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Krainer G, Jacquat RPB, Schneider MM, Welsh TJ, Fan J, Peter QAE, Andrzejewska EA, Šneiderienė G, Czekalska MA, Ausserwoeger H, Chai L, Arter WE, Saar KL, Herling TW, Franzmann TM, Kosmoliaptsis V, Alberti S, Hartl FU, Lee SF, Knowles TPJ. Single-molecule digital sizing of proteins in solution. Nat Commun 2024; 15:7740. [PMID: 39231922 PMCID: PMC11375031 DOI: 10.1038/s41467-024-50825-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 07/23/2024] [Indexed: 09/06/2024] Open
Abstract
The physical characterization of proteins in terms of their sizes, interactions, and assembly states is key to understanding their biological function and dysfunction. However, this has remained a difficult task because proteins are often highly polydisperse and present as multicomponent mixtures. Here, we address this challenge by introducing single-molecule microfluidic diffusional sizing (smMDS). This approach measures the hydrodynamic radius of single proteins and protein assemblies in microchannels using single-molecule fluorescence detection. smMDS allows for ultrasensitive sizing of proteins down to femtomolar concentrations and enables affinity profiling of protein interactions at the single-molecule level. We show that smMDS is effective in resolving the assembly states of protein oligomers and in characterizing the size of protein species within complex mixtures, including fibrillar protein aggregates and nanoscale condensate clusters. Overall, smMDS is a highly sensitive method for the analysis of proteins in solution, with wide-ranging applications in drug discovery, diagnostics, and nanobiotechnology.
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Affiliation(s)
- Georg Krainer
- Institute of Molecular Biosciences (IMB), University of Graz, Humboldtstraße 50, 8010, Graz, Austria.
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Raphael P B Jacquat
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Matthias M Schneider
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
- Department of Cellular Biochemistry, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Timothy J Welsh
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Jieyuan Fan
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Quentin A E Peter
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Ewa A Andrzejewska
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Greta Šneiderienė
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Magdalena A Czekalska
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Hannes Ausserwoeger
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Lin Chai
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - William E Arter
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Kadi L Saar
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Therese W Herling
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Titus M Franzmann
- Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47/49, 01307, Dresden, Germany
| | - Vasilis Kosmoliaptsis
- Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
- NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, University of Cambridge, Hills Road, Cambridge, CB2 0QQ, UK
- NIHR Cambridge Biomedical Research Centre, University of Cambridge, Hills Road, Cambridge, CB2 0QQ, UK
| | - Simon Alberti
- Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47/49, 01307, Dresden, Germany
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
- Munich Cluster for Systems Neurology (SyNergy), Feodor-Lynen-Str. 17, 81377, Munich, Germany
| | - Steven F Lee
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Ave, Cambridge, CB3 0HE, UK.
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2
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Coskuner-Weber O. Structures prediction and replica exchange molecular dynamics simulations of α-synuclein: A case study for intrinsically disordered proteins. Int J Biol Macromol 2024; 276:133813. [PMID: 38996889 DOI: 10.1016/j.ijbiomac.2024.133813] [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: 06/10/2024] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 07/14/2024]
Abstract
In recent years, a variety of three-dimensional structure prediction tools, including AlphaFold2, AlphaFold3, I-TASSER, C-I-TASSER, Phyre2, ESMFold, and RoseTTAFold, have been employed in the investigation of intrinsically disordered proteins. However, a comprehensive validation of these tools specifically for intrinsically disordered proteins has yet to be conducted. In this study, we utilize AlphaFold2, AlphaFold3, I-TASSER, C-I-TASSER, Phyre2, ESMFold, and RoseTTAFold to predict the structure of a model intrinsically disordered α-synuclein protein. Additionally, extensive replica exchange molecular dynamics simulations of the intrinsically disordered protein are conducted. The resulting structures from both structure prediction tools and replica exchange molecular dynamics simulations are analyzed for radius of gyration, secondary and tertiary structure properties, as well as Cα and Hα chemical shift values. A comparison of the obtained results with experimental data reveals that replica exchange molecular dynamics simulations provide results in excellent agreement with experimental observations. However, none of the structure prediction tools utilized in this study can fully capture the structural characteristics of the model intrinsically disordered protein. This study shows that a cluster of ensembles are required for intrinsically disordered proteins. Artificial-intelligence based structure prediction tools such as AlphaFold3 and C-I-TASSER could benefit from stochastic sampling or Monte Carlo simulations for generating an ensemble of structures for intrinsically disordered proteins.
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Affiliation(s)
- Orkid Coskuner-Weber
- Turkish-German University, Molecular Biotechnology, Sahinkaya Caddesi, No. 106, Beykoz, Istanbul 34820, Turkey.
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3
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Wasim A, Menon S, Mondal J. Modulation of α-synuclein aggregation amid diverse environmental perturbation. eLife 2024; 13:RP95180. [PMID: 39087984 PMCID: PMC11293868 DOI: 10.7554/elife.95180] [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] [Indexed: 08/02/2024] Open
Abstract
Intrinsically disordered protein α-synuclein (αS) is implicated in Parkinson's disease due to its aberrant aggregation propensity. In a bid to identify the traits of its aggregation, here we computationally simulate the multi-chain association process of αS in aqueous as well as under diverse environmental perturbations. In particular, the aggregation of αS in aqueous and varied environmental condition led to marked concentration differences within protein aggregates, resembling liquid-liquid phase separation (LLPS). Both saline and crowded settings enhanced the LLPS propensity. However, the surface tension of αS droplet responds differently to crowders (entropy-driven) and salt (enthalpy-driven). Conformational analysis reveals that the IDP chains would adopt extended conformations within aggregates and would maintain mutually perpendicular orientations to minimize inter-chain electrostatic repulsions. The droplet stability is found to stem from a diminished intra-chain interactions in the C-terminal regions of αS, fostering inter-chain residue-residue interactions. Intriguingly, a graph theory analysis identifies small-world-like networks within droplets across environmental conditions, suggesting the prevalence of a consensus interaction patterns among the chains. Together these findings suggest a delicate balance between molecular grammar and environment-dependent nuanced aggregation behavior of αS.
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Affiliation(s)
- Abdul Wasim
- Tata Institute of Fundamental ResearchHyderabadIndia
| | - Sneha Menon
- Tata Institute of Fundamental ResearchHyderabadIndia
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4
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Zhaliazka K, Kurouski D. Elucidation of molecular mechanisms by which amyloid β 1-42 fibrils exert cell toxicity. Biochim Biophys Acta Mol Cell Biol Lipids 2024; 1869:159510. [PMID: 38759921 DOI: 10.1016/j.bbalip.2024.159510] [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: 03/28/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/19/2024]
Abstract
Abrupt aggregation of amyloid β1-42 (Aβ1-42) peptide in the frontal lobe is the expected underlying cause of Alzheimer's disease (AD). β-Sheet-rich oligomers and fibrils formed by Aβ1-42 exert high cell toxicity. A growing body of evidence indicates that lipids can uniquely alter the secondary structure and toxicity of Aβ1-42 aggregates. At the same time, underlying molecular mechanisms that determine this difference in toxicity of amyloid aggregates remain unclear. Using a set of molecular and biophysical assays to determine the molecular mechanism by which Aβ1-42 aggregates formed in the presence of cholesterol, cardiolipin, and phosphatidylcholine exert cell toxicity. Our findings demonstrate that rat neuronal cells exposed to Aβ1-42 fibrils formed in the presence of lipids with different chemical structure exert drastically different magnitude and dynamic of unfolded protein response (UPR) in the endoplasmic reticulum (ER) and mitochondria (MT). We found that the opposite dynamics of UPR in MT and ER in the cells exposed to Aβ1-42: cardiolipin fibrils and Aβ1-42 aggregates formed in a lipid-free environment. We also found that Aβ1-42: phosphatidylcholine fibrils upregulated ER UPR simultaneously downregulating the UPR response of MT, whereas Aβ1-42: cholesterol fibrils suppressed the UPR response of ER and upregulated UPR response of MT. We also observed progressively increasing ROS production that damages mitochondrial membranes and other cell organelles, ultimately leading to cell death.
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Affiliation(s)
- Kiryl Zhaliazka
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, United States
| | - Dmitry Kurouski
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, United States; Department of Biomedical Engineering, Texas A&M University, College Station, TX 77843, United States.
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5
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Anbaraki A, Dindar Z, Mousavi-Jarrahi Z, Ghasemi A, Moeini Z, Evini M, Saboury AA, Seyedarabi A. The novel anti-fibrillary effects of volatile compounds α-asarone and β-caryophyllene on tau protein: Towards promising therapeutic agents for Alzheimer's disease. Int J Biol Macromol 2024; 271:132401. [PMID: 38761902 DOI: 10.1016/j.ijbiomac.2024.132401] [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: 10/23/2023] [Revised: 05/11/2024] [Accepted: 05/13/2024] [Indexed: 05/20/2024]
Abstract
The abnormal deposition of tau protein is one of the critical causes of tauopathies including Alzheimer's disease (AD). In recent years, there has been great interest in the use of essential oils and volatile compounds in aromatherapy for treating AD, since volatile compounds can directly reach the brain through intranasal administration. The volatile compounds α-asarone (ASA) and β-caryophyllene (BCP) have revealed various important neuroprotective properties, useful in treating AD. In this study, the volatile compounds ASA and BCP were assessed for their effectiveness in preventing tau fibrillation, disassembly of pre-formed tau fibrils, and disaggregation of tau aggregates. SDS-PAGE and AFM analyses revealed that ASA and BCP inhibited tau fibrillation/aggregation and decreased the mean size of tau oligomers. Tau samples treated with ASA and BCP, showed a reduction in ThT and ANS fluorescence intensities, and a decrease in the β-sheet content. Additionally, ASA and BCP disassembled the pre-formed tau fibrils to the granular and linear oligomeric intermediates. Treatment of neuroblastoma SH-SY5Y cells with tau samples treated with ASA and BCP, revealed protective effects as shown by reduced toxicity of the cells, due to the inhibition of tau fibrillation/aggregation. Overall, ASA and BCP appeared to be promising therapeutic candidates for AD.
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Affiliation(s)
- Afrooz Anbaraki
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Zahra Dindar
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | | | - Atiyeh Ghasemi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Zahra Moeini
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Mina Evini
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Arefeh Seyedarabi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
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6
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Dolui S, Roy A, Pal U, Kundu S, Pandit E, N Ratha B, Pariary R, Saha A, Bhunia A, Maiti NC. Raman Spectroscopic Insights of Phase-Separated Insulin Aggregates. ACS PHYSICAL CHEMISTRY AU 2024; 4:268-280. [PMID: 38800728 PMCID: PMC11117687 DOI: 10.1021/acsphyschemau.3c00065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 05/29/2024]
Abstract
Phase-separated protein accumulation through the formation of several aggregate species is linked to the pathology of several human disorders and diseases. Our current investigation envisaged detailed Raman signature and structural intricacy of bovine insulin in its various forms of aggregates produced in situ at an elevated temperature (60 °C). The amide I band in the Raman spectrum of the protein in its native-like conformation appeared at 1655 cm-1 and indicated the presence of a high content of α-helical structure as prepared freshly in acidic pH. The disorder content (turn and coils) also was predominately present in both the monomeric and oligomeric states and was confirmed by the presence shoulder amide I maker band at ∼1680 cm-1. However, the band shifted to ∼1671 cm-1 upon the transformation of the protein solution into fibrillar aggregates as produced for a longer time of incubation. The protein, however, maintained most of its helical conformation in the oligomeric phase; the low-frequency backbone α-helical conformation signal at ∼935 cm-1 was similar to that of freshly prepared aqueous protein solution enriched in helical conformation. The peak intensity was significantly weak in the fibrillar aggregates, and it appeared as a good Raman signature to follow the phase separation and the aggregation behavior of insulin and similar other proteins. Tyrosine phenoxy moieties in the protein may maintained its H-bond donor-acceptor integrity throughout the course of fibril formation; however, it entered in more hydrophobic environment in its journey of fibril formation. In addition, it was noticed that oligomeric bovine insulin maintained the orientation/conformation of the disulfide bonds. However, in the fibrillar state, the disulfide linkages became more strained and preferred to maintain a single conformation state.
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Affiliation(s)
- Sandip Dolui
- Structural
Biology and Bioinformatics Division, Indian
Institute of Chemical Biology, Council of Scientific and Industrial
Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Anupam Roy
- Structural
Biology and Bioinformatics Division, Indian
Institute of Chemical Biology, Council of Scientific and Industrial
Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Uttam Pal
- Structural
Biology and Bioinformatics Division, Indian
Institute of Chemical Biology, Council of Scientific and Industrial
Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Shubham Kundu
- Structural
Biology and Bioinformatics Division, Indian
Institute of Chemical Biology, Council of Scientific and Industrial
Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Esha Pandit
- Structural
Biology and Bioinformatics Division, Indian
Institute of Chemical Biology, Council of Scientific and Industrial
Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Bhisma N Ratha
- Department
of Chemical Sciences, Bose Institute, Unified Academic Campus, Salt Lake,
Sector V, Kolkata 700091, India
| | - Ranit Pariary
- Department
of Chemical Sciences, Bose Institute, Unified Academic Campus, Salt Lake,
Sector V, Kolkata 700091, India
| | - Achintya Saha
- Department
of Chemical Technology, University of Calcutta, 92 Acharya Prafulla Chandra Road, Calcutta 700009, India
| | - Anirban Bhunia
- Department
of Chemical Sciences, Bose Institute, Unified Academic Campus, Salt Lake,
Sector V, Kolkata 700091, India
| | - Nakul C. Maiti
- Structural
Biology and Bioinformatics Division, Indian
Institute of Chemical Biology, Council of Scientific and Industrial
Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India
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Matveyenka M, Zhaliazka K, Kurouski D. Macrophages and Natural Killers Degrade α-Synuclein Aggregates. Mol Pharm 2024; 21:2565-2576. [PMID: 38635186 PMCID: PMC11080468 DOI: 10.1021/acs.molpharmaceut.4c00160] [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: 02/13/2024] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 04/19/2024]
Abstract
Amyloid oligomers and fibrils are protein aggregates that exert a high cell toxicity. Efficient degradation of these protein aggregates can minimize the spread and progression of neurodegeneration. In this study, we investigate the properties of natural killer (NK) cells and macrophages in the degradation of α-synuclein (α-Syn) aggregates grown in a lipid-free environment and in the presence of phosphatidylserine and cholesterol (PS/Cho), which are lipids that are directly associated with the onset and progression of Parkinson's disease. We found that both types of α-Syn aggregates were endocytosed by neurons, which caused strong damage to cell endosomes. Our results also indicated that PS/Cho vesicles drastically increased the toxicity of α-Syn fibrils formed in their presence compared to the toxicity of α-Syn aggregates grown in a lipid-free environment. Both NK cells and macrophages were able to degrade α-Syn and α-Syn/Cho monomers, oligomers, and fibrils. Quantitative analysis of protein degradation showed that macrophages demonstrated substantially more efficient internalization and degradation of amyloid aggregates in comparison to NK cells. We also found that amyloid aggregates induced the proliferation of macrophages and NK cells and significantly changed the expression of their cytokines and chemokines.
