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Muthu SA, Qureshi A, Sharma R, Bisaria I, Parvez S, Grover S, Ahmad B. Redesigning the kinetics of lysozyme amyloid aggregation by cephalosporin molecules. J Biomol Struct Dyn 2024:1-16. [PMID: 38682862 DOI: 10.1080/07391102.2024.2335304] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 03/20/2024] [Indexed: 05/01/2024]
Abstract
In lysozyme amyloidosis, fibrillar aggregates of lysozyme are associated with severe renal, hepatic, and gastrointestinal manifestations, with no definite therapy. Current drugs are now being tested in amyloidosis clinical trials as aggregation inhibitors to mitigate disease progression. The tetracycline group among antimicrobials in use is in phase II of clinical trials, whereas some macrolides and cephalosporins have shown neuroprotection. In the present study, two cephalosporins, ceftazidime (CZD) and cefotaxime (CXM), and a glycopeptide, vancomycin (VNC), are evaluated for inhibition of amyloid aggregation of hen egg white lysozyme (HEWL) under two conditions (i) 4 M guanidine hydrochloride (GuHCl) at pH 6.5 and 37° C, (ii) At pH 1.5 and 65 °C. Fluorescence quench titration and molecular docking methods report that CZD, CXM, and VNC interact more strongly with the partially folded intermediates (PFI) in comparison to the protein's natural state (N). However, only CZD and CXM proficiently inhibit the aggregation. Transmission electron microscopy, tinctorial assessments, and aggregation kinetics all support oligomer-level inhibition. Transition structures in CZD-HEWL and CXM-HEWL aggregation are shown by circular dichroism (CD). On the other hand, kinetic variables and soluble fraction assays point to a localized association of monomers. Intrinsic fluorescence (IF),1-Anilino 8-naphthalene sulphonic acid, and CD demonstrate structural and conformational modifications redesigning the PFI. GuHCl-induced unfolding and differential scanning fluorimetry suggested that the PFI monomers bound to CZD and CXM exhibited partial stability. Our results present two mechanisms that function in both solution conditions, creating a novel avenue for the screening of putative inhibitors for drug repurposing. We extend our proposed mechanisms in the designing of physical inhibitors of amyloid aggregation considering shorter time frames and foolproof methods.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shivani A Muthu
- Protein Assembly Laboratory, Department of Medical Elementology and Toxicology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
- Department of Molecular Medicine, School of Interdisciplinary Studies, Jamia Hamdard, New Delhi, India
| | - Afnaan Qureshi
- Protein Assembly Laboratory, Department of Medical Elementology and Toxicology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Rahul Sharma
- Department of Molecular Medicine, School of Interdisciplinary Studies, Jamia Hamdard, New Delhi, India
| | - Ishita Bisaria
- Protein Assembly Laboratory, Department of Medical Elementology and Toxicology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Suhel Parvez
- Department of Medical Elementology and Toxicology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Sonam Grover
- Department of Molecular Medicine, School of Interdisciplinary Studies, Jamia Hamdard, New Delhi, India
| | - Basir Ahmad
- Protein Assembly Laboratory, Department of Medical Elementology and Toxicology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
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2
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Florio D, Luciano P, Di Natale C, Marasco D. The effects of histidine substitution of aromatic residues on the amyloidogenic properties of the fragment 264-277 of nucleophosmin 1. Bioorg Chem 2024; 147:107404. [PMID: 38678777 DOI: 10.1016/j.bioorg.2024.107404] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/15/2024] [Accepted: 04/25/2024] [Indexed: 05/01/2024]
Abstract
Histidine (His) plays a key role in mediating protein interactions and its unique side chain determines pH responsive self-assembling processes and thus in the formation of nanostructures. In this study, To identify novel self-assembling bioinspired sequences, we analyzed a series of peptide sequences obtained through the point mutation of aromatic residues of 264-277 fragment of nucleophosmin 1 (NPM1) with single and double histidines. Through several orthogonal biophysical techniques and under different pH and ionic strength conditions we evaluated the effects of these substitutions in the amyloidogenic features of derived peptides. The results clearly indicate that both the type of aromatic mutated residue and its position can have different effect on amyloid-like behaviors. They corroborate the crucial role exerted by Tyr271 in the self-assembling process of CTD of NPM1 in AML mutated form and add novel insights in the accurate investigation of how side chain orientations can determine successful design of innovative bioinspired materials.
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Affiliation(s)
- Daniele Florio
- Department of Pharmacy, University of Naples "Federico II", 80131 Naples, Italy
| | - Paolo Luciano
- Department of Pharmacy, University of Naples "Federico II", 80131 Naples, Italy
| | - Concetta Di Natale
- Department of Ingegneria Chimica, dei Materiali e della Produzione Industriale (DICMAPI), Italy
| | - Daniela Marasco
- Department of Pharmacy, University of Naples "Federico II", 80131 Naples, Italy.
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3
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Mohammadi S, Seyedalipour B, Hashemi SZ, Hosseinkhani S, Mohseni M. Implications of ALS-Associated Mutations on Biochemical and Biophysical Features of hSOD1 and Aggregation Formation. Biochem Genet 2024:10.1007/s10528-023-10619-y. [PMID: 38196030 DOI: 10.1007/s10528-023-10619-y] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 12/02/2023] [Indexed: 01/11/2024]
Abstract
One of the recognized motor neuron degenerative disorders is amyotrophic lateral sclerosis (ALS). By now, several mutations have been reported and linked to ALS patients, some of which are induced by mutations in the human superoxide dismutase (hSOD1) gene. The ALS-provoking mutations are located throughout the structure of hSOD1 and promote the propensity to aggregate. Despite numerous investigations, the underlying mechanism related to the toxicity of mutant hSOD1 through the gain of a toxic function is still vague. We surveyed two mutant forms of hSOD1 by removing and adding cysteine at positions 146 and 72, respectively, to investigate the biochemical characterization and amyloid formation. Our findings predicted the harmful and destabilizing impact of two SOD1 mutants using multiple programs. The specific activity of the wild-type form was about 1.42- and 1.92-fold higher than that of C146R and G72C mutants, respectively. Comparative structural studies using CD spectropolarimetry, and intrinsic and ANS fluorescence showed alterations in secondary structure content, exposure of hydrophobic patches, and structural compactness of WT-hSOD1 vs. mutants. We demonstrated that two mutants were able to promote amyloid-like aggregates under amyloid induction circumstances (50-mM Tris-HCl pH 7.4, 0.2-M KSCN, 50-mM DTT, 37 °C, 190 rpm). Monitoring aggregates were done using an enhancement in thioflavin T fluorescence and alterations in Congo red absorption. The mutants accelerated fibrillation with subsequently greater fluorescence amplitude and a shorter lag time compared to WT-SOD1. These findings support the aggregation of ALS-associated SOD1 mutants as an integral part of ALS pathology.
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Affiliation(s)
- Saeede Mohammadi
- Department of Molecular and Cell Biology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran
| | - Bagher Seyedalipour
- Department of Molecular and Cell Biology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran.
| | - Seyedeh Zohreh Hashemi
- Department of Molecular and Cell Biology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran
| | - Saman Hosseinkhani
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mojtaba Mohseni
- Department of Microbiology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran
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4
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Lin Y. Preparation of Tau Condensates by Liquid-Liquid Phase Separation to Study Tau Amyloid Aggregation. Methods Mol Biol 2024; 2754:185-192. [PMID: 38512667 DOI: 10.1007/978-1-0716-3629-9_10] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
Protein liquid-liquid phase separation (LLPS) has been associated with protein amyloid aggregation. Amyloid aggregation of tau is a hallmark of Alzheimer's disease and other neurodegenerative diseases. This protocol provides steps to prepare tau condensates via LLPS, so that researchers can further study its driving forces and its relationship with tau amyloid aggregation.
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Affiliation(s)
- Yanxian Lin
- Department of Biomolecular Science and Engineering, University of California, Santa Barbara, CA, USA
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5
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Fitzner L, Hasler M, Heyn TR, Schwarz K, Keppler JK. UVB pretreatment of β-lactoglobulin affects the temperature-induced formation of functional amyloid-like aggregates and promotes oxidative degradation. Food Chem 2023; 429:136898. [PMID: 37516047 DOI: 10.1016/j.foodchem.2023.136898] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/11/2023] [Accepted: 07/14/2023] [Indexed: 07/31/2023]
Abstract
Unfolding in combination with or without acid hydrolysis is crucial for the formation of functional amyloid (fibrillar) or amyloid-like (worm-like) β-lactoglobulin (BLG) aggregates, which can be induced through temperature treatment for several hours at pH 2-4. A preceding conformational destabilization of BLG might affect its aggregation. We investigated ultraviolet (UV) B radiation as conformational perturbing treatment to facilitate temperature-induced protein aggregation. 2-h UVB pretreated BLG (UV-BLG) exhibited an accelerated worm-like aggregation at pH 3.5, while at pH 2 the formation of fibrils was decelerated. The UV-induced conformational destabilization lowered the thermal stability and thus facilitates unfolding during thermal treatment. Thereby, the formation of covalent and non-covalent intermolecular interactions was favored, which promoted assembly of intact proteins resulting in worm-like aggregates. The oxidative degradation of UV-BLG was suggested to alter fibrillation-prone protein regions and thereby impede peptide assembly.
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Affiliation(s)
- Laura Fitzner
- Institute of Human Nutrition and Food Science, Division Food Technology, Christian-Albrechts-University of Kiel, Heinrich-Hecht-Platz 10, 24118 Kiel, Germany.
| | - Mario Hasler
- Lehrfach Variationsstatistik, Christian-Albrechts-University of Kiel, Hermann-Rodewald-Strasse 9, 24118 Kiel, Germany.
| | - Timon R Heyn
- Institute of Human Nutrition and Food Science, Division Food Technology, Christian-Albrechts-University of Kiel, Heinrich-Hecht-Platz 10, 24118 Kiel, Germany.
| | - Karin Schwarz
- Institute of Human Nutrition and Food Science, Division Food Technology, Christian-Albrechts-University of Kiel, Heinrich-Hecht-Platz 10, 24118 Kiel, Germany.
| | - Julia Katharina Keppler
- Laboratory of Food Process Engineering, Wageningen University & Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands.
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Tvrdoňová M, Borovská B, Salayová A, Rončák R, Michalčin P, Bednáriková Z, Gažová Z. Design and synthesis of novel carbohydrate-amino acid hybrids and their antioxidant and anti-β- amyloid aggregation activity. Bioorg Chem 2023; 137:106636. [PMID: 37290376 DOI: 10.1016/j.bioorg.2023.106636] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/10/2023]
Abstract
Herein we report the synthesis of new furanoid sugar amino acids and thioureas, prepared by coupling aromatic amino acids and dipeptides with isothiocyanato- functionalized ribofuranose ring. Since carbohydrate-derived structures possess many biological activities, synthesized compounds were evaluated as anti-amyloid and antioxidant agents. The anti-amyloid activity of the studied compounds was evaluated based on their potential to destroy amyloid fibrils of intrinsically disordered Aβ40 peptide and globular hen egg-white (HEW) lysozyme. The destructive efficiency of the compounds differed between the studied peptides. While the destruction activity of the compounds on the HEW lysozyme amyloid fibrils was negligible, the effect on Aβ40 amyloid fibrils was significantly higher. Furanoid sugar α-amino acid 1 and its dipeptide derivatives 8 (Trp-Trp) and 11 (Trp-Tyr) were the most potent anti-Aβ fibrils compounds. The antioxidant properties of synthesized compounds were estimated by three complementary in vitro assays (DPPH, ABTS, and FRAP). The ABTS assay was the most sensitive for assessing the radical scavenging activity of all tested compounds compared to the DPPH test. Significant antioxidant activity was detected for compounds in the group of aromatic amino acids depending on the present amino acid, with the highest activity in the case of dipeptides 11 and 12 containing the Tyr and Trp moiety. Regarding the FRAP assay, the best reducing antioxidant potential revealed Trp-containing compounds 5, 10, and 12.
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Affiliation(s)
- Monika Tvrdoňová
- Department of Organic Chemistry, Institute of Chemical Sciences, P.J. Šafárik University, Moyzesova 11, 040 01 Košice, Slovakia.
| | - Barbora Borovská
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Košice, Slovakia
| | - Aneta Salayová
- Department of Chemistry, Biochemistry and Biophysics, University of Veterinary Medicine and Pharmacy in Košice, Komenského 73, 041 81 Košice, Slovakia
| | - Róbert Rončák
- Department of Organic Chemistry, Institute of Chemical Sciences, P.J. Šafárik University, Moyzesova 11, 040 01 Košice, Slovakia
| | - Peter Michalčin
- Department of Organic Chemistry, Institute of Chemical Sciences, P.J. Šafárik University, Moyzesova 11, 040 01 Košice, Slovakia
| | - Zuzana Bednáriková
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Košice, Slovakia
| | - Zuzana Gažová
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Košice, Slovakia
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Salehi N, Lohrasebi A, Bordbar AK. Preventing the amyloid-beta peptides accumulation on the cell membrane by applying GHz electric fields: A molecular dynamic simulation. J Mol Graph Model 2023; 123:108516. [PMID: 37216829 DOI: 10.1016/j.jmgm.2023.108516] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 05/03/2023] [Accepted: 05/07/2023] [Indexed: 05/24/2023]
Abstract
Alzheimer's disease is associated with accumulating different amyloid peptides on the nerve cell membranes. The non-thermal effects of the GHz electric fields in this topic have yet to be well recognized. Hence, in this study, the impacts of 1 and 5 GHz electric fields on the amyloid peptide proteins accumulation on the cell membrane have been investigated, utilizing molecular dynamics (MD) simulation. The obtained results indicated that this range of electric fields did not significantly affect the peptide structure. Moreover, it was found that the peptide penetration into the membrane was increased as the field frequency was increased when the system was exposed to a 20 mv/nm oscillating electric field. In addition, it was observed that the protein-membrane interaction is reduced significantly in the presence of the 70 mv/nm electric field. The molecular level results reported in this study could be helpful in better understanding Alzheimer's disease.
