1
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Goto Y, Nakajima K, Yamamoto S, Yamaguchi K. Supersaturation, a Critical Factor Underlying Proteostasis of Amyloid Fibril Formation. J Mol Biol 2024; 436:168475. [PMID: 38311232 DOI: 10.1016/j.jmb.2024.168475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/10/2024]
Abstract
From a physicochemical viewpoint, amyloid fibril formation is a phase transition from soluble to crystal-like sates limited by supersaturation. It occurs only above solubility (i.e., the solubility limit) coupled with a breakdown of supersaturation. Although many studies have examined the role of molecular chaperones in the context of proteostasis, the role of supersaturation has not been addressed. Moreover, although molecular chaperone-dependent disaggregations have been reported for preformed amyloid fibrils, amyloid fibrils will not dissolve above the solubility of monomers, even if agitations fragment long fibrils to shorter amyloid particles. On the other hand, on considering a reversible and coupled equilibrium of interactions, folding/unfolding and amyloid formation/disaggregation, molecules stabilizing native states can work as a disaggregase reversing the amyloid fibrils to monomers. It is likely that the proteostasis network has various intra- and extracellular components which disaggregate preformed amyloid fibrils as well as prevent amyloid formation. Further studies with a view of solubility and supersaturation will be essential for comprehensive understanding of proteostasis.
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Affiliation(s)
- Yuji Goto
- Microsonochemistry Joint Research Chair, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Kichitaro Nakajima
- Microsonochemistry Joint Research Chair, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Suguru Yamamoto
- Division of Clinical Nephrology and Rheumatology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan
| | - Keiichi Yamaguchi
- Microsonochemistry Joint Research Chair, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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2
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Nakajima K, Ota T, Toda H, Yamaguchi K, Goto Y, Ogi H. Surface Modification of Ultrasonic Cavitation by Surfactants Improves Detection Sensitivity of α-Synuclein Amyloid Seeds. ACS Chem Neurosci 2024; 15:1643-1651. [PMID: 38546732 DOI: 10.1021/acschemneuro.4c00071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2024] Open
Abstract
The rapid amplification and sensitive detection of α-synuclein (αSyn) seeds is an efficient approach for the early diagnosis of Parkinson's disease. Ultrasonication stands out as a promising method for the rapid amplification of αSyn seeds because of its robust fibril fragmentation capability. However, ultrasonication also induces the primary nucleation of αSyn monomers, deteriorating the seed detection sensitivity by generating seed-independent fibrils. In this study, we show that an addition of surfactants to the αSyn monomer solution during αSyn seed detection under ultrasonication remarkably improves the detection sensitivity of the αSyn seeds by a factor of 100-1000. Chemical kinetic analysis reveals that these surfactants reduce the rate of primary nucleation while promoting the fragmentation of the αSyn fibrils under ultrasonication. These effects are attributed to the modification of the ultrasonic cavitation surface by the surfactants. Our study enhances the utility of ultrasonication in clinical assays targeting αSyn seeds as the Parkinson's disease biomarker.
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Affiliation(s)
- Kichitaro Nakajima
- Graduate School of Engineering, Osaka University, Yamadaoka 2-2, Suita, Osaka 565-0871, Japan
| | - Tomoki Ota
- Graduate School of Engineering, Osaka University, Yamadaoka 2-2, Suita, Osaka 565-0871, Japan
| | - Hajime Toda
- Graduate School of Engineering, Osaka University, Yamadaoka 2-2, Suita, Osaka 565-0871, Japan
| | - Keiichi Yamaguchi
- Graduate School of Engineering, Osaka University, Yamadaoka 2-2, Suita, Osaka 565-0871, Japan
| | - Yuji Goto
- Graduate School of Engineering, Osaka University, Yamadaoka 2-2, Suita, Osaka 565-0871, Japan
| | - Hirotsugu Ogi
- Graduate School of Engineering, Osaka University, Yamadaoka 2-2, Suita, Osaka 565-0871, Japan
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3
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Imomnazarov K, Lopez-Scarim J, Bagheri I, Joers V, Tansey MG, Martín-Peña A. Biochemical Fractionation of Human α-Synuclein in a Drosophila Model of Synucleinopathies. Int J Mol Sci 2024; 25:3643. [PMID: 38612454 PMCID: PMC11011978 DOI: 10.3390/ijms25073643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/19/2024] [Accepted: 03/19/2024] [Indexed: 04/14/2024] Open
Abstract
Synucleinopathies are a group of central nervous system pathologies that are characterized by the intracellular accumulation of misfolded and aggregated α-synuclein in proteinaceous depositions known as Lewy Bodies (LBs). The transition of α-synuclein from its physiological to pathological form has been associated with several post-translational modifications such as phosphorylation and an increasing degree of insolubility, which also correlate with disease progression in post-mortem specimens from human patients. Neuronal expression of α-synuclein in model organisms, including Drosophila melanogaster, has been a typical approach employed to study its physiological effects. Biochemical analysis of α-synuclein solubility via high-speed ultracentrifugation with buffers of increasing detergent strength offers a potent method for identification of α-synuclein biochemical properties and the associated pathology stage. Unfortunately, the development of a robust and reproducible method for the evaluation of human α-synuclein solubility isolated from Drosophila tissues has remained elusive. Here, we tested different detergents for their ability to solubilize human α-synuclein carrying the pathological mutation A53T from the brains of aged flies. We also assessed the effect of sonication on the solubility of human α-synuclein and optimized a protocol to discriminate the relative amounts of soluble/insoluble human α-synuclein from dopaminergic neurons of the Drosophila brain. Our data established that, using a 5% SDS buffer, the three-step protocol separates cytosolic soluble, detergent-soluble and insoluble proteins in three sequential fractions according to their chemical properties. This protocol shows that sonication breaks down α-synuclein insoluble complexes from the fly brain, making them soluble in the SDS buffer and thus enriching the detergent-soluble fraction of the protocol.