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Affiliation(s)
- Mikhail Matveyenka
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
| | - Kiryl Zhaliazka
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
| | - Dmitry Kurouski
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
- Department
of Biomedical Engineering, Texas A&M
University, College Station, Texas 77843, United States
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8
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Charles-Achille S, Janot JM, Cayrol B, Balme S. Influence of Seed structure on Volume distribution of α-Synuclein Oligomer at Early Stages of Aggregation using nanopipette. Chembiochem 2024; 25:e202300748. [PMID: 38240074 DOI: 10.1002/cbic.202300748] [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: 11/01/2023] [Revised: 01/18/2024] [Indexed: 02/04/2024]
Abstract
Understanding α-synuclein aggregation is crucial in the context of Parkinson's disease. The objective of this study was to investigate the influence of aggregation induced by preformed seeding on the volume of oligomers during the early stages, using a label-free, single-molecule characterization approach. By utilizing nanopipettes of varying sizes, the volume of the oligomers can be calculated from the amplitude of the current blockade and pipette geometry. Further investigation of the aggregates formed over time in the presence of added seeds revealed an acceleration in the formation of large aggregates and the existence of multiple distinct populations of oligomers. Additionally, we observed that spontaneously formed seeds inhibited the formation of smaller oligomers, in contrast to the effect of HNE seeds. These results suggest that the seeds play a crucial role in the formation of oligomers and their sizes during the early stages of aggregation, whereas the classical thioflavin T assay remains negative.
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Affiliation(s)
- Saly Charles-Achille
- Institut Européen des Membranes, UMR5635 University of Montpellier ENCSM CNRS, Place Eugène Bataillon, 34095, Montpellier cedex 5, France
| | - Jean-Marc Janot
- Institut Européen des Membranes, UMR5635 University of Montpellier ENCSM CNRS, Place Eugène Bataillon, 34095, Montpellier cedex 5, France
| | - Bastien Cayrol
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, 34000, Montpellier, France
| | - Sebastien Balme
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, 34000, Montpellier, France
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9
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Chavarría C, Ivagnes R, Zeida A, Piñeyro MD, Souza JM. Revisiting the role of 3-nitrotyrosine residues in the formation of alpha-synuclein oligomers and fibrils. Arch Biochem Biophys 2024; 752:109858. [PMID: 38104957 DOI: 10.1016/j.abb.2023.109858] [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: 09/07/2023] [Revised: 12/04/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
Nitration of tyrosine residues in alpha-synuclein (a-syn) has been detected in different synucleinopathies, including Parkinson's disease. The potential role of 3-nitrotyrosine formation in a-syn, as an oxidative post-translational modification, is still elusive. In this work, we generated well-characterized tyrosine nitrated a-syn monomers and studied their capability to form oligomers and fibrils. We constructed tyrosine to phenylalanine mutants, containing a single tyrosine residue, a-syn mutant Y(125/133/136)F and Y(39/125/133)F) and assessed the impact in a-syn biophysical properties. Nitrated wild-type a-syn and the Y-F mutants, with one 3-nitrotyrosine residue in either the protein's N-terminal or C-terminal region, showed inhibition of fibril formation but retained the capacity of oligomer formation. The inhibition of a-syn fibrillation occurs even when an important amount of unmodified a-syn is still present. We characterized oligomers from both nitrated and non-nitrated forms of the wild-type protein and the mutant forms obtained. Our results indicate that the formation of 3-nitrotyrosine in a-syn could induce an off-pathway oligomer formation which may have an important impact in the development of synucleinopathies.
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Affiliation(s)
- Cecilia Chavarría
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Av. Gral. Flores 2125, Montevideo, 11800, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Av. Gral. Flores 2125, Montevideo, 11800, Uruguay
| | - Rodrigo Ivagnes
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Av. Gral. Flores 2125, Montevideo, 11800, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Av. Gral. Flores 2125, Montevideo, 11800, Uruguay
| | - Ari Zeida
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Av. Gral. Flores 2125, Montevideo, 11800, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Av. Gral. Flores 2125, Montevideo, 11800, Uruguay
| | - María Dolores Piñeyro
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Av. Gral. Flores 2125, Montevideo, 11800, Uruguay; Laboratorio de Interacciones Hospedero-Patógeno, Unidad de Biología Molecular, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo, 11400, Uruguay
| | - José M Souza
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Av. Gral. Flores 2125, Montevideo, 11800, Uruguay; Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Av. Gral. Flores 2125, Montevideo, 11800, Uruguay.
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10
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Zhaliazka K, Ali A, Kurouski D. Phospholipids and Cholesterol Determine Molecular Mechanisms of Cytotoxicity of α-Synuclein Oligomers and Fibrils. ACS Chem Neurosci 2024; 15:371-381. [PMID: 38166409 DOI: 10.1021/acschemneuro.3c00671] [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] [Indexed: 01/04/2024] Open
Abstract
Progressive loss of dopaminergic (DA) neurons in the substantia nigra pars compacta, hypothalamus, and thalamus is a hallmark of Parkinson's disease. Neuronal death is linked to the abrupt aggregation of α-synuclein (α-Syn), a small membrane protein that regulates cell vesicle trafficking. α-Syn aggregation rate, as well as the secondary structure and toxicity of α-Syn fibrils, could be uniquely altered by lipids. However, molecular mechanisms that determine such a remarkable difference in the toxicity of α-Syn fibrils formed in the presence of lipids remain unclear. In this study, we used a set of molecular assays to determine the molecular mechanism by which α-Syn fibrils formed in the presence of phosphatidylcholine (PC), cardiolipin (CL), and cholesterol (Cho) exert cell toxicity. We found that rat dopaminergic cells exposed to α-Syn fibrils formed in the presence of different lipids exert drastically different magnitudes and dynamics of unfolded protein response (UPR) in the endoplasmic reticulum (ER) and mitochondria (MT). Specifically, α-Syn:CL were found to cause the strongest, whereas α-Syn fibrils formed in the absence of lipids had the lowest magnitude of the UPR cell response. We also found the opposite dynamics of the ER- and MT-UPR responses in rat dopaminergic cells exposed to protein aggregates. These results could suggest that facing severe ER stress, dopaminergic cells suppress MT-UPR response, enabling the maximal ATP production to restore their normal physiological function. These findings help to better understand complex mechanisms of cell toxicity of amyloid aggregates and ultimately find neuroprotective drug candidates that will be able to suppress the spread of Parkinson's disease.
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Affiliation(s)
- Kiryl Zhaliazka
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Abid Ali
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Dmitry Kurouski
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States
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Cui Z, Guo FY, Li L, Lu F, Jin CH, Wang X, Liu F. Brazilin-7-acetate, a novel potential drug of Parkinson's disease, hinders the formation of α-synuclein fibril, mitigates cytotoxicity, and decreases oxidative stress. Eur J Med Chem 2024; 264:115965. [PMID: 38056304 DOI: 10.1016/j.ejmech.2023.115965] [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: 09/25/2023] [Revised: 11/06/2023] [Accepted: 11/13/2023] [Indexed: 12/08/2023]
Abstract
Parkinson's disease (PD) is a prevalent neurodegenerative disorder characterized by the accumulation of α-synuclein (α-Syn) aggregates. However, there are currently no effective therapies for PD. Brazilin, an inhibitor of α-Syn aggregation, is unstable and toxic. Therefore, we have developed and synthesized derivatives of brazilin. One of these derivatives, called brazilin-7-acetate (B-7-A), has shown reduced toxicity and a stronger effect on inhibiting α-Syn aggregation. It showed that B-7-A prevented the formation of α-Syn fibers and disrupted existing fibers in a dosage-dependent manner. Additionally, B-7-A significantly reduced the cytotoxicity of α-Syn aggregates and alleviated oxidative stress in PC12 cells. The beneficial effects of B-7-A were also confirmed using the Caenorhabditis elegans model. These effects included preventing the accumulation of α-Syn clumps, improving behavior disorder, increasing lifespan, reducing oxidative stress, and protecting against lipid oxidation and loss. Finally, B-7-A showed good ADMET properties in silico. Based on these findings, B-7-A exhibits potential as a prospective treatment for PD.
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Affiliation(s)
- Zhan Cui
- College of Biotechnology, Tianjin University of Science & Technology, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, Tianjin, China
| | - Fang-Yan Guo
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Yanbian University, Yanji, Jilin Province, China
| | - Li Li
- College of Science, Tianjin University of Science & Technology, China
| | - Fuping Lu
- College of Biotechnology, Tianjin University of Science & Technology, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, Tianjin, China
| | - Cheng-Hua Jin
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Yanbian University, Yanji, Jilin Province, China.
| | - Xiangming Wang
- Department of Cell Biology, School of Basic Medical Science, Capital Medical University, Beijing, China.
| | - Fufeng Liu
- College of Biotechnology, Tianjin University of Science & Technology, Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, Tianjin, China.
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12
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Mondal A, Dolui S, Dhabal S, Kundu S, Das L, Bhattacharjee A, Maiti NC. Structure specific neuro-toxicity of α-synuclein oligomer. Int J Biol Macromol 2023; 253:126683. [PMID: 37666396 DOI: 10.1016/j.ijbiomac.2023.126683] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/06/2023]
Abstract
Parkinson's disease (PD) is linked to α-synuclein (aS) aggregation and deposition of amyloid in the substantia nigra region of the brain tissues. In the current investigation we produced two distinct classes of aS oligomer of differed protein conformation, stability and compared their toxic nature to cultured neuronal cells. Lyophilized oligomer (LO) was produced in storage of aS at-20 °C for 7 days and it was enriched with loosely hold molten globule like structure with residues having preferences for α-helical conformational space. The size of the oligomer was 4-5.5 nm under AFM. This kind of oligomer exhibited potential toxicity towards neuronal cell lines and did not transform into compact β-sheet rich amyloid fiber even after incubation at 37 °C for several days. Formation of another type of oligomer was often observed in the lag phase of aS fibrillation that often occurred at an elevated temperature (37 °C). This kind of heat induced oligomer (IO) was more hydrophobic and relatively less toxic to neuronal cells compared to lyophilized oligomer (LO). Importantly, initiation of hydrophobic zipping of aS caused the transformation of IO into thermodynamically stable β-sheet rich amyloid fibril. On the other hand, the presence of molten globule like conformation in LO, rendered greater toxicity to cultured neuronal cells.
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Affiliation(s)
- Animesh Mondal
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India; Department of Zoology, Government General Degree College-Mangalkote, Purba Bardhaman, West Bengal 713132, India.
| | - Sandip Dolui
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Sukhamoy Dhabal
- Department of Biotechnology, National Institute of Technology-Durgapur, Mahatma Gandhi Rd, A-Zone, Durgapur, West Bengal 713209, India
| | - Shubham Kundu
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Lopamudra Das
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Ashish Bhattacharjee
- Department of Biotechnology, National Institute of Technology-Durgapur, Mahatma Gandhi Rd, A-Zone, Durgapur, West Bengal 713209, India
| | - Nakul C Maiti
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, 4, Raja S.C. Mullick Road, Kolkata 700032, India.
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13
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Harper M, Nudurupati U, Workman RJ, Lakoba TI, Perez N, Nelson D, Ou Y, Punihaole D. Toward determining amyloid fibril structures using experimental constraints from Raman spectroscopy. J Chem Phys 2023; 159:225101. [PMID: 38078532 PMCID: PMC10720587 DOI: 10.1063/5.0177437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 11/20/2023] [Indexed: 12/17/2023] Open
Abstract
We present structural models for three different amyloid fibril polymorphs prepared from amylin20-29 (sequence SNNFGAILSS) and amyloid-β25-35 (Aβ25-35) (sequence GSNKGAIIGLM) peptides. These models are based on the amide C=O bond and Ramachandran ψ-dihedral angle data from Raman spectroscopy, which were used as structural constraints to guide molecular dynamics (MD) simulations. The resulting structural models indicate that the basic structural motif of amylin20-29 and Aβ25-35 fibrils is extended β-strands. Our data indicate that amylin20-29 forms both antiparallel and parallel β-sheet fibril polymorphs, while Aβ25-35 forms a parallel β-sheet fibril structure. Overall, our work lays the foundation for using Raman spectroscopy in conjunction with MD simulations to determine detailed molecular-level structural models of amyloid fibrils in a manner that complements gold-standard techniques, such as solid-state nuclear magnetic resonance and cryogenic electron microscopy.
