Aβ42, especially at positions 10 and 12, affects the rate of fibril mass generated via secondary nucleation. Cryo-electron micrographs reveal that most of the mutants with lower hydrophobicity form fibrils that are markedly longer than WT Aβ42, in line with the reduced secondary nucleation rates for these peptides. The dominance of secondary nucleation, however, is still retained in the aggregation mechanism of these mutants because the rate of primary nucleation is even more reduced. This highlights that secondary nucleation is a general phenomenon that is not dependent on any one particular feature of the peptide and is rather robust to sequence perturbations.
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Affiliation(s)
- Dev Thacker
- Department
of Biochemistry and Structural Biology, Lund University, Lund22362, Sweden
| | - Amanda Willas
- Department
of Biochemistry and Structural Biology, Lund University, Lund22362, Sweden
| | - Alexander J. Dear
- Department
of Biochemistry and Structural Biology, Lund University, Lund22362, Sweden
- Centre
for Misfolding Diseases, Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, U.K.
| | - Sara Linse
- Department
of Biochemistry and Structural Biology, Lund University, Lund22362, Sweden
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2
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Kopp J, Bayer B, Slouka C, Striedner G, Dürkop M, Spadiut O. Fundamental insights in early-stage inclusion body formation. Microb Biotechnol 2022; 16:893-900. [PMID: 35830603 PMCID: PMC10128139 DOI: 10.1111/1751-7915.14117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 11/28/2022] Open
Abstract
Early-stage inclusion body formation is still mysterious. Literature is ambiguous about the existence of rod-shaped protein aggregates, a potential sponge-like inclusion body scaffold as well as the number of inclusion bodies per Escherichia coli cell. In this study, we verified the existence of rod-shaped inclusion bodies, confirmed their porous morphology, the presence of multiple protein aggregates per cell and modelled inclusion body formation as function of the number of generations.
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Affiliation(s)
- Julian Kopp
- Research Division Integrated Bioprocess Development, Institute of Chemical, Environmental and Bioscience, Vienna, Austria
| | - Benjamin Bayer
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria.,Novasign GmbH, Vienna, Austria
| | - Christoph Slouka
- Research Division Integrated Bioprocess Development, Institute of Chemical, Environmental and Bioscience, Vienna, Austria
| | - Gerald Striedner
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria.,Novasign GmbH, Vienna, Austria
| | - Mark Dürkop
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria.,Novasign GmbH, Vienna, Austria
| | - Oliver Spadiut
- Research Division Integrated Bioprocess Development, Institute of Chemical, Environmental and Bioscience, Vienna, Austria
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Martínez-Miguel M, Tatkiewicz W, Köber M, Ventosa N, Veciana J, Guasch J, Ratera I. Methods for the Characterization of Protein Aggregates. Methods Mol Biol 2022; 2406:479-497. [PMID: 35089576 DOI: 10.1007/978-1-0716-1859-2_29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The physicochemical characterization of protein aggregates yields an important contribution to further our understanding on many diseases for which the formation of protein aggregates is one of the pathological hallmarks. On the other hand, bacterial inclusion bodies (IBs) have recently been shown to be highly pure proteinaceous aggregates of a few hundred nanometers, produced by recombinant bacteria supporting the biological activities of the embedded polypeptides. Despite the wide spectrum of uses of IBs as functional and biocompatible materials upon convenient engineering, very few is known about their physicochemical properties.In this chapter we present methods for the characterization of protein aggregates as particulate materials relevant to their physicochemical and nanoscale properties.Specifically, we describe the use of dynamic light scattering (DLS) for sizing, nanoparticle tracking analysis for sizing and counting, and zeta potential measurements for the determination of colloidal stability. To study the morphology of protein aggregates we present the use of atomic force microscopy (AFM) and scanning electron microscopy (SEM). Cryo-transmission electron microscopy (cryo-TEM) will be used for the determination of the internal structuration. Moreover, wettability and nanomechanical characterization can be performed using contact angle (CA) and force spectroscopic AFM (FS-AFM) measurements of the proteinaceous nanoparticles, respectively. Finally, the 4'4-dithiodipyridine (DTDP) method is presented as a way of relatively quantifying accessible sulfhydryl groups in the structure of the nanoparticle .The physical principles of the methods are briefly described and examples are given to help clarify capabilities of each technique.