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Affiliation(s)
- N Salehi
- Department of Chemistry, University of Isfahan, Isfahan, 81746-73441, Iran
| | - A Lohrasebi
- Department of Physics, University of Isfahan, Isfahan, 81746-73441, Iran.
| | - A K Bordbar
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, CA, USA.
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8
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Garcarova I, Valusova E, Shlapa Y, Belous A, Musatov A, Siposova K. Surface-modified cerium dioxide nanoparticles with improved anti-amyloid and preserved nanozymatic activity. Colloids Surf B Biointerfaces 2023; 227:113356. [PMID: 37201447 DOI: 10.1016/j.colsurfb.2023.113356] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 05/06/2023] [Accepted: 05/13/2023] [Indexed: 05/20/2023]
Abstract
Cerium dioxide nanoparticles (CeO2 NPs) are used increasingly in nanotechnology and particularly in biotechnology and bioresearch. Thus, CeO2 NPs have been successfully tested in vitro as a potential therapeutic agent for various pathologies associated with oxidative stress, including the formation of protein amyloid aggregates. In this study, to increase the anti-amyloidogenic efficiency and preserve the antioxidant potential, the surface of the synthesized CeO2 NPs is modified with a nonionic, sugar-based surfactant, dodecyl maltoside (DDM), which is known for its high anti-amyloidogenic activity and biocompatibility. Dynamic light scattering and Fourier transform infrared spectroscopy demonstrated successful modification by DDM. The apparent hydrodynamic diameters of CeO2 NPs and DDM-modified NPs (CeO2@DDM NPs) are found to be ⁓180 nm and ⁓260 nm, respectively. A positive zeta potential value of + 30.5 mV for CeO2 NPs and + 22.5 mV for CeO2 @DDM NPs suggest sufficient stability and good dispersion of NPs in an aqueous solution. A combination of Thioflavin T fluorescence analysis and atomic force microscopy is used to assess the effect of nanoparticles on the formation of insulin amyloid fibrils. Results show that the fibrillization of insulin is inhibited by both, naked and modified NPs in a dose-dependent manner. However, while the IC50 of naked NPs is found to be ∼270 ± 13 µg/mL, the surface-modified NPs are 50% more efficient with IC50 equaled to 135 ± 7 µg/mL. In addition, both, the naked CeO2 NPs and DDM-modified NPs displayed an antioxidant activity expressed as oxidase-, catalase- and SOD-like activity. Therefore, the resulting nanosized material is very well suited to prove or disprove the hypothesis that oxidative stress plays a role in the formation of amyloid fibrils.
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Affiliation(s)
- Ivana Garcarova
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Kosice, Slovakia
| | - Eva Valusova
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Kosice, Slovakia
| | - Yuliia Shlapa
- Department of Solid-State Chemistry, V. I. Vernadsky Institute of General & Inorganic Chemistry of the NAS of Ukraine, 32/34 Palladina ave., Kyiv 03142, Ukraine
| | - Anatolii Belous
- Department of Solid-State Chemistry, V. I. Vernadsky Institute of General & Inorganic Chemistry of the NAS of Ukraine, 32/34 Palladina ave., Kyiv 03142, Ukraine
| | - Andrey Musatov
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Kosice, Slovakia.
| | - Katarina Siposova
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Kosice, Slovakia.
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9
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Antosova A, Gancar M, Bednarikova Z, Marek J, Bystrenova E, Gazova Z. The influence of cations on α-lactalbumin amyloid aggregation. J Biol Inorg Chem 2022; 27:679-689. [PMID: 36151481 PMCID: PMC9569292 DOI: 10.1007/s00775-022-01962-3] [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: 03/17/2022] [Accepted: 09/05/2022] [Indexed: 11/24/2022]
Abstract
There is limited knowledge regarding α-lactalbumin amyloid aggregation and its mechanism. We examined the formation of α-lactalbumin amyloid fibrils (α-LAF) in the presence of cations (Mg2+, Ca2+, Na+, K+, NH4+, and Cs+) in the form of chloride salts at two concentrations. We have shown that studied cations affect the conformation of α-lactalbumin, the kinetics of its amyloid formation, morphology, and secondary structure of α-LAF in a different manner. The higher salts concentration significantly accelerated the aggregation process. Both salt concentrations stabilized α-lactalbumin's secondary structure. However, the presence of divalent cations resulted in shorter fibrils with less β-sheet content. Moreover, strongly hydrated Mg2+ significantly altered α-lactalbumin's tertiary structure, followed by Na+, NH4+, K+, and weakly hydrated Cs+. On the other hand, Ca2+, despite being also strongly hydrated, stabilized the tertiary structure, supposedly due to its high affinity towards α-lactalbumin. Yet, Ca2+ was not able to inhibit α-lactalbumin amyloid aggregation.
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Affiliation(s)
- Andrea Antosova
- Institute of Experimental Physics Slovak Academy of Sciences, Watsonova 47, 040 01, Kosice, Slovakia
| | - Miroslav Gancar
- Institute of Experimental Physics Slovak Academy of Sciences, Watsonova 47, 040 01, Kosice, Slovakia
| | - Zuzana Bednarikova
- Institute of Experimental Physics Slovak Academy of Sciences, Watsonova 47, 040 01, Kosice, Slovakia
| | - Jozef Marek
- Institute of Experimental Physics Slovak Academy of Sciences, Watsonova 47, 040 01, Kosice, Slovakia
| | - Eva Bystrenova
- Consiglio Nazionale Delle Ricerche, Istituto Per Lo Studio Dei Materiali Nanostrutturati (CNR-ISMN), via P. Gobetti 101, 40129, Bologna, Italy.
| | - Zuzana Gazova
- Institute of Experimental Physics Slovak Academy of Sciences, Watsonova 47, 040 01, Kosice, Slovakia.
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Prebble DW, Er S, Hlushchuk I, Domanskyi A, Airavaara M, Ekins MG, Mellick GD, Carroll AR. α-Synuclein binding activity of the plant growth promoter asterubine. Bioorg Med Chem Lett 2022; 64:128677. [PMID: 35301136 DOI: 10.1016/j.bmcl.2022.128677] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/05/2022] [Accepted: 03/12/2022] [Indexed: 11/02/2022]
Abstract
Preventing the aggregation of certain amyloid proteins has the potential to slow down the progression of diseases like Alzheimer's, Parkinson's, and type 2 diabetes mellitus. During a high-throughput screen of 300 Australian marine invertebrate extracts, the extract of the marine sponge Thorectandra sp. 4408 displayed binding activity to the Parkinson's disease-associated protein, α-synuclein. Isolation of the active component led to its identification as the known plant growth promoter asterubine (1). This molecule shares distinct structural similarities with potent amyloid beta aggregation inhibitors tramiprosate (homotaurine) and ALZ-801. Herein we report the isolation, NMR data acquired in DMSO and α-synuclein binding activity of asterubine (1).
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Affiliation(s)
- Dale W Prebble
- School of Environment and Science, Griffith University (Gold Coast Campus), Parklands Drive, Southport, QLD 4222, Australia; Griffith Institute for Drug Discovery, Griffith University (Brisbane Innovation Park), Don Young Road, Nathan, QLD 4111, Australia
| | - Safak Er
- Faculty of Pharmacy, University of Helsinki, Helsinki 00014, Finland; Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00014, Finland
| | - Irena Hlushchuk
- Faculty of Pharmacy, University of Helsinki, Helsinki 00014, Finland
| | - Andrii Domanskyi
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00014, Finland
| | - Mikko Airavaara
- Faculty of Pharmacy, University of Helsinki, Helsinki 00014, Finland; Neuroscience Center, HiLIFE, University of Helsinki, Helsinki 00014, Finland
| | - Merrick G Ekins
- Griffith Institute for Drug Discovery, Griffith University (Brisbane Innovation Park), Don Young Road, Nathan, QLD 4111, Australia; Queensland Museum, South Brisbane BC, QLD 4101, Australia
| | - George D Mellick
- School of Environment and Science, Griffith University (Gold Coast Campus), Parklands Drive, Southport, QLD 4222, Australia; Griffith Institute for Drug Discovery, Griffith University (Brisbane Innovation Park), Don Young Road, Nathan, QLD 4111, Australia
| | - Anthony R Carroll
- School of Environment and Science, Griffith University (Gold Coast Campus), Parklands Drive, Southport, QLD 4222, Australia; Griffith Institute for Drug Discovery, Griffith University (Brisbane Innovation Park), Don Young Road, Nathan, QLD 4111, Australia.
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11
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Samantray S, Schumann W, Illig AM, Carballo-Pacheco M, Paul A, Barz B, Strodel B. Molecular Dynamics Simulations of Protein Aggregation: Protocols for Simulation Setup and Analysis with Markov State Models and Transition Networks. Methods Mol Biol 2022; 2340:235-79. [PMID: 35167078 DOI: 10.1007/978-1-0716-1546-1_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Protein disorder and aggregation play significant roles in the pathogenesis of numerous neurodegenerative diseases, such as Alzheimer's and Parkinson's diseases. The end products of the aggregation process in these diseases are highly structured amyloid fibrils. Though in most cases, small, soluble oligomers formed during amyloid aggregation are the toxic species. A full understanding of the physicochemical forces that drive protein aggregation is thus required if one aims for the rational design of drugs targeting the formation of amyloid oligomers. Among a multitude of biophysical and biochemical techniques that are employed for studying protein aggregation, molecular dynamics (MD) simulations at the atomic level provide the highest temporal and spatial resolution of this process, capturing key steps during the formation of amyloid oligomers. Here we provide a step-by-step guide for setting up, running, and analyzing MD simulations of aggregating peptides using GROMACS. For the analysis, we provide the scripts that were developed in our lab, which allow to determine the oligomer size and inter-peptide contacts that drive the aggregation process. Moreover, we explain and provide the tools to derive Markov state models and transition networks from MD data of peptide aggregation.
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12
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A P, Agrawal M, Dethe MR, Ahmed H, Yadav A, Gupta U, Alexander A. Nose-to-brain drug delivery for the treatment of Alzheimer's Disease: Current advancements and challenges. Expert Opin Drug Deliv 2022; 19:87-102. [PMID: 35040728 DOI: 10.1080/17425247.2022.2029845] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 12/16/2022]
Abstract
INTRODUCTION The irreversible destruction of neurons, progressive loss of memory and cognitive behavior, high cost of therapy, and impact on society desire a better, effective, and affordable treatment of AD. The nose-to-brain drug delivery approach holds a great potential to access the brain without any hindrance of BBB and result in higher bioavailability thus better therapeutic efficacy of anti-AD drugs. AREAS COVERED The present review article highlighted the current facts and worldwide statistics of AD and its detailed etiology. Followed by barriers to brain delivery, nose-to-brain delivery, their limitations, and amalgamation with various novel carrier systems. We have emphasized recent advancements in nose-to-brain delivery using mucoadhesive, stimuli-responsive carriers, polymeric nanoparticles, lipid nanoparticles, protein/peptide delivery for treatment of AD. EXPERT OPINION The available therapies are symptomatic, mitigate the symptoms of AD at the initial stages. In this lieu, nose-to-brain delivery has the ability to overcome these limitations and increase drug bioavailability in the brain. Various novel strategies including stimuli-responsive systems, nanoparticles, etc. enhance the nasal drug permeation, protects the drug, and enhance its therapeutic potency. Although, successful preclinical data does not assure the clinical success of the therapy and hence exhaustive clinical investigations are needed to make the therapy available for patients.
