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Cascella R, Banchelli M, Abolghasem Ghadami S, Ami D, Gagliani MC, Bigi A, Staderini T, Tampellini D, Cortese K, Cecchi C, Natalello A, Adibi H, Matteini P, Chiti F. An in situ and in vitro investigation of cytoplasmic TDP-43 inclusions reveals the absence of a clear amyloid signature. Ann Med 2023; 55:72-88. [PMID: 36495262 PMCID: PMC9746631 DOI: 10.1080/07853890.2022.2148734] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Introduction: Several neurodegenerative conditions are associated with a common histopathology within neurons of the central nervous system, consisting of the deposition of cytoplasmic inclusions of TAR DNA-binding protein 43 (TDP-43). Such inclusions have variably been described as morphologically and molecularly ordered aggregates having amyloid properties, as filaments without the cross-β-structure and dye binding specific for amyloid, or as amorphous aggregates with no defined structure and fibrillar morphology.Aims and Methods: Here we have expressed human full-length TDP-43 in neuroblastoma x spinal cord 34 (NSC-34) cells to investigate the morphological, structural, and tinctorial properties of TDP-43 inclusions in situ. We have used last-generation amyloid diagnostic probes able to cross the cell membrane and detect amyloid in the cytoplasm and have adopted Raman and Fourier transform infrared microspectroscopies to study in situ the secondary structure of the TDP-43 protein in the inclusions. We have then used transmission electron microscopy to study the morphology of the TDP-43 inclusions.Results: The results show the absence of amyloid dye binding, the lack of an enrichment of cross-β structure in the inclusions, and of a fibrillar texture in the round inclusions. The aggregates formed in vitro from the purified protein under conditions in which it is initially native also lack all these characteristics, ruling out a clear amyloid-like signature.Conclusions: These findings indicate a low propensity of TDP-43 to form amyloid fibrils and even non-amyloid filaments, under conditions in which the protein is initially native and undergoes its typical nucleus-to-cell mislocalization. It cannot be excluded that filaments emerge on the long time scale from such inclusions, but the high propensity of the protein to form initially other types of inclusions appear to be an essential characteristic of TDP-43 proteinopathies.KEY MESSAGESCytoplasmic inclusions of TDP-43 formed in NSC-34 cells do not stain with amyloid-diagnostic dyes, are not enriched with cross-β structure, and do not show a fibrillar morphology.TDP-43 assemblies formed in vitro from pure TDP-43 do not have any hallmarks of amyloid.
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Affiliation(s)
- Roberta Cascella
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Martina Banchelli
- Institute of Applied Physics "Nello Carrara", National Research Council, Sesto Fiorentino, Italy
| | | | - Diletta Ami
- Department of Biotechnologies and Biosciences, University of Milano-Bicocca, Milan, Italy.,Milan Center of Neuroscience (NeuroMI), Milan, Italy
| | - Maria Cristina Gagliani
- Cellular Electron Microscopy Laboratory, Department of Experimental Medicine, University of Genova, Genoa, Italy
| | - Alessandra Bigi
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Tommaso Staderini
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Davide Tampellini
- U 1195 INSERM-Université Paris-Saclay, Paris, France.,Institut Professeur Baulieu, Paris, France
| | - Katia Cortese
- Cellular Electron Microscopy Laboratory, Department of Experimental Medicine, University of Genova, Genoa, Italy
| | - Cristina Cecchi
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Antonino Natalello
- Department of Biotechnologies and Biosciences, University of Milano-Bicocca, Milan, Italy.,Milan Center of Neuroscience (NeuroMI), Milan, Italy
| | - Hadi Adibi
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Paolo Matteini
- Institute of Applied Physics "Nello Carrara", National Research Council, Sesto Fiorentino, Italy
| | - Fabrizio Chiti
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
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2
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Malik A, Khan JM, Alhomida AS, Ola MS, Alokail MS, Khan MS, Alenad AM, Altwaijry N, Alafaleq NO, Odeibat H. Agitation does not induce fibrillation in reduced hen egg-white lysozyme at physiological temperature and pH. J Mol Recognit 2023; 36:e3009. [PMID: 36841950 DOI: 10.1002/jmr.3009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 02/27/2023]
Abstract
Several proteins and peptides tend to form an amyloid fibril, causing a range of unrelated diseases, from neurodegenerative to certain types of cancer. In the native state, these proteins are folded and soluble. However, these proteins acquired β-sheet amyloid fibril due to unfolding and aggregation. The conversion mechanism from well-folded soluble into amorphous or amyloid fibril is not well understood yet. Here, we induced unfolding and aggregation of hen egg-white lysozyme (HEWL) by reducing agent dithiothreitol and applied mechanical sheering force by constant shaking (1000 rpm) on the thermostat for 7 days. Our turbidity results showed that reduced HEWL rapidly formed aggregates, and a plateau was attained in nearly 5 h of incubation in both shaking and non-shaking conditions. The turbidity was lower in the shaking condition than in the non-shaking condition. The thioflavin T binding and transmission electron micrographs showed that reduced HEWL formed amorphous aggregates in both conditions. Far-UV circular dichroism results showed that reduced HEWL lost nearly all alpha-helical structure, and β-sheet secondary structure was not formed in both conditions. All the spectroscopic and microscopic results showed that reduced HEWL formed amorphous aggregates under both conditions.
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Affiliation(s)
- Ajamaluddin Malik
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Javed Masood Khan
- Department of Food Science and Nutrition, Faculty of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah S Alhomida
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Shamsul Ola
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Majed S Alokail
- Protein Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohd Shahnawaz Khan
- Protein Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Amal M Alenad
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Nojood Altwaijry
- Protein Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Nouf Omar Alafaleq
- Protein Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Hamza Odeibat
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
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3
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Chaaban H, Vallooran JJ, van de Weert M, Foderà V. Ion-Mediated Morphological Diversity in Protein Amyloid Systems. J Phys Chem Lett 2022; 13:3586-3593. [PMID: 35426676 DOI: 10.1021/acs.jpclett.2c00182] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Salt ions are considered among the major determinants ruling protein folding, stability, and self-assembly in the context of amyloid-related diseases, protein drug development, and functional biomaterials. Here, we report that Hofmeister ions not only determine the rate constants of the aggregation reaction for human insulin and hen egg white lysozyme but also control the generation of a plethora of amyloid-like morphologies ranging from the nanoscale to the microscale. We anticipate that the latter is a result of a balance between colloidal and conformational stability combined with an ion-specific effect and highlight the importance of salt ions in controlling the biological functions of protein aggregates.