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Affiliation(s)
- Marc Martínez-Miguel
- Institut de Ciència de Materials de Barcelona, ICMAB-CSIC and CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Campus UAB, Bellaterra, Spain
| | - Witold Tatkiewicz
- Institut de Ciència de Materials de Barcelona, ICMAB-CSIC and CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Campus UAB, Bellaterra, Spain
| | - Mariana Köber
- Institut de Ciència de Materials de Barcelona, ICMAB-CSIC and CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Campus UAB, Bellaterra, Spain
| | - Nora Ventosa
- Institut de Ciència de Materials de Barcelona, ICMAB-CSIC and CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Campus UAB, Bellaterra, Spain
| | - Jaume Veciana
- Institut de Ciència de Materials de Barcelona, ICMAB-CSIC and CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Campus UAB, Bellaterra, Spain
| | - Judith Guasch
- Institut de Ciència de Materials de Barcelona, ICMAB-CSIC and CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Campus UAB, Bellaterra, Spain
- Dynamic Biomimetics for Cancer Immunotherapy, Max Planck Partner Group, ICMAB-CSIC, Campus UAB, Bellaterra, Spain
| | - Imma Ratera
- Institut de Ciència de Materials de Barcelona, ICMAB-CSIC and CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Campus UAB, Bellaterra, Spain.
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4
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Kaldmäe M, Leppert A, Chen G, Sarr M, Sahin C, Nordling K, Kronqvist N, Gonzalvo-Ulla M, Fritz N, Abelein A, Laίn S, Biverstål H, Jörnvall H, Lane DP, Rising A, Johansson J, Landreh M. High intracellular stability of the spidroin N-terminal domain in spite of abundant amyloidogenic segments revealed by in-cell hydrogen/deuterium exchange mass spectrometry. FEBS J 2019; 287:2823-2833. [PMID: 31815338 PMCID: PMC7383493 DOI: 10.1111/febs.15169] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 11/01/2019] [Accepted: 12/05/2019] [Indexed: 12/22/2022]
Abstract
Proteins require an optimal balance of conformational flexibility and stability in their native environment to ensure their biological functions. A striking example is spidroins, spider silk proteins, which are stored at extremely high concentrations in soluble form, yet undergo amyloid-like aggregation during spinning. Here, we elucidate the stability of the highly soluble N-terminal domain (NT) of major ampullate spidroin 1 in the Escherichia coli cytosol as well as in inclusion bodies containing fibrillar aggregates. Surprisingly, we find that NT, despite being largely composed of amyloidogenic sequences, showed no signs of concentration-dependent aggregation. Using a novel intracellular hydrogen/deuterium exchange mass spectrometry (HDX-MS) approach, we reveal that NT adopts a tight fold in the E. coli cytosol and in this manner conceals its aggregation-prone regions by maintaining a tight fold under crowded conditions. Fusion of NT to the unstructured amyloid-forming Aβ40 peptide, on the other hand, results in the formation of fibrillar aggregates. However, HDX-MS indicates that the NT domain is only partially incorporated into these aggregates in vivo. We conclude that NT is able to control its aggregation to remain functional under the extreme conditions in the spider silk gland.
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Affiliation(s)
- Margit Kaldmäe
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Biomedicum, Solna, Sweden
| | - Axel Leppert
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Huddinge, Sweden
| | - Gefei Chen
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Huddinge, Sweden
| | - Medoune Sarr
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Huddinge, Sweden
| | - Cagla Sahin
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Biomedicum, Solna, Sweden
| | - Kerstin Nordling
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Huddinge, Sweden
| | - Nina Kronqvist
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Huddinge, Sweden
| | - Marta Gonzalvo-Ulla
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Biomedicum, Solna, Sweden.,Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Nicolas Fritz
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Biomedicum, Solna, Sweden
| | - Axel Abelein
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Huddinge, Sweden
| | - Sonia Laίn
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Biomedicum, Solna, Sweden
| | - Henrik Biverstål
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Huddinge, Sweden.,Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Hans Jörnvall
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Biomedicum, Solna, Sweden
| | - David P Lane
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Biomedicum, Solna, Sweden
| | - Anna Rising
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Huddinge, Sweden.,Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jan Johansson
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Huddinge, Sweden
| | - Michael Landreh
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Biomedicum, Solna, Sweden
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