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Kuzmina NV, Gavrilova AA, Fefilova AS, Romanovich AE, Kuznetsova IM, Turoverov KK, Fonin AV. Von-Hippel Lindau protein amyloid formation. The role of GST-tag. Biochem Biophys Res Commun 2024; 715:150008. [PMID: 38685186 DOI: 10.1016/j.bbrc.2024.150008] [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: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/02/2024]
Abstract
In the last decade, much attention was given to the study of physiological amyloid fibrils. These structures include A-bodies, which are the nucleolar fibrillar formations that appear in the response to acidosis and heat shock, and disassemble after the end of stress. One of the proteins involved in the biogenesis of A-bodies, regardless of the type of stress, is Von-Hippel Lindau protein (VHL). Known also as a tumor suppressor, VHL is capable to form amyloid fibrils both in vitro and in vivo in response to the environment acidification. As with most amyloidogenic proteins fusion with various tags is used to increase the solubility of VHL. Here, we first performed AFM-study of fibrils formed by VHL protein and by VHL fused with GST-tag (GST-VHL) at acidic conditions. It was shown that formed by full-length VHL fibrils are short heterogenic structures with persistent length of 2400 nm and average contour length of 409 nm. GST-tag catalyzes VHL amyloid fibril formation, superimpose chirality, increases length and level of hierarchy, but decreases rigidity of amyloid fibrils. The obtained data indicate that tagging can significantly affect the fibrillogenesis of the target protein.
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Affiliation(s)
- Natalia V Kuzmina
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Bldg. 4, 31, Leninskiy ave., 119071, Moscow, Russia
| | - Anastasia A Gavrilova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., 194064, St. Petersburg, Russia
| | - Anna S Fefilova
- Center of Genomic Regulation (GRC), Barcelona Institute of Science and Technology, Barcelona, 08003, Spain
| | - Anna E Romanovich
- Resource Center of Molecular and Cell Technologies, St-Petersburg State University Research Park, Universitetskaya Emb. 7-9, 199034, St. Petersburg, Russia
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., 194064, St. Petersburg, Russia
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., 194064, St. Petersburg, Russia
| | - Alexander V Fonin
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., 194064, St. Petersburg, Russia.
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2
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Koroleva ON, Kuzmina NV, Dubrovin EV, Drutsa VL. Atomic force microscopy of spherical intermediates on the pathway to fibril formation of influenza A virus nuclear export protein. Microsc Res Tech 2024; 87:1131-1145. [PMID: 38270267 DOI: 10.1002/jemt.24499] [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: 08/25/2023] [Revised: 01/02/2024] [Accepted: 01/07/2024] [Indexed: 01/26/2024]
Abstract
The nuclear export protein of the influenza A virus (NEP) is involved in many important processes of the virus life cycle. This makes it an attractive target for the treatment of a disease caused by a virus. Previously it has been shown, that recombinant variants of NEP are highly prone to aggregation in solution under various conditions with the formation of amyloid-like aggregates. In the present work, the amyloid nature of NEP aggregates was evidenced by Congo red binding assays. Atomic force microscopy has shown that NEP can form two types of spherical nanoparticles, which provide an alternative pathway for the formation of amyloid-like fibrils. Type I of these "fibrillogenic" spheres, formed under physiological conditions, represents the micelle-like particles with height 10-60 nm, which can generate worm-like flexible fibrils with the diameter 2.5-4.0 nm, length 20-500 nm and the Young's modulus ~73 MPa. Type II spherical aggregates with size of about 400-1000 nm, formed at elevated temperatures, includes fractions of drop-like and vesicle-like particles, generating more rigid amyloid-like fibrils with height of ~8 nm, and length of up to 2 μm. The hypothetical mechanism of fibril formation via nanospherical structures was suggested. RESEARCH HIGHLIGHTS: AFM has revealed two types of the influenza A virus nuclear export protein spherical aggregates. They provide an alternative pathway for the formation of amyloid-like fibrils. The mechanism of fibril formation via spherical structures is suggested.