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Affiliation(s)
- Prabakaran A
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER-Guwahati), Sila, Changsari, Kamrup, Guwahati, Assam, India, 781101
| | - Mukta Agrawal
- School of Pharmacy & Technology Management, SVKM's Narsee Monjee Institute of Management Studies (NMIMS), Hyderabad, India, 509301
| | - Mithun Rajendra Dethe
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER-Guwahati), Sila, Changsari, Kamrup, Guwahati, Assam, India, 781101
| | - Hafiz Ahmed
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER-Guwahati), Sila, Changsari, Kamrup, Guwahati, Assam, India, 781101
| | - Awesh Yadav
- National Institute of Pharmaceutical Education and Research, Raebareli, Uttar Pradesh, India, 226002
| | - Umesh Gupta
- Department of Pharmacy, School of Chemical Sciences and Pharmacy, Central University of Rajasthan, Bandarsindri, Ajmer, Rajasthan, India, 305817
| | - Amit Alexander
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER-Guwahati), Sila, Changsari, Kamrup, Guwahati, Assam, India, 781101
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13
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Ziaunys M, Mikalauskaite K, Veiveris D, Sakalauskas A, Smirnovas V. Superoxide dismutase-1 alters the rate of prion protein aggregation and resulting fibril conformation. Arch Biochem Biophys 2022; 715:109096. [PMID: 34848178 DOI: 10.1016/j.abb.2021.109096] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/22/2021] [Accepted: 11/24/2021] [Indexed: 11/02/2022]
Abstract
The assembly of amyloidogenic proteins into highly-structured fibrillar aggregates is related to the onset and progression of several amyloidoses, including neurodegenerative Alzheimer's or Parkinson's diseases. Despite years of research and a general understanding of the process of such aggregate formation, there are currently still very few drugs and treatment modalities available. One of the factors that is relatively insufficiently understood is the cross-interaction between different amyloid-forming proteins. In recent years, it has been shown that several of these proteins or their aggregates can alter each other's fibrillization properties, however, there are still many unknowns in the amyloid interactome. In this work, we examine the interaction between amyloid disease-related prion protein and superoxide dismutase-1. We show that not only does superoxide dismutase-1 increase the lag time of prion protein fibril formation, but it also changes the conformation of the resulting aggregates.
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Affiliation(s)
- Mantas Ziaunys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
| | - Kamile Mikalauskaite
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Dominykas Veiveris
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Andrius Sakalauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Vytautas Smirnovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
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14
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Abu-Hussien M, Viswanathan GK, Simhaev L, Paul A, Engel H, Gazit E, Segal D. The contribution of individual residues of an aggregative hexapeptide derived from the human γD-crystallin to its amyloidogenicity. Int J Biol Macromol 2022; 201:182-92. [PMID: 34998884 DOI: 10.1016/j.ijbiomac.2021.12.192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/22/2021] [Accepted: 12/30/2021] [Indexed: 11/24/2022]
Abstract
Human γD-crystallin protein is abundant in the lens and is essential for preserving lens transparency. With age the protein may lose its native structure resulting in the formation of cataract. We recently reported an aggregative peptide, 41Gly-Cys-Trp-Met-Leu-Tyr46 from the human γD-crystallin, termed GDC6, exhibiting amyloidogenic properties in vitro. Here, we aimed to determine the contribution of each residue of the GDC6 to its amyloidogenicity. Molecular dynamic (MD) simulations revealed that the residues Trp, Leu, and Tyr played an important role in the amyloidogenicity of GDC6 by facilitating inter-peptide main-chain hydrogen bonds, and π-π interactions. MD predictions were further validated using single-, double- and triple-alanine-substituted GDC6 peptides in which their amyloidogenic propensity was individually evaluated using complementary biophysical techniques including Thioflavin T assay, turbidity assay, CD spectroscopy, and TEM imaging. Results revealed that the substitution of Trp, Leu, and Tyr together by Ala completely abolished aggregation of GDC6 in vitro, highlighting their importance in the amyloidogenicity of GDC6.
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15
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Caballero AB, Gamez P, Sabate R, Espargaró A. Anti-Amyloid Drug Screening Methods Using Bacterial Inclusion Bodies. Methods Mol Biol 2022; 2538:165-188. [PMID: 35951300 DOI: 10.1007/978-1-0716-2529-3_12] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Amyloid aggregation is linked to a number of human disorders that range from non-neurological illnesses such as type 2 diabetes to neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. The formation of insoluble protein aggregates with amyloid conformation inside bacteria, namely, in bacterial inclusion bodies, offers the possibility to use bacteria as simple models to study amyloid aggregation processes and potential effects of both anti-amyloid drugs and/or pro-aggregative compounds. This chapter describes fast, simple, inexpensive, highly reproducible, and tunable in vitro and in cellulo methods that use bacterial inclusion bodies as preliminary screening tools for anti-amyloid drugs.
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Affiliation(s)
- Ana B Caballero
- NanoBIC, Department of Inorganic and Organic Chemistry, Faculty of Chemistry, University of Barcelona, Barcelona, Catalonia, Spain
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, Barcelona, Catalonia, Spain
| | - Patrick Gamez
- NanoBIC, Department of Inorganic and Organic Chemistry, Faculty of Chemistry, University of Barcelona, Barcelona, Catalonia, Spain
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, Barcelona, Catalonia, Spain
- Catalan Institution for Research and Advanced Studies, Passeig Lluís Companys 23, Barcelona, Catalonia, Spain
| | - Raimon Sabate
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, Barcelona, Catalonia, Spain
- Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Catalonia, Spain
| | - Alba Espargaró
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, Barcelona, Catalonia, Spain.
- Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Catalonia, Spain.
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16
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Zhang Y, Liu Y, Zhao W, Sun Y. Hydroxylated single-walled carbon nanotube inhibits β2m 21-31 fibrillization and disrupts pre-formed proto-fibrils. Int J Biol Macromol 2021; 193:1-7. [PMID: 34687758 DOI: 10.1016/j.ijbiomac.2021.10.103] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 09/01/2021] [Revised: 10/11/2021] [Accepted: 10/14/2021] [Indexed: 11/17/2022]
Abstract
Pathological aggregation of amyloid polypeptides is associated with numerous degenerative diseases. Preventing aggregation and clearing amyloid deposits are considered as promising strategies against amyloidosis. With the capacity of crossing the blood-brain barrier and good biocompatibility, the hydroxylated single-walled carbon nanotube (SWCNT-OH) has been shown with excellent anti-amyloid properties. Here, we systematically studied the SWCNT-OH effects on the fibrillization of the β2m21-31 peptides utilizing all-atom discrete molecular dynamics (DMD) simulation. Our results demonstrated the isolated β2m21-31 peptides first nucleated into unstructured oligomers followed by coil-to-sheet conformational conversions in oligomers with at least six peptides. The elongation and lateral surfaces of the preformed β-sheet could catalyze the other unstructured monomers and small oligomers converted into β-sheet formations via dock-lock fibril growth and secondary nucleation processes. Eventually, the β2m21-31 peptides would self-assemble into well-ordered cross-β structures. Regardless of isolated monomers or well-defined cross-β assemblies, the β2m21-31 would attach on the surfaces of SWCNT-OH adopting unstructured formations indicating the SWCNT-OH not only inhibited the fibrillization of β2m21-31 but also destroyed pre-formed proto-fibrils. Overall, our study displays a complete picture of the fibrillization mechanism of β2m21-31 and the amyloid inhibitory mechanism of SWCNT-OH, offering new insight into the de-novo design of anti-amyloid inhibitors.
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Affiliation(s)
- Yu Zhang
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Yuying Liu
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Wenhui Zhao
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Yunxiang Sun
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China.
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17
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Lacroix E, Pereira L, Yoo B, Coyle KM, Chandhok S, Zapf R, Marijan D, Morin RD, Vlachos S, Harden N, Audas TE. Evolutionary conservation of systemic and reversible amyloid aggregation. J Cell Sci 2021; 134:273507. [PMID: 34704593 DOI: 10.1242/jcs.258907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 05/13/2021] [Accepted: 10/19/2021] [Indexed: 12/30/2022] Open
Abstract
In response to environmental stress, human cells have been shown to form reversible amyloid aggregates within the nucleus, termed amyloid bodies (A-bodies). These protective physiological structures share many of the biophysical characteristics associated with the pathological amyloids found in Alzheimer's and Parkinson's disease. Here, we show that A-bodies are evolutionarily conserved across the eukaryotic domain, with their detection in Drosophila melanogaster and Saccharomyces cerevisiae marking the first examples of these functional amyloids being induced outside of a cultured cell setting. The conditions triggering amyloidogenesis varied significantly among the species tested, with results indicating that A-body formation is a severe, but sublethal, stress response pathway that is tailored to the environmental norms of an organism. RNA-sequencing analyses demonstrate that the regulatory low-complexity long non-coding RNAs that drive A-body aggregation are both conserved and essential in human, mouse and chicken cells. Thus, the identification of these natural and reversible functional amyloids in a variety of evolutionarily diverse species highlights the physiological significance of this protein conformation, and will be informative in advancing our understanding of both functional and pathological amyloid aggregation events. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Emma Lacroix
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada.,Center for Cell Biology, Development, and Disease, Burnaby, BC V5A 1S6, Canada
| | - Lionel Pereira
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada.,Center for Cell Biology, Development, and Disease, Burnaby, BC V5A 1S6, Canada
| | - Byoungjoo Yoo
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Krysta M Coyle
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Sahil Chandhok
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada.,Center for Cell Biology, Development, and Disease, Burnaby, BC V5A 1S6, Canada
| | - Richard Zapf
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada.,Center for Cell Biology, Development, and Disease, Burnaby, BC V5A 1S6, Canada
| | - Dane Marijan
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada.,Center for Cell Biology, Development, and Disease, Burnaby, BC V5A 1S6, Canada
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Stephanie Vlachos
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Nicholas Harden
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada.,Center for Cell Biology, Development, and Disease, Burnaby, BC V5A 1S6, Canada
| | - Timothy E Audas
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada.,Center for Cell Biology, Development, and Disease, Burnaby, BC V5A 1S6, Canada
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18
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Strodel B. Energy landscapes of protein aggregation and conformation switching in intrinsically disordered proteins. J Mol Biol 2021; 433:167182. [PMID: 34358545 DOI: 10.1016/j.jmb.2021.167182] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/28/2021] [Accepted: 07/28/2021] [Indexed: 11/24/2022]
Abstract
The protein folding problem was apparently solved recently by the advent of a deep learning method for protein structure prediction called AlphaFold. However, this program is not able to make predictions about the protein folding pathways. Moreover, it only treats about half of the human proteome, as the remaining proteins are intrinsically disordered or contain disordered regions. By definition these proteins differ from natively folded proteins and do not adopt a properly folded structure in solution. However these intrinsically disordered proteins (IDPs) also systematically differ in amino acid composition and uniquely often become folded upon binding to an interaction partner. These factors preclude solving IDP structures by current machine-learning methods like AlphaFold, which also cannot solve the protein aggregation problem, since this meta-folding process can give rise to different aggregate sizes and structures. An alternative computational method is provided by molecular dynamics simulations that already successfully explored the energy landscapes of IDP conformational switching and protein aggregation in multiple cases. These energy landscapes are very different from those of 'simple' protein folding, where one energy funnel leads to a unique protein structure. Instead, the energy landscapes of IDP conformational switching and protein aggregation feature a number of minima for different competing low-energy structures. In this review, I discuss the characteristics of these multifunneled energy landscapes in detail, illustrated by molecular dynamics simulations that elucidated the underlying conformational transitions and aggregation processes.
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Affiliation(s)
- Birgit Strodel
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany; Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitätstrasse 1, 40225Düsseldorf, Germany
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19
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Ramshini H, Rostami S. Dual function of Selenium nanoparticles: Inhibition or induction of lysozyme amyloid aggregation and evaluation of their cell based cytotoxicity. Arch Ital Biol 2021; 159:82-94. [PMID: 34184240 DOI: 10.12871/00039829202123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Aberrant protein aggregation and the formation of amyloid deposits are associated with numerous neuro- and non-neurodegenerative disorders. Thus, one potential strategy is to eliminate these deposits by halting amyloid aggregation. Selenium nanoparticles (Se-NPs) have great potential in biomedicine for various therapeutic and diagnostic purposes and also have the ability to inhibit amyloid fibrillation. Herein, Hen Egg White Lysozyme (HEWL) was chosen as a protein model, and rod-like Se-NPs with diameters ranging from 90 to 120 nm were synthesized and the influence of shape and concentration of the particles on HEWL fibrillation was investigated. The effect of the nanoparticles on HEWL amyloid formation was analyzed using thioflavin T and Congo red binding assays, atomic force microscopy, and cytotoxicity assays. In the present study, it has been observed that these particles have a dual function in various concentrations. Using lower concentrations of Se-NPs ranging from 3-30 μg/ml, the Thioflavin T (ThT) fluorescence intensity decreased significantly by 60%, with an increased lag time compared to that of the control. While HEWL fibrillation substantially increased upon co-incubation with a higher concentration of these particles (300-2400μg/ml), and these results were verified by AFM, Congo red, and MTT assay. We showed that inhibitory or inductive influences of Se-NPs on the hen egg-white lysozyme (HEWL) amyloid aggregation are achieved via different independent mechanisms. These results demonstrate that dual-activity of Se-NPs might be a valuable targeting system for inhibiting amyloid aggregation, and thus, may play a useful role in new therapeutic and diagnostic strategies for amyloid-related disorders.