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Affiliation(s)
- Khondamir Imomnazarov
- Center for Translational Research in Neurodegenerative Disease, Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA; (K.I.); (J.L.-S.); (I.B.); (V.J.); (M.G.T.)
| | - Joshua Lopez-Scarim
- Center for Translational Research in Neurodegenerative Disease, Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA; (K.I.); (J.L.-S.); (I.B.); (V.J.); (M.G.T.)
| | - Ila Bagheri
- Center for Translational Research in Neurodegenerative Disease, Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA; (K.I.); (J.L.-S.); (I.B.); (V.J.); (M.G.T.)
| | - Valerie Joers
- Center for Translational Research in Neurodegenerative Disease, Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA; (K.I.); (J.L.-S.); (I.B.); (V.J.); (M.G.T.)
| | - Malú Gámez Tansey
- Center for Translational Research in Neurodegenerative Disease, Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA; (K.I.); (J.L.-S.); (I.B.); (V.J.); (M.G.T.)
- Fixel Institute for Neurological Diseases, Department of Neurology, University of Florida, Gainesville, FL 32610, USA
| | - Alfonso Martín-Peña
- Center for Translational Research in Neurodegenerative Disease, Department of Neuroscience, McKnight Brain Institute, University of Florida, Gainesville, FL 32610, USA; (K.I.); (J.L.-S.); (I.B.); (V.J.); (M.G.T.)
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4
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Imomnazarov K, Lopez-Scarim J, Bagheri I, Joers V, Tansey MG, Martín-Peña A. Biochemical fractionation of human α-Synuclein in a Drosophila model of synucleinopathies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.579034. [PMID: 38370694 PMCID: PMC10871193 DOI: 10.1101/2024.02.05.579034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Synucleinopathies are a group of central nervous system pathologies that are characterized by neuronal accumulation of misfolded and aggregated α-synuclein in proteinaceous depositions known as Lewy Bodies (LBs). The transition of α-synuclein from its physiological to pathological form has been associated with several post-translational modifications such as phosphorylation and an increasing degree of insolubility, which also correlate with disease progression in postmortem specimens from human patients. Neuronal expression of α-synuclein in model organisms, including Drosophila melanogaster, has been a typical approach employed to study its physiological effects. Biochemical analysis of α-synuclein solubility via high-speed ultracentrifugation with buffers of increasing detergent strength offers a potent method for identification of α-synuclein biochemical properties and the associated pathology stage. Unfortunately, the development of a robust and reproducible method for evaluation of human α-synuclein solubility isolated from Drosophila tissues has remained elusive. Here, we tested different detergents for their ability to solubilize human α-synuclein carrying the pathological mutation A53T from brains of aged flies. We also assessed the effect of sonication on solubility of human α-synuclein and optimized a protocol to discriminate relative amounts of soluble/insoluble human α-synuclein from dopaminergic neurons of the Drosophila brain. Our data established that, using a 5% SDS buffer, the 3-step protocol distinguishes between cytosolic soluble proteins in fraction 1, detergent-soluble proteins in fraction 2 and insoluble proteins in fraction 3. This protocol shows that sonication breaks down α-synuclein insoluble complexes from the fly brain, making them soluble in the SDS buffer and enriching fraction 2 of the protocol.