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Affiliation(s)
- Hussein Chaaban
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Center for Biopharmaceuticals and Biobarriers in Drug Delivery, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Nano-Science Center, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Jijo J Vallooran
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Center for Biopharmaceuticals and Biobarriers in Drug Delivery, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Marco van de Weert
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Center for Biopharmaceuticals and Biobarriers in Drug Delivery, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Nano-Science Center, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Vito Foderà
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Center for Biopharmaceuticals and Biobarriers in Drug Delivery, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Nano-Science Center, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
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4
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Nirwal S, Bharathi V, Patel BK. Amyloid-like aggregation of bovine serum albumin at physiological temperature induced by cross-seeding effect of HEWL amyloid aggregates. Biophys Chem 2021; 278:106678. [PMID: 34492451 DOI: 10.1016/j.bpc.2021.106678] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 08/28/2021] [Accepted: 08/29/2021] [Indexed: 01/16/2023]
Abstract
BSA can form amyloid-like aggregates in vitro at 65 °C. Heterologous amyloid can proposedly cross-seed other protein's aggregation, however, general mechanisms and driving conditions remain to be vividly elucidated. Here, we examined if pre-formed HEWL amyloid can cross-seed the aggregation of BSA at physiological temperature, 37 °C, and whether the efficacy depends on the BSA conformation. We find that at pH 3.0, 37 °C where BSA manifests exposure of abundant hydrophobic patches, HEWL amyloid efficiently drives BSA into ThT-positive, sarkosyl-resistant, β-sheet rich amyloid-like aggregates exhibiting fibrils in TEM. On the contrary, HEWL amyloid fails to cross-seed the BSA aggregation at pH 7.0, 37 °C where BSA has largely internalized hydrophobic patches. Strikingly, human lysozyme amyloid could also cross-seed human serum albumin aggregation at pH 3.0, 37 °C. Thus, heterologous amyloid cross-seeding can help overcome the energy-barrier for aggregation of other proteins that, for any reason, may have perturbed and promiscuous structural conformation at physiological temperatures.
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Affiliation(s)
- Sadhana Nirwal
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Vidhya Bharathi
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Basant K Patel
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India.
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5
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Sirangelo I, Iannuzzi C. Understanding the Role of Protein Glycation in the Amyloid Aggregation Process. Int J Mol Sci 2021; 22:ijms22126609. [PMID: 34205510 PMCID: PMC8235188 DOI: 10.3390/ijms22126609] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 02/06/2023] Open
Abstract
Protein function and flexibility is directly related to the native distribution of its structural elements and any alteration in protein architecture leads to several abnormalities and accumulation of misfolded proteins. This phenomenon is associated with a range of increasingly common human disorders, including Alzheimer and Parkinson diseases, type II diabetes, and a number of systemic amyloidosis characterized by the accumulation of amyloid aggregates both in the extracellular space of tissues and as intracellular deposits. Post-translational modifications are known to have an active role in the in vivo amyloid aggregation as able to affect protein structure and dynamics. Among them, a key role seems to be played by non-enzymatic glycation, the most unwanted irreversible modification of the protein structure, which strongly affects long-living proteins throughout the body. This study provided an overview of the molecular effects induced by glycation on the amyloid aggregation process of several protein models associated with misfolding diseases. In particular, we analyzed the role of glycation on protein folding, kinetics of amyloid formation, and amyloid cytotoxicity in order to shed light on the role of this post-translational modification in the in vivo amyloid aggregation process.
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6
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Poothong J, Jang I, Kaufman RJ. Defects in Protein Folding and/or Quality Control Cause Protein Aggregation in the Endoplasmic Reticulum. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2021; 59:115-143. [PMID: 34050864 DOI: 10.1007/978-3-030-67696-4_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Protein aggregation is now a common hallmark of numerous human diseases, most of which involve cytosolic aggregates including Aβ (AD) and ⍺-synuclein (PD) in Alzheimer's disease and Parkinson's disease. However, it is also evident that protein aggregation can also occur in the lumen of the endoplasmic reticulum (ER) that leads to specific diseases due to loss of protein function or detrimental effects on the host cell, the former is inherited in a recessive manner where the latter are dominantly inherited. However, the mechanisms of protein aggregation, disaggregation and degradation in the ER are not well understood. Here we provide an overview of factors that cause protein aggregation in the ER and how the ER handles aggregated proteins. Protein aggregation in the ER can result from intrinsic properties of the protein (hydrophobic residues in the ER), oxidative stress or nutrient depletion. The ER has quality control mechanisms [chaperone functions, ER-associated protein degradation (ERAD) and autophagy] to ensure only correctly folded proteins exit the ER and enter the cis-Golgi compartment. Perturbation of protein folding in the ER activates the unfolded protein response (UPR) that evolved to increase ER protein folding capacity and efficiency and degrade misfolded proteins. Accumulation of misfolded proteins in the ER to a level that exceeds the ER-chaperone folding capacity is a major factor that exacerbates protein aggregation. The most significant ER resident protein that prevents protein aggregation in the ER is the heat shock protein 70 (HSP70) homologue, BiP/GRP78, which is a peptide-dependent ATPase that binds unfolded/misfolded proteins and releases them upon ATP binding. Since exogenous factors can also reduce protein misfolding and aggregation in the ER, such as chemical chaperones and antioxidants, these treatments have potential therapeutic benefit for ER protein aggregation-associated diseases.