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Affiliation(s)
- H Ramshini
- Department of Biology, Payam Noor University, P. O. Box: 19395-3697, Tehran, Iran. E-mail:
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20
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Antosova A, Gancar M, Bednarikova Z, Marek J, Zahn D, Dutz S, Gazova Z. Surface-modified magnetite nanoparticles affect lysozyme amyloid fibrillization. Biochim Biophys Acta Gen Subj 2021; 1865:129941. [PMID: 34090976 DOI: 10.1016/j.bbagen.2021.129941] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 05/17/2021] [Accepted: 06/01/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND The surface of nanoparticles (NPs) is an important factor affecting the process of poly/peptides' amyloid aggregation. We have investigated the in vitro effect of trisodium citrate (TC), gum arabic (GA) and citric acid (CA) surface-modified magnetite nanoparticles (COAT-MNPs) on hen egg-white lysozyme (HEWL) amyloid fibrillization and mature HEWL fibrils. METHODS Dynamic light scattering (DLS) was used to characterize the physico-chemical properties of studied COAT-MNPs and determine the adsorption potential of their surface towards HEWL. The anti-amyloid properties were studied using thioflavin T (ThT) and tryptophan (Trp) intrinsic fluorescence assays, and atomic force microscopy (AFM). The morphology of amyloid aggregates was analyzed using Gwyddion software. The cytotoxicity of COAT-MNPs was determined utilizing Trypan blue (TB) assay. RESULTS Agents used for surface modification affect the COAT-MNPs physico-chemical properties and modulate their anti-amyloid potential. The results from ThT and intrinsic fluorescence showed that the inhibitory activities result from the more favorable interactions of COAT-MNPs with early pre-amyloid species, presumably reducing nuclei and oligomers formation necessary for amyloid fibrillization. COAT-MNPs also possess destroying potential, which is presumably caused by the interaction with hydrophobic residues of the fibrils, resulting in the interruption of an interface between β-sheets stabilizing the amyloid fibrils. CONCLUSION COAT-MNPs were able to inhibit HEWL fibrillization and destroy mature fibrils with different efficacy depending on their properties, TC-MNPs being the most potent nanoparticles. GENERAL SIGNIFICANCE The study reports findings regarding the general impact of nanoparticles' surface modifications on the amyloid aggregation of proteins.
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Affiliation(s)
- A Antosova
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Košice, Slovakia
| | - M Gancar
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Košice, Slovakia
| | - Z Bednarikova
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Košice, Slovakia
| | - J Marek
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Košice, Slovakia
| | - D Zahn
- Institute of Biomedical Engineering and Informatics (BMTI), Technische Universität Ilmenau, Ilmenau, Germany
| | - S Dutz
- Institute of Biomedical Engineering and Informatics (BMTI), Technische Universität Ilmenau, Ilmenau, Germany
| | - Z Gazova
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Košice, Slovakia.
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21
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Ghadami SA, Ahmadi Z, Moosavi-Nejad Z. The albumin-based nanoparticle formation in relation to protein aggregation. Spectrochim Acta A Mol Biomol Spectrosc 2021; 252:119489. [PMID: 33524819 DOI: 10.1016/j.saa.2021.119489] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 01/05/2021] [Accepted: 01/11/2021] [Indexed: 06/12/2023]
Abstract
Albumin is an attractive protein for the preparation of nanoparticle with possible therapeutic applications, due to its biodegradable, nontoxic, non-immunogenic, and metabolizable properties. Many studies have investigated the formation of albumin nanoparticles, generally by the desolvation or coacervation approaches. One of the most important parameters that should be considered in the formation of nanoparticles is their morphology (size and shape). There are many proposals to control the nanoparticle size, but it remains a challenge for researchers yet. In this study, we showed that control of BSA-based nanoparticles/microparticles size could be achieved by varying the temperature and pH and therefore controlling the rate of aggregation. The aggregation behavior was monitored by UV-Vis spectroscopy, SEM, and dye-binding assay. Our results provide more options for the size and shape control of BSA-based nanoparticle in natural buffer systems. The aggregation of BSA at different temperatures within the range of 50-80 °C were studied under the effect of different pHs in the range of 4.7-6.2. In this research, we found that protein aggregation under extreme conditions of pH and temperature, or at the pH near to pI appears to be amorphous, and at the pH above the pI seems to be the amyloid fibril structure. In some instances where the aggregation is neither too fast nor too slow, in the initial phase of the aggregation process, nanoparticle structures can be identified and separated by mechanistic approaches. This observation suggests that the best condition for monitoring the formation of albumin-based nanoparticles could be pH 5.7, 70 °C. Satisfactory rationalization of all aspects of our experimental observation requires further and more detailed study.
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Affiliation(s)
| | - Zahra Ahmadi
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
| | - Zahra Moosavi-Nejad
- Department of Biotechnology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.
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22
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Li C, Ma Y, Liu X, Huang R, Su R, Qi W, Che J, He Z. Synergistic effect of polystyrene nanoplastics and contaminants on the promotion of insulin fibrillation. Ecotoxicol Environ Saf 2021; 214:112115. [PMID: 33691242 DOI: 10.1016/j.ecoenv.2021.112115] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 02/11/2021] [Accepted: 02/26/2021] [Indexed: 06/12/2023]
Abstract
Nanoplastics (NPs) are becoming an emerging pollutant of global concern. A potential risk of NPs is that they can serve as carriers and synergistically function with other contaminants to cause diseases. A variety of diseases such as Alzheimer's disease are related to the generation of amyloid fibrils, and insulin is typically used as a model to study the fibrillation process. In this study, we examined the fibrillation of insulin promoted by polystyrene nanoplastics (PSNPs) alone and synergistically with organic contaminants (denoted as X, X = pyrene, bisphenol A, 2,2',4,4'-tetrabromodiphenyl ether, 4,4'-dihydroxydiphenylmethane, or 4-nonylphenol) having different polarities using thioflavin T fluorescence assays, dynamic light scattering, and circular dichroism spectroscopy. The presence of PSNPs and small organic contaminants decreased the lag phase time (tlag) for insulin fibrillation from 54.6 h to 35-51 h and their combination (PS-X) enhanced this process (tlag = 21-30 h). Notably, the lag phase time for insulin fibrillation with PS-nonpolar contaminants, PS-weakly polar contaminants, and PS-polar contaminants is around 20.8, 26.7, and 30.1 h, respectively, indicating the synergistic effect of PS-nonpolar contaminants or PS-weakly polar contaminants was more obvious than that of PS-polar contaminants. Moreover, molecular dynamic simulation reveal the interactions between insulin and PSs or small organic contaminants are primarily driven by van der Waals forces and hydrophobic interactions. Overall, the findings of this study underscore the potentially significant environmental impact of small organic contaminants assisting NPs in promoting insulin fibrillation.
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Affiliation(s)
- Chuanxi Li
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China
| | - Yingying Ma
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China
| | - Xiao Liu
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China; State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, PR China
| | - Renliang Huang
- School of Marine Science and Technology, Tianjin University, Tianjin 300072, PR China.
| | - Rongxin Su
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China; School of Marine Science and Technology, Tianjin University, Tianjin 300072, PR China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China.
| | - Wei Qi
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China.
| | - Jinjing Che
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, PR China
| | - Zhimin He
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
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23
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Ghosh N, Kundu LM. In-situ side-chain peptide cyclization as a breaker strategy against the amyloid aggregating peptide. Bioorg Med Chem 2021; 33:116017. [PMID: 33486160 DOI: 10.1016/j.bmc.2021.116017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 02/07/2023]
Abstract
Accumulation and deposition of misfolded amyloid β (Aβ) peptide outside the nerve cells are one of the major causes of Alzheimer's disease (AD). To date, one of the promising therapeutic strategies for AD is to block the early steps associated with the aggregation of Aβ peptide. We have developed synthetic breaker peptides derived from the original Aβ sequences that undergo self-cyclization in situ. We have focussed and replaced Val-18 (of Aβ) by side-chain modified glutamic acid (Glu-OBn) to generate adequate turn through in-situ peptide cyclization to disrupt the β-sheet structure of Aβ. The disruption of amyloid fibril formation and the mechanism of the 'inhibition of aggregation' were studied by various biophysical methods, such as ThT-assay, TEM, Congo-red birefringence study. CD and FTIR spectroscopy were used to characterize the conformational change during the aggregation process. Results suggest that designed breaker peptides may be useful to inhibit and disrupt not only Aβ peptide but related peptides that undergo aggregation.
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Ziaunys M, Sakalauskas A, Mikalauskaite K, Smirnovas V. Exploring the occurrence of thioflavin-T-positive insulin amyloid aggregation intermediates. PeerJ 2021; 9:e10918. [PMID: 33614299 PMCID: PMC7881721 DOI: 10.7717/peerj.10918] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 11/05/2020] [Accepted: 01/18/2021] [Indexed: 12/12/2022] Open
Abstract
The aggregation of proteins is considered to be the main cause of several neurodegenerative diseases. Despite much progress in amyloid research, the process of fibrillization is still not fully understood, which is one of the main reasons why there are still very few effective treatments available. When the aggregation of insulin, a model amyloidogenic protein, is tracked using thioflavin-T (ThT), an amyloid specific dye, there is an anomalous occurrence of double-sigmoidal aggregation kinetics. Such an event is likely related to the formation of ThT-positive intermediates, which may affect the outcome of both aggregation kinetic data, as well as final fibril structure. In this work we explore insulin fibrillization under conditions, where both normal and double-sigmoidal kinetics are observed and show that, despite their dye-binding properties and random occurrence, the ThT-positive intermediates do not significantly alter the overall aggregation process.
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Affiliation(s)
- Mantas Ziaunys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Andrius Sakalauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Kamile Mikalauskaite
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Vytautas Smirnovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
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25
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Camino JD, Gracia P, Cremades N. The role of water in the primary nucleation of protein amyloid aggregation. Biophys Chem 2020; 269:106520. [PMID: 33341693 DOI: 10.1016/j.bpc.2020.106520] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/26/2020] [Accepted: 11/30/2020] [Indexed: 12/18/2022]
Abstract
The understanding of the complex conformational landscape of amyloid aggregation and its modulation by relevant physicochemical and cellular factors is a prerequisite for elucidating some of the molecular basis of pathology in amyloid related diseases, and for developing and evaluating effective disease-specific therapeutics to reduce or eliminate the underlying sources of toxicity in these diseases. Interactions of proteins with solvating water have been long considered to be fundamental in mediating their function and folding; however, the relevance of water in the process of protein amyloid aggregation has been largely overlooked. Here, we provide a perspective on the role water plays in triggering primary amyloid nucleation of intrinsically disordered proteins (IDPs) based on recent experimental evidences. The initiation of amyloid aggregation likely results from the synergistic effect between both protein intermolecular interactions and the properties of the water hydration layer of the protein surface. While the self-assembly of both hydrophobic and hydrophilic IDPs would be thermodynamically favoured due to large water entropy contributions, large desolvation energy barriers are expected, particularly for the nucleation of hydrophilic IDPs. Under highly hydrating conditions, primary nucleation is slow, being facilitated by the presence of nucleation-active surfaces (heterogeneous nucleation). Under conditions of poor water activity, such as those found in the interior of protein droplets generated by liquid-liquid phase separation, however, the desolvation energy barrier is significantly reduced, and nucleation can occur very rapidly in the bulk of the solution (homogeneous nucleation), giving rise to structurally distinct amyloid polymorphs. Water, therefore, plays a key role in modulating the transition free energy of amyloid nucleation, thus governing the initiation of the process, and dictating the type of preferred primary nucleation and the type of amyloid polymorph generated, which could vary depending on the particular microenvironment that the protein molecules encounter in the cell.
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Affiliation(s)
- José D Camino
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Unit BIFI-IQFR(CSIC), Universidad de Zaragoza, Zaragoza 50018, Spain
| | - Pablo Gracia
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Unit BIFI-IQFR(CSIC), Universidad de Zaragoza, Zaragoza 50018, Spain
| | - Nunilo Cremades
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Unit BIFI-IQFR(CSIC), Universidad de Zaragoza, Zaragoza 50018, Spain.
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26
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Saghir AE, Farrugia G, Vassallo N. The human islet amyloid polypeptide in protein misfolding disorders: Mechanisms of aggregation and interaction with biomembranes. Chem Phys Lipids 2020; 234:105010. [PMID: 33227292 DOI: 10.1016/j.chemphyslip.2020.105010] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/06/2020] [Accepted: 11/09/2020] [Indexed: 02/09/2023]
Abstract
Human islet amyloid polypeptide (hIAPP), otherwise known as amylin, is a 37-residue peptide hormone which is reported to be a common factor in protein misfolding disorders such as type-2 diabetes mellitus, Alzheimer's disease and Parkinson's disease, due to deposition of insoluble hIAPP amyloid in the pancreas and brain. Multiple studies point to the importance of the peptide's interaction with biological membranes and the cytotoxicity of hIAPP species. Here, we discuss the aggregation pathways of hIAPP amyloid fibril formation and focus on the complex interplay between membrane-mediated assembly of hIAPP and the associated mechanisms of membrane damage caused by the peptide species. Mitochondrial membranes, which are unique in their lipid composition, are proposed as prime targets for the early intracellular formation of hIAPP toxic entities. We suggest that future studies should include more physiologically-relevant and in-cell studies to allow a more accurate model of in vivo interactions. Finally, we underscore an urgent need for developing effective therapeutic strategies aimed at hindering hIAPP-phospholipid interactions.
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Affiliation(s)
- Adam El Saghir
- Dept. of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta; Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Gianluca Farrugia
- Dept. of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta; Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Neville Vassallo
- Dept. of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta; Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta.