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Affiliation(s)
- Olga N Koroleva
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Natalia V Kuzmina
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Evgeniy V Dubrovin
- Faculty of Physics, Lomonosov Moscow State University, Moscow, Russian Federation
- National University of Science and Technology, MISIS, Moscow, Russian Federation
| | - Valeriy L Drutsa
- A.N.Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
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3
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Heesink G, van den Oetelaar MCM, Semerdzhiev SA, Ottmann C, Brunsveld L, Blum C, Claessens MMAE. 14-3-3τ as a Modulator of Early α-Synuclein Multimerization and Amyloid Formation. ACS Chem Neurosci 2024; 15:1926-1936. [PMID: 38635928 PMCID: PMC11066837 DOI: 10.1021/acschemneuro.4c00100] [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: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/20/2024] Open
Abstract
The aggregation of α-synuclein (αS) plays a key role in Parkinson's disease (PD) etiology. While the onset of PD is age-related, the cellular quality control system appears to regulate αS aggregation throughout most human life. Intriguingly, the protein 14-3-3τ has been demonstrated to delay αS aggregation and the onset of PD in various models. However, the molecular mechanisms behind this delay remain elusive. Our study confirms the delay in αS aggregation by 14-3-3τ, unveiling a concentration-dependent relation. Utilizing microscale thermophoresis (MST) and single-molecule burst analysis, we quantified the early αS multimers and concluded that these multimers exhibit properties that classify them as nanoscale condensates that form in a cooperative process, preceding the critical nucleus for fibril formation. Significantly, the αS multimer formation mechanism changes dramatically in the presence of scaffold protein 14-3-3τ. Our data modeling suggests that 14-3-3τ modulates the multimerization process, leading to the creation of mixed multimers or co-condensates, comprising both αS and 14-3-3τ. These mixed multimers form in a noncooperative process. They are smaller, more numerous, and distinctively not on the pathway to amyloid formation. Importantly, 14-3-3τ thus acts in the very early stage of αS multimerization, ensuring that αS does not aggregate but remains soluble and functional. This offers long-sought novel entries for the pharmacological modulation of PD.
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Affiliation(s)
- Gobert Heesink
- Nanobiophysics,
Faculty of Science and Technology, MESA + Institute for Nanotechnology
and Technical Medical Centre, University
of Twente, Enschede 7500 AE, The Netherlands
| | - Maxime C. M. van den Oetelaar
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
for Complex Molecular Systems, Eindhoven
University of Technology, Eindhoven 5600 MB, The Netherlands
| | - Slav A. Semerdzhiev
- Nanobiophysics,
Faculty of Science and Technology, MESA + Institute for Nanotechnology
and Technical Medical Centre, University
of Twente, Enschede 7500 AE, The Netherlands
| | - Christian Ottmann
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
for Complex Molecular Systems, Eindhoven
University of Technology, Eindhoven 5600 MB, The Netherlands
| | - Luc Brunsveld
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
for Complex Molecular Systems, Eindhoven
University of Technology, Eindhoven 5600 MB, The Netherlands
| | - Christian Blum
- Nanobiophysics,
Faculty of Science and Technology, MESA + Institute for Nanotechnology
and Technical Medical Centre, University
of Twente, Enschede 7500 AE, The Netherlands
| | - Mireille M. A. E. Claessens
- Nanobiophysics,
Faculty of Science and Technology, MESA + Institute for Nanotechnology
and Technical Medical Centre, University
of Twente, Enschede 7500 AE, The Netherlands
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4
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Galkin M, Priss A, Kyriukha Y, Shvadchak V. Navigating α-Synuclein Aggregation Inhibition: Methods, Mechanisms, and Molecular Targets. CHEM REC 2024; 24:e202300282. [PMID: 37919046 DOI: 10.1002/tcr.202300282] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 10/08/2023] [Indexed: 11/04/2023]
Abstract
Parkinson's disease is a yet incurable, age-related neurodegenerative disorder characterized by the aggregation of small neuronal protein α-synuclein into amyloid fibrils. Inhibition of this process is a prospective strategy for developing a disease-modifying treatment. We overview here small molecule, peptide, and protein inhibitors of α-synuclein fibrillization reported to date. Special attention was paid to the specificity of inhibitors and critical analysis of their action mechanisms. Namely, the importance of oxidation of polyphenols and cross-linking of α-synuclein into inhibitory dimers was highlighted. We also compared strategies of targeting monomeric, oligomeric, and fibrillar α-synuclein species, thoroughly discussed the strong and weak sides of different approaches to testing the inhibitors.