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Affiliation(s)
- Madeline Harper
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, USA
| | - Uma Nudurupati
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, USA
| | - Riley J. Workman
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Taras I. Lakoba
- Department of Mathematics and Statistics, University of Vermont, Burlington, Vermont 05405, USA
| | - Nicholas Perez
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, USA
| | - Delaney Nelson
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, USA
| | - Yangguang Ou
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, USA
| | - David Punihaole
- Department of Chemistry, University of Vermont, Burlington, Vermont 05405, USA
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14
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Maurer M, Lazaridis T. Transmembrane β-Barrel Models of α-Synuclein Oligomers. J Chem Inf Model 2023; 63:7171-7179. [PMID: 37963823 DOI: 10.1021/acs.jcim.3c00997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
The aggregation of α-synuclein is implicated in a number of neurodegenerative diseases, such as Parkinson's and Multiple System Atrophy, but the role of these aggregates in disease development is not clear. One possible mechanism of cytotoxicity is the disturbance or permeabilization of cell membranes by certain types of oligomers. However, no high-resolution structure of such membrane-embedded complexes has ever been determined. Here we construct and evaluate putative transmembrane β-barrels formed by this protein. Examination of the α-synuclein sequence reveals two regions that could form membrane-embedded β-hairpins: 64-92 (the NAC), and 35-56, which harbors many familial Parkinson's mutations. The stability of β-barrels formed by these hairpins is examined first in implicit membrane pores and then by multimicrosecond all-atom simulations. We find that a NAC region barrel remains stably inserted and hydrated for at least 10 μs. A 35-56 barrel remains stably inserted in the membrane but dehydrates and collapses if all His50 are neutral or if His50 is replaced by Q. If half of the His50 are doubly protonated, the barrel takes an oval shape but remains hydrated for at least 10 μs. Possible implications of these findings for α-synuclein pathology are discussed.
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Affiliation(s)
- Manuela Maurer
- Department of Chemistry & Biochemistry, City College of New York/CUNY, 160 Convent Ave, New York, New York 10031, United States
| | - Themis Lazaridis
- Department of Chemistry & Biochemistry, City College of New York/CUNY, 160 Convent Ave, New York, New York 10031, United States
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15
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Bai Y, Zhang S, Dong H, Liu Y, Liu C, Zhang X. Advanced Techniques for Detecting Protein Misfolding and Aggregation in Cellular Environments. Chem Rev 2023; 123:12254-12311. [PMID: 37874548 DOI: 10.1021/acs.chemrev.3c00494] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Protein misfolding and aggregation, a key contributor to the progression of numerous neurodegenerative diseases, results in functional deficiencies and the creation of harmful intermediates. Detailed visualization of this misfolding process is of paramount importance for improving our understanding of disease mechanisms and for the development of potential therapeutic strategies. While in vitro studies using purified proteins have been instrumental in delivering significant insights into protein misfolding, the behavior of these proteins in the complex milieu of living cells often diverges significantly from such simplified environments. Biomedical imaging performed in cell provides cellular-level information with high physiological and pathological relevance, often surpassing the depth of information attainable through in vitro methods. This review highlights a variety of methodologies used to scrutinize protein misfolding within biological systems. This includes optical-based methods, strategies leaning on mass spectrometry, in-cell nuclear magnetic resonance, and cryo-electron microscopy. Recent advancements in these techniques have notably deepened our understanding of protein misfolding processes and the features of the resulting misfolded species within living cells. The progression in these fields promises to catalyze further breakthroughs in our comprehension of neurodegenerative disease mechanisms and potential therapeutic interventions.
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Affiliation(s)
- Yulong Bai
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Shengnan Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Hui Dong
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- University of the Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Xin Zhang
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
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16
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Ahmed R, Unal M, Gautam R, Uppuganti S, Derasari S, Mahadevan-Jansen A, Nyman JS. Sensitivity of the amide I band to matrix manipulation in bone: a Raman micro-spectroscopy and spatially offset Raman spectroscopy study. Analyst 2023; 148:4799-4809. [PMID: 37602820 PMCID: PMC10528211 DOI: 10.1039/d3an00527e] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
The fracture resistance of bone arises from the hierarchical arrangement of minerals, collagen fibrils (i.e., cross-linked triple helices of α1 and α2 collagen I chains), non-collagenous proteins, and water. Raman spectroscopy (RS) is not only sensitive to the relative fractions of these constituents, but also to the secondary structure of bone proteins. To assess the ability of RS to detect differences in the protein structure, we quantified the effect of sequentially autoclaving (AC) human cortical bone at 100 °C (∼34.47 kPa) and then at 120 °C (∼117.21 kPa) on the amide I band using a commercial Raman micro-spectroscopy (μRS) instrument and custom spatially offset RS (SORS) instrument in which rings of collection fiber optics are offset from the central excitation fiber optics within a hand-held, cylindrical probe. Being clinically viable, measurements by SORS involved collecting Raman spectra of cadaveric femur mid-shafts (5 male & 5 female donors) through layers of a tissue mimic. Otherwise, μRS and SORS measurements were acquired directly from each bone. AC-related changes in the helical status of collagen I were assessed using amide I sub-peak ratios (intensity, I, at ∼1670 cm-1 relative to intensities at ∼1610 cm-1 and ∼1640 cm-1). The autoclaving manipulation significantly decreased the selected amide I sub-peak ratios as well as shifted peaks at ∼1605 cm-1 (μRS), ∼1636 cm-1 (SORS) and ∼1667 cm-1 in both μRS and SORS. Compared to μRS, SORS detected more significant differences in the amide I sub-peak ratios when the fiber optic probe was directly applied to bone. SORS also detected AC-related decreases in I1670/I1610 and I1670/I1640 when spectra were acquired through layers of the tissue mimic with a thickness ≤2 mm by the 7 mm offset ring, but not with the 5 mm or 6 mm offset ring. Overall, the SORS instrument was more sensitive than the conventional μRS instrument to pressure- and temperature-related changes in the organic matrix that affect the fracture resistance of bone, but SORS analysis of the amide I band is limited to an overlying thickness layer of 2 mm.
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Affiliation(s)
- Rafay Ahmed
- Department of Orthopaedic Surgery, Vanderbilt University Medical Center, 1215 21st Ave. S., Suite 4200, Nashville, TN 37232, USA
| | - Mustafa Unal
- Department of Bioengineering, Karamanoglu Mehmetbey University, Karaman, Türkiye 70200
- Department of Biophysics, Faculty of Medicine, Karamanoglu Mehmetbey University, Karaman, Türkiye 70200.
| | - Rekha Gautam
- Biophotonics@Tyndall, IPIC, Tyndall National Institute, Cork, Ireland
- Department of Biomedical Engineering, Vanderbilt University, 5824 Stevenson Center, Nashville, TN 37232, USA
- Vanderbilt Biophotonics Center, 410 24th Ave. S., Nashville, TN 37232, USA
| | - Sasidhar Uppuganti
- Department of Orthopaedic Surgery, Vanderbilt University Medical Center, 1215 21st Ave. S., Suite 4200, Nashville, TN 37232, USA
| | - Shrey Derasari
- Department of Biomedical Engineering, Vanderbilt University, 5824 Stevenson Center, Nashville, TN 37232, USA
- Vanderbilt Biophotonics Center, 410 24th Ave. S., Nashville, TN 37232, USA
| | - Anita Mahadevan-Jansen
- Department of Biomedical Engineering, Vanderbilt University, 5824 Stevenson Center, Nashville, TN 37232, USA
- Vanderbilt Biophotonics Center, 410 24th Ave. S., Nashville, TN 37232, USA
| | - Jeffry S Nyman
- Department of Orthopaedic Surgery, Vanderbilt University Medical Center, 1215 21st Ave. S., Suite 4200, Nashville, TN 37232, USA
- Department of Biomedical Engineering, Vanderbilt University, 5824 Stevenson Center, Nashville, TN 37232, USA
- Department of Veterans Affairs, Tennessee Valley Healthcare System, 1310 24th Ave. S., Nashville, TN 37212, USA
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17
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Feng F, Song X, Tan Z, Tu Y, Xiao L, Xie P, Ma Y, Sun X, Ma J, Rong L, He L. Cooperative assembly of a designer peptide and silk fibroin into hybrid nanofiber gels for neural regeneration after spinal cord injury. SCIENCE ADVANCES 2023; 9:eadg0234. [PMID: 37352345 PMCID: PMC10289662 DOI: 10.1126/sciadv.adg0234] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 05/17/2023] [Indexed: 06/25/2023]
Abstract
Local reconstruction of a permissive environment with biomaterials is a promising strategy to treat spinal cord injury (SCI). We reported a hybrid hydrogel fabricated from a small functional self-assembling peptide (F-SAP) and large silk fibroin (SF). The diffusion of SF micelles into F-SAP solution was driven by the dynamic synergy between osmotic pressure and F-SAP/SF electrostatic interactions, resulting in the rearrangement of SF micelles and the formation of rod-like filaments with axes nearly perpendicular to F-SAP nanofibers. Spectroscopy analysis, including circular dichroism, Raman and fluorescence, indicated conformation changes of SF from random coil to β sheet, which contributed to enhanced mechanical properties of the resultant hybrid hydrogel. Furthermore, the F-SAP/SF hybrid hydrogel coupled with controlled release of NT-3 provided a permissive environment for neural regeneration by providing nanofibrous substrates for regenerating axons, inflammatory modulation and remyelination, consequently resulting in improved locomotion and electrophysiological properties. This hydrogel could be used as a long-term stent in vivo for the treatment of SCI.
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Affiliation(s)
- Feng Feng
- Department of Spine Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Xiyong Song
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki 00014, Finland
| | - Zan Tan
- Department of Spine Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Yujie Tu
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Longyou Xiao
- Department of Spine Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Pengfei Xie
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yahao Ma
- College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xiumin Sun
- Department of Spine Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Junwu Ma
- Department of Spine Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Limin Rong
- Department of Spine Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Liumin He
- Department of Spine Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
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18
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Kaur G, Mankoo OK, Goyal D, Goyal B. Unveiling How Hydroxytyrosol Destabilizes α-Syn Oligomers Using Molecular Simulations. J Phys Chem B 2023. [PMID: 37319389 DOI: 10.1021/acs.jpcb.3c02434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The etiology of Parkinson's disease (PD) is mainly linked to the α-synuclein (α-Syn) fibrillogenesis. Hydroxytyrosol (HT), also known as 3,4-dihydroxyphenylethanol, is a naturally occurring polyphenol, found in extra virgin olive oil, and has been shown to have cardioprotective, anticancer, antiobesity, and antidiabetic properties. HT has neuroprotective benefits in neurodegenerative diseases and lessens the severity of PD by reducing the aggregation of α-Syn and destabilizing the preformed toxic α-Syn oligomers. However, the molecular mechanism by which HT destabilizes α-Syn oligomers and alleviates the accompanying cytotoxicity remains unexplored. The impact of HT on the α-Syn oligomer structure and its potential binding mechanism was examined in this work by employing molecular dynamics (MD) simulations. The secondary structure analysis depicted that HT significantly reduces the β-sheet and concomitantly increases the coil content of α-Syn trimer. Visualization of representative conformations from the clustering analysis depicted the hydrogen bond interactions of the hydroxyl groups in HT with the N-terminal and nonamyloid-β component (NAC) region residues of α-Syn trimer, which, in turn, leads to the weakening of interchain interactions in α-Syn trimer and resulted in the disruption of the α-Syn oligomer. The binding free energy calculations depict that HT binds favorably to α-Syn trimer (ΔGbinding = -23.25 ± 7.86 kcal/mol) and a notable reduction in the interchain binding affinity of α-Syn trimer on the incorporation of HT, which, in turn, highlights its potential to disrupt α-Syn oligomers. The current research provided mechanistic insights into the destabilization of α-Syn trimer by HT, which, in turn, will provide new clues for developing therapeutics against PD.
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Affiliation(s)
- Gagandeep Kaur
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib-140406, Punjab, India
| | - Opinder Kaur Mankoo
- Department of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib-140406, Punjab, India
| | - Deepti Goyal
- Department of Chemistry, DAV College, Sector 10, Chandigarh-160011, India
| | - Bhupesh Goyal
- School of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala-147004, Punjab, India
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19
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Pandit E, Das L, Das AK, Dolui S, Saha S, Pal U, Mondal A, Chowdhury J, Biswas SC, Maiti NC. Single point mutations at the S129 residue of α-synuclein and their effect on structure, aggregation, and neurotoxicity. Front Chem 2023; 11:1145877. [PMID: 37304685 PMCID: PMC10250651 DOI: 10.3389/fchem.2023.1145877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/10/2023] [Indexed: 06/13/2023] Open
Abstract
Parkinson's disease is an age-related neurological disorder, and the pathology of the disease is linked to different types of aggregates of α-synuclein or alpha-synuclein (aS), which is an intrinsically disordered protein. The C-terminal domain (residues 96-140) of the protein is highly fluctuating and possesses random/disordered coil conformation. Thus, the region plays a significant role in the protein's solubility and stability by an interaction with other parts of the protein. In the current investigation, we examined the structure and aggregation behavior of two artificial single point mutations at a C-terminal residue at position 129 that represent a serine residue in the wild-type human aS (wt aS). Circular Dichroism (CD) and Raman spectroscopy were performed to analyse the secondary structure of the mutated proteins and compare it to the wt aS. Thioflavin T assay and atomic force microscopy imaging helped in understanding the aggregation kinetics and type of aggregates formed. Finally, the cytotoxicity assay gave an idea about the toxicity of the aggregates formed at different stages of incubation due to mutations. Compared to wt aS, the mutants S129A and S129W imparted structural stability and showed enhanced propensity toward the α-helical secondary structure. CD analysis showed proclivity of the mutant proteins toward α-helical conformation. The enhancement of α-helical propensity lengthened the lag phase of fibril formation. The growth rate of β-sheet-rich fibrillation was also reduced. Cytotoxicity tests on SH-SY5Y neuronal cell lines established that the S129A and S129W mutants and their aggregates were potentially less toxic than wt aS. The average survivability rate was ∼40% for cells treated with oligomers (presumably formed after 24 h of incubation of the freshly prepared monomeric protein solution) produced from wt aS and ∼80% for cells treated with oligomers obtained from mutant proteins. The relative structural stability with α-helical propensity of the mutants could be a plausible reason for their slow rate of oligomerization and fibrillation, and this was also the possible reason for reduced toxicity to neuronal cells.