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27
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Siposova K, Kozar T, Stupakova M, Musatov A. Complementary experimental and computational analysis of the effects of non-ionic detergents and phospholipids on insulin amyloid aggregation. Colloids Surf B Biointerfaces 2020; 197:111428. [PMID: 33129101 DOI: 10.1016/j.colsurfb.2020.111428] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 07/13/2020] [Revised: 10/05/2020] [Accepted: 10/17/2020] [Indexed: 10/23/2022]
Abstract
Amphiphilic compounds, both detergents and lipids, are important tools for in vitro analysis of water-soluble and integral membrane proteins. A key question is whether these two groups of amphiphilic molecules use the same pathway to affect structural and functional integrity of proteins. In the present study, we tested the effect of non-ionic detergent dodecyl maltoside (DDM), two phospholipids, 1,2-dimyristoyl-sn-glycero-3- phosphocholine (DMPC), 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC), and the detergent-phospholipid mixtures on insulin amyloidogenesis in vitro. Amyloidogenesis of insulin is significantly affected by DDM in a time-and dose-dependent manner, but only slightly affected by either of phospholipids. Addition of DHPC or DMPC to detergent does not alter the inhibiting pattern, suggesting that DDM preferably binds to insulin. The molecular modeling revealed that DDM and the phospholipids occupy equivalent binding sites. DDM, due to the presence of maltose with several oxygen atoms (hydroxylic, glycosidic and ring) is involved in more hydrogen bonds than DHPC or DMPC. Hydrophobic interactions are important factors to stabilize both, DDM and phospholipids in their binding sites. Our results indicate that certain detergents (applying DDM as an example) and selected phospholipids are not always interchangeable in their use to investigate the effect of amphiphilic compounds on the behavior of amyloid-prone proteins.
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Affiliation(s)
- Katarina Siposova
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Kosice, Slovakia.
| | - Tibor Kozar
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, P. J. Safarik University, Jesenna 5, 040 01 Kosice, Slovakia.
| | - Michaela Stupakova
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Kosice, Slovakia
| | - Andrey Musatov
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Kosice, Slovakia
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28
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Marasco D, Vicidomini C, Krupa P, Cioffi F, Huy PDQ, Li MS, Florio D, Broersen K, De Pandis MF, Roviello GN. Plant isoquinoline alkaloids as potential neurodrugs: A comparative study of the effects of benzo[c]phenanthridine and berberine-based compounds on β- amyloid aggregation. Chem Biol Interact 2021; 334:109300. [PMID: 33098838 DOI: 10.1016/j.cbi.2020.109300] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/17/2020] [Accepted: 10/21/2020] [Indexed: 12/15/2022]
Abstract
Herein we present a comparative study of the effects of isoquinoline alkaloids belonging to benzo[c]phenanthridine and berberine families on β-amyloid aggregation. Results obtained using a Thioflavine T (ThT) fluorescence assay and circular dichroism (CD) spectroscopy suggested that the benzo[c]phenanthridine nucleus, present in both sanguinarine and chelerythrine molecules, was directly involved in an inhibitory effect of Aβ1-42 aggregation. Conversely, coralyne, that contains the isomeric berberine nucleus, significantly increased propensity for Aβ1-42 to aggregate. Surface Plasmon Resonance (SPR) experiments provided quantitative estimation of these interactions: coralyne bound to Aβ1-42 with an affinity (KD = 11.6 μM) higher than benzo[c]phenanthridines. Molecular docking studies confirmed that all three compounds are able to recognize Aβ1-42 in different aggregation forms suggesting their effective capacity to modulate the Aβ1-42 self-recognition mechanism. Molecular dynamics simulations indicated that coralyne increased the β-content of Aβ1-42, in early stages of aggregation, consistent with fluorescence-based promotion of the Aβ1-42 self-recognition mechanism by this alkaloid. At the same time, sanguinarine induced Aβ1-42 helical conformation corroborating its ability to delay aggregation as experimentally proved in vitro. The investigated compounds were shown to interfere with aggregation of Aβ1-42 demonstrating their potential as starting leads for the development of therapeutic strategies in neurodegenerative diseases.
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Mondal S, Vashi Y, Ghosh P, Roy D, Barthakur M, Kumar S, Iyer PK. Amyloid Targeting "Artificial Chaperone" Impairs Oligomer Mediated Neuronal Damage and Mitochondrial Dysfunction Associated with Alzheimer's Disease. ACS Chem Neurosci 2020; 11:3277-3287. [PMID: 32941009 DOI: 10.1021/acschemneuro.0c00387] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 12/20/2022] Open
Abstract
Alzheimer's disease (AD) is an irreversible memory disorder associated with multiple neuropathological events including amyloid aggregation that triggers oxidative stress and mitochondrial dysfunction in humans. Herein, a new artificial chaperone, benzimidazole functionalized polyfluorene (PFBZ) is reported to efficiently sequester toxic amyloid beta (Aβ) by binding at their 'amyloidogenic domain' (Aβ16-21) with unprecedented selectivity and prevent amyloid-mediated neuronal damage in a wild-type (WT) mouse model. An accurate dose of PFBZ chaperone successfully attenuated an amyloid triggered internal hemorrhage and pyknosis in the cerebral cortex of WT mice. The structural advantage of the polymer results in an efficient Cu(II) chelation arresting a redox cycle to prevent reactive oxygen species (ROS) generation and protect mitochondria from ROS mediated damage. This was further evidenced by caspase activation and mitochondrial membrane potential (MMP) biomarkers and was complemented by brain histology and electron microscopy data which revealed that the PFBZ chaperone provided a protective coating over the amyloid surface and resists from interacting with cell membrane and prevents inducing toxicity. This conjugated polymer artificial chaperone-based nanodrug showed exceptional properties such as its multipotent and highly biocompatible nature, the first of its kind with specific amyloid (Aβ16-21) targeting behavior, bioimaging, and BBB permeability with a potential to suppress amyloid triggered neurotoxicity implicated in numerous human disorders through a rare synergistic mechanism.
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Affiliation(s)
- Subrata Mondal
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Yoya Vashi
- Department of Bioscience and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Priyam Ghosh
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Dhrubajyoti Roy
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Manash Barthakur
- Department of Zoology, Pub Kamrup College, Baihata Chariali, Kamrup 781381, Assam, India
| | - Sachin Kumar
- Department of Bioscience and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Parameswar Krishnan Iyer
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
- Center for Nanotechnology, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
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30
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Di Natale C, Florio D, Di Somma S, Di Matteo A, Federici L, Netti PA, Morelli G, Malfitano AM, Marasco D. Proteostasis unbalance of nucleophosmin 1 in Acute Myeloid Leukemia: An aggregomic perspective. Int J Biol Macromol 2020; 164:3501-3507. [PMID: 32890557 DOI: 10.1016/j.ijbiomac.2020.08.248] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [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: 05/18/2020] [Revised: 08/31/2020] [Accepted: 08/31/2020] [Indexed: 01/22/2023]
Abstract
The role exerted by the nucleus in the regulation of proteostasis in both health and disease is recognized of outmost importance, even though not fully understood. Many recent investigations are focused on its ability to modulate and coordinate protein quality control machineries in mammalian cells. Nucleophosmin 1 (NPM1) is one of the most abundant nucleolar proteins and its gene is mutated in ~30% of Acute Myeloid Leukemia (AML) patients. Mutations are localized in the C-terminal domain of the protein and cause cytoplasmatically delocalized and possibly aggregated forms of NPM1 (NPM1c+). Therapeutic interventions targeted on NPM1c+ are in demand and, to this end, deeper knowledge of NPM1c+ behavior in the blasts' cytosol is required. Here by means of complementary biophysical techniques we compared the conformational and aggregative behavior of the entire C-terminal domains of NPM1wt and type A NPM1c+ (bearing the most common mutation). Overall data show that only Cterm_mutA is able to form amyloid-like assemblies with fibrillar morphology and that the oligomers are toxic in human neuroblastoma SHSY cells. This study adds a novel piece of knowledge to the comprehension of the molecular roles exerted by cytoplasmatic NPM1c+ and suggests the exploitation of the amyloidogenic propensity of NPM1c+ as a new strategy for targeting AML with NPM1 mutations.
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Affiliation(s)
- Concetta Di Natale
- Department of Pharmacy, University of Naples "Federico II", 80134, Italy; Center for Advanced Biomaterial for Health Care (CABHC), Istituto Italiano di Tecnologia, Naples, Italy; Interdisciplinary Research Centre on Biomaterials (CRIB), University of Naples Federico II, P.le Tecchio 80, Naples 80125, Italy
| | - Daniele Florio
- Department of Pharmacy, University of Naples "Federico II", 80134, Italy
| | - Sarah Di Somma
- Department of Translational Medical Science, University of Naples Federico II, 80131 Napoli, Italy
| | - Adele 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, 00185 Rome, Italy
| | - Luca Federici
- Center of Advanced Studies and Technology (CAST) and Department of Clinical, Oral and Biotechnological Sciences, University of Chieti "G. d'Annunzio", 66100 Chieti, Italy
| | - Paolo Antonio Netti
- Center for Advanced Biomaterial for Health Care (CABHC), Istituto Italiano di Tecnologia, Naples, Italy; Interdisciplinary Research Centre on Biomaterials (CRIB), University of Naples Federico II, P.le Tecchio 80, Naples 80125, Italy; Department of Chemical Materials and Industrial Production (DICMAPI), University of Naples Federico II, P.le Tecchio 80, Naples 80125, Italy
| | - Giancarlo Morelli
- Department of Pharmacy, University of Naples "Federico II", 80134, Italy
| | - Anna Maria Malfitano
- Department of Translational Medical Science, University of Naples Federico II, 80131 Napoli, Italy
| | - Daniela Marasco
- Department of Pharmacy, University of Naples "Federico II", 80134, Italy.
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31
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Liang J, Pitsillou E, Man AYL, Madzima S, Bresnehan SM, Nakai ME, Hung A, Karagiannis TC. Utilisation of the OliveNet™ Library to investigate phenolic compounds using molecular modelling studies in the context of Alzheimer's disease. Comput Biol Chem 2020; 87:107271. [PMID: 32521495 DOI: 10.1016/j.compbiolchem.2020.107271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 12/18/2019] [Revised: 04/24/2020] [Accepted: 04/26/2020] [Indexed: 01/05/2023]
Abstract
Alzheimer's disease (AD) is a debilitating neurodegenerative disease that affects over 47 million people worldwide, and is the most common form of dementia. There is a vast body of literature demonstrating that the disease is caused by an accumulation of toxic extracellular amyloid-β (Aβ) peptides and intracellular neurofibrillary tangles that consist of hyperphosphorylated tau. Adherence to the Mediterranean diet has been shown to reduce the incidence of AD and the phenolic compounds in extra virgin olive oil, including oleocanthal, have gained a significant amount of attention. A large number of these ligands have been described in the pre-existing literature and 222 of these compounds have been characterised in the OliveNet™ database. In this study, molecular docking was used to screen the 222 phenolic compounds from the OliveNet™ database and assess their ability to bind to various forms of the Aβ and tau proteins. The phenolic ligands were found to be binding strongly to the hairpin-turn of the Aβ1-40 and Aβ1-42 monomers, and binding sites were also identified in the tau fibril protein structures. Luteolin-4'-O-rutinoside, oleuricine A, isorhoifolin, luteolin-7-O-rutinoside, cyanidin-3-O-rutinoside and luteolin-7,4-O-diglucoside were predicted to be novel lead compounds. Molecular dynamics (MD) simulations performed using well-known olive ligands bound to Aβ1-42 oligomers highlighted that future work may examine potential anti-aggregating properties of novel compounds in the OliveNet™ database. This may lead to the development and evaluation of new compounds that may have efficacy against Alzheimer's disease.
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Affiliation(s)
- Julia Liang
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Prahran, VIC 3004, Australia; School of Science, RMIT University, VIC 3001, Australia
| | - Eleni Pitsillou
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Prahran, VIC 3004, Australia; Department of Microbiology and Immunology (Pathology), The University of Melbourne, Parkville, VIC 3052, Australia
| | - Abella Y L Man
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Prahran, VIC 3004, Australia; Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Sibonginkosi Madzima
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Prahran, VIC 3004, Australia; Department of Microbiology and Immunology (Pathology), The University of Melbourne, Parkville, VIC 3052, Australia
| | - Sarah M Bresnehan
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Prahran, VIC 3004, Australia; Department of Microbiology and Immunology (Pathology), The University of Melbourne, Parkville, VIC 3052, Australia
| | - Michael E Nakai
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Prahran, VIC 3004, Australia; Department of Microbiology and Immunology (Pathology), The University of Melbourne, Parkville, VIC 3052, Australia
| | - Andrew Hung
- School of Science, RMIT University, VIC 3001, Australia
| | - Tom C Karagiannis
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Prahran, VIC 3004, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3052, Australia.