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Affiliation(s)
- Khondamir Imomnazarov
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute
| | - Joshua Lopez-Scarim
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute
| | - Ila Bagheri
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute
| | - Valerie Joers
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute
| | - Malú Gámez Tansey
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute
- Fixel Institute for Neurological Diseases, University of Florida
| | - Alfonso Martín-Peña
- Department of Neuroscience, Center for Translational Research in Neurodegenerative Disease, McKnight Brain Institute
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5
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Malik A, Khan JM, Al-Amri AM, Altwaijry N, Sharma P, Alhomida A, Sen P. Hexametaphosphate, a Common Food Additive, Aggregated the Hen Egg White Lysozyme. ACS OMEGA 2023; 8:44086-44092. [PMID: 38027328 PMCID: PMC10666150 DOI: 10.1021/acsomega.3c06210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 09/25/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023]
Abstract
Polyphosphate polymers are chains of phosphate monomers chemically bonded together via phosphoanhydride bonds. They are found in all prokaryotic and eukaryotic organisms and are among the earliest, most anionic, and most mysterious molecules known. They are everywhere, from small cellular components to additives in our food. There is a strong association between hyperphosphatemia and mortality. That is why it is crucial to assess how polyphosphates, as food additives, affect the quality of edible proteins. This study investigated the effect of inexpensive and widely used food additives (hexametaphosphate labeled as E452) on bakery items, meat products, fish, and soft drinks. Using various spectroscopic and microscopic techniques, we examined how hexametaphosphate affected the aggregation propensity, structure, and stability of a commonly used food protein: hen egg white lysozyme (HEWL). The solubility of HEWL is affected in a bimodal fashion by the concentration of hexametaphosphate. The bimodal concentration-dependent effect was also observed in the tertiary and secondary structural changes. Hexametaphosphate-induced HEWL aggregates were amorphous, as evidenced by ThT fluorescence, far-UV CD, and TEM imaging. This study showed that the food additive (hexametaphosphate) may denature and aggregate proteins and may lead to undesirable health issues.
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Affiliation(s)
- Ajamaluddin Malik
- Department
of Biochemistry, College of Science, King
Saud University, Riyadh 11451, Saudi Arabia
| | - Javed Masood Khan
- Department
of Food Science and Nutrition, Faculty of Food and Agricultural Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| | - Abdulaziz M. Al-Amri
- Department
of Biochemistry, College of Science, King
Saud University, Riyadh 11451, Saudi Arabia
| | - Nojood Altwaijry
- Department
of Biochemistry, College of Science, King
Saud University, Riyadh 11451, Saudi Arabia
| | - Prerna Sharma
- Geisinger
Commonwealth School of Medicine Scranton, Scranton, Pennsylvania 18509-3240, United States
| | - Abdullah Alhomida
- Department
of Biochemistry, College of Science, King
Saud University, Riyadh 11451, Saudi Arabia
| | - Priyankar Sen
- Centre
for Bioseparation Technology, VIT University, Vellore 632014, India
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6
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Roterman I, Stapor K, Konieczny L. Structural Specificity of Polymorphic Forms of α-Synuclein Amyloid. Biomedicines 2023; 11:biomedicines11051324. [PMID: 37238996 DOI: 10.3390/biomedicines11051324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/16/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
The structural transformation producing amyloids is a phenomenon that sheds new light on the protein folding problem. The analysis of the polymorphic structures of the α-synuclein amyloid available in the PDB database allows analysis of the amyloid-oriented structural transformation itself, but also the protein folding process as such. The polymorphic amyloid structures of α-synuclein analyzed employing the hydrophobicity distribution (fuzzy oil drop model) reveal a differentiation with a dominant distribution consistent with the micelle-like system (hydrophobic core with polar shell). This type of ordering of the hydrophobicity distribution covers the entire spectrum from the example with all three structural units (single chain, proto-fibril, super-fibril) exhibiting micelle-like form, through gradually emerging examples of local disorder, to structures with an extremely different structuring pattern. The water environment directing protein structures towards the generation of ribbon micelle-like structures (concentration of hydrophobic residues in the center of the molecule forming a hydrophobic core with the exposure of polar residues on the surface) also plays a role in the amyloid forms of α-synuclein. The polymorphic forms of α-synuclein reveal local structural differentiation with a common tendency to accept the micelle-like structuralization in certain common fragments of the polypeptide chain of this protein.