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Affiliation(s)
- Esha Pandit
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, India
| | - Lopamudra Das
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, India
| | - Anoy Kumar Das
- Cell Biology and Physiology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Sandip Dolui
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, India
| | - Saumen Saha
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, India
| | - Uttam Pal
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, India
| | - Animesh Mondal
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, India
| | | | - Subhas C. Biswas
- Cell Biology and Physiology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Nakul C. Maiti
- Structural Biology and Bioinformatics Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, India
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20
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Colniță A, Toma VA, Brezeștean IA, Tahir MA, Dina NE. A Review on Integrated ZnO-Based SERS Biosensors and Their Potential in Detecting Biomarkers of Neurodegenerative Diseases. BIOSENSORS 2023; 13:bios13050499. [PMID: 37232860 DOI: 10.3390/bios13050499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/15/2023] [Accepted: 04/20/2023] [Indexed: 05/27/2023]
Abstract
Surface-enhanced Raman spectroscopy (SERS) applications in clinical diagnosis and spectral pathology are increasing due to the potential of the technique to bio-barcode incipient and differential diseases via real-time monitoring of biomarkers in fluids and in real-time via biomolecular fingerprinting. Additionally, the rapid advancements in micro/nanotechnology have a visible influence in all aspects of science and life. The miniaturization and enhanced properties of materials at the micro/nanoscale transcended the confines of the laboratory and are revolutionizing domains such as electronics, optics, medicine, and environmental science. The societal and technological impact of SERS biosensing by using semiconductor-based nanostructured smart substrates will be huge once minor technical pitfalls are solved. Herein, challenges in clinical routine testing are addressed in order to understand the context of how SERS can perform in real, in vivo sampling and bioassays for early neurodegenerative disease (ND) diagnosis. The main interest in translating SERS into clinical practice is reinforced by the practical advantages: portability of the designed setups, versatility in using nanomaterials of various matter and costs, readiness, and reliability. As we will present in this review, in the frame of technology readiness levels (TRL), the current maturity reached by semiconductor-based SERS biosensors, in particular that of zinc oxide (ZnO)-based hybrid SERS substrates, is situated at the development level TRL 6 (out of 9 levels). Three-dimensional, multilayered SERS substrates that provide additional plasmonic hot spots in the z-axis are of key importance in designing highly performant SERS biosensors for the detection of ND biomarkers.
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Affiliation(s)
- Alia Colniță
- Department of Molecular and Biomolecular Physics, National Institute for Research and Development of Isotopic and Molecular Technologies, 67-103 Donat, 400293 Cluj-Napoca, Romania
| | - Vlad-Alexandru Toma
- Department of Molecular and Biomolecular Physics, National Institute for Research and Development of Isotopic and Molecular Technologies, 67-103 Donat, 400293 Cluj-Napoca, Romania
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeș-Bolyai University, 5-7 Clinicilor, 400006 Cluj-Napoca, Romania
- Institute of Biological Research, Department of Biochemistry and Experimental Biology, 48 Republicii, Branch of NIRDBS Bucharest, 400015 Cluj-Napoca, Romania
| | - Ioana Andreea Brezeștean
- Department of Molecular and Biomolecular Physics, National Institute for Research and Development of Isotopic and Molecular Technologies, 67-103 Donat, 400293 Cluj-Napoca, Romania
| | - Muhammad Ali Tahir
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention, Department of Environmental Science & Engineering, Fudan University, Shanghai 200433, China
| | - Nicoleta Elena Dina
- Department of Molecular and Biomolecular Physics, National Institute for Research and Development of Isotopic and Molecular Technologies, 67-103 Donat, 400293 Cluj-Napoca, Romania
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21
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Maity A, Mondal A, Kundu S, Shome G, Misra R, Singh A, Pal U, Mandal AK, Bera K, Maiti NC. Naringenin-Functionalized Gold Nanoparticles and Their Role in α-Synuclein Stabilization. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:7231-7248. [PMID: 37094111 DOI: 10.1021/acs.langmuir.2c03259] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Misfolding and self-assembly of several intrinsically disordered proteins into ordered β-sheet-rich amyloid aggregates emerged as hallmarks of several neurodegenerative disorders such as Alzheimer's and Parkinson's diseases. Here we show how the naringenin-embedded nanostructure effectively retards aggregation and fibril formation of α-synuclein, which is strongly associated with the pathology of Parkinson's-like diseases. Naringenin is a polyphenolic compound from a plant source, and in our current investigation, we reported the one-pot synthesis of naringenin-coated spherical and monophasic gold nanoparticles (NAR-AuNPs) under optimized conditions. The average hydrodynamic diameter of the produced nanoparticle was ∼24 nm and showed a distinct absorption band at 533 nm. The zeta potential of the nanocomposite was ∼-22 mV and indicated the presence of naringenin on the surface of nanoparticles. Core-level XPS spectrum analysis showed prominent peaks at 84.02 and 87.68 eV, suggesting the zero oxidation state of metal in the nanostructure. Additionally, the peaks at 86.14 and 89.76 eV were due to the Au-O bond, induced by the hydroxyl groups of the naringenin molecule. The FT-IR analysis further confirmed strong interactions of the molecule with the gold nanosurface via the phenolic oxygen group. The composite surface was found to interact with monomeric α-synuclein and caused a red shift in the nanoparticle absorption band by ∼5 nm. The binding affinity of the composite nanostructure toward α-synuclein was in the micromolar range (Ka∼ 5.02 × 106 M-1) and may produce a protein corona over the gold nanosurface. A circular dichroism study showed that the nanocomposite can arrest the conformational fluctuation of the protein and hindered its transformation into a compact cross-β-sheet conformation, a prerequisite for amyloid fibril formation. Furthermore, it was found that naringenin and its nanocomplex did not perturb the viability of neuronal cells. It thus appeared that engineering of the nanosurface with naringenin could be an alternative strategy in developing treatment approaches for Parkinson's and other diseases linked to protein conformation.
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Affiliation(s)
- Anupam Maity
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata 700032, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre, (CSIR-HRDC) Campus, Postal Staff College Area, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201 002, India
| | - Animesh Mondal
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata 700032, India
| | - Shubham Kundu
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata 700032, India
| | - Gourav Shome
- Division of Molecular Medicine, Bose Institute, Kolkata 700091, India
| | - Rajdip Misra
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata 700032, India
| | - Aakriti Singh
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata 700032, India
| | - Uttam Pal
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata 700032, India
| | - Atin Kumar Mandal
- Division of Molecular Medicine, Bose Institute, Kolkata 700091, India
| | - Kaushik Bera
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata 700032, India
- Department of Chemistry, The Heritage School, 994 Chowbaga Road, Anandapur, East Kolkata Twp, Kolkata 700107, India
| | - Nakul C Maiti
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata 700032, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre, (CSIR-HRDC) Campus, Postal Staff College Area, Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201 002, India
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22
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Verma G, Bhat R. The Anthocyanidin Peonidin Interferes with an Early Step in the Fibrillation Pathway of α-Synuclein and Modulates It toward Amorphous Aggregates. ACS Chem Neurosci 2023. [PMID: 37011370 DOI: 10.1021/acschemneuro.2c00726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023] Open
Abstract
Parkinson's disease (PD) is characterized by progressive degeneration of the dopaminergic neurons in the brain, accompanied by the accumulation of proteinaceous inclusions, Lewy bodies (LB), mainly comprised of alpha synuclein (α-syn) aggregates. The heterogeneity and the transient nature of the intermediate species formed in the α-syn fibrillation pathway have made it difficult to develop an effective therapeutic intervention. Therefore, any therapeutic molecule that could prevent as well as treat PD would be of great interest. Anthocyanidins are natural flavonoid compounds that have been shown to have neuroprotective properties and to modulate factors that cause neuronal death. Herein, we have explored the modulation and inhibition of α-syn fibrillation by the anthocyanidins cyanidin, delphinidin, and peonidin using a number of biophysical and structural tools. α-Syn fibrillation monitored using thioflavin T (ThT) fluorescence and light scattering suggested concentration dependent inhibition of α-syn fibrillation by all the three anthocyanidins. While cyanidin and delphinidin induced the formation of oligomers and small fibrillar structures of α-syn, respectively, peonidin led to the formation of amorphous aggregates, as observed by Atomic Force Microscopy (AFM). Peonidin proved to be most effective of the three anthocyanidins toward alleviating cell toxicity of SH-SY5Y neuroblastoma cells at concentrations where α-synuclein fibrillation was completely suppressed. Hence, the inhibition mechanism of peonidin was further explored by studying its interaction with α-syn using titration calorimetry and molecular docking. The results show its weak binding (in mM range) to the NAC region of α-syn through hydrogen bonding interactions. Also, circular dichroism and Raman spectroscopy revealed the structural aspects of peonidin-induced α-syn amorphous aggregates showing alpha helical structures with exposed Phe and Tyr regions. Due to the neuroprotective nature of peonidin, the findings reported here are significant and can be further explored toward developing a modifying therapy that could address both disease onset as well as the progression of PD.
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Affiliation(s)
- Geetika Verma
- School of Biotechnology Jawaharlal Nehru University, New Delhi 110067, India
| | - Rajiv Bhat
- School of Biotechnology Jawaharlal Nehru University, New Delhi 110067, India
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23
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Zhaliazka K, Kurouski D. Nanoscale imaging of individual amyloid aggregates extracted from brains of Alzheimer and Parkinson patients reveals presence of lipids in α-synuclein but not in amyloid β 1-42 fibrils. Protein Sci 2023; 32:e4598. [PMID: 36823759 PMCID: PMC10019452 DOI: 10.1002/pro.4598] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 02/02/2023] [Accepted: 02/15/2023] [Indexed: 02/25/2023]
Abstract
Abrupt aggregation of misfolded proteins is the underlying molecular cause of Alzheimer disease (AD) and Parkinson disease (PD). Both AD and PD are severe pathologies that affect millions of people around the world. A small 42 amino acid long peptide, known as amyloid β (Aβ), aggregates in the frontal cortex of AD patients forming oligomers and fibrils, highly toxic protein aggregates that cause progressive neuron death. Similar aggregates of α-synuclein (α-Syn), a small protein that facilitates neurotransmitter release, are observed in the midbrain, hypothalamus, and thalamus of people with PD. In this study, we utilized the innovative nano-Infrared imaging technique to investigate the structural organization of individual Aβ and α-syn fibrils postmortem extracted from brains of AD and PD patients, respectively. We observed two morphologically different Aβ and α-Syn fibril polymorphs in each patient's brain. One had twisted topology, whereas another exhibited flat tape-like morphology. We found that both polymorphs shared the same parallel β-sheet-dominated secondary structure. These findings suggested that both fibril polymorphs were built from structurally similar if not identical filaments that coiled forming twisted fibrils or associated side-by-side in the case of straight Aβ and α-Syn fibrils. Nano-Infrared analysis of individual protein aggregates also revealed the presence of lipids in the structure of both twisted and tape-like α-Syn fibrils that were not observed in any of the Aβ fibril polymorphs. These findings demonstrate that lipid membranes can play a critically important role in the onset and progression of PD.
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Affiliation(s)
- Kiryl Zhaliazka
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTexasUSA
| | - Dmitry Kurouski
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTexasUSA
- Department of Biomedical EngineeringTexas A&M UniversityCollege StationTexasUSA
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24
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Savva L, Platts JA. How Cu(II) binding affects structure and dynamics of α-synuclein revealed by molecular dynamics simulations. J Inorg Biochem 2023; 239:112068. [PMID: 36403437 DOI: 10.1016/j.jinorgbio.2022.112068] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/08/2022] [Accepted: 11/08/2022] [Indexed: 11/15/2022]
Abstract
We report accelerated molecular dynamics simulations of α-Synuclein and its complex with two Cu(II) ions bound to experimentally determined binding sites. Adding two Cu(II) ions, one bound to the N-terminal region and one to the C-terminus, decreases size and flexibility of the peptide while introducing significant new contacts within and between N-terminus and non-Aβ component (NAC). Cu(II) ions also alter the pattern of secondary structure within the peptide, inducing more and longer-lasting elements of secondary structure such as β-strands and hairpins. Free energy surfaces, obtained from reweighting the accelerated molecular dynamics boost potential, further demonstrate the restriction on size and flexibility that results from binding of copper ions.
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Affiliation(s)
- Loizos Savva
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK
| | - James A Platts
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK..
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25
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Matveyenka M, Rizevsky S, Pellois JP, Kurouski D. Lipids uniquely alter rates of insulin aggregation and lower toxicity of amyloid aggregates. Biochim Biophys Acta Mol Cell Biol Lipids 2023; 1868:159247. [PMID: 36272517 PMCID: PMC10401553 DOI: 10.1016/j.bbalip.2022.159247] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/14/2022] [Accepted: 10/02/2022] [Indexed: 02/25/2023]
Abstract
Amyloid formation is a hallmark of many medical diseases including diabetes type 2, Alzheimer's and Parkinson diseases. Under these pathological conditions, misfolded proteins self-assemble forming oligomers and fibrils, structurally heterogeneous aggregates that exhibit a large variety of shapes and forms. A growing body of evidence points to drastic changes in the lipid profile in organs affected by amyloidogenic diseases. In this study, we investigated the extent to which individual phospho- and sphingolipids, as well as their mixtures can impact insulin aggregation. Our results show that lipids and their mixtures uniquely alter rates of insulin aggregation simultaneously changing the secondary structure of protein aggregates that are grown in their presence. These structurally different protein-lipid aggregates impact cell viability to different extent while using distinct mechanisms of toxicity. These findings suggest that irreversible changes in lipid profiles of organs may trigger formation of toxic protein species that in turn are responsible for the onset and progression of amyloidogenic diseases.