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Affiliation(s)
- Juthakorn Poothong
- Degenerative Diseases Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Insook Jang
- Degenerative Diseases Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Randal J Kaufman
- Degenerative Diseases Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
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7
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Umerani MJ, Pratakshya P, Chatterjee A, Cerna Sanchez JA, Kim HS, Ilc G, Kovačič M, Magnan C, Marmiroli B, Sartori B, Kwansa AL, Orins H, Bartlett AW, Leung EM, Feng Z, Naughton KL, Norton-Baker B, Phan L, Long J, Allevato A, Leal-Cruz JE, Lin Q, Baldi P, Bernstorff S, Plavec J, Yingling YG, Gorodetsky AA. Structure, self-assembly, and properties of a truncated reflectin variant. Proc Natl Acad Sci U S A 2020; 117:32891-32901. [PMID: 33323484 PMCID: PMC7780002 DOI: 10.1073/pnas.2009044117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Naturally occurring and recombinant protein-based materials are frequently employed for the study of fundamental biological processes and are often leveraged for applications in areas as diverse as electronics, optics, bioengineering, medicine, and even fashion. Within this context, unique structural proteins known as reflectins have recently attracted substantial attention due to their key roles in the fascinating color-changing capabilities of cephalopods and their technological potential as biophotonic and bioelectronic materials. However, progress toward understanding reflectins has been hindered by their atypical aromatic and charged residue-enriched sequences, extreme sensitivities to subtle changes in environmental conditions, and well-known propensities for aggregation. Herein, we elucidate the structure of a reflectin variant at the molecular level, demonstrate a straightforward mechanical agitation-based methodology for controlling this variant's hierarchical assembly, and establish a direct correlation between the protein's structural characteristics and intrinsic optical properties. Altogether, our findings address multiple challenges associated with the development of reflectins as materials, furnish molecular-level insight into the mechanistic underpinnings of cephalopod skin cells' color-changing functionalities, and may inform new research directions across biochemistry, cellular biology, bioengineering, and optics.
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Affiliation(s)
- Mehran J. Umerani
- Department of Materials Science and Engineering, University of California, Irvine, CA 92697
| | | | - Atrouli Chatterjee
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697
| | - Juana A. Cerna Sanchez
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697
| | - Ho Shin Kim
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC 27695
| | - Gregor Ilc
- Slovenian NMR Centre, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Matic Kovačič
- Slovenian NMR Centre, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Christophe Magnan
- Department of Computer Science, University of California, Irvine, CA 92697
| | - Benedetta Marmiroli
- Institute of Inorganic Chemistry, Graz University of Technology, 8010 Graz, Austria
| | - Barbara Sartori
- Institute of Inorganic Chemistry, Graz University of Technology, 8010 Graz, Austria
| | - Albert L. Kwansa
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC 27695
| | - Helen Orins
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697
| | - Andrew W. Bartlett
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697
| | - Erica M. Leung
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697
| | - Zhijing Feng
- Department of Materials Science and Engineering, University of California, Irvine, CA 92697
| | - Kyle L. Naughton
- Department of Physics and Astronomy, University of California, Irvine, CA 92697
| | | | - Long Phan
- Department of Materials Science and Engineering, University of California, Irvine, CA 92697
| | - James Long
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697
| | - Alex Allevato
- Department of Materials Science and Engineering, University of California, Irvine, CA 92697
| | - Jessica E. Leal-Cruz
- Department of Materials Science and Engineering, University of California, Irvine, CA 92697
| | - Qiyin Lin
- Irvine Materials Research Institute, University of California, Irvine, CA 92697
| | - Pierre Baldi
- Department of Computer Science, University of California, Irvine, CA 92697
| | | | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Yaroslava G. Yingling
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC 27695
| | - Alon A. Gorodetsky
- Department of Materials Science and Engineering, University of California, Irvine, CA 92697
- Department of Chemistry, University of California, Irvine, CA 92697
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697
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8
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Santorelli D, Rocchio S, Fata F, Silvestri I, Angelucci F, Imperi F, Marasco D, Diaferia C, Gigli L, Demitri N, Federici L, Di Matteo A, Travaglini-Allocatelli C. The folding and aggregation properties of a single KH-domain protein: Ribosome binding factor A (RbfA) from Pseudomonas aeruginosa. Biochim Biophys Acta Gen Subj 2020; 1865:129780. [PMID: 33157160 DOI: 10.1016/j.bbagen.2020.129780] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 10/13/2020] [Accepted: 11/01/2020] [Indexed: 11/25/2022]
Abstract
BACKGROUND Ribosome-binding factor A from the pathogenic bacterium Pseudomonas aeruginosa (PaRbfA) is a small ribosome assembly factor, composed by a single KH domain, involved in the maturation of the 30S subunit. These domains are characterized by the ability to bind RNA or ssDNA and are often located in proteins involved in a variety of cellular functions. However, although the ability of proteins to fold properly, to misfold or to aggregate is of paramount importance for their cellular functions, limited information is available on these dynamic properties in the case of KH domains. METHODS PaRbfA thermodynamic stability and folding mechanism: Far-UV CD and fluorescence spectroscopy, stopped-flow kinetics and chevron plot analysis, site-directed mutagenesis. Fibrils characterization: FT-IR spectroscopy, Thioflavin T fluorescence, Transmission Electron Microscopy (TEM) and X-ray fibrils diffraction. RESULTS Quantitative analysis of the (un)folding kinetics of PaRbfA show that, in vitro, the protein folds via a 3-states mechanism involving a transiently populated folding intermediate. We also provide experimental evidences that PaRbfA can form ordered fibrils endowed with cross-β structure even in mild conditions. CONCLUSION These results lead to the hypothesis that the folding intermediate of PaRbfA may expose (some of) the predicted amyloidogenic regions, which could act as aggregation nuclei in the fibrillogenesis. GENERAL SIGNIFICANCE The methodological approach presented herein could be readily adapted to verify the ability of other KH domain proteins to form cross-β structured fibrils and to transiently populate a folding intermediate.