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Affiliation(s)
- Maksym Galkin
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Anastasiia Priss
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Yevhenii Kyriukha
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri, 63110, United States
| | - Volodymyr Shvadchak
- Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, Ivano-Frankivsk, Ukraine
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Sundaria N, Upadhyay A, Prasad A, Prajapati VK, Poluri KM, Mishra A. Neurodegeneration & imperfect ageing: Technological limitations and challenges? Mech Ageing Dev 2021; 200:111574. [PMID: 34562507 DOI: 10.1016/j.mad.2021.111574] [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: 05/30/2021] [Revised: 08/29/2021] [Accepted: 09/21/2021] [Indexed: 11/18/2022]
Abstract
Cellular homeostasis is regulated by the protein quality control (PQC) machinery, comprising multiple chaperones and enzymes. Studies suggest that the loss of the PQC mechanisms in neurons may lead to the formation of abnormal inclusions that may lead to neurological disorders and defective aging. The questions could be raised how protein aggregate formation precisely engenders multifactorial molecular pathomechanism in neuronal cells and affects different brain regions? Such questions await thorough investigation that may help us understand how aberrant proteinaceous bodies lead to neurodegeneration and imperfect aging. However, these studies face multiple technological challenges in utilizing available tools for detailed characterizations of the protein aggregates or amyloids and developing new techniques to understand the biology and pathology of proteopathies. The lack of detection and analysis methods has decelerated the pace of the research in amyloid biology. Here, we address the significance of aggregation and inclusion formation, followed by exploring the evolutionary contribution of these structures. We also provide a detailed overview of current state-of-the-art techniques and advances in studying amyloids in the diseased brain. A comprehensive understanding of the structural, pathological, and clinical characteristics of different types of aggregates (inclusions, fibrils, plaques, etc.) will aid in developing future therapies.
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Affiliation(s)
- Naveen Sundaria
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology, Jodhpur, Rajasthan, 342037, India
| | - Arun Upadhyay
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology, Jodhpur, Rajasthan, 342037, India
| | - Amit Prasad
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH‑8 Bandarsindri, Ajmer, Rajasthan, 305817, India
| | - Krishna Mohan Poluri
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology, Jodhpur, Rajasthan, 342037, India.
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Wild-type GBA1 increases the α-synuclein tetramer-monomer ratio, reduces lipid-rich aggregates, and attenuates motor and cognitive deficits in mice. Proc Natl Acad Sci U S A 2021; 118:2103425118. [PMID: 34326260 PMCID: PMC8346893 DOI: 10.1073/pnas.2103425118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The mechanisms responsible for brain α-synuclein (αS) dyshomeostasis, caused by Gaucher’s GBA1 mutations that increase Parkinson’s disease (PD) risk, are largely unknown. We previously showed that abrogating physiological αS tetramers by a familial PD-E46K–amplified 3K mutation produces PD-like syndrome in mice and that treatment with stearoyl-CoA desaturase inhibitors increased a portion of the αS tetramers, benefitting the motor phenotypes. Here, we show that—similar to previous findings in GBA1-mutant PD culture—GCase elevation prolonged the stabilization of wild-type and 3K mutant αS tetramers in wtGBA1–transduced mouse brains, improving lysosomal integrity and motor and cognitive phenotypes. These data help elucidating lipid modulators that impact the αS physiological state in vivo and the development of PD therapeutic approaches. Loss-of-function mutations in acid beta-glucosidase 1 (GBA1) are among the strongest genetic risk factors for Lewy body disorders such as Parkinson’s disease (PD) and Lewy body dementia (DLB). Altered lipid metabolism in PD patient–derived neurons, carrying either GBA1 or PD αS mutations, can shift