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Affiliation(s)
- Mikhail Matveyenka
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, United States
| | - Stanislav Rizevsky
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, United States; Department of Biotechnology, Binh Duong University, Thu Dau Mot 820000, Viet Nam
| | - Jean-Philippe Pellois
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, United States
| | - Dmitry Kurouski
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, United States; Department of Biomedical Engineering, Texas A&M University, College Station, TX 77843, United States.
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26
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Hauptmann A, Hoelzl G, Mueller M, Bechtold-Peters K, Loerting T. Raman Marker Bands for Secondary Structure Changes of Frozen Therapeutic Monoclonal Antibody Formulations During Thawing. J Pharm Sci 2023; 112:51-60. [PMID: 36279956 DOI: 10.1016/j.xphs.2022.10.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 10/16/2022] [Accepted: 10/16/2022] [Indexed: 11/06/2022]
Abstract
In this work we use Raman spectroscopy for protein characterization in the frozen state. We investigate the behavior of frozen therapeutic monoclonal antibody IgG1 formulation upon thawing by Raman spectroscopy. Secondary and tertiary structure of the protein in three different mab formulations in the frozen state are followed through observation of marker bands for α-helix, β-sheet and random coil. We identify the tyrosine intensity ratio I856/I830 as a marker for mab aggregation. Upon fast cooling (40 °C/min) to -80 °C we observe a significant increase of random coil and α -helical structures, while this is not the case for slower cooling (20 °C/min) to -80 °C. Most changes in the protein's secondary structure are observed in the course of thawing in the range up to -20 °C, when passing through the glass transitions and cold-crystallization of the two types of freeze-concentrated solutions formed through macro- and microcryoconcentration. An increase of protein concentration and the addition of mannitol suppress secondary structural changes but do no impact on aggregation.
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Affiliation(s)
| | | | | | | | - Thomas Loerting
- Institute of Physical Chemistry, University Innsbruck, Innsbruck, Austria.
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27
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Saurabh A, Prabhu NP. Concerted enhanced-sampling simulations to elucidate the helix-fibril transition pathway of intrinsically disordered α-Synuclein. Int J Biol Macromol 2022; 223:1024-1041. [PMID: 36379279 DOI: 10.1016/j.ijbiomac.2022.11.079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/19/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022]
Abstract
Fibril formation of α-synuclein is linked with Parkinson's disease. The intrinsically disordered nature of α-syn provides extensive conformational plasticity and becomes difficult to characterize its transition pathway from native monomeric to disease-associated fibril form. We implemented different simulation methods such as steered dynamics-umbrella sampling, and replica-exchange and conventional MD simulations to access various conformational states of α-syn. Nineteen distinct intermediate structures were identified by free energy landscape and cluster analysis. They were then sorted based on secondary structure and solvent exposure of fibril-core residues to illustrate the fibril dissociation pathway. The analysis showed that following the initial dissociation of the polypeptide chain from the fibril, α-syn might form either compact-conformations by long-range interactions or extended-conformations stabilized by local interactions. This leads α-syn to adapt two different pathways. The secondary structure, solvation, contact distance, interaction energies and backbone dihedrals of thirty-two selected residues were analyzed for all the 19 intermediates. The results suggested that formation of β-turns, reorganization of salt bridges, and dihedral changes in the hydrophobic regions are the major driving forces for helix-fibril transition. Structural features of the intermediates also correlated with the earlier experimental and computational studies. The study provides critical information on the fibrillation pathway of α-syn.
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Affiliation(s)
- Archi Saurabh
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India
| | - N Prakash Prabhu
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India.
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28
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Ranasinghe JC, Wang Z, Huang S. Raman Spectroscopy on Brain Disorders: Transition from Fundamental Research to Clinical Applications. BIOSENSORS 2022; 13:27. [PMID: 36671862 PMCID: PMC9855372 DOI: 10.3390/bios13010027] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/13/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Brain disorders such as brain tumors and neurodegenerative diseases (NDs) are accompanied by chemical alterations in the tissues. Early diagnosis of these diseases will provide key benefits for patients and opportunities for preventive treatments. To detect these sophisticated diseases, various imaging modalities have been developed such as computed tomography (CT), magnetic resonance imaging (MRI), and positron emission tomography (PET). However, they provide inadequate molecule-specific information. In comparison, Raman spectroscopy (RS) is an analytical tool that provides rich information about molecular fingerprints. It is also inexpensive and rapid compared to CT, MRI, and PET. While intrinsic RS suffers from low yield, in recent years, through the adoption of Raman enhancement technologies and advanced data analysis approaches, RS has undergone significant advancements in its ability to probe biological tissues, including the brain. This review discusses recent clinical and biomedical applications of RS and related techniques applicable to brain tumors and NDs.
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Affiliation(s)
| | | | - Shengxi Huang
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA
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29
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Vaikath N, Sudhakaran I, Abdi I, Gupta V, Majbour N, Ghanem S, Abdesselem H, Vekrellis K, El-Agnaf O. Structural and Biophysical Characterization of Stable Alpha-Synuclein Oligomers. Int J Mol Sci 2022; 23:ijms232314630. [PMID: 36498957 PMCID: PMC9740078 DOI: 10.3390/ijms232314630] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/14/2022] [Accepted: 11/19/2022] [Indexed: 11/25/2022] Open
Abstract
The aggregation of α-synuclein (α-syn) into neurotoxic oligomers and fibrils is an important pathogenic feature of synucleinopatheis, including Parkinson's disease (PD). A further characteristic of PD is the oxidative stress that results in the formation of aldehydes by lipid peroxidation. It has been reported that the brains of deceased patients with PD contain high levels of protein oligomers that are cross-linked to these aldehydes. Increasing evidence also suggests that prefibrillar oligomeric species are more toxic than the mature amyloid fibrils. However, due to the heterogenous and metastable nature, characterization of the α-syn oligomeric species has been challenging. Here, we generated and characterized distinct α-syn oligomers in vitro in the presence of DA and lipid peroxidation products 4-hydroxy-2-nonenal (HNE) and 4-oxo-2-nonenal (ONE). HNE and ONE oligomer were stable towards the treatment with SDS, urea, and temperature. The secondary structure analysis revealed that only HNE and ONE oligomers contain β-sheet content. In the seeding assay, both DA and ONE oligomers significantly accelerated the aggregation. Furthermore, all oligomeric preparations were found to seed the aggregation of α-syn monomers in vitro and found to be cytotoxic when added to SH-SY5Y cells. Finally, both HNE and ONE α-syn oligomers can be used as a calibrator in an α-syn oligomers-specific ELISA.
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Affiliation(s)
- Nishant Vaikath
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha P.O. Box 5825, Qatar
- Correspondence:
| | - Indulekha Sudhakaran
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha P.O. Box 5825, Qatar
| | - Ilham Abdi
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha P.O. Box 5825, Qatar
| | - Vijay Gupta
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha P.O. Box 5825, Qatar
| | - Nour Majbour
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha P.O. Box 5825, Qatar
| | - Simona Ghanem
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha P.O. Box 5825, Qatar
| | - Houari Abdesselem
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha P.O. Box 5825, Qatar
| | - Kostas Vekrellis
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
| | - Omar El-Agnaf
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha P.O. Box 5825, Qatar
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30
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León-Bejarano F, Méndez MO, Alba A, Rodríguez-Leyva I, González FJ, Rodríguez-Aranda MDC, Guevara E, Guirado-López RA, Ramírez-Elías MG. Raman Spectroscopy Study of Skin Biopsies from Patients with Parkinson's Disease: Trends in Alpha-Synuclein Aggregation from the Amide I Region. APPLIED SPECTROSCOPY 2022; 76:1317-1328. [PMID: 35506336 DOI: 10.1177/00037028221101634] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Parkinson's disease (PD) is one of the most common neurological pathologies with a high prevalence worldwide. PD is characterized by Lewy bodies, whose major component is the aggregates of α-synuclein (αSyn) protein. Interestingly, recent works have demonstrated that skin biopsy studies are a promising diagnostic tool for evaluating α-synucleinopathies. In this sense, this work focuses on the detection of αSyn in skin biopsies employing Raman spectroscopy, using three different approaches: (i) the in vitro Raman spectrum of α-synuclein, (ii) the ex vivo Raman spectra of human skin biopsies from healthy and Parkinson's disease patients, and (iii) theoretical calculations of the Raman spectra obtained from different model αSyn fragments using density functional theory (DFT). Significant differences in the intensity and location of Raman active frequencies in the amide I region were found when comparing healthy and PD subjects related to α-synuclein conformational changes and variations in their aggregation behavior. In samples from healthy patients, we identified well-known Raman peaks at 1655, 1664, and 1680 cm-1 associated with the normal state of the protein. In PD subjects, shifted Raman bands and intensity variations were found at 1650, 1670, and 1687 cm-1 associated with aggregated forms of the protein. DFT calculations reveal that the shape of the amide I Raman peak in model αSyn fragments strongly depends on the degree of aggregation. Sizable frequency shifts and intensity variations are found within the highly relevant 1600-1700 cm-1 domain, revealing the sensitivity of the amide I Raman band to the changes in the local atomic environment. Interestingly, we obtain that the presence of surrounding waters also affects the structure of the amide I band, leading to the appearance of new peaks on the low-frequency side and a notable broadening of the Raman spectra. These results strongly suggest that, through Raman spectroscopy, it is possible to infer the presence of aggregated forms of αSyn in skin biopsies, a result that could have important implications for understanding α-synuclein related diseases.
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Affiliation(s)
- Fabiola León-Bejarano
- Facultad de Ciencias, 27773Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - Martín O Méndez
- Facultad de Ciencias, 27773Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
- Laboratorio Nacional CI3M, Facultad de Ciencias, 27773Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - Alfonso Alba
- Facultad de Ciencias, 27773Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
- Laboratorio Nacional CI3M, Facultad de Ciencias, 27773Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | | | - Francisco J González
- Coordinación para la Innovación y Aplicación de la Ciencia y la Tecnología (CIACyT), 27773Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - María Del Carmen Rodríguez-Aranda
- Coordinación para la Innovación y Aplicación de la Ciencia y la Tecnología (CIACyT), 27773Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - Edgar Guevara
- Coordinación para la Innovación y Aplicación de la Ciencia y la Tecnología (CIACyT), 27773Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
- CONACYT-Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | | | - Miguel G Ramírez-Elías
- Facultad de Ciencias, 27773Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
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31
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Zhaliazka K, Kurouski D. Nanoscale Characterization of Parallel and Antiparallel β-Sheet Amyloid Beta 1-42 Aggregates. ACS Chem Neurosci 2022; 13:2813-2820. [PMID: 36122250 PMCID: PMC10405294 DOI: 10.1021/acschemneuro.2c00180] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Abrupt aggregation of amyloid beta (Aβ) peptide is strongly associated with Alzheimer's disease. In this study, we used atomic force microscopy-infrared (AFM-IR) spectroscopy to characterize the secondary structure of Aβ oligomers, protofibrils and fibrils formed at the early (4 h), middle (24 h), and late (72 h) stages of protein aggregation. This innovative spectroscopic approach allows for label-free nanoscale structural characterization of individual protein aggregates. Using AFM-IR, we found that at the early stage of protein aggregation, oligomers with parallel β-sheet dominated. However, these species exhibited slower rates of fibril formation compared to the oligomers with antiparallel β-sheet, which first appeared in the middle stage. These antiparallel β-sheet oligomers rapidly propagated into fibrils that were simultaneously observed together with parallel β-sheet fibrils at the late stage of protein aggregation. Our findings showed that aggregation of Aβ is a complex process that yields several distinctly different aggregates with dissimilar toxicities.
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Affiliation(s)
- Kiryl Zhaliazka
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Dmitry Kurouski
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States.,Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States
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32
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Matveyenka M, Zhaliazka K, Rizevsky S, Kurouski D. Lipids uniquely alter secondary structure and toxicity of lysozyme aggregates. FASEB J 2022; 36:e22543. [PMID: 36094052 PMCID: PMC10427241 DOI: 10.1096/fj.202200841r] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/03/2022] [Accepted: 08/29/2022] [Indexed: 08/17/2023]
Abstract
Abrupt aggregation of misfolded proteins is a hallmark of the large group of amyloid pathologies that include diabetes type 2, Alzheimer and Parkinson's diseases. Protein aggregation yields oligomers and fibrils, β-sheet-rich structures that exert cell toxicity. Microscopic examination of amyloid deposits reveals the presence of lipids membranes, which suggests that lipids can be involved in the process of pathogenic protein assembly. In this study, we show that lipids can uniquely alter the aggregation rates of lysozyme, a protein that is associated with systemic amyloidosis. Specifically, cardiolipin (CL), ceramide (CER), and sphingomyelin (SM) accelerate, phosphatidylcholine (PC) strongly inhibits, whereas phosphatidylserine (PS) has no effect on the rate of protein aggregation. Furthermore, lipids uniquely alter the secondary structure of lysozyme aggregates. Furthermore, we found that lysozyme aggregates grown in the presence of CL, CER, SM, PS, and CL:PC mixtures exert significantly lower production of reactive oxygen species and mitochondrial dysfunction compared to lysozyme:PC aggregates and lysozyme fibrils grown in the lipid-free environment. These findings suggest that a change in the lipid composition of cell membranes, which is taken place upon neurodegeneration, may trigger the formation of toxic protein species that otherwise would not be formed.