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Affiliation(s)
- D Santorelli
- Department of Biochemical Sciences "A Rossi Fanelli" - Sapienza, University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - S Rocchio
- Department of Biochemical Sciences "A Rossi Fanelli" - Sapienza, University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy; Institute of Molecular Biology and Pathology, National Research Council of Italy, c/o Department of Biochemical Sciences "A Rossi Fanelli" - Sapienza, University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy
| | - F Fata
- Department of Health, Life and Environmental Sciences, University of L'Aquila, P.le Salvatore Tommasi 1, 76100 L'Aquila, Italy
| | - I Silvestri
- Department of Health, Life and Environmental Sciences, University of L'Aquila, P.le Salvatore Tommasi 1, 76100 L'Aquila, Italy
| | - F Angelucci
- Department of Health, Life and Environmental Sciences, University of L'Aquila, P.le Salvatore Tommasi 1, 76100 L'Aquila, Italy
| | - F Imperi
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy
| | - D Marasco
- Department of Pharmacy, University of Naples "Federico II", Via Mezzocannone 16, 80134 Naples, Italy
| | - C Diaferia
- Department of Pharmacy, University of Naples "Federico II", Via Mezzocannone 16, 80134 Naples, Italy
| | - L Gigli
- Elettra - Sincrotrone Trieste, S.S. 14 Km 163.5, Area Science Park, 34149 Basovizza, Trieste, Italy
| | - N Demitri
- Elettra - Sincrotrone Trieste, S.S. 14 Km 163.5, Area Science Park, 34149 Basovizza, Trieste, Italy
| | - L Federici
- Department of Medical, Oral and Biotechnological Sciences and Center for Advanced Studies and Technology (CAST), University of Chieti "G. d'Annunzio", Via dei Vestini 31 - 66100, Chieti, Italy
| | - A Di Matteo
- Institute of Molecular Biology and Pathology, National Research Council of Italy, c/o Department of Biochemical Sciences "A Rossi Fanelli" - Sapienza, University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy.
| | - C Travaglini-Allocatelli
- Department of Biochemical Sciences "A Rossi Fanelli" - Sapienza, University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy.
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9
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Iadanza MG, Jackson MP, Hewitt EW, Ranson NA, Radford SE. A new era for understanding amyloid structures and disease. Nat Rev Mol Cell Biol 2019; 19:755-773. [PMID: 30237470 DOI: 10.1038/s41580-018-0060-8] [Citation(s) in RCA: 568] [Impact Index Per Article: 113.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The aggregation of proteins into amyloid fibrils and their deposition into plaques and intracellular inclusions is the hallmark of amyloid disease. The accumulation and deposition of amyloid fibrils, collectively known as amyloidosis, is associated with many pathological conditions that can be associated with ageing, such as Alzheimer disease, Parkinson disease, type II diabetes and dialysis-related amyloidosis. However, elucidation of the atomic structure of amyloid fibrils formed from their intact protein precursors and how fibril formation relates to disease has remained elusive. Recent advances in structural biology techniques, including cryo-electron microscopy and solid-state NMR spectroscopy, have finally broken this impasse. The first near-atomic-resolution structures of amyloid fibrils formed in vitro, seeded from plaque material and analysed directly ex vivo are now available. The results reveal cross-β structures that are far more intricate than anticipated. Here, we describe these structures, highlighting their similarities and differences, and the basis for their toxicity. We discuss how amyloid structure may affect the ability of fibrils to spread to different sites in the cell and between organisms in a prion-like manner, along with their roles in disease. These molecular insights will aid in understanding the development and spread of amyloid diseases and are inspiring new strategies for therapeutic intervention.
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Affiliation(s)
- Matthew G Iadanza
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Matthew P Jackson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Eric W Hewitt
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
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10
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Wei Z, Huang Q. Developing organogel-based Pickering emulsions with improved freeze-thaw stability and hesperidin bioaccessibility. Food Hydrocoll 2019. [DOI: 10.1016/j.foodhyd.2019.01.050] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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11
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Inhibition of amyloid fibril formation in the variable domain of λ6 light chain mutant Wil caused by the interaction between its unfolded state and epigallocatechin-3-O-gallate. Biochim Biophys Acta Gen Subj 2018; 1862:2570-2578. [DOI: 10.1016/j.bbagen.2018.08.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 07/27/2018] [Accepted: 08/03/2018] [Indexed: 12/12/2022]
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12
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Very rapid amyloid fibril formation by a bacterial lipase in the absence of a detectable lag phase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:652-663. [DOI: 10.1016/j.bbapap.2017.03.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 03/03/2017] [Accepted: 03/14/2017] [Indexed: 02/01/2023]
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13
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Amyloid formation of growth hormone in presence of zinc: Relevance to its storage in secretory granules. Sci Rep 2016; 6:23370. [PMID: 27004850 PMCID: PMC4804206 DOI: 10.1038/srep23370] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 03/04/2016] [Indexed: 11/16/2022] Open
Abstract
Amyloids are cross-β-sheet fibrillar aggregates, associated with various human diseases and native functions such as protein/peptide hormone storage inside secretory granules of neuroendocrine cells. In the current study, using amyloid detecting agents, we show that growth hormone (GH) could be stored as amyloid in the pituitary of rat. Moreover, to demonstrate the formation of GH amyloid in vitro, we studied various conditions (solvents, glycosaminoglycans, salts and metal ions) and found that in presence of zinc metal ions (Zn(II)), GH formed short curvy fibrils. The amyloidogenic nature of these fibrils was examined by Thioflavin T binding, Congo Red binding, transmission electron microscopy and X-ray diffraction. Our biophysical studies also suggest that Zn(II) initiates the early oligomerization of GH that eventually facilitates the fibrillation process. Furthermore, using immunofluorescence study of pituitary tissue, we show that GH in pituitary significantly co-localizes with Zn(II), suggesting the probable role of zinc in GH aggregation within secretory granules. We also found that GH amyloid formed in vitro is capable of releasing monomers. The study will help to understand the possible mechanism of GH storage, its regulation and monomer release from the somatotrophs of anterior pituitary.