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Affiliation(s)
- Irena Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University-Medical College, Medyczna 7, 30-688 Krakow, Poland
| | - Katarzyna Stapor
- Department of Applied Informatics, Silesian University of Technology, Akademicka 2A, 44-100 Gliwice, Poland
| | - Leszek Konieczny
- Medical Biochemistry, Jagiellonian University-Medical College, Kopernika 7, 31-034 Krakow, Poland
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7
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Altwaijry N, Almutairi GS, Khan MS, Alokail MS, Alafaleq N, Ali R. The effect of novel antihypertensive drug valsartan on lysozyme aggregation: A combined in situ and in silico study. Heliyon 2023; 9:e15270. [PMID: 37123968 PMCID: PMC10130856 DOI: 10.1016/j.heliyon.2023.e15270] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 03/10/2023] [Accepted: 03/31/2023] [Indexed: 05/02/2023] Open
Abstract
Protein misfolding can result in amyloid fiber aggregation, which is associated with various types of diseases. Therefore, preventing or treating abnormally folded proteins may provide therapeutic intervention for these diseases. Valsartan (VAL) is an angiotensin II receptor blocker (ARB) that is used to treat hypertension. In this study, we examine the anti-aggregating effect of VAL against hen egg-white lysozyme (HEWL) amyloid fibrils through spectroscopy, docking, and microscopic analysis. In vitro formation of HEWL amyloid fibrils was indicated by increased turbidity, RLS (Rayleigh light scattering), and ThT fluorescence intensity. 10 μM VAL, amyloid/aggregation was inhibited up to 83% and 72% as measured by ThT and RLS respectively. In contrast, 100 μM VAL significantly increases the fibril aggregation of HEWL. CD spectroscopy results show a stabilization of HEWL α-helical structures in the presence of 10 μM VAL while the increase in β-sheet was detected at 100 μM concentration of VAL. The hydrophobicity of HEWL was increased at 100 μM VAL, suggesting the promotion of aggregation via its self-association. Steady-state quenching revealed that VAL and HEWL interact spontaneously via hydrogen bonds and van der Waals forces. Transmission electron microscopy (TEM) images illustrate that the needle-like fibers of HEWL amyloid were reduced at 10 μM VAL, while at 100 μM the fibrils of amyloid were increased. Additionally, our computational studies showed that VAL could bind to two binding sites within HEWL. In the BS-1 domain of HEWL, VAL binds to ASN59, ILE98, ILE58, TRP108, VAL109, SER50, ASP52, ASN59, ALA107, and TRP108 residues with a binding energy of -9.72 kcal mol-1. Also, it binds to GLU7, ALA10, ALA11, CYS6, ARG128, and ARG14 in the BS-2 domain with a binding energy of -5.89 kcal mol-1. VAL, therefore, appears to have dual effect against HEWL aggregation. We suggest that VAL stabilizes HEWL's aggregation-prone region (APR) at 10 μM, preventing aggregation. Also, we assume that at 100 μM, VAL occupies BS-2 beside BS-1 and destabilizes the folding structure of HEWL, resulting in aggregation. Further studies are needed to investigate the mechanism of action and determine its potential side effects.
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Affiliation(s)
- Nojood Altwaijry
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
- Corresponding author.
| | - Ghaliah S. Almutairi
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohd Shahhnawaz Khan
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
- Corresponding author.
| | - Majed S. Alokail
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Nouf Alafaleq
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Rizwan Ali
- King Abdullah International Medial Research Center (KAIMRC), Medical Research Core Facility and Platforms (MRCFP), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Ministry of National Guard Health Affairs (MNGHA), Riyadh, 11481, Saudi Arabia
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8
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Effect of Antihypertensive Drug (Chlorothiazide) on Fibrillation of Lysozyme: A Combined Spectroscopy, Microscopy, and Computational Study. Int J Mol Sci 2023; 24:ijms24043112. [PMID: 36834523 PMCID: PMC9959601 DOI: 10.3390/ijms24043112] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/14/2023] [Accepted: 01/18/2023] [Indexed: 02/08/2023] Open
Abstract
Amyloid fibrils abnormally accumulate together in the human body under certain conditions, which can result in lethal conditions. Thus, blocking this aggregation may prevent or treat this disease. Chlorothiazide (CTZ) is a diuretic and is used to treat hypertension. Several previous studies suggest that diuretics prevent amyloid-related diseases and reduce amyloid aggregation. Thus, in this study we examine the effects of CTZ on hen egg white lysozyme (HEWL) aggregation using spectroscopic, docking, and microscopic approaches. Our results showed that under protein misfolding conditions of 55 °C, pH 2.0, and 600 rpm agitation, HEWL aggregated as evidenced by the increased turbidity and Rayleigh light scattering (RLS). Furthermore, thioflavin-T, as well as trans electron microscope (TEM) analysis confirmed the formation of amyloid structures. An anti-aggregation effect of CTZ is observed on HEWL aggregations. Circular dichroism (CD), TEM, and Thioflavin-T fluorescence show that both CTZ concentrations reduce the formation of amyloid fibrils as compared to fibrillated. The turbidity, RLS, and ANS fluorescence increase with CTZ increasing. This increase is attributed to the formation of a soluble aggregation. As evidenced by CD analysis, there was no significant difference in α-helix content and β-sheet content between at 10 µM CTZ and 100 µM. A TEM analysis of HEWL coincubated with CTZ at different concentrations validated all the above-mentioned results. The TEM results show that CTZ induces morphological changes in the typical structure of amyloid fibrils. The steady-state quenching study demonstrated that CTZ and HEWL bind spontaneously via hydrophobic interactions. HEWL-CTZ also interacts dynamically with changes in the environment surrounding tryptophan. Computational results revealed the binding of CTZ to ILE98, GLN57, ASP52, TRP108, TRP63, TRP63, ILE58, and ALA107 residues in HEWL via hydrophobic interactions and hydrogen bonds with a binding energy of -6.58 kcal mol-1. We suggest that at 10 µM and 100 μM, CTZ binds to the aggregation-prone region (APR) of HEWL and stabilizes it, thus preventing aggregation. Based on these findings, we can conclude that CTZ has antiamyloidogenic activity and can prevent fibril aggregation.