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Affiliation(s)
- Mikhail Matveyenka
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Kiryl Zhaliazka
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Stanislav Rizevsky
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
- Department of Biotechnology, Binh Duong University, Thu Dau Mot, Vietnam
| | - Dmitry Kurouski
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas, USA
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Dou T, Kurouski D. Phosphatidylcholine and Phosphatidylserine Uniquely Modify the Secondary Structure of α-Synuclein Oligomers Formed in Their Presence at the Early Stages of Protein Aggregation. ACS Chem Neurosci 2022; 13:2380-2385. [PMID: 35904551 PMCID: PMC10405296 DOI: 10.1021/acschemneuro.2c00355] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Abrupt aggregation of α-synuclein (α-Syn) leads to a formation of highly toxic protein oligomers. These aggregates are the underlying molecular cause of an onset of the irreversible degeneration of dopaminergic neurons in midbrain, hypothalamus, and thalamus, a pathology known as Parkinson's disease. The transient nature of oligomers, as well as their structural and morphological heterogeneity, limits the use of cryo-electron microscopy and solid-state NMR, classical tools of structural biology, for elucidation of their secondary structure. Despite this limitation, numerous pieces of experimental evidence suggest that phospholipids can uniquely alter the structure and toxicity of oligomers. In this study, we utilize an innovative nano-infrared imaging technique, also known as atomic force microscopy infrared (AFM-IR) spectroscopy, to examine the structure of individual α-Syn oligomers grown in the presence of phosphatidylcholine (α-Syn:PC) and phosphatidylserine (α-Syn:PS). We determined the amount of the parallel and the antiparallel β-sheets, as well as the amount the α-helix and the unordered protein, in the secondary structure of α-Syn:PC and α-Syn:PS formed at day 2 (D2), 8 (D8), and 15 (D15) after initiation of protein aggregation. We found a gradual decrease in the amount of the parallel β-sheet in both α-Syn:PC and α-Syn:PS from D2 to D15 together with an increase in the α-helix and the unordered protein secondary structure. We infer that this is due to the presence of lipids in the structure of oligomers that prevent an expansion of the parallel β-sheet upon interaction of the oligomers with monomeric α-Syn.
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Affiliation(s)
- Tianyi Dou
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Dmitry Kurouski
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States.,Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States
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Savva L, Platts JA. Evaluation of implicit solvent models in molecular dynamics simulation of α-Synuclein. J Biomol Struct Dyn 2022:1-16. [PMID: 35670576 DOI: 10.1080/07391102.2022.2082534] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
We report conventional and accelerated molecular dynamics simulations of α-Synuclein, designed to assess performance of using different starting conformation, solvation environment and force field combination. Backbone and sidechain chemical shifts, radius of gyration, presence of β-hairpin structures in KTK(E/Q)GV repeats and secondary structure percentages were used to evaluate how variations in forcefield, solvation model and simulation protocol provide results that correlate with experimental findings. We show that with suitable choice of forcefield and solvent, ff03ws and OBC implicit model, respectively, acceptable reproduction of experimental data on size and secondary structure is obtained by both conventional and accelerated MD. In contrast to the implicit solvent model, simulations in explicit TIP4P/2005 solvent do not properly represent size or secondary structure of α-Synuclein.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Loizos Savva
- School of Chemistry, Cardiff University, Cardiff, UK
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35
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Galamba N. Aggregation of a Parkinson's Disease-Related Peptide: When Does Urea Weaken Hydrophobic Interactions? ACS Chem Neurosci 2022; 13:1769-1781. [PMID: 35616516 PMCID: PMC9775218 DOI: 10.1021/acschemneuro.2c00169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
While the exact cause of neurodegenerative diseases such as Alzheimer's disease and Parkinson's disease is not completely understood, compelling evidence implicates the aggregation of specific proteins and peptides. Co-solvents can provide molecular insight into protein aggregation mechanisms and the chemical nature of potential aggregation inhibitors. Here, we study, through molecular simulations, the hydration and binding free energies of an amphiphilic peptide from the nonamyloid-β component (NAC), a key aggregation-prone domain of α-synuclein, in water and an 8 M aqueous urea solution. Isoleucine, glycine, and serine peptides of the same length are also studied to unravel the role of urea in the hydration and aggregation of hydrophobic and hydrophilic domains. A strong impact of urea in hindering the aggregation of the NAC subdomain is observed. A slightly weaker aggregation inhibition is observed for the Gly and Ser peptides, whereas a much lower aggregation inhibitory activity is found for the Ile peptide, seemingly contrasting with urea's protein unfolding mechanism. This behavior is shown to derive from a lower profusion of urea next to the hydrophobic side chains and the backbone of the Ile's peptide in the dimeric form. As a consequence, β-sheets, formed upon aggregation, remain nearly intact. Hydrophilic neighbor groups in the amphiphilic NAC subdomain, however, are shown to anchor enough urea to weaken hydrophobic interactions and disrupt β-sheet structures. Our results indicate that urea's activity is potentiated in amphiphilic domains and that potential drugs could disrupt hydrophobic β-sheet-rich regions while not binding primarily to hydrophobic amino acids.
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36
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Synhaivska O, Bhattacharya S, Campioni S, Thompson D, Nirmalraj PN. Single-Particle Resolution of Copper-Associated Annular α-Synuclein Oligomers Reveals Potential Therapeutic Targets of Neurodegeneration. ACS Chem Neurosci 2022; 13:1410-1421. [PMID: 35414168 PMCID: PMC9073932 DOI: 10.1021/acschemneuro.2c00021] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
![]()
Metal ions stabilize
protein–protein interactions and can
modulate protein aggregation. Here, using liquid-based atomic force
microscopy and molecular dynamics simulations, we study the concentration-dependent
effect of Cu2+ ions on the aggregation pathway of α-synuclein
(α-Syn) proteins, which play a key role in the pathology of
Parkinson’s disease. The full spectrum of α-Syn aggregates
in the presence and absence of Cu2+ ions from monomers
to mature fibrils was resolved and quantified at the gold–water
interface. Raman spectroscopy confirmed the atomic force microscopy
(AFM) findings on the heterogeneity in aggregated states of α-Syn.
The formation of annular oligomers was exclusively detected upon incubating
α-Syn with Cu2+ ions. Our findings emphasize the
importance of targeting annular α-Syn protein oligomers for
therapeutic intervention and their potential role as biomarkers for
early detection and monitoring progression of neurodegeneration.
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Affiliation(s)
- Olena Synhaivska
- Transport at Nanoscale Interfaces Laboratory, Swiss Federal Laboratories for Materials Science and Technology, Dübendorf CH-8600, Switzerland
| | - Shayon Bhattacharya
- Department of Physics, Bernal Institute, University of Limerick, Limerick V94T9PX, Ireland
| | - Silvia Campioni
- Functional Materials Laboratory, Swiss Federal Laboratories for Materials Science and Technology, Dübendorf CH-8600, Switzerland
| | - Damien Thompson
- Department of Physics, Bernal Institute, University of Limerick, Limerick V94T9PX, Ireland
| | - Peter Niraj Nirmalraj
- Transport at Nanoscale Interfaces Laboratory, Swiss Federal Laboratories for Materials Science and Technology, Dübendorf CH-8600, Switzerland
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Rizevsky S, Matveyenka M, Kurouski D. Nanoscale Structural Analysis of a Lipid-Driven Aggregation of Insulin. J Phys Chem Lett 2022; 13:2467-2473. [PMID: 35266717 PMCID: PMC9169669 DOI: 10.1021/acs.jpclett.1c04012] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Abrupt aggregation of misfolded proteins is a hallmark of a large number of severe pathologies, including diabetes types 1 and 2, Alzheimer, and Parkinson diseases. A growing body of evidence suggests that lipids can uniquely change rates of amyloid-associated proteins as well as modify the structure of formed oligomers and fibrils. In this study, we utilize atomic force microscopy infrared (AFM-IR) spectroscopy, also known as nano-IR spectroscopy, to examine the structure of individual insulin oligomers, protofilaments, and fibrils grown in the presence of phospholipids. Our findings show that AFM-IR spectra of insulin oligomers have strong signals of C-H and PO2- vibrations, which points on the presence of lipids in the oligomer structure. Furthermore, substantial shifts in lipid vibrations in AFM-IR spectra of the oligomers relative to the corresponding bands of pure lipids have been observed. This points on strong interactions between a lipid and a protein that are developed at the stage of the oligomer formation.
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Affiliation(s)
- Stanislav Rizevsky
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
- Department of Biotechnology, Binh Duong University, Thu Dau Mot 820000, Vietnam
| | - Mikhail Matveyenka
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
| | - Dmitry Kurouski
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, United States
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States
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38
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Lye YS, Chen YR. TAR DNA-binding protein 43 oligomers in physiology and pathology. IUBMB Life 2022; 74:794-811. [PMID: 35229461 DOI: 10.1002/iub.2603] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/19/2022] [Accepted: 01/28/2022] [Indexed: 11/08/2022]
Abstract
TAR DNA-binding protein 43 (TDP-43) is an RNA/DNA-binding protein involved in RNA regulation and diseases. In 2006, TDP-43 inclusions were found in the disease lesions of several neurodegenerative diseases. It is the pathological hallmark in both amyotrophic lateral sclerosis and frontotemporal lobar dementia. It also presents in a large portion of patients with Alzheimer's disease. TDP-43 is prone to aggregate; however, the role of TDP-43 oligomers remains poorly understood in both physiological and pathological conditions. In this review, we emphasize the role of oligomeric TDP-43 in both physiological and pathological conditions and discuss the potential mechanisms of oligomer formation. Finally, we suggest therapeutic strategies against the TDP-43 oligomers in neurodegenerative diseases.
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Affiliation(s)
- Yuh Shen Lye
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.,Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Cheng Kung University and Academia Sinica, Taipei, Taiwan
| | - Yun-Ru Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.,Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Cheng Kung University and Academia Sinica, Taipei, Taiwan
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39
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Xu CK, Castellana-Cruz M, Chen SW, Du Z, Meisl G, Levin A, Mannini B, Itzhaki LS, Knowles TPJ, Dobson CM, Cremades N, Kumita JR. The Pathological G51D Mutation in Alpha-Synuclein Oligomers Confers Distinct Structural Attributes and Cellular Toxicity. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27041293. [PMID: 35209093 PMCID: PMC8879557 DOI: 10.3390/molecules27041293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/02/2022] [Accepted: 02/10/2022] [Indexed: 12/17/2022]
Abstract
A wide variety of oligomeric structures are formed during the aggregation of proteins associated with neurodegenerative diseases. Such soluble oligomers are believed to be key toxic species in the related disorders; therefore, identification of the structural determinants of toxicity is of upmost importance. Here, we analysed toxic oligomers of α-synuclein and its pathological variants in order to identify structural features that could be related to toxicity and found a novel structural polymorphism within G51D oligomers. These G51D oligomers can adopt a variety of β-sheet-rich structures with differing degrees of α-helical content, and the helical structural content of these oligomers correlates with the level of induced cellular dysfunction in SH-SY5Y cells. This structure–function relationship observed in α-synuclein oligomers thus presents the α-helical structure as another potential structural determinant that may be linked with cellular toxicity in amyloid-related proteins.
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Affiliation(s)
- Catherine K. Xu
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; (C.K.X.); (M.C.-C.); (G.M.); (A.L.); (B.M.); (T.P.J.K.)
| | - Marta Castellana-Cruz
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; (C.K.X.); (M.C.-C.); (G.M.); (A.L.); (B.M.); (T.P.J.K.)
| | - Serene W. Chen
- Department of Life Sciences, South Kensington Campus, Imperial College London, London SW7 2AZ, UK;
| | - Zhen Du
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK; (Z.D.); (L.S.I.)
| | - Georg Meisl
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; (C.K.X.); (M.C.-C.); (G.M.); (A.L.); (B.M.); (T.P.J.K.)
| | - Aviad Levin
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; (C.K.X.); (M.C.-C.); (G.M.); (A.L.); (B.M.); (T.P.J.K.)
| | - Benedetta Mannini
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; (C.K.X.); (M.C.-C.); (G.M.); (A.L.); (B.M.); (T.P.J.K.)
| | - Laura S. Itzhaki
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK; (Z.D.); (L.S.I.)
| | - Tuomas P. J. Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; (C.K.X.); (M.C.-C.); (G.M.); (A.L.); (B.M.); (T.P.J.K.)
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
| | - Christopher M. Dobson
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; (C.K.X.); (M.C.-C.); (G.M.); (A.L.); (B.M.); (T.P.J.K.)
| | - Nunilo Cremades
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Mariano Esquillor, Edificio I+D+I, 50018 Zaragoza, Spain
- Correspondence: (N.C.); (J.R.K.)
| | - Janet R. Kumita
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK; (Z.D.); (L.S.I.)
- Correspondence: (N.C.); (J.R.K.)
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40
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Martínez-Miguel M, Tatkiewicz W, Köber M, Ventosa N, Veciana J, Guasch J, Ratera I. Methods for the Characterization of Protein Aggregates. Methods Mol Biol 2022; 2406:479-497. [PMID: 35089576 DOI: 10.1007/978-1-0716-1859-2_29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The physicochemical characterization of protein aggregates yields an important contribution to further our understanding on many diseases for which the formation of protein aggregates is one of the pathological hallmarks. On the other hand, bacterial inclusion bodies (IBs) have recently been shown to be highly pure proteinaceous aggregates of a few hundred nanometers, produced by recombinant bacteria supporting the biological activities of the embedded polypeptides. Despite the wide spectrum of uses of IBs as functional and biocompatible materials upon convenient engineering, very few is known about their physicochemical properties.In this chapter we present methods for the characterization of protein aggregates as particulate materials relevant to their physicochemical and nanoscale properties.Specifically, we describe the use of dynamic light scattering (DLS) for sizing, nanoparticle tracking analysis for sizing and counting, and zeta potential measurements for the determination of colloidal stability. To study the morphology of protein aggregates we present the use of atomic force microscopy (AFM) and scanning electron microscopy (SEM). Cryo-transmission electron microscopy (cryo-TEM) will be used for the determination of the internal structuration. Moreover, wettability and nanomechanical characterization can be performed using contact angle (CA) and force spectroscopic AFM (FS-AFM) measurements of the proteinaceous nanoparticles, respectively. Finally, the 4'4-dithiodipyridine (DTDP) method is presented as a way of relatively quantifying accessible sulfhydryl groups in the structure of the nanoparticle .The physical principles of the methods are briefly described and examples are given to help clarify capabilities of each technique.