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14
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Liu Z, Reddy G, Thirumalai D. Folding PDZ2 Domain Using the Molecular Transfer Model. J Phys Chem B 2016; 120:8090-101. [PMID: 26926418 DOI: 10.1021/acs.jpcb.6b00327] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Zhenxing Liu
- Department of Physics, Beijing Normal University , Beijing 100875, China
| | - Govardhan Reddy
- Solid State and Structural Chemistry Unit, Indian Institute of Science , Bangalore, Karnataka 560012, India
| | - D Thirumalai
- Biophysics Program, Institute for Physical Science and Technology and Department of Chemistry and Biochemistry, University of Maryland , College Park, Maryland 20742, United States
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15
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Del Poggetto E, Bemporad F, Tatini F, Chiti F. Mutations of Profilin-1 Associated with Amyotrophic Lateral Sclerosis Promote Aggregation Due to Structural Changes of Its Native State. ACS Chem Biol 2015; 10:2553-63. [PMID: 26226631 DOI: 10.1021/acschembio.5b00598] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The PFN1 gene, coding for profilin-1, has recently been associated with familial amyotrophic lateral sclerosis (fALS), as three mutations, namely C71G, M114T, and G118V, have been found in patients with familial forms of the disease and another, E117G, has been proposed to be a moderate risk factor for disease onset. In this work, we have purified the four profilin-1 variants along with the wild-type protein. The resulting aggregates appear to be fibrillar, to have a weak binding to ThT, and to possess a significant amount of intermolecular β-sheet structure. Using ThT fluorescence assays, far-UV circular dichroism, and dynamic light scattering, we found that all four variants have an aggregation propensity higher than that of the wild-type counterpart. In particular, the C71G mutation was found to induce the most dramatic change in aggregation, followed by the G118V and M114T substitutions and then the E117G mutation. Such a propensity was found not to strictly correlate with the conformational stability in this group of profilin-1 variants, determined using both urea-induced denaturation at equilibrium and folding/unfolding kinetics. However, it correlated with structural changes of the folded states, as monitored with far-UV circular dichroism, intrinsic fluorescence spectroscopy, ANS binding, acrylamide quenching, and dynamic light scattering. Overall, the results suggest that all four mutations increase the tendency of profilin-1 to aggregate and that such aggregation behavior is largely determined by the mutation-induced structural changes occurring in the folded state of the protein.
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Affiliation(s)
- Edoardo Del Poggetto
- Department
of Biomedical Experimental and Clinical Sciences, Section of Biochemistry, University of Florence, Viale Morgagni 50, I-50134, Florence, Italy
| | - Francesco Bemporad
- Department
of Biomedical Experimental and Clinical Sciences, Section of Biochemistry, University of Florence, Viale Morgagni 50, I-50134, Florence, Italy
| | - Francesca Tatini
- Institute
of Applied Physics Nello Carrara, National Research Council, Via
Madonna del Piano 10, I-50019, Sesto Fiorentino (FI), Italy
| | - Fabrizio Chiti
- Department
of Biomedical Experimental and Clinical Sciences, Section of Biochemistry, University of Florence, Viale Morgagni 50, I-50134, Florence, Italy
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16
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Moayedzadeh S, Madadlou A, Khosrowshahi asl A. Formation mechanisms, handling and digestibility of food protein nanofibrils. Trends Food Sci Technol 2015. [DOI: 10.1016/j.tifs.2015.05.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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17
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Probing the interplay between amyloidogenic proteins and membranes using lipid monolayers and bilayers. Adv Colloid Interface Sci 2014; 207:81-92. [PMID: 24200086 DOI: 10.1016/j.cis.2013.10.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 10/11/2013] [Accepted: 10/13/2013] [Indexed: 11/21/2022]
Abstract
Many degenerative diseases such as Alzheimer's and Parkinson's involve proteins that have a tendency to misfold and aggregate eventually forming amyloid fibers. This review describes the use of monolayers, bilayers, supported membranes, and vesicles as model systems that have helped elucidate the mechanisms and consequences of the interactions between amyloidogenic proteins and membranes. These are twofold: membranes favor the formation of amyloid structures and these induce damage in those membranes. We describe studies that show how interfaces, especially charged ones, favor amyloidogenic protein aggregation by several means. First, surfaces increase the effective protein concentration reducing a three-dimensional system to a two-dimensional one. Second, charged surfaces allow electrostatic interactions with the protein. Anionic lipids as well as rafts, rich in cholesterol and gangliosides, prove to play an especially important role. Finally, these amphipathic systems also offer a hydrophobic environment favoring conformational changes, oligomerization, and eventual formation of mature fibers. In addition, we examine several models for membrane permeabilization: protein pores, leakage induced by extraction of lipids, chaotic pores, and membrane tension, presenting illustrative examples of experimental evidence in support of these models. The picture that emerges from recent work is one where more than one mechanism is in play. Which mechanism prevails depends on the protein, its aggregation state, and the lipid environment in which the interactions occur.