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Konijnenberg E, Tijms BM, Gobom J, Dobricic V, Bos I, Vos S, Tsolaki M, Verhey F, Popp J, Martinez-Lage P, Vandenberghe R, Lleó A, Frölich L, Lovestone S, Streffer J, Bertram L, Blennow K, Teunissen CE, Veerhuis R, Smit AB, Scheltens P, Zetterberg H, Visser PJ. APOE ε4 genotype-dependent cerebrospinal fluid proteomic signatures in Alzheimer's disease. Alzheimers Res Ther 2020; 12:65. [PMID: 32460813 PMCID: PMC7254647 DOI: 10.1186/s13195-020-00628-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 05/06/2020] [Indexed: 02/04/2023]
Abstract
Background Aggregation of amyloid β into plaques in the brain is one of the earliest pathological events in Alzheimer’s disease (AD). The exact pathophysiology leading to dementia is still uncertain, but the apolipoprotein E (APOE) ε4 genotype plays a major role. We aimed to identify the molecular pathways associated with amyloid β aggregation using cerebrospinal fluid (CSF) proteomics and to study the potential modifying effects of APOE ε4 genotype. Methods We tested 243 proteins and protein fragments in CSF comparing 193 subjects with AD across the cognitive spectrum (65% APOE ε4 carriers, average age 75 ± 7 years) against 60 controls with normal CSF amyloid β, normal cognition, and no APOE ε4 allele (average age 75 ± 6 years). Results One hundred twenty-nine proteins (53%) were associated with aggregated amyloid β. APOE ε4 carriers with AD showed altered concentrations of proteins involved in the complement pathway and glycolysis when cognition was normal and lower concentrations of proteins involved in synapse structure and function when cognitive impairment was moderately severe. APOE ε4 non-carriers with AD showed lower expression of proteins involved in synapse structure and function when cognition was normal and lower concentrations of proteins that were associated with complement and other inflammatory processes when cognitive impairment was mild. Repeating analyses for 114 proteins that were available in an independent EMIF-AD MBD dataset (n = 275) showed that 80% of the proteins showed group differences in a similar direction, but overall, 28% effects reached statistical significance (ranging between 6 and 87% depending on the disease stage and genotype), suggesting variable reproducibility. Conclusions These results imply that AD pathophysiology depends on APOE genotype and that treatment for AD may need to be tailored according to APOE genotype and severity of the cognitive impairment.
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Affiliation(s)
- Elles Konijnenberg
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit Amsterdam, PO Box 7057, 1007 MB, Amsterdam, The Netherlands
| | - Betty M Tijms
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit Amsterdam, PO Box 7057, 1007 MB, Amsterdam, The Netherlands.
| | - Johan Gobom
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden.,Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Valerija Dobricic
- Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Lübeck, Germany
| | - Isabelle Bos
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit Amsterdam, PO Box 7057, 1007 MB, Amsterdam, The Netherlands.,Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Alzheimer Centre Limburg, Maastricht University, Maastricht, The Netherlands
| | - Stephanie Vos
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Alzheimer Centre Limburg, Maastricht University, Maastricht, The Netherlands
| | - Magda Tsolaki
- 1st Department of Neurology, AHEPA University Hospital, Thessaloniki, Macedonia, Greece
| | - Frans Verhey
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Alzheimer Centre Limburg, Maastricht University, Maastricht, The Netherlands
| | - Julius Popp
- Department of Psychiatry, University Hospital of Lausanne, Lausanne, Switzerland
| | - Pablo Martinez-Lage
- Department of Neurology, Center for Research and Advanced Therapies, CITA-Alzheimer Foundation, San Sebastian, Spain
| | | | - Alberto Lleó
- Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Lutz Frölich
- Department of Geriatric Psychiatry, Zentralinstitut für Seelische Gesundheit, University of Heidelberg, Mannheim, Germany
| | - Simon Lovestone
- Department of Psychiatry, University of Oxford, Oxford, UK.,Janssen R&D, Beerse, Belgium
| | - Johannes Streffer
- Early Clinical Neurology, UCB Biopharma SPRL, Braine-l'Alleud, Belgium.,Present Address: Janssen R&D, LLC, Beerse, Belgium
| | - Lars Bertram
- Lübeck Interdisciplinary Platform for Genome Analytics, University of Lübeck, Lübeck, Germany.,School of Public Health, Imperial College London, London, UK.,Department of Psychology, University of Oslo, Oslo, Norway
| | - Kaj Blennow
- Clinical Neurochemistry Lab, Institute of Neuroscience and Physiology, Sahlgrenska University Hospital, Mölndal, Sweden.,Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, University of Gothenburg, Mölndal, Sweden
| | - Charlotte E Teunissen
- Neurochemistry Laboratory and Biobank, Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Robert Veerhuis
- Neurochemistry Laboratory and Biobank, Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Department of Psychiatry, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - August B Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, The Netherlands
| | - Philip Scheltens
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit Amsterdam, PO Box 7057, 1007 MB, Amsterdam, The Netherlands
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, University of Gothenburg, Mölndal, Sweden.,Neurochemistry Laboratory and Biobank, Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK.,UK Dementia Research Institute, London, UK
| | - Pieter Jelle Visser
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit Amsterdam, PO Box 7057, 1007 MB, Amsterdam, The Netherlands.,Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Alzheimer Centre Limburg, Maastricht University, Maastricht, The Netherlands.,Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Instutet, Stockholm, Sweden
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Wood A, Chau E, Yang Y, Kim JR. A KLVFFAE-Derived Peptide Probe for Detection of Alpha-Synuclein Fibrils. Appl Biochem Biotechnol 2020; 190:1411-24. [PMID: 31776941 DOI: 10.1007/s12010-019-03197-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 11/11/2019] [Indexed: 12/27/2022]
Abstract
Aggregation of an amyloid protein, α-synuclein (αS), is a critical step in the neurodegenerative pathway of Parkinson's diseases (PD). Specific detection of amyloid conformers (i.e., monomers, oligomers, and fibrils) produced during αS aggregation is critical in better understanding a molecular basis of PD and developing a diagnostic tool. While various molecular probes are available for detection of αS fibrils, which may serve as a reservoir of toxic αS aggregate forms, these probes suffer from limited conformer-specificity and operational flexibility. In the present study, we explored the potential of non-self-aggregating peptides derived from the highly aggregation-prone KLVFFAE region of an amyloid protein, β-amyloid, as molecular probes for αS aggregates. We show that of the four peptides tested (KLVFWAK, ELVFWAE, and their C-terminal capping variants, all of which were attached with fluorescein isothiocyanate at their respective N-termini), KLVFWAK with C-terminal capping was selectively bound to αS fibrils over monomers and oligomers and readily used for monitoring αS fibrilization. Our analyses suggest that binding of the peptide to αS fibrils is mediated by both electrostatic and hydrophobic interactions. We anticipate that our peptide can readily be optimized for conformer-specificity and operational flexibility. Overall, this study presents the creation of a KLVFFAE-based molecular probe for αS fibrils and demonstrates fine-tuning of its conformer-specificity by terminal mutations and capping.
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Yakupova EI, Bobylev AG, Bobyleva LG, Vikhlyantsev IM. Study of the complement activation by amyloid aggregates of smooth muscle titin in vitro. J Immunoassay Immunochem 2019; 41:132-143. [PMID: 31744373 DOI: 10.1080/15321819.2019.1694943] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The giant muscle protein, titin, is the third most abundant protein in muscle (after myosin and actin). It was shown previously that smooth muscle titin (SMT) with a molecular mass of 500 kDa can form in vitro amorphous amyloid aggregates in two conditions: in solution of low ionic strength (0.15 M Glycine-KOH, pH 7.0) (SMT(Gly) aggregates) and in solution with ionic strength in the physiological range (0.2 M KCl, 20 mM imidazole, pH 7.2-7.4) (SMT(KCl) aggregates). Such aggregation in vivo, which may play a pathological or functional role, is not excluded. In view of the fact that some pathological amyloids can activate the classical and alternative pathways of complement system, we investigated the binding of complement component C1q and C3b to smooth muscle titin amyloid aggregates. The binding of С1q and C3b to SMT aggregates was not observed with ELISA assay. Since SMT aggregates do not activate the complement system, they are hardly implicated in the inflammatory process caused by muscle damage in amyloidoses.Abbreviations: SMT: smooth muscle titin; SMT(KCl) aggregates: SMT aggregates in solution containing 0.2 M KCl, 10 mM imidazole, pH 7.0; SMT(Gly) aggregates: SMT aggregates in solution containing 0.15 M glycine-KOH, pH 7.2-7.4; MAC: membrane attack complex; DLS: dynamic light scattering; NHS: Normal Human Serum.
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Affiliation(s)
- Elmira I Yakupova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Russia
| | - Alexander G Bobylev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Russia.,Faculty of Biophysics and medicobiological sciences, Pushchino State Institute of Natural Sciences, Pushchino, Russia
| | - Liya G Bobyleva
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Russia
| | - Ivan M Vikhlyantsev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Russia.,Faculty of Biophysics and medicobiological sciences, Pushchino State Institute of Natural Sciences, Pushchino, Russia
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Esmaeili S, Ghobadi N, Akbari V, Moradi S, Shahlaie M, Ghobadi S, Jalalvand AR, Amani M, Khodarahmi R. Pyridine-2,3-dicarboxylate, quinolinic acid, induces 1N4R Tau amyloid aggregation in vitro: Another evidence for the detrimental effect of the inescapable endogenous neurotoxin. Chem Biol Interact 2020; 315:108884. [PMID: 31678113 DOI: 10.1016/j.cbi.2019.108884] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 10/18/2019] [Accepted: 10/26/2019] [Indexed: 01/19/2023]
Abstract
Quinolinic acid (QA) known as a neuro-active metabolite associated with the kynurenine pathway. At high concentrations, QA is often involved in the initiation and development of several human neurologic diseases, like Alzheimer's disease. Because of the QA action as the NMDA receptor, it is considered as a potent excitotoxin in vivo. Since it is probable that different mechanisms are employed by QA, activation of NMDA receptors cannot fully explain the revealed toxicity and it is even believed that there are multiple unknown mechanisms/targets leading to QA cytotoxicity. Herein we report accelerated amyloid oligomerization of 1N4R Tau under the effect of QA, in vitro, then the molecular structure, morphology and toxicity of the protein aggregate were documented by using various theoretical/experimental approaches. The possible mechanism of action of QA-induced Tau oligomerization has also been explored.
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Lv Z, Hashemi M, Banerjee S, Zagorski K, Rochet JC, Lyubchenko YL. Assembly of α-synuclein aggregates on phospholipid bilayers. Biochim Biophys Acta Proteins Proteom 2019; 1867:802-812. [PMID: 31226488 PMCID: PMC6661114 DOI: 10.1016/j.bbapap.2019.06.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/29/2019] [Accepted: 06/14/2019] [Indexed: 01/17/2023]
Abstract
The spontaneous self-assembly of α-synuclein (α-syn) into aggregates of different morphologies is associated with the development of Parkinson's disease. However, the mechanism behind the spontaneous assembly remains elusive. The current study shows a novel effect of phospholipid bilayers on the assembly of the α-syn aggregates. Using time-lapse atomic force microscopy, it was discovered that α-syn assembles into aggregates on bilayer surfaces, even at the nanomolar concentration range. The efficiency of the aggregation process depends on the membrane composition, with the greatest efficiency observed for of 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-l-serine (POPS). Importantly, assembled aggregates can dissociate from the surface, suggesting that on-surface aggregation is a mechanism by which pathological aggregates may be produced. Computational modeling revealed that dimers of α-syn assembled rapidly, through the membrane-bound monomer on POPS bilayer, due to an aggregation-prone orientation of α-syn. Interaction of α-syn with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) leads to a binding mode that does not induce a fast assembly of the dimer. Based on these findings, we propose a model in which the interaction of α-syn with membranes plays a critical role initiating the formation of α-syn aggregates and the overall aggregation process.
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Affiliation(s)
- Zhengjian Lv
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, United States of America; Bruker Nano Surfaces Division, 112 Robin Hill Road, Goleta, Santa Barbara, CA 93117, United States of America
| | - Mohtadin Hashemi
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, United States of America
| | - Siddhartha Banerjee
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, United States of America
| | - Karen Zagorski
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, United States of America
| | - Jean-Christophe Rochet
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, United States of America; Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN, United States of America
| | - Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, United States of America.
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Vilasi S, Carrotta R, Ricci C, Rappa GC, Librizzi F, Martorana V, Ortore MG, Mangione MR. Inhibition of Aβ 1-42 Fibrillation by Chaperonins: Human Hsp60 Is a Stronger Inhibitor than Its Bacterial Homologue GroEL. ACS Chem Neurosci 2019; 10:3565-3574. [PMID: 31298838 DOI: 10.1021/acschemneuro.9b00183] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Alzheimer's disease is a chronic neurodegenerative disease characterized by the accumulation of pathological aggregates of amyloid beta peptide. Many efforts have been focused on understanding peptide aggregation pathways and on identification of molecules able to inhibit aggregation in order to find an effective therapy. As a result, interest in neuroprotective proteins, such as molecular chaperones, has increased as their normal function is to assist in protein folding or to facilitate the disaggregation and/or clearance of abnormal aggregate proteins. Using biophysical techniques, we evaluated the effects of two chaperones, human Hsp60 and bacterial GroEL, on the fibrillogenesis of Aβ1-42. Both chaperonins interfere with Aβ1-42 aggregation, but the effect of Hsp60 is more significant and correlates with its more pronounced flexibility and stronger interaction with ANS, an indicator of hydrophobic regions. Dose-dependent ThT fluorescence kinetics and SAXS experiments reveal that Hsp60 does not change the nature of the molecular processes stochastically leading to the formation of seeds, but strongly delays them by recognition of hydrophobic sites of some peptide species crucial for triggering amyloid formation. Hsp60 reduces the initial chaotic heterogeneity of Aβ1-42 sample at high concentration regimes. The understanding of chaperone action in counteracting pathological aggregation could be a starting point for potential new therapeutic strategies against neurodegenerative diseases.
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Affiliation(s)
- Silvia Vilasi
- Institute of Biophysics, National Research Council, Palermo 90146, Italy
| | - Rita Carrotta
- Institute of Biophysics, National Research Council, Palermo 90146, Italy
| | - Caterina Ricci
- Department of Life and Environmental Sciences, Marche Polytechnic University, Ancona 60131, Italy
| | | | - Fabio Librizzi
- Institute of Biophysics, National Research Council, Palermo 90146, Italy
| | - Vincenzo Martorana
- Institute of Biophysics, National Research Council, Palermo 90146, Italy
| | - Maria Grazia Ortore
- Department of Life and Environmental Sciences, Marche Polytechnic University, Ancona 60131, Italy
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Banerjee S, Lyubchenko YL. Interaction of Amyloidogenic Proteins with Membranes and Molecular Mechanism for the Development of Alzheimer's disease. Alzheimers Res Ther Open Access 2019; 2:106. [PMID: 33135011 PMCID: PMC7597641] [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] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Molecular mechanism of diseases like Alzheimer's disease (AD) and Parkinson's diseases (PD) is associated with misfolding of specific proteins, such as amyloid beta (Aβ) proteins in the case of AD, followed by their self-assembly into toxic oligomers along with the formation of amyloid fibrils assembled as plaques in the brain. Interaction of Aβ with membrane can lead to membrane damage; this process is considered as the major factor associated with the AD development. Additionally, membrane can facilitate the aggregation process of Aβ proteins. This important property of membranes is discussed in this review. A specific emphasis is given to the recently discovered property of cellular membranes to catalyze the initial step of Aβ aggregation process by which self-assembly of Aβ can be observed at physiologically low concentrations of Aβ proteins. At such low concentrations, no spontaneous aggregation occurs in the bulk solution. This fact was a major weakness of the protein aggregation model for AD. The catalytic property of membrane surfaces towards Aβ aggregation depends on the membrane composition. This finding suggests a number of novel ideas on the development of treatments and preventions for AD, which is briefly discussed in the review.
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Affiliation(s)
| | - YL Lyubchenko
- Corresponding author: Yuri L Lyubchenko Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA, Tel: 1-402-559-1971;
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Abstract
From that time AgNPs become one of the most accessible and important antibacterial agents in our world, thousands of papers published regarding investigating all aspects of these materials. When the time elapsed and novel methods contrived to follow the fingerprint of AgNPs in the in vivo models, some critical concerns and arguments also appeared between researchers about the safety of these compounds for living cells and vital organs. The paper by Dehvari and Ghahaghaei published in Volume 108 International Journal of Biological Macromolecules, pages 1128-1139 (Dehvari and Ghahghaei, 2018) suffered some errors from safety concerns to obscurities in the results essentially needing the amendment to enhance its quality. Though the author(s) idea is commended enough, nevertheless, I could not find a profound trace with their results, and my concerns are discussed in detail as the following lines.
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Affiliation(s)
- Hassan Rasouli
- Medical Biology Research Center (MBRC), Kermanshah University of Medical Science, Kermanshah, Iran..
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Di Natale C, La Manna S, Malfitano AM, Di Somma S, Florio D, Scognamiglio PL, Novellino E, Netti PA, Marasco D. Structural insights into amyloid structures of the C-terminal region of nucleophosmin 1 in type A mutation of acute myeloid leukemia. Biochim Biophys Acta Proteins Proteom 2019; 1867:637-644. [PMID: 30710643 DOI: 10.1016/j.bbapap.2019.01.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 01/11/2019] [Accepted: 01/26/2019] [Indexed: 12/22/2022]
Abstract
Acute myeloid leukemia (AML) is a clinically and a molecularly heterogeneous disease characterized by the accumulation of undifferentiated and uncontrolled proliferation of hematopoietic progenitor cells. The sub-group named "AML with gene mutations" includes mutations in nucleophosmin (NPM1) assumed as a distinct leukemic entity. NPM1 is an abundant multifunctional protein belonging to the nucleoplasmin family of nuclear chaperones. AML mutated protein is translocated into the cytoplasm (NPM1c+) retaining all functional domains except the loss of a unique NoLs (nucleolar localization signal) at the C-term domain (CTD) and the subsequent disruption of a three helix bundle as tertiary structure. The oligomeric state of NPM1 is of outmost importance for its biological roles and our previous studies linked an aggregation propensity of distinct regions of CTD to leukomogenic potentials of AML mutations. Here we investigated a polypeptide spanning the third and second helices of the bundle of type A mutated CTD. By a combination of several techniques, we ascertained the amyloid character of the aggregates and of fibrils resulting from a self-recognition mechanism. Further amyloid assemblies resulted cytoxic in MTT assay strengthening a new idea of a therapeutic strategy in AML consisting in the self-degradation of mutated NPM1.
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Affiliation(s)
- Concetta Di Natale
- Department of Pharmacy, University of Naples "Federico II", Italy; Center for Advanced Biomaterial for Health Care (CABHC), Istituto Italiano di Tecnologia, Naples, Italy
| | - Sara La Manna
- Department of Pharmacy, University of Naples "Federico II", Italy
| | | | - Sarah Di Somma
- Department of Translational Medicine, University of Naples "Federico II", Italy
| | - Daniele Florio
- Department of Pharmacy, University of Naples "Federico II", Italy
| | | | - Ettore Novellino
- Department of Pharmacy, University of Naples "Federico II", Italy
| | - Paolo Antonio Netti
- Center for Advanced Biomaterial for Health Care (CABHC), Istituto Italiano di Tecnologia, Naples, Italy
| | - Daniela Marasco
- Department of Pharmacy, University of Naples "Federico II", Italy.
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Boza-Serrano A, Ruiz R, Sanchez-Varo R, García-Revilla J, Yang Y, Jimenez-Ferrer I, Paulus A, Wennström M, Vilalta A, Allendorf D, Davila JC, Stegmayr J, Jiménez S, Roca-Ceballos MA, Navarro-Garrido V, Swanberg M, Hsieh CL, Real LM, Englund E, Linse S, Leffler H, Nilsson UJ, Brown GC, Gutierrez A, Vitorica J, Venero JL, Deierborg T. Galectin-3, a novel endogenous TREM2 ligand, detrimentally regulates inflammatory response in Alzheimer's disease. Acta Neuropathol 2019; 138:251-73. [PMID: 31006066 DOI: 10.1007/s00401-019-02013-z] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 04/12/2019] [Accepted: 04/12/2019] [Indexed: 12/15/2022]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disease in which the formation of extracellular aggregates of amyloid beta (Aβ) peptide, fibrillary tangles of intraneuronal tau and microglial activation are major pathological hallmarks. One of the key molecules involved in microglial activation is galectin-3 (gal3), and we demonstrate here for the first time a key role of gal3 in AD pathology. Gal3 was highly upregulated in the brains of AD patients and 5xFAD (familial Alzheimer's disease) mice and found specifically expressed in microglia associated with Aβ plaques. Single-nucleotide polymorphisms in the LGALS3 gene, which encodes gal3, were associated with an increased risk of AD. Gal3 deletion in 5xFAD mice attenuated microglia-associated immune responses, particularly those associated with TLR and TREM2/DAP12 signaling. In vitro data revealed that gal3 was required to fully activate microglia in response to fibrillar Aβ. Gal3 deletion decreased the Aβ burden in 5xFAD mice and improved cognitive behavior. Interestingly, a single intrahippocampal injection of gal3 along with Aβ monomers in WT mice was sufficient to induce the formation of long-lasting (2 months) insoluble Aβ aggregates, which were absent when gal3 was lacking. High-resolution microscopy (stochastic optical reconstruction microscopy) demonstrated close colocalization of gal3 and TREM2 in microglial processes, and a direct interaction was shown by a fluorescence anisotropy assay involving the gal3 carbohydrate recognition domain. Furthermore, gal3 was shown to stimulate TREM2-DAP12 signaling in a reporter cell line. Overall, our data support the view that gal3 inhibition may be a potential pharmacological approach to counteract AD.
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Trumbore CN, Paik J, Fay D, Vachet RW. Preliminary Capillary Flow Experiments with Amyloid-β, Possible Needle and Capillary Aβ Adsorption, and a Proposal for Drug Evaluation Under Shear Conditions. J Alzheimers Dis 2019; 72:751-760. [PMID: 31640094 PMCID: PMC6918921 DOI: 10.3233/jad-190522] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2019] [Indexed: 01/08/2023]
Abstract
Amyloid-β (Aβ) solution injections into an aqueous mobile phase moving through narrow bore stainless-steel capillary tubing results in adsorption of at least 99% Aβ within the tubing or injection valve. However, if flow is stopped for a period of 5-10 minutes, then started, wall desorption yields Aβ-containing molecules in the new effluent. The amount of desorbed Aβ-containing effluent depends on flow rate, period of flow cessation, and number of successive Aβ injections into the same tube without cleaning between injections. Unexpected multiple chromatographic peaks in these experiments seem to imply "separation" of released, previously adsorbed Aβ-containing products in the empty capillary tubing. These preliminary experiments raise questions about possible errors in Alzheimer's disease (AD) spinal tap analyses, which use stainless-steel needles of approximately the same inner diameter and encounter similar flow rates as those in our capillary experiments. Microliter syringes and HPLC connectors also contain stainless-steel tubing that have similar inner diameter dimensions and similar flow rates. The capillary system involved in these experiments has previously been proposed as a model system for studying the effects of shear on Aβ within the brain because it offers a research environment that provides highly restrictive flow through very small dimension channels. A suggestion is made for the use of this system in exploratory anti-amyloid drug studies in which both the drug and Aβ are injected in the same solution so that both drug and Aβ are subjected to the same shear environment. Reduction in adsorbed Aβ is suggested as an indicator of effective anti-Aβ drugs.
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Affiliation(s)
- Conrad N. Trumbore
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Jennie Paik
- Department of Chemistry, University of Massachusetts, Amhurst, MA, USA
| | - David Fay
- Department of Chemistry, University of Massachusetts, Amhurst, MA, USA
| | - Richard W. Vachet
- Department of Chemistry, University of Massachusetts, Amhurst, MA, USA
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43
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Sun Y, Kakinen A, Xing Y, Pilkington EH, Davis TP, Ke PC, Ding F. Nucleation of β-rich oligomers and β-barrels in the early aggregation of human islet amyloid polypeptide. Biochim Biophys Acta Mol Basis Dis 2018; 1865:434-444. [PMID: 30502402 DOI: 10.1016/j.bbadis.2018.11.021] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/10/2018] [Accepted: 11/26/2018] [Indexed: 10/27/2022]
Abstract
The self-assembly of human islet amyloid polypeptide (hIAPP) into β-sheet rich amyloid aggregates is associated with pancreatic β-cell death in type 2 diabetes (T2D). Prior experimental studies of hIAPP aggregation reported the early accumulation of α-helical intermediates before the rapid conversion into β-sheet rich amyloid fibrils, as also corroborated by our experimental characterizations with transmission electron microscopy and Fourier transform infrared spectroscopy. Although increasing evidence suggests that small oligomers populating early hIAPP aggregation play crucial roles in cytotoxicity, structures of these oligomer intermediates and their conformational conversions remain unknown, hindering our understanding of T2D disease mechanism and therapeutic design targeting these early aggregation species. We further applied large-scale discrete molecule dynamics simulations to investigate the oligomerization of full-length hIAPP, employing multiple molecular systems of increasing number of peptides. We found that the oligomerization process was dynamic, involving frequent inter-oligomeric exchanges. On average, oligomers had more α-helices than β-sheets, consistent with ensemble-based experimental measurements. However, in ~4-6% independent simulations, β-rich oligomers expected as the fibrillization intermediates were observed, especially in the pentamer and hexamer simulations. These β-rich oligomers could adopt β-barrel conformations, recently postulated to be the toxic oligomer species but only observed computationally in the aggregates of short amyloid protein fragments. Free-energy analysis revealed high energies of these β-rich oligomers, supporting the nucleated conformational changes of oligomers in amyloid aggregation. β-barrel oligomers of full-length hIAPP with well-defined three-dimensional structures may play an important pathological role in T2D etiology and may be a therapeutic target for the disease.
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Affiliation(s)
- Yunxiang Sun
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Aleksandr Kakinen
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Yanting Xing
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Emily H Pilkington
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia; Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Thomas P Davis
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia; Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Pu Chun Ke
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia.
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA.
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Siposova K, Sedlak E, Kozar T, Nemergut M, Musatov A. Dual effect of non-ionic detergent Triton X-100 on insulin amyloid formation. Colloids Surf B Biointerfaces 2018; 173:709-718. [PMID: 30384267 DOI: 10.1016/j.colsurfb.2018.10.039] [Citation(s) in RCA: 12] [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] [Received: 07/11/2018] [Revised: 10/10/2018] [Accepted: 10/15/2018] [Indexed: 10/28/2022]
Abstract
Atomic force microscopy, Thioflavin T (ThT) fluorescence assay, circular dichroism spectroscopy, differential scanning calorimetry, and molecular modeling techniques have been employed to investigate the amyloid aggregation of insulin in the presence of non-ionic detergent, Triton X-100 (TX-100). In contrast to recently described inhibition of lysozyme amyloid formation by non-ionic detergents (Siposova, 2017), the amyloid aggregation of insulin in the presence of sub-micellar TX-100 concentration exhibits two dissimilar phases. The first, inhibition phase, is observed at the protein to detergent molar ratio of 1:0.1 to 1:1. During this phase, the insulin amyloid fibril formation is inhibited by TX-100 up to ∼60%. The second, "morphological" phase, is observed at increasing detergent concentration, corresponding to protein:detergent molar ratio of ∼1:1 - 1:10. Under these conditions a significant increase of the steady-state ThT fluorescence intensities and a dramatically changed morphology of the insulin fibrils were observed. Increasing of the detergent concentration above the CMC led to complete inhibition of amyloidogenesis. Analysis of the experimental and molecular modeling results suggests an existence of up to six TX-100 binding sites within dimer of insulin with different binding energy. The physiological relevance of the results is discussed.
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Affiliation(s)
- Katarina Siposova
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01, Kosice, Slovakia.
| | - Erik Sedlak
- Center for Interdisciplinary Biosciences, TIP - P.J. Safarik University, Jesenna 5, 041 54, Kosice, Slovakia
| | - Tibor Kozar
- Center for Interdisciplinary Biosciences, TIP - P.J. Safarik University, Jesenna 5, 041 54, Kosice, Slovakia; Laboratory of Information Technologies, Joint Institute for Nuclear Research, Joliot-Curie 6, 141980, Dubna, Moscow Region, Russia
| | - Michal Nemergut
- Department of Biophysics, Faculty of Science, P.J. Safarik University, Jesenna 5, 041 54, Kosice, Slovakia
| | - Andrey Musatov
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01, Kosice, Slovakia
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Hornedo-Ortega R, Cerezo AB, Troncoso AM, Garcia-Parrilla MC. Corrigendum to "Protective effects of hydroxytyrosol against α-synuclein toxicity on PC12 cells and fibril formation" [Food Chem. Toxicol. 120 (2018) 41-49]. Food Chem Toxicol 2018; 121:719. [PMID: 30253891 DOI: 10.1016/j.fct.2018.09.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Ruth Hornedo-Ortega
- Departmento de Nutrición y Bromatología, Toxicología y Medicina Legal, Área de Nutrición y Bromatología, Facultad de Farmacia, Universidad de Sevilla, C/Profesor, García González, 2, 41012, Sevilla, Spain
| | - Ana B Cerezo
- Departmento de Nutrición y Bromatología, Toxicología y Medicina Legal, Área de Nutrición y Bromatología, Facultad de Farmacia, Universidad de Sevilla, C/Profesor, García González, 2, 41012, Sevilla, Spain
| | - Ana M Troncoso
- Departmento de Nutrición y Bromatología, Toxicología y Medicina Legal, Área de Nutrición y Bromatología, Facultad de Farmacia, Universidad de Sevilla, C/Profesor, García González, 2, 41012, Sevilla, Spain
| | - M Carmen Garcia-Parrilla
- Departmento de Nutrición y Bromatología, Toxicología y Medicina Legal, Área de Nutrición y Bromatología, Facultad de Farmacia, Universidad de Sevilla, C/Profesor, García González, 2, 41012, Sevilla, Spain.
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Tsunoda T, Takase M, Shigemori H. Structure-activity relationship of clovamide and its related compounds for the inhibition of amyloid β aggregation. Bioorg Med Chem 2018; 26:3202-3209. [PMID: 29706525 DOI: 10.1016/j.bmc.2018.04.044] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [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: 04/03/2018] [Revised: 04/18/2018] [Accepted: 04/20/2018] [Indexed: 11/29/2022]
Abstract
Alzheimer's disease (AD), a neurodegenerative disorder, is characterized by aggregation of amyloid β-protein (Aβ). Aβ aggregates through β-sheet formation and induces cytotoxicity against neuronal cells. Inhibition of Aβ aggregation by naturally occurring compounds is thus a promising strategy for the treatment of AD. We have already reported that caffeoylquinic acids and phenylethanoid glycosides, which possess two or more catechol moieties, strongly inhibited Aβ aggregation. Clovamide (1) containing two catechol moieties, isolated from cacao beans (Theobroma cacao L.), is believed to exhibit preventive effects on Aβ aggregation. To investigate the structure-activity relationship of clovamide (1) for the inhibition of Aβ aggregation, we synthesized 1 and related compounds 2-11 through reaction between l-DOPA, d-DOPA, l-tyrosine, or l-phenylalanine and caffeic acid, p-coumaric acid, or cinnamic acid, and compounds 12 and 13 were derived from 1. Among tested compounds 1-13, those containing one or two catechol moieties exhibited potent anti-aggregation activity, whereas the non-catechol-type related compounds showed little or no activity. This suggests that at least one catechol moiety is essential for inhibition of Aβ42 aggregation, and this activity increases depending on the number of catechol moieties. Consequently, clovamide (1) and its related compounds may be a promising therapeutic option for inhibiting Aβ-mediated pathology in AD.
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Affiliation(s)
- Tatsuhiko Tsunoda
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Mio Takase
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Hideyuki Shigemori
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan.
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Ge X, Sun Y, Ding F. Structures and dynamics of β-barrel oligomer intermediates of amyloid-beta16-22 aggregation. Biochim Biophys Acta Biomembr 2018; 1860:1687-1697. [PMID: 29550287 DOI: 10.1016/j.bbamem.2018.03.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 03/06/2018] [Accepted: 03/07/2018] [Indexed: 01/13/2023]
Abstract
Accumulating evidence suggests that soluble oligomers are more toxic than final fibrils of amyloid aggregations. Among the mixture of inter-converting intermediates with continuous distribution of sizes and secondary structures, oligomers in the β-barrel conformation - a common class of protein folds with a closed β-sheet - have been postulated as the toxic species with well-defined three-dimensional structures to perform pathological functions. A common mechanism for amyloid toxicity, therefore, implies that all amyloid peptides should be able to form β-barrel oligomers as the aggregation intermediates. Here, we applied all-atom discrete molecular dynamics (DMD) simulations to evaluate the formation of β-barrel oligomers and characterize their structures and dynamics in the aggregation of a seven-residue amyloid peptide, corresponding to the amyloid core of amyloid-β with a sequence of 16KLVFFAE22 (Aβ16-22). We carried out aggregation simulations with various numbers of peptides to study the size dependence of aggregation dynamics and assembly structures. Consistent with previous computational studies, we observed the formation of β-barrel oligomers in all-atom DMD simulations. Using a network-based approach to automatically identify β-barrel conformations, we systematically characterized β-barrels of various sizes. Our simulations revealed the conformational inter-conversion between β-barrels and double-layer β-sheets due to increased structural strains upon forming a closed β-barrel while maximizing backbone hydrogen bonds. The potential of mean force analysis further characterized the free energy barriers between these two states. The obtained structural and dynamic insights of β-barrel oligomers may help better understand the molecular mechanism of oligomer toxicities and design novel therapeutics targeting the toxic β-barrel oligomers. This article is part of a Special Issue entitled: Protein Aggregation and Misfolding at the Cell Membrane Interface edited by Ayyalusamy Ramamoorthy.
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Affiliation(s)
- Xinwei Ge
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Yunxiang Sun
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States.
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Abstract
Nanoimaging methods, atomic force microscopy (AFM) in particular, are widely used to study the interaction of biological molecules with the supported lipid bilayer (SLB), which itself is a traditional model for cellular membranes. Success in these studies is based on the availability of a stable SLB for the required observation period, which can extend several hours. The application of AFM requires that the SLB have a smooth morphology, thus enabling visualization of proteins and other molecules on its surface. Herein, we describe protocols for SLB assembly by using 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine (POPS) on a mica support. Our methodology enables us to assemble defect-free POPC and POPS SLBs that remain stable for at least 8 h. The application of such smooth and stable surfaces is illustrated by monitoring of the on-surface aggregation of amyloid proteins with the use of time-lapse AFM.
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Affiliation(s)
- Zhengjian Lv
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, USA
- Bruker Nano Surfaces Division, Santa Barbara, CA, USA
| | - Siddhartha Banerjee
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, USA
| | - Karen Zagorski
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, USA
| | - Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, USA.
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Socias SB, González-Lizárraga F, Avila CL, Vera C, Acuña L, Sepulveda-Diaz JE, Del-Bel E, Raisman-Vozari R, Chehin RN. Exploiting the therapeutic potential of ready-to-use drugs: Repurposing antibiotics against amyloid aggregation in neurodegenerative diseases. Prog Neurobiol 2017; 162:17-36. [PMID: 29241812 DOI: 10.1016/j.pneurobio.2017.12.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [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: 07/20/2017] [Revised: 12/07/2017] [Accepted: 12/07/2017] [Indexed: 01/02/2023]
Abstract
Neurodegenerative diseases are chronic and progressive disorders that affect specific regions of the brain, causing gradual disability and suffering that results in a complete inability of patients to perform daily functions. Amyloid aggregation of specific proteins is the most common biological event that is responsible for neuronal death and neurodegeneration in various neurodegenerative diseases. Therapeutic agents capable of interfering with the abnormal aggregation are required, but traditional drug discovery has fallen short. The exploration of new uses for approved drugs provides a useful alternative to fill the gap between the increasing incidence of neurodegenerative diseases and the long-term assessment of classical drug discovery technologies. Drug re-profiling is currently the quickest possible transition from bench to bedside. In this way, experimental evidence shows that some antibiotic compounds exert neuroprotective action through anti-aggregating activity on disease-associated proteins. The finding that many antibiotics can cross the blood-brain barrier and have been used for several decades without serious toxic effects makes them excellent candidates for therapeutic switching towards neurological disorders. The present review is, to our knowledge, the first extensive evaluation and analysis of the anti-amyloidogenic effect of different antibiotics on well-known disease-associated proteins. In addition, we propose a common structural signature derived from the antiaggregant antibiotic molecules that could be relevant to rational drug discovery.
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Affiliation(s)
- Sergio B Socias
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, and Instituto de Química Biológica "Dr. Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, UNT. Chacabuco 461, T4000ILI, San Miguel de Tucumán, Argentina, Argentina
| | - Florencia González-Lizárraga
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, and Instituto de Química Biológica "Dr. Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, UNT. Chacabuco 461, T4000ILI, San Miguel de Tucumán, Argentina, Argentina
| | - Cesar L Avila
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, and Instituto de Química Biológica "Dr. Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, UNT. Chacabuco 461, T4000ILI, San Miguel de Tucumán, Argentina, Argentina
| | - Cecilia Vera
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, and Instituto de Química Biológica "Dr. Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, UNT. Chacabuco 461, T4000ILI, San Miguel de Tucumán, Argentina, Argentina
| | - Leonardo Acuña
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, and Instituto de Química Biológica "Dr. Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, UNT. Chacabuco 461, T4000ILI, San Miguel de Tucumán, Argentina, Argentina; Sorbonne Universite, UPMC Univ Paris 06, INSERM, CNRS, UM75, U1127, UMR 7225, Institut du Cerveau et de la Moelle Epinière, Paris, France
| | - Julia E Sepulveda-Diaz
- Sorbonne Universite, UPMC Univ Paris 06, INSERM, CNRS, UM75, U1127, UMR 7225, Institut du Cerveau et de la Moelle Epinière, Paris, France
| | - Elaine Del-Bel
- Department of Morphology, Physiology and Stomatology, Faculty of Odontology of Ribeirão Preto, University of São Paulo, Brazil; Center of Interdisciplinary Research on Applied Neurosciences (NAPNA), University of São Paulo, Brazil
| | - Rita Raisman-Vozari
- Sorbonne Universite, UPMC Univ Paris 06, INSERM, CNRS, UM75, U1127, UMR 7225, Institut du Cerveau et de la Moelle Epinière, Paris, France.
| | - Rosana N Chehin
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, and Instituto de Química Biológica "Dr. Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, UNT. Chacabuco 461, T4000ILI, San Miguel de Tucumán, Argentina, Argentina.
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Cremades N, Dobson CM. The contribution of biophysical and structural studies of protein self-assembly to the design of therapeutic strategies for amyloid diseases. Neurobiol Dis 2017; 109:178-190. [PMID: 28709995 DOI: 10.1016/j.nbd.2017.07.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [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: 01/09/2017] [Revised: 06/26/2017] [Accepted: 07/10/2017] [Indexed: 01/26/2023] Open
Abstract
Many neurodegenerative disorders, including Alzheimer's, Parkinson's and the prion diseases, are characterized by a conformational conversion of normally soluble proteins or peptides into pathological species, by a process of misfolding and self-assembly that leads ultimately to the formation of amyloid fibrils. Recent studies support the idea that multiple intermediate species with a wide variety of degrees of neuronal toxicity are generated during such processes. The development of a high level of knowledge of the nature and structure of the pathogenic amyloid species would significantly enhance efforts to underline the molecular origins of these disorders and also to develop both accurate diagnoses and effective therapeutic interventions for these types of conditions. In this review, we discuss recent biophysical and structural information concerning different types of amyloid aggregates and the way in which such information can guide rational therapeutic approaches designed to target specific pathogenic events that occur during the development of these highly debilitating and increasingly common diseases.
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Affiliation(s)
- Nunilo Cremades
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Unit BIFI-IQFR(CSIC), Universidad de Zaragoza, Zaragoza 50018, Spain.
| | - Christopher M Dobson
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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