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Affiliation(s)
- Marc Martínez-Miguel
- Institut de Ciència de Materials de Barcelona, ICMAB-CSIC and CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Campus UAB, Bellaterra, Spain
| | - Witold Tatkiewicz
- Institut de Ciència de Materials de Barcelona, ICMAB-CSIC and CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Campus UAB, Bellaterra, Spain
| | - Mariana Köber
- Institut de Ciència de Materials de Barcelona, ICMAB-CSIC and CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Campus UAB, Bellaterra, Spain
| | - Nora Ventosa
- Institut de Ciència de Materials de Barcelona, ICMAB-CSIC and CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Campus UAB, Bellaterra, Spain
| | - Jaume Veciana
- Institut de Ciència de Materials de Barcelona, ICMAB-CSIC and CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Campus UAB, Bellaterra, Spain
| | - Judith Guasch
- Institut de Ciència de Materials de Barcelona, ICMAB-CSIC and CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Campus UAB, Bellaterra, Spain
- Dynamic Biomimetics for Cancer Immunotherapy, Max Planck Partner Group, ICMAB-CSIC, Campus UAB, Bellaterra, Spain
| | - Imma Ratera
- Institut de Ciència de Materials de Barcelona, ICMAB-CSIC and CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Campus UAB, Bellaterra, Spain.
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41
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Bhattacharya S, Xu L, Thompson D. Characterization of Amyloidogenic Peptide Aggregability in Helical Subspace. Methods Mol Biol 2022; 2340:401-448. [PMID: 35167084 DOI: 10.1007/978-1-0716-1546-1_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Prototypical amyloidogenic peptides amyloid-β (Aβ) and α-synuclein (αS) can undergo helix-helix associations via partially folded helical conformers, which may influence pathological progression to Alzheimer's (AD) and Parkinson's disease (PD), respectively. At the other extreme, stable folded helical conformers have been reported to resist self-assembly and amyloid formation. Experimental characterisation of such disparities in aggregation profiles due to subtle differences in peptide stabilities is precluded by the conformational heterogeneity of helical subspace. The diverse physical models used in molecular simulations allow sampling distinct regions of the phase space and are extensive in capturing the ensemble of rich helical subspace. Robust and powerful computational predictive methods utilizing network theory and free energy mapping can model the origin of helical population shifts in amyloidogenic peptides, which highlight their inherent aggregability. In this chapter, we discuss computational models, methods, design rules, and strategies to identify the driving force behind helical self-assembly and the molecular origin of aggregation resistance in helical intermediates of Aβ42 and αS. By extensive multiscale mapping of intrapeptide interactions, we show that the computational models can capture features that are otherwise imperceptible to experiments. Our models predict that targeting terminal residues may allow modulation and control of initial pathogenic aggregability of amyloidogenic peptides.
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Affiliation(s)
- Shayon Bhattacharya
- Department of Physics, Bernal Institute, University of Limerick, Limerick, Ireland
| | - Liang Xu
- Department of Physics, Bernal Institute, University of Limerick, Limerick, Ireland
| | - Damien Thompson
- Department of Physics, Bernal Institute, University of Limerick, Limerick, Ireland.
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Gadhe L, Sakunthala A, Mukherjee S, Gahlot N, Bera R, Sawner AS, Kadu P, Maji SK. Intermediates of α-synuclein aggregation: Implications in Parkinson's disease pathogenesis. Biophys Chem 2021; 281:106736. [PMID: 34923391 DOI: 10.1016/j.bpc.2021.106736] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/27/2021] [Accepted: 11/27/2021] [Indexed: 12/11/2022]
Abstract
Cytoplasmic deposition of aberrantly misfolded α-synuclein (α-Syn) is a common feature of synucleinopathies, including Parkinson's disease (PD). However, the precise pathogenic mechanism of α-Syn in synucleinopathies remains elusive. Emerging evidence has suggested that α-Syn may contribute to PD pathogenesis in several ways; wherein the contribution of fibrillar species, for exerting toxicity and disease transmission, cannot be neglected. Further, the oligomeric species could be the most plausible neurotoxic species causing neuronal cell death. However, understanding the structural and molecular insights of these oligomers are very challenging due to the heterogeneity and transient nature of the species. In this review, we discuss the recent advancements in understanding the formation and role of α-Syn oligomers in PD pathogenesis. We also summarize the different types of α-Syn oligomeric species and potential mechanisms to exert neurotoxicity. Finally, we address the possible ways to target α-Syn as a promising approach against PD and the possible future directions.
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Affiliation(s)
- Laxmikant Gadhe
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Arunima Sakunthala
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Semanti Mukherjee
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Nitisha Gahlot
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Riya Bera
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Ajay Singh Sawner
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Pradeep Kadu
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Samir K Maji
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India.
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43
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The role of amyloids in Alzheimer's and Parkinson's diseases. Int J Biol Macromol 2021; 190:44-55. [PMID: 34480905 DOI: 10.1016/j.ijbiomac.2021.08.197] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 11/23/2022]
Abstract
With varying clinical symptoms, most neurodegenerative diseases are associated with abnormal loss of neurons. They share the same common pathogenic mechanisms involving misfolding and aggregation, and these visible aggregates of proteins are deposited in the central nervous system. Amyloid formation is thought to arise from partial unfolding of misfolded proteins leading to the exposure of hydrophobic surfaces, which interact with other similar structures and give rise to form dimers, oligomers, protofibrils, and eventually mature fibril aggregates. Accumulating evidence indicates that amyloid oligomers, not amyloid fibrils, are the most toxic species that causes Alzheimer's disease (AD) and Parkinson's disease (PD). AD has recently been recognized as the 'twenty-first century plague', with an incident rate of 1% at 60 years of age, which then doubles every fifth year. Currently, 5.3 million people in the US are afflicted with this disease, and the number of cases is expected to rise to 13.5 million by 2050. PD, a disorder of the brain, is the second most common form of dementia, characterized by difficulty in walking and movement. Keeping the above views in mind, in this review we have focused on the roles of amyloid in neurodegenerative diseases including AD and PD, the involvement of amyloid in mitochondrial dysfunction leading to neurodegeneration, are also considered in the review.
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44
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Chau E, Kim H, Shin J, Martinez A, Kim JR. Inhibition of alpha-synuclein aggregation by AM17, a synthetic resveratrol derivative. Biochem Biophys Res Commun 2021; 574:85-90. [PMID: 34454326 DOI: 10.1016/j.bbrc.2021.08.049] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/29/2021] [Accepted: 08/18/2021] [Indexed: 10/20/2022]
Abstract
Parkinson's disease (PD) is linked to the aberrant self-assembly of the amyloid protein, α-synuclein (αS), where αS monomers aggregate to form oligomers and fibrils. Out of the three conformers, αS oligomers are the major toxic agents in PD, while αS fibrils may work as a reservoir for toxic oligomeric conformers. Thus, compounds that inhibit aggregation of αS monomers and disaggregate αS oligomers and fibrils may serve as therapeutic agents against PD. In this regard, resveratrol and its synthetic derivatives (e.g., AM17, which contains a copper ion-selective ionophoric motif) have previously been examined for their inhibitory effects on aggregation of amyloid proteins, such as the β-amyloid peptide implicated in Alzheimer's disease. In the current study, we employed an array of experimental tools, such as Thioflavin T fluorescence, transmission electron microscopy, immuno-dot blot assays, SDS- and native-PAGE, and circular dichroism, to determine the impact of AM17 and resveratrol on αS aggregation. To the best of our knowledge, we show for the first time that AM17 not only inhibits aggregation of αS monomers but also disaggregates αS oligomers and fibrils, independent of the copper ions. Similar αS aggregation inhibitory effects were observed with resveratrol only in the presence of the copper ion. The present study supports the high promise of applicability of AM17 as an effective amyloid aggregation inhibitor for various conformers and protein sequences.
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Affiliation(s)
- Edward Chau
- Department of Chemical and Biomolecular Engineering, New York University, 6 MetroTech Center, Brooklyn, NY, 11201, USA
| | - Hyunjoo Kim
- Department of Chemical and Biomolecular Engineering, New York University, 6 MetroTech Center, Brooklyn, NY, 11201, USA
| | - Jineun Shin
- Department of Biomedical Engineering, New York University, 6 MetroTech Center, Brooklyn, NY, 11201, USA
| | - Alberto Martinez
- Department of Chemistry, New York City College of Technology, 300 Jay St, Brooklyn, NY, 11201, USA
| | - Jin Ryoun Kim
- Department of Chemical and Biomolecular Engineering, New York University, 6 MetroTech Center, Brooklyn, NY, 11201, USA.
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45
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Sevgi F, Brauchle EM, Carvajal Berrio DA, Schenke-Layland K, Casadei N, Salker MS, Riess O, Singh Y. Imaging of α-Synuclein Aggregates in a Rat Model of Parkinson's Disease Using Raman Microspectroscopy. Front Cell Dev Biol 2021; 9:664365. [PMID: 34568310 PMCID: PMC8461246 DOI: 10.3389/fcell.2021.664365] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 06/14/2021] [Indexed: 11/18/2022] Open
Abstract
A hallmark of Parkinson’s disease (PD) is the formation of Lewy bodies in the brain. Lewy bodies are rich in the aggregated form of misfolded α-Synuclein (α-Syn). The brain from PD patients can only be analyzed after postmortem, therefore, limiting the diagnosis of PD to the manifestation of motor symptoms. In PD patients and animal models, phosphorylated α-Syn was detected in the peripheral tissues including the gut, thus, raising the hypothesis that early-stage PD could be diagnosed based on colon tissue biopsies. Non-invasive marker-free technologies represent ideal methods to potentially detect aggregated α-Syn in vivo. Raman microspectroscopy has been established for the detection of molecular changes such as alterations of protein structures. Using Raman imaging and microspectroscopy, we analyzed the olfactory bulb in the brain and the muscularis mucosae of colon tissue sections of a human BAC-SNCA transgenic (TG) rat model. Raman images from TG and WT rats were investigated using principal component analysis (PCA) and true component analysis (TCA). Spectral components indicated protein aggregates (spheroidal oligomers) in the TG rat brain and in the colon tissues even at a young age but not in WT. In summary, we have demonstrated that Raman imaging is capable of detecting α-Syn aggregates in colon tissues of a PD rat model and making it a promising tool for future use in PD pathology.
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Affiliation(s)
- Fide Sevgi
- Department of Women's Health, Research Institute for Women's Health, Eberhard Karls Tübingen University, Tübingen, Germany
| | - Eva M Brauchle
- Department of Women's Health, Research Institute for Women's Health, Eberhard Karls Tübingen University, Tübingen, Germany.,Natural and Medical Sciences Institute (NMI), Tübingen University, Reutlingen, Germany.,Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University Tübingen, Tübingen, Germany
| | - Daniel A Carvajal Berrio
- Department of Women's Health, Research Institute for Women's Health, Eberhard Karls Tübingen University, Tübingen, Germany.,Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University Tübingen, Tübingen, Germany
| | - Katja Schenke-Layland
- Department of Women's Health, Research Institute for Women's Health, Eberhard Karls Tübingen University, Tübingen, Germany.,Natural and Medical Sciences Institute (NMI), Tübingen University, Reutlingen, Germany.,Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University Tübingen, Tübingen, Germany.,Department of Medicine/Cardiology, Cardiovascular Research Laboratories, David Geffen School of Medicine at UCLA, Los Angeles, CA, United States
| | - Nicolas Casadei
- Institute of Medical Genetics and Applied Genomics, Eberhard Karls Tübingen University, Tübingen, Germany
| | - Madhuri S Salker
- Department of Women's Health, Research Institute for Women's Health, Eberhard Karls Tübingen University, Tübingen, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, Eberhard Karls Tübingen University, Tübingen, Germany
| | - Yogesh Singh
- Department of Women's Health, Research Institute for Women's Health, Eberhard Karls Tübingen University, Tübingen, Germany.,Institute of Medical Genetics and Applied Genomics, Eberhard Karls Tübingen University, Tübingen, Germany
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46
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Näsström T, Dahlberg T, Malyshev D, Ådén J, Andersson PO, Andersson M, Karlsson BCG. Synthetic NAC 71-82 Peptides Designed to Produce Fibrils with Different Protofilament Interface Contacts. Int J Mol Sci 2021; 22:ijms22179334. [PMID: 34502242 PMCID: PMC8431055 DOI: 10.3390/ijms22179334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 11/17/2022] Open
Abstract
Alpha-synucleinopathies are featured by fibrillar inclusions in brain cells. Although α-synuclein fibrils display structural diversity, the origin of this diversity is not fully understood. We used molecular dynamics simulations to design synthetic peptides, based on the NAC 71-82 amino acid fragment of α-synuclein, that govern protofilament contacts and generation of twisted fibrillar polymorphs. Four peptides with structures based on either single or double fragments and capped or non-capped ends were selected for further analysis. We determined the fibrillar yield and the structures from these peptides found in the solution after fibrillisation using protein concentration determination assay and circular dichroism spectroscopy. In addition, we characterised secondary structures formed by individual fibrillar complexes using laser-tweezers Raman spectroscopy. Results suggest less mature fibrils, based on the lower relative β-sheet content for double- than single-fragment peptide fibrils. We confirmed this structural difference by TEM analysis which revealed, in addition to short protofibrils, more elongated, twisted and rod-like fibril structures in non-capped and capped double-fragment peptide systems, respectively. Finally, time-correlated single-photon counting demonstrated a difference in the Thioflavin T fluorescence lifetime profiles upon fibril binding. It could be proposed that this difference originated from morphological differences in the fibril samples. Altogether, these results highlight the potential of using peptide models for the generation of fibrils that share morphological features relevant for disease, e.g., twisted and rod-like polymorphs.