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18
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Capitini C, Conti S, Perni M, Guidi F, Cascella R, De Poli A, Penco A, Relini A, Cecchi C, Chiti F. TDP-43 inclusion bodies formed in bacteria are structurally amorphous, non-amyloid and inherently toxic to neuroblastoma cells. PLoS One 2014; 9:e86720. [PMID: 24497973 PMCID: PMC3907574 DOI: 10.1371/journal.pone.0086720] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 12/13/2013] [Indexed: 12/13/2022] Open
Abstract
Accumulation of ubiquitin-positive, tau- and α-synuclein-negative intracellular inclusions of TDP-43 in the central nervous system represents the major hallmark correlated to amyotrophic lateral sclerosis and frontotemporal lobar degeneration with ubiquitin-positive inclusions. Such inclusions have variably been described as amorphous aggregates or more structured deposits having an amyloid structure. Following the observations that bacterial inclusion bodies generally consist of amyloid aggregates, we have overexpressed full-length TDP-43 and C-terminal TDP-43 in E. coli, purified the resulting full-length and C-terminal TDP-43 containing inclusion bodies (FL and Ct TDP-43 IBs) and subjected them to biophysical analyses to assess their structure/morphology. We show that both FL and Ct TDP-43 aggregates contained in the bacterial IBs do not bind amyloid dyes such as thioflavin T and Congo red, possess a disordered secondary structure, as inferred using circular dichroism and infrared spectroscopies, and are susceptible to proteinase K digestion, thus possessing none of the hallmarks for amyloid. Moreover, atomic force microscopy revealed an irregular structure for both types of TDP-43 IBs and confirmed the absence of amyloid-like species after proteinase K treatment. Cell biology experiments showed that FL TDP-43 IBs were able to impair the viability of cultured neuroblastoma cells when added to their extracellular medium and, more markedly, when transfected into their cytosol, where they are at least in part ubiquitinated and phosphorylated. These data reveal an inherently high propensity of TDP-43 to form amorphous aggregates, which possess, however, an inherently high ability to cause cell dysfunction. This indicates that a gain of toxic function caused by TDP-43 deposits is effective in TDP-43 pathologies, in addition to possible loss of function mechanisms originating from the cellular mistrafficking of the protein.
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Affiliation(s)
- Claudia Capitini
- Section of Biochemistry, Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Florence, Italy
| | - Simona Conti
- Section of Biochemistry, Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Florence, Italy
| | - Michele Perni
- Section of Biochemistry, Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Florence, Italy
| | - Francesca Guidi
- Section of Biochemistry, Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Florence, Italy
| | - Roberta Cascella
- Section of Biochemistry, Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Florence, Italy
| | - Angela De Poli
- Section of Biochemistry, Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Florence, Italy
| | - Amanda Penco
- Department of Physics, University of Genoa, Genoa, Italy
| | | | - Cristina Cecchi
- Section of Biochemistry, Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Florence, Italy
| | - Fabrizio Chiti
- Section of Biochemistry, Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Florence, Italy
- * E-mail:
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19
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Hill SE, Donegan RK, Lieberman RL. The glaucoma-associated olfactomedin domain of myocilin forms polymorphic fibrils that are constrained by partial unfolding and peptide sequence. J Mol Biol 2013; 426:921-35. [PMID: 24333014 DOI: 10.1016/j.jmb.2013.12.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 11/06/2013] [Accepted: 12/02/2013] [Indexed: 12/26/2022]
Abstract
The glaucoma-associated olfactomedin domain of myocilin (myoc-OLF) is a recent addition to the growing list of disease-associated amyloidogenic proteins. Inherited, disease-causing myocilin variants aggregate intracellularly instead of being secreted to the trabecular meshwork, which is a scenario toxic to trabecular meshwork cells and leads to early onset of ocular hypertension, the major risk factor for glaucoma. Here we systematically structurally and biophysically dissected myoc-OLF to better understand its amyloidogenesis. Under mildly destabilizing conditions, wild-type myoc-OLF adopts non-native structures that readily fibrillize when incubated at a temperature just below the transition for tertiary unfolding. With buffers at physiological pH, two main endpoint fibril morphologies are observed: (a) straight fibrils common to many amyloids and (b) unique micron-length, ~300 nm or larger diameter, species that lasso oligomers, which also exhibit classical spectroscopic amyloid signatures. Three disease-causing variants investigated herein exhibit non-native tertiary structures under physiological conditions, leading to a variety of growth rates and a fibril morphologies. In particular, the well-documented D380A variant, which lacks calcium, forms large circular fibrils. Two amyloid-forming peptide stretches have been identified, one for each of the main fibril morphologies observed. Our study places myoc-OLF within the larger landscape of the amylome and provides insight into the diversity of myoc-OLF aggregation that plays a role in glaucoma pathogenesis.
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Affiliation(s)
- Shannon E Hill
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive Northwest, Atlanta, GA 30332-0400, USA
| | - Rebecca K Donegan
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive Northwest, Atlanta, GA 30332-0400, USA
| | - Raquel L Lieberman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive Northwest, Atlanta, GA 30332-0400, USA.
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20
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Shokri MM, Ahmadian S, Bemporad F, Khajeh K, Chiti F. Amyloid fibril formation by a normally folded protein in the absence of denaturants and agitation. Amyloid 2013; 20:226-32. [PMID: 24053331 DOI: 10.3109/13506129.2013.830246] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The conversion of normally folded proteins into amyloid-like fibrils is an important process in protein chemistry, biology, pathology and biotechnology. This process generally requires harsh conditions, such as pH extremes, organic cosolvents, high temperatures, high pressures or shear forces. Such conditions promote aggregation because they partially unfold structured proteins or allow the sampling of locally unfolded native-like states, both of which possibly represent amyloidogenic states. Here we report the formation of amyloid-like fibrils by the lipase from Pseudomonas sp. under conditions that are close to physiological, that is, in the absence of denaturants and agitation. The resulting aggregates bind thioflavin T and Congo red, causing their characteristic spectral changes observed in the presence of amyloid fibrils. They possess a significant quantity of β-sheet structure, as detected with Fourier transform infrared and far-UV circular dichroism spectroscopies, and appear fibrillar using transmission electron microscopy. These results indicate that the lipase from Pseudomonas sp. can be a useful model system for the characterization of a key process, such as amyloid fibril formation under physiological conditions.
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21
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Buttstedt A, Wostradowski T, Ihling C, Hause G, Sinz A, Schwarz E. Different morphology of amyloid fibrils originating from agitated and non-agitated conditions. Amyloid 2013; 20:86-92. [PMID: 23570235 DOI: 10.3109/13506129.2013.784962] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In vitro amyloid formation has been suggested to be a common property of any polypeptide chain depending on particular environmental conditions although in vivo amyloid fibril formation can be promoted by point mutations or triplet expansions. Here, we explored the influence of agitation on fibril formation of amyloidogenic alanine segments fused to Cold Shock Protein B (CspB) of Bacillus subtilis. While without agitation fibril formation was clearly dependent on the presence of an amyloidogenic alanine segment, fibril formation was independent of the amyloidogenic segment under agitation. Agitation even led to fibrillation of native CspB lacking the amyloidogenic segment. Furthermore, agitation not only influenced the kinetics of fibril formation, but also resulted in completely different fibril morphologies. These results indicate that experimental conditions can alter the region that undergoes a conformational change during in vitro fibrillation. Moreover, the data show that deductions from in vitro assays on in vivo fibril formation mechanisms are afflicted with a certain degree of uncertainty and therefore need to be cautiously discussed.