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9
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Singla D, Bhattacharya M. Salt-Induced Dissolution of Protein Aggregates. J Phys Chem B 2022; 126:8760-8770. [PMID: 36283072 DOI: 10.1021/acs.jpcb.2c06555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Protein aggregation is mediated by a complex interplay of noncovalent interactions and is associated with a broad range of aspects from debilitating human diseases to the food industry and therapeutic biotechnology. Deciphering the intricate roles of noncovalent interactions is of paramount importance for the design of effective inhibitory and disaggregation strategies, which remains a formidable challenge. By using a combination of spectroscopic and microscopic tools, here we show that the surfactant-mediated protein aggregation can be modulated by an intriguing interplay of hydrophobic and electrostatic effects. Additionally, our results illuminate the unique role of salt as a potent disaggregation inducer that alters the protein-surfactant electrostatic interactions and triggers the dissolution of preformed protein aggregates resulting in restoring the native protein structure. This unusual salt-induced dissolution and refolding offers a unique approach to regulating the balance between protein self-assembly and disassembly and will offer a potent strategy to design electrostatically targeted inhibitors.
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Affiliation(s)
- Deepika Singla
- School of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Thapar Technology Campus, Bhadson Road, Patiala, Punjab147004, India
| | - Mily Bhattacharya
- School of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Thapar Technology Campus, Bhadson Road, Patiala, Punjab147004, India
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10
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Supersaturation-Dependent Formation of Amyloid Fibrils. Molecules 2022; 27:molecules27144588. [PMID: 35889461 PMCID: PMC9321232 DOI: 10.3390/molecules27144588] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 07/11/2022] [Accepted: 07/12/2022] [Indexed: 01/27/2023] Open
Abstract
The supersaturation of a solution refers to a non-equilibrium phase in which the solution is trapped in a soluble state, even though the solute’s concentration is greater than its thermodynamic solubility. Upon breaking supersaturation, crystals form and the concentration of the solute decreases to its thermodynamic solubility. Soon after the discovery of the prion phenomena, it was recognized that prion disease transmission and propagation share some similarities with the process of crystallization. Subsequent studies exploring the structural and functional association between amyloid fibrils and amyloidoses solidified this paradigm. However, recent studies have not necessarily focused on supersaturation, possibly because of marked advancements in structural studies clarifying the atomic structures of amyloid fibrils. On the other hand, there is increasing evidence that supersaturation plays a critical role in the formation of amyloid fibrils and the onset of amyloidosis. Here, we review the recent evidence that supersaturation plays a role in linking unfolding/folding and amyloid fibril formation. We also introduce the HANABI (HANdai Amyloid Burst Inducer) system, which enables high-throughput analysis of amyloid fibril formation by the ultrasonication-triggered breakdown of supersaturation. In addition to structural studies, studies based on solubility and supersaturation are essential both to developing a comprehensive understanding of amyloid fibrils and their roles in amyloidosis, and to developing therapeutic strategies.
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11
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Moors TE, Mona D, Luehe S, Duran-Pacheco G, Spycher L, Mundigl O, Kaluza K, Huber S, Hug MN, Kremer T, Ritter M, Dziadek S, Dernick G, van de Berg WDJ, Britschgi M. Multi-platform quantitation of alpha-synuclein human brain proteoforms suggests disease-specific biochemical profiles of synucleinopathies. Acta Neuropathol Commun 2022; 10:82. [PMID: 35659116 PMCID: PMC9164351 DOI: 10.1186/s40478-022-01382-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/16/2022] [Indexed: 12/02/2022] Open
Abstract
Based on immunostainings and biochemical analyses, certain post-translationally modified alpha-synuclein (aSyn) variants, including C-terminally truncated (CTT) and Serine-129 phosphorylated (pSer129) aSyn, are proposed to be involved in the pathogenesis of synucleinopathies such as Parkinson’s disease with (PDD) and without dementia (PD), dementia with Lewy bodies (DLB), and multiple system atrophy (MSA). However, quantitative information about aSyn proteoforms in the human brain in physiological and different pathological conditions is still limited. To address this, we generated sequential biochemical extracts of the substantia nigra, putamen and hippocampus from 28 donors diagnosed and neuropathologically-confirmed with different synucleinopathies (PD/PDD/DLB/MSA), as well as Alzheimer’s disease, progressive supranuclear palsy, and aged normal subjects. The tissue extracts were used to build a reverse phase array including 65 aSyn antibodies for detection. In this multiplex approach, we observed increased immunoreactivity in donors with synucleinopathies compared to controls in detergent-insoluble fractions, mainly for antibodies against CT aSyn and pSer129 aSyn. In addition, despite of the restricted sample size, clustering analysis suggested disease-specific immunoreactivity signatures in patient groups with different synucleinopathies. We aimed to validate and quantify these findings using newly developed immunoassays towards total, 119 and 122 CTT, and pSer129 aSyn. In line with previous studies, we found that synucleinopathies shared an enrichment of post-translationally modified aSyn in detergent-insoluble fractions compared to the other analyzed groups. Our measurements allowed for a quantitative separation of PDD/DLB patients from other synucleinopathies based on higher detergent-insoluble pSer129 aSyn concentrations in the hippocampus. In addition, we found that MSA stood out due to enrichment of CTT and pSer129 aSyn also in the detergent-soluble fraction of the SN and putamen. Together, our results achieved by multiplexed and quantitative immunoassay-based approaches in human brain extracts of a limited sample set point to disease-specific biochemical aSyn proteoform profiles in distinct neurodegenerative disorders.
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12
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Development of HANABI, an ultrasonication-forced amyloid fibril inducer. Neurochem Int 2021; 153:105270. [PMID: 34954259 DOI: 10.1016/j.neuint.2021.105270] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/16/2021] [Accepted: 12/21/2021] [Indexed: 12/20/2022]
Abstract
Amyloid fibrils involved in amyloidoses are crystal-like aggregates, which are formed by breaking supersaturation of denatured proteins. Ultrasonication is an efficient method of agitation for breaking supersaturation and thus inducing amyloid fibrils. By combining an ultrasonicator and a microplate reader, we developed the HANABI (HANdai Amyloid Burst Inducer) system that enables high-throughput analysis of amyloid fibril formation. Among high-throughput approaches of amyloid fibril assays, the HANABI system has advantages in accelerating and detecting spontaneous amyloid fibril formation. HANABI is also powerful for amplifying a tiny amount of preformed amyloid fibrils by seeding. Thus, HANABI will contribute to creating therapeutic strategies against amyloidoses by identifying their biomarkers.
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13
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So M, Kimura Y, Yamaguchi K, Sugiki T, Fujiwara T, Aguirre C, Ikenaka K, Mochizuki H, Kawata Y, Goto Y. Polyphenol-solubility alters amyloid fibril formation of α-synuclein. Protein Sci 2021; 30:1701-1713. [PMID: 34046949 DOI: 10.1002/pro.4130] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/10/2021] [Accepted: 05/18/2021] [Indexed: 12/18/2022]
Abstract
Amyloid fibril formation is associated with various amyloidoses, including neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. Amyloid fibrils form above the solubility of amyloidogenic proteins or peptides upon breaking supersaturation, followed by a nucleation and elongation mechanism, which is similar to the crystallization of solutes. Many additives, including salts, detergents, and natural compounds, promote or inhibit amyloid formation. However, the underlying mechanisms of the opposing effects are unclear. We examined the effects of two polyphenols, that is, epigallocatechin gallate (EGCG) and kaempferol-7─O─glycoside (KG), with high and low solubilities, respectively, on the amyloid formation of α-synuclein (αSN). EGCG and KG inhibited and promoted amyloid formation of αSN, respectively, when monitored by thioflavin T (ThT) fluorescence or transmission electron microscopy (TEM). Nuclear magnetic resonance (NMR) analysis revealed that, although interactions of αSN with soluble EGCG increased the solubility of αSN, thus inhibiting amyloid formation, interactions of αSN with insoluble KG reduced the solubility of αSN, thereby promoting amyloid formation. Our study suggests that opposing effects of polyphenols on amyloid formation of proteins and peptides can be interpreted based on the solubility of polyphenols.
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Affiliation(s)
- Masatomo So
- Institute for Protein Research, Osaka University, Osaka, Japan.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Yuto Kimura
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Keiichi Yamaguchi
- Institute for Protein Research, Osaka University, Osaka, Japan.,Global Center for Medical Engineering and Informatics, Osaka University, Osaka, Japan
| | | | | | - Cesar Aguirre
- Institute for Protein Research, Osaka University, Osaka, Japan.,Department of Neurology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Kensuke Ikenaka
- Department of Neurology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Hideki Mochizuki
- Department of Neurology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yasushi Kawata
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, Japan
| | - Yuji Goto
- Institute for Protein Research, Osaka University, Osaka, Japan.,Global Center for Medical Engineering and Informatics, Osaka University, Osaka, Japan
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14
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Yamaguchi K, So M, Aguirre C, Ikenaka K, Mochizuki H, Kawata Y, Goto Y. Polyphosphates induce amyloid fibril formation of α-synuclein in concentration-dependent distinct manners. J Biol Chem 2021; 296:100510. [PMID: 33676889 PMCID: PMC8059054 DOI: 10.1016/j.jbc.2021.100510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 11/17/2022] Open
Abstract
Polyphosphates (polyPs), chains of phosphate residues found in species across nature from bacteria to mammals, were recently reported to accelerate the amyloid fibril formation of many proteins. How polyPs facilitate this process, however, remains unknown. To gain insight into their mechanisms, we used various physicochemical approaches to examine the effects of polyPs of varying chain lengths on ultrasonication-dependent α-synuclein (α-syn) amyloid formation. Although orthophosphate and diphosphate exhibited a single optimal concentration of amyloid formation, triphosphate and longer-chain phosphates exhibited two optima, with the second at a concentration lower than that of orthophosphate or diphosphate. The second optimum decreased markedly as the polyP length increased. This suggested that although the optima at lower polyP concentrations were caused by interactions between negatively charged phosphate groups and the positive charges of α-syn, the optima at higher polyP concentrations were caused by the Hofmeister salting-out effects of phosphate groups, where the effects do not depend on the net charge. NMR titration experiments of α-syn with tetraphosphate combined with principal component analysis revealed that, at low tetraphosphate concentrations, negatively charged tetraphosphates interacted with positively charged "KTK" segments in four KTKEGV repeats located at the N-terminal region. At high concentrations, hydrated tetraphosphates affected the surface-exposed hydrophilic groups of compact α-syn. Taken together, our results suggest that long-chain polyPs consisting of 60 to 70 phosphates induce amyloid formation at sub-μM concentrations, which are comparable with the concentrations of polyPs in the blood or tissues. Thus, these findings may identify a role for polyPs in the pathogenesis of amyloid-related diseases.
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Affiliation(s)
- Keiichi Yamaguchi
- Global Center for Medical Engineering and Informatics, Osaka University, Osaka, Japan; Institute for Protein Research, Osaka University, Osaka, Japan
| | - Masatomo So
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - César Aguirre
- Institute for Protein Research, Osaka University, Osaka, Japan; Department of Neurology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Kensuke Ikenaka
- Department of Neurology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Hideki Mochizuki
- Department of Neurology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yasushi Kawata
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, Japan
| | - Yuji Goto
- Global Center for Medical Engineering and Informatics, Osaka University, Osaka, Japan; Institute for Protein Research, Osaka University, Osaka, Japan.
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15
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Nguyen PH, Ramamoorthy A, Sahoo BR, Zheng J, Faller P, Straub JE, Dominguez L, Shea JE, Dokholyan NV, De Simone A, Ma B, Nussinov R, Najafi S, Ngo ST, Loquet A, Chiricotto M, Ganguly P, McCarty J, Li MS, Hall C, Wang Y, Miller Y, Melchionna S, Habenstein B, Timr S, Chen J, Hnath B, Strodel B, Kayed R, Lesné S, Wei G, Sterpone F, Doig AJ, Derreumaux P. Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis. Chem Rev 2021; 121:2545-2647. [PMID: 33543942 PMCID: PMC8836097 DOI: 10.1021/acs.chemrev.0c01122] [Citation(s) in RCA: 385] [Impact Index Per Article: 128.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein misfolding and aggregation is observed in many amyloidogenic diseases affecting either the central nervous system or a variety of peripheral tissues. Structural and dynamic characterization of all species along the pathways from monomers to fibrils is challenging by experimental and computational means because they involve intrinsically disordered proteins in most diseases. Yet understanding how amyloid species become toxic is the challenge in developing a treatment for these diseases. Here we review what computer, in vitro, in vivo, and pharmacological experiments tell us about the accumulation and deposition of the oligomers of the (Aβ, tau), α-synuclein, IAPP, and superoxide dismutase 1 proteins, which have been the mainstream concept underlying Alzheimer's disease (AD), Parkinson's disease (PD), type II diabetes (T2D), and amyotrophic lateral sclerosis (ALS) research, respectively, for many years.
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Affiliation(s)
- Phuong H Nguyen
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Bikash R Sahoo
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jie Zheng
- Department of Chemical & Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Peter Faller
- Institut de Chimie, UMR 7177, CNRS-Université de Strasbourg, 4 rue Blaise Pascal, 67000 Strasbourg, France
| | - John E Straub
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Laura Dominguez
- Facultad de Química, Departamento de Fisicoquímica, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - Nikolay V Dokholyan
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
- Department of Chemistry, and Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, London SW7 2AZ, U.K
- Molecular Biology, University of Naples Federico II, Naples 80138, Italy
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Saeed Najafi
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics & Faculty of Applied Sciences, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
| | - Antoine Loquet
- Institute of Chemistry & Biology of Membranes & Nanoobjects, (UMR5248 CBMN), CNRS, Université Bordeaux, Institut Européen de Chimie et Biologie, 33600 Pessac, France
| | - Mara Chiricotto
- Department of Chemical Engineering and Analytical Science, University of Manchester, Manchester M13 9PL, U.K
| | - Pritam Ganguly
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - James McCarty
- Chemistry Department, Western Washington University, Bellingham, Washington 98225, United States
| | - Mai Suan Li
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 700000, Vietnam
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Carol Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Yiming Wang
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Yifat Miller
- Department of Chemistry and The Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | | | - Birgit Habenstein
- Institute of Chemistry & Biology of Membranes & Nanoobjects, (UMR5248 CBMN), CNRS, Université Bordeaux, Institut Européen de Chimie et Biologie, 33600 Pessac, France
| | - Stepan Timr
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Jiaxing Chen
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Brianna Hnath
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Rakez Kayed
- Mitchell Center for Neurodegenerative Diseases, and Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Sylvain Lesné
- Department of Neuroscience, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Science, Multiscale Research Institute of Complex Systems, Fudan University, Shanghai 200438, China
| | - Fabio Sterpone
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Andrew J Doig
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, U.K
| | - Philippe Derreumaux
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
- Laboratory of Theoretical Chemistry, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
- Faculty of Pharmacy, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
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16
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Ramis R, Ortega-Castro J, Vilanova B, Adrover M, Frau J. Unraveling the NaCl Concentration Effect on the First Stages of α-Synuclein Aggregation. Biomacromolecules 2020; 21:5200-5212. [PMID: 33140640 DOI: 10.1021/acs.biomac.0c01292] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Intraneuronal aggregation of the intrinsically disordered protein α-synuclein is at the core of Parkinson's disease and related neurodegenerative disorders. Several reports show that the concentration of salts in the medium heavily affects its aggregation rate and fibril morphology, but a characterization of the individual monomeric conformations underlying these effects is still lacking. In this work, we have applied our α-synuclein-optimized coarse-grained molecular dynamics approach to decipher the structural features of the protein monomer under a range of NaCl concentrations (0.0-1.0 M). The results show that key intramolecular contacts between the terminal domains are lost at intermediate concentrations (leading to extended conformations likely to fibrillate), but recovered at high concentrations (leading to compact conformations likely to evolve toward amorphous aggregates). The pattern of direct interactions of the terminal α-synuclein domains with Na+ and Cl- ions plays a key role in explaining this effect. Our results are consistent with a recent study reporting a fibrillation enhancement at moderate NaCl concentrations but an inhibition at higher concentrations. The present work will contribute to improving our understanding of the structural features of monomeric α-synuclein, determining its NaCl-induced fibrillation propensity and the molecular basis of synucleinopathies, necessary for the future development of disease-halting therapies.
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Affiliation(s)
- Rafael Ramis
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain.,Institut d'Investigació Sanitària Illes Balears (IdISBa), 07020 Palma de Mallorca, Spain
| | - Joaquín Ortega-Castro
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain.,Institut d'Investigació Sanitària Illes Balears (IdISBa), 07020 Palma de Mallorca, Spain
| | - Bartolomé Vilanova
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain.,Institut d'Investigació Sanitària Illes Balears (IdISBa), 07020 Palma de Mallorca, Spain
| | - Miquel Adrover
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain.,Institut d'Investigació Sanitària Illes Balears (IdISBa), 07020 Palma de Mallorca, Spain
| | - Juan Frau
- Institut Universitari d'Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain.,Institut d'Investigació Sanitària Illes Balears (IdISBa), 07020 Palma de Mallorca, Spain
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