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Affiliation(s)
- Thomas Näsström
- Physical Pharmacy Laboratory, Linnaeus University Centre for Biomaterials Chemistry, Linnaeus University, SE-392 31 Kalmar, Sweden;
| | - Tobias Dahlberg
- The Biophysics and Biophotonics Group, Department of Physics, Umeå University, SE-901 87 Umeå, Sweden; (T.D.); (D.M.); (M.A.)
| | - Dmitry Malyshev
- The Biophysics and Biophotonics Group, Department of Physics, Umeå University, SE-901 87 Umeå, Sweden; (T.D.); (D.M.); (M.A.)
| | - Jörgen Ådén
- Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden;
| | - Per Ola Andersson
- Department of Material Science and Engineering, Applied Materials Science, Uppsala University, SE-751 03 Uppsala, Sweden;
| | - Magnus Andersson
- The Biophysics and Biophotonics Group, Department of Physics, Umeå University, SE-901 87 Umeå, Sweden; (T.D.); (D.M.); (M.A.)
| | - Björn C. G. Karlsson
- Physical Pharmacy Laboratory, Linnaeus University Centre for Biomaterials Chemistry, Linnaeus University, SE-392 31 Kalmar, Sweden;
- Correspondence:
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47
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Imanbekova M, Suarasan S, Rojalin T, Mizenko RR, Hilt S, Mathur M, Lepine P, Nicouleau M, Mohamed NV, Durcan TM, Carney RP, Voss JC, Wachsmann-Hogiu S. Identification of amyloid beta in small extracellular vesicles via Raman spectroscopy. NANOSCALE ADVANCES 2021; 3:4119-4132. [PMID: 34355118 PMCID: PMC8276787 DOI: 10.1039/d1na00330e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 06/07/2021] [Indexed: 05/20/2023]
Abstract
One of the hallmarks of Alzheimer's disease (AD) pathogenesis is believed to be the production and deposition of amyloid-beta (Aβ) peptide into extracellular plaques. Existing research indicates that extracellular vesicles (EVs) can carry Aβ associated with AD. However, characterization of the EVs-associated Aβ and its conformational variants has yet to be realized. Raman spectroscopy is a label-free and non-destructive method that is able to assess the biochemical composition of EVs. This study reports for the first time the Raman spectroscopic fingerprint of the Aβ present in the molecular cargo of small extracellular vesicles (sEVs). Raman spectra were measured from sEVs isolated from Alzheimer's disease cell culture model, where secretion of Aβ is regulated by tetracycline promoter, and from midbrain organoids. The averaged spectra of each sEV group showed considerable variation as a reflection of the biochemical content of sEVs. Spectral analysis identified more intense Raman peaks at 1650 cm-1 and 2930 cm-1 attributable to the Aβ peptide incorporated in sEVs produced by the Alzheimer's cell culture model. Subsequent analysis of the spectra by principal component analysis differentiated the sEVs of the Alzheimer's disease cell culture model from the control groups of sEVs. Moreover, the results indicate that Aβ associated with secreted sEVs has a α-helical secondary structure and the size of a monomer or small oligomer. Furthermore, by analyzing the lipid content of sEVs we identified altered fatty acid chain lengths in sEVs that carry Aβ that may affect the fluidity of the EV membrane. Overall, our findings provide evidence supporting the use of Raman spectroscopy for the identification and characterization of sEVs associated with potential biomarkers of neurological disorders such as toxic proteins.
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Affiliation(s)
| | - Sorina Suarasan
- Department of Bioengineering, McGill University Montreal QC H3A 0E9 Canada
| | - Tatu Rojalin
- Department of Biomedical Engineering, University of California Davis CA 95616 USA
| | - Rachel R Mizenko
- Department of Biomedical Engineering, University of California Davis CA 95616 USA
| | - Silvia Hilt
- Department of Biochemistry & Molecular Medicine, University of California Davis CA 95616 USA
| | - Meghna Mathur
- The Early Drug Discovery Unit (EDDU), Montreal Neurological Institute and Hospital, McGill University Montreal QC H3A 2B4 Canada
| | - Paula Lepine
- The Early Drug Discovery Unit (EDDU), Montreal Neurological Institute and Hospital, McGill University Montreal QC H3A 2B4 Canada
| | - Michael Nicouleau
- The Early Drug Discovery Unit (EDDU), Montreal Neurological Institute and Hospital, McGill University Montreal QC H3A 2B4 Canada
| | - Nguyen-Vi Mohamed
- The Early Drug Discovery Unit (EDDU), Montreal Neurological Institute and Hospital, McGill University Montreal QC H3A 2B4 Canada
| | - Thomas M Durcan
- The Early Drug Discovery Unit (EDDU), Montreal Neurological Institute and Hospital, McGill University Montreal QC H3A 2B4 Canada
| | - Randy P Carney
- Department of Biomedical Engineering, University of California Davis CA 95616 USA
| | - John C Voss
- Department of Biochemistry & Molecular Medicine, University of California Davis CA 95616 USA
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48
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Candelise N, Scaricamazza S, Salvatori I, Ferri A, Valle C, Manganelli V, Garofalo T, Sorice M, Misasi R. Protein Aggregation Landscape in Neurodegenerative Diseases: Clinical Relevance and Future Applications. Int J Mol Sci 2021; 22:ijms22116016. [PMID: 34199513 PMCID: PMC8199687 DOI: 10.3390/ijms22116016] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 05/28/2021] [Accepted: 05/29/2021] [Indexed: 12/13/2022] Open
Abstract
Intrinsic disorder is a natural feature of polypeptide chains, resulting in the lack of a defined three-dimensional structure. Conformational changes in intrinsically disordered regions of a protein lead to unstable β-sheet enriched intermediates, which are stabilized by intermolecular interactions with other β-sheet enriched molecules, producing stable proteinaceous aggregates. Upon misfolding, several pathways may be undertaken depending on the composition of the amino acidic string and the surrounding environment, leading to different structures. Accumulating evidence is suggesting that the conformational state of a protein may initiate signalling pathways involved both in pathology and physiology. In this review, we will summarize the heterogeneity of structures that are produced from intrinsically disordered protein domains and highlight the routes that lead to the formation of physiological liquid droplets as well as pathogenic aggregates. The most common proteins found in aggregates in neurodegenerative diseases and their structural variability will be addressed. We will further evaluate the clinical relevance and future applications of the study of the structural heterogeneity of protein aggregates, which may aid the understanding of the phenotypic diversity observed in neurodegenerative disorders.
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Affiliation(s)
- Niccolò Candelise
- Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy; (S.S.); (I.S.); (A.F.); (C.V.)
- Institute of Translational Pharmacology, National Research Council, 00133 Rome, Italy
- Correspondence: ; Tel.: +39-338-891-2668
| | - Silvia Scaricamazza
- Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy; (S.S.); (I.S.); (A.F.); (C.V.)
| | - Illari Salvatori
- Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy; (S.S.); (I.S.); (A.F.); (C.V.)
- Department of Experimental Medicine, University of Rome “La Sapienza”, 00161 Rome, Italy; (V.M.); (T.G.); (M.S.); (R.M.)
| | - Alberto Ferri
- Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy; (S.S.); (I.S.); (A.F.); (C.V.)
- Institute of Translational Pharmacology, National Research Council, 00133 Rome, Italy
| | - Cristiana Valle
- Fondazione Santa Lucia IRCCS, c/o CERC, 00143 Rome, Italy; (S.S.); (I.S.); (A.F.); (C.V.)
- Institute of Translational Pharmacology, National Research Council, 00133 Rome, Italy
| | - Valeria Manganelli
- Department of Experimental Medicine, University of Rome “La Sapienza”, 00161 Rome, Italy; (V.M.); (T.G.); (M.S.); (R.M.)
| | - Tina Garofalo
- Department of Experimental Medicine, University of Rome “La Sapienza”, 00161 Rome, Italy; (V.M.); (T.G.); (M.S.); (R.M.)
| | - Maurizio Sorice
- Department of Experimental Medicine, University of Rome “La Sapienza”, 00161 Rome, Italy; (V.M.); (T.G.); (M.S.); (R.M.)
| | - Roberta Misasi
- Department of Experimental Medicine, University of Rome “La Sapienza”, 00161 Rome, Italy; (V.M.); (T.G.); (M.S.); (R.M.)
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49
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Wells C, Brennan S, Keon M, Ooi L. The role of amyloid oligomers in neurodegenerative pathologies. Int J Biol Macromol 2021; 181:582-604. [PMID: 33766600 DOI: 10.1016/j.ijbiomac.2021.03.113] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 02/18/2021] [Accepted: 03/19/2021] [Indexed: 11/25/2022]
Abstract
Many neurodegenerative diseases are rooted in the activities of amyloid-like proteins which possess conformations that spread to healthy proteins. These include Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD) and amyotrophic lateral sclerosis (ALS). While their clinical manifestations vary, their protein-level mechanisms are remarkably similar. Aberrant monomeric proteins undergo conformational shifts, facilitating aggregation and formation of solid fibrils. However, there is growing evidence that intermediate oligomeric stages are key drivers of neuronal toxicity. Analysis of protein dynamics is complicated by the fact that nucleation and growth of amyloid-like proteins is not a linear pathway. Feedback within this pathway results in exponential acceleration of aggregation, but activities exerted by oligomers and fibrils can alter cellular interactions and the cellular environment as a whole. The resulting cascade of effects likely contributes to the late onset and accelerating progression of amyloid-like protein disorders and the widespread effects they have on the body. In this review we explore the amyloid-like proteins associated with AD, PD, HD and ALS, as well as the common mechanisms of amyloid-like protein nucleation and aggregation. From this, we identify core elements of pathological progression which have been targeted for therapies, and which may become future therapeutic targets.
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Affiliation(s)
- Cameron Wells
- GenieUs Genomics, Sydney, NSW 2010, Australia; University of New South Wales, Sydney, NSW 2052, Australia
| | | | - Matt Keon
- GenieUs Genomics, Sydney, NSW 2010, Australia
| | - Lezanne Ooi
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia; School of Chemistry and Molecular Bioscience, and Molecular Horizons, University of Wollongong, Wollongong, NSW 2522, Australia; GenieUs Genomics, Sydney, NSW 2010, Australia
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50
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Devitt G, Crisford A, Rice W, Weismiller HA, Fan Z, Commins C, Hyman BT, Margittai M, Mahajan S, Mudher A. Conformational fingerprinting of tau variants and strains by Raman spectroscopy. RSC Adv 2021; 11:8899-8915. [PMID: 34381596 PMCID: PMC8330415 DOI: 10.1039/d1ra00870f] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 02/18/2021] [Indexed: 12/11/2022] Open
Abstract
Tauopathies are a group of disorders in which the deposition of abnormally folded tau protein accompanies neurodegeneration. The development of methods for detection and classification of pathological changes in protein conformation are desirable for understanding the factors that influence the structural polymorphism of aggregates in tauopathies. We have previously demonstrated the utility of Raman spectroscopy for the characterization and discrimination of different protein aggregates, including tau, based on their unique conformational signatures. Building on this, in the present study, we assess the utility of Raman spectroscopy for characterizing and distinguishing different conformers of the same protein which in the case of tau are unique tau strains generated in vitro. We now investigate the impact of aggregation environment, cofactors, post-translational modification and primary sequence on the Raman fingerprint of tau fibrils. Using quantitative conformational fingerprinting and multivariate statistical analysis, we found that the aggregation of tau in different buffer conditions resulted in the formation of distinct fibril strains. Unique spectral markers were identified for tau fibrils generated using heparin or RNA cofactors, as well as for phosphorylated tau. We also determined that the primary sequence of the tau monomer influenced the conformational signature of the resulting tau fibril, including 2N4R, 0N3R, K18 and P301S tau variants. These results highlight the conformational polymorphism of tau fibrils, which is reflected in the wide range of associated neurological disorders. Furthermore, the analyses presented in this study provide a benchmark for the Raman spectroscopic characterization of tau strains, which may shed light on how the aggregation environment, cofactors and post-translational modifications influence tau conformation in vivo in future studies.
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Affiliation(s)
- George Devitt
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton Highfield Southampton SO17 1BJ UK .,School of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton Highfield Southampton SO17 1BJ UK.,Institute for Life Sciences, University of Southampton Highfield Southampton SO17 1BJ UK
| | - Anna Crisford
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton Highfield Southampton SO17 1BJ UK .,School of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton Highfield Southampton SO17 1BJ UK
| | - William Rice
- School of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton Highfield Southampton SO17 1BJ UK
| | - Hilary A Weismiller
- Department of Chemistry and Biochemistry, University of Denver 2190 E. Iliff Ave. Denver CO 80208 USA
| | - Zhanyun Fan
- Department of Neurology, Harvard Medical School, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital Charlestown MA 02129 USA
| | - Caitlin Commins
- Department of Neurology, Harvard Medical School, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital Charlestown MA 02129 USA
| | - Bradley T Hyman
- Department of Neurology, Harvard Medical School, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital Charlestown MA 02129 USA
| | - Martin Margittai
- Department of Chemistry and Biochemistry, University of Denver 2190 E. Iliff Ave. Denver CO 80208 USA
| | - Sumeet Mahajan
- School of Chemistry, Faculty of Engineering and Physical Sciences, University of Southampton Highfield Southampton SO17 1BJ UK.,Institute for Life Sciences, University of Southampton Highfield Southampton SO17 1BJ UK
| | - Amrit Mudher
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton Highfield Southampton SO17 1BJ UK .,Institute for Life Sciences, University of Southampton Highfield Southampton SO17 1BJ UK
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