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Affiliation(s)
- Anja Buttstedt
- Facultatea de Zootehnie şi Biotehnologii, Universitatea de Ştiinţe Agricole şi Medicină Veterinară, Calea Mănăştur 3-5, 400372 Cluj-Napoca, Romania.
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22
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Torchio GM, Ermácora MR, Sica MP. Equilibrium unfolding of the PDZ domain of β2-syntrophin. Biophys J 2012; 102:2835-44. [PMID: 22735534 DOI: 10.1016/j.bpj.2012.05.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Revised: 04/23/2012] [Accepted: 05/04/2012] [Indexed: 10/28/2022] Open
Abstract
β2-syntrophin, a dystrophin-associated protein, plays a pivotal role in insulin secretion by pancreatic β-cells. It contains a PDZ domain (β2S-PDZ) that, in complex with protein-tyrosine phosphatase ICA512, anchors the dense insulin granules to actin filaments. The phosphorylation state of β2-syntrophin allosterically regulates the affinity of β2S-PDZ for ICA512, and the disruption of the complex triggers the mobilization of the insulin granule stores. Here, we investigate the thermal unfolding of β2S-PDZ at different pH and urea concentrations. Our results indicate that, unlike other PDZ domains, β2S-PDZ is marginally stable. Thermal denaturation experiments show broad transitions and cold denaturation, and a two-state model fit reveals a significant unfolded fraction under physiological conditions. Furthermore, T(m) and T(max) denaturant-dependent shifts and noncoincidence of melting curves monitored at different wavelengths suggest that two-state and three-state models fail to explain the equilibrium data properly and are in better agreement with a downhill scenario. Its higher stability at pH >9 and the results of molecular dynamics simulations indicate that this behavior of β2S-PDZ might be related to its charge distribution. All together, our results suggest a link between the conformational plasticity of the native ensemble of this PDZ domain and the regulation of insulin secretion.
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Affiliation(s)
- Gabriela María Torchio
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina
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23
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Macchi F, Hoffmann SV, Carlsen M, Vad B, Imparato A, Rischel C, Otzen DE. Mechanical stress affects glucagon fibrillation kinetics and fibril structure. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:12539-12549. [PMID: 21877745 DOI: 10.1021/la202125c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Mechanical stress can strongly influence the capability of a protein to aggregate and the kinetics of aggregation, but there is little insight into the underlying mechanism. Here we study the effect of different mechanical stress conditions on the fibrillation of the peptide hormone glucagon, which forms different fibrils depending on temperature, pH, ionic strength, and concentration. A combination of spectroscopic and microscopic data shows that fibrillar polymorphism can also be induced by mechanical stress. We observed two classes of fibrils: a low-stress and a high-stress class, which differ in their kinetic profiles, secondary structure as well as morphology and that are able to self-propagate in a template-dependent fashion. The bending rigidity of the low-stress fibrils is sensitive to the degree of mechanical perturbation. We propose a fibrillation model, where interfaces play a fundamental role in the switch between the two fibrillar classes. Our work also raises the cautionary note that mechanical perturbation is a potential source of variability in the study of fibrillation mechanisms and fibril structures.
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Affiliation(s)
- Francesca Macchi
- iNANO, Center for Insoluble Protein Structures (inSPIN), Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark
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24
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Li J, Hoop CL, Kodali R, Sivanandam VN, van der Wel PCA. Amyloid-like fibrils from a domain-swapping protein feature a parallel, in-register conformation without native-like interactions. J Biol Chem 2011; 286:28988-28995. [PMID: 21715337 PMCID: PMC3190706 DOI: 10.1074/jbc.m111.261750] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Revised: 06/21/2011] [Indexed: 11/06/2022] Open
Abstract
The formation of amyloid-like fibrils is characteristic of various diseases, but the underlying mechanism and the factors that determine whether, when, and how proteins form amyloid, remain uncertain. Certain mechanisms have been proposed based on the three-dimensional or runaway domain swapping, inspired by the fact that some proteins show an apparent correlation between the ability to form domain-swapped dimers and a tendency to form fibrillar aggregates. Intramolecular β-sheet contacts present in the monomeric state could constitute intermolecular β-sheets in the dimeric and fibrillar states. One example is an amyloid-forming mutant of the immunoglobulin binding domain B1 of streptococcal protein G, which in its native conformation consists of a four-stranded β-sheet and one α-helix. Under native conditions this mutant adopts a domain-swapped dimer, and it also forms amyloid-like fibrils, seemingly in correlation to its domain-swapping ability. We employ magic angle spinning solid-state NMR and other methods to examine key structural features of these fibrils. Our results reveal a highly rigid fibril structure that lacks mobile domains and indicate a parallel in-register β-sheet structure and a general loss of native conformation within the mature fibrils. This observation contrasts with predictions that native structure, and in particular intermolecular β-strand interactions seen in the dimeric state, may be preserved in "domain-swapping" fibrils. We discuss these observations in light of recent work on related amyloid-forming proteins that have been argued to follow similar mechanisms and how this may have implications for the role of domain-swapping propensities for amyloid formation.
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Affiliation(s)
- Jun Li
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260
| | - Cody L Hoop
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260
| | - Ravindra Kodali
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260
| | - V N Sivanandam
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260
| | - Patrick C A van der Wel
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260.
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25
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Murciano-Calles J, Cobos ES, Mateo PL, Camara-Artigas A, Martinez JC. An oligomeric equilibrium intermediate as the precursory nucleus of globular and fibrillar supramacromolecular assemblies in a PDZ domain. Biophys J 2010; 99:263-72. [PMID: 20655855 DOI: 10.1016/j.bpj.2010.04.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Revised: 03/26/2010] [Accepted: 04/01/2010] [Indexed: 11/26/2022] Open
Abstract
The equilibrium unfolding at neutral pH of the third PDZ domain of PSD95, as followed by DSC, is characterized by the presence of an equilibrium intermediate with clear signs of oligomerization. DLS and SEC measurements indicate that at 60-70 degrees C small oligomers populate, showing a typical beta-sheet far-UV CD spectrum. These intermediate species lead to the formation of rodlike particulates of approximately 12 nm, which remain in solution after 2 weeks incubation and grow until they adopt annular/spherical shapes of approximately 50 nm and protofibrils, which are subsequently fully transformed into fibrils. The fibrils can also disaggregate after the addition of 1:1 buffer dilution followed by cooling to room temperature, thus returning to the initial monomeric state. Growth kinetics, as shown by ThT and ANS fluorescence, show that the organization of the different supramacromolecular structures comes from a common nucleation unit, the small oligomers, which organize themselves before reaching the incubation temperature of 60 degrees C. Our experiments point toward the existence of a well-defined reversible, stepwise, and downhill organization of the processes involved in the association-dissociation of the intermediate. We estimate the enthalpy change accompanying the association-dissociation equilibria to be 130 kJ x mol(-1). Furthermore, the coalescence under essentially reversible conditions of different kinds of supramacromolecular assemblies renders this protein system highly interesting for biophysical studies aimed at our further understanding of amyloid pathological conditions.
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Affiliation(s)
- Javier Murciano-Calles
- Department of Physical Chemistry and Institute of Biotechnology, Faculty of Sciences, University of Granada, Granada, Spain
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26
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Gregori M, Cassina V, Brogioli D, Salerno D, De Kimpe L, Scheper W, Masserini M, Mantegazza F. Stability of Aβ (1-42) peptide fibrils as consequence of environmental modifications. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2010; 39:1613-23. [DOI: 10.1007/s00249-010-0619-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Revised: 06/15/2010] [Accepted: 07/14/2010] [Indexed: 01/05/2023]
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27
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Manno M, Giacomazza D, Newman J, Martorana V, San Biagio PL. Amyloid gels: precocious appearance of elastic properties during the formation of an insulin fibrillar network. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:1424-1426. [PMID: 19916492 DOI: 10.1021/la903340v] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The formation of insulin amyloid fibrils is important not only for the development of reliable drugs but also for modeling the basic properties of protein self-assembly. Fibrillation kinetics is typically characterized by an initial apparent lag phase related to the formation of oligomers, protofibrils, and aggregation nuclei. Afterwards, aggregation proceeds over a wide range of length scales via fibril elongation, thickening, and/or flocculation and eventual gelation. By light scattering and rheological techniques, we reveal the structural details hidden in the apparent lag phase and we show the unexpected appearance of noteworthy elastic properties concurrently with initial fibril nucleation and elongation preceding the formation of the larger structures and the gel network.
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Affiliation(s)
- Mauro Manno
- Institute of Biophysics at Palermo, Italian National Research Council, via Ugo La Malfa 153, I90146 Palermo, Italy.
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28
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Solomon JP, Yonemoto IT, Murray AN, Price JL, Powers ET, Balch WE, Kelly JW. The 8 and 5 kDa fragments of plasma gelsolin form amyloid fibrils by a nucleated polymerization mechanism, while the 68 kDa fragment is not amyloidogenic. Biochemistry 2009; 48:11370-80. [PMID: 19904968 PMCID: PMC2907741 DOI: 10.1021/bi901368e] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Familial amyloidosis of Finnish type (FAF), or gelsolin amyloidosis, is a systemic amyloid disease caused by a mutation (D187N/Y) in domain 2 of human plasma gelsolin, resulting in domain 2 misfolding within the secretory pathway. When D187N/Y gelsolin passes through the Golgi, furin endoproteolysis within domain 2 occurs as a consequence of the abnormal conformations that enable furin to bind and cleave, resulting in the secretion of a 68 kDa C-terminal fragment (amino acids 173-755, C68). The C68 fragment is cleaved upon secretion from the cell by membrane type 1 matrix metalloprotease (MT1-MMP), affording the 8 and 5 kDa fragments (amino acids 173-242 and 173-225, respectively) comprising the amyloid fibrils in FAF patients. Herein, we show that the 8 and 5 kDa gelsolin fragments form amyloid fibrils by a nucleated polymerization mechanism. In addition to demonstrating the expected concentration dependence of a nucleated polymerization reaction, the addition of preformed amyloid fibrils, or "seeds", was shown to bypass the requirement for the formation of a high-energy nucleus, accelerating 8 and 5 kDa D187N gelsolin amyloidogenesis. The C68 fragment can form small oligomers, but not amyloid fibrils, even when seeded with preformed 8 kDa fragment plasma gelsolin fibrils. Because the 68 kDa fragment of gelsolin does not form amyloid fibrils in vitro or in a recently published transgenic mouse model of FAF, we propose that administration of an MT1-MMP inhibitor could be an effective strategy for the treatment of FAF.
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Affiliation(s)
- James P. Solomon
- Departments of Chemistry and Molecular and Experimental Medicine and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037 USA
| | - Isaac T. Yonemoto
- Departments of Chemistry and Molecular and Experimental Medicine and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037 USA
| | - Amber N. Murray
- Departments of Chemistry and Molecular and Experimental Medicine and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037 USA
| | - Joshua L. Price
- Departments of Chemistry and Molecular and Experimental Medicine and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037 USA
| | - Evan T. Powers
- Departments of Chemistry and Molecular and Experimental Medicine and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037 USA
| | - William E. Balch
- Departments of Cell Biology and Chemical Physiology and the Institute for Childhood and Neglected Diseases, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037 USA
| | - Jeffery W. Kelly
- Departments of Chemistry and Molecular and Experimental Medicine and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037 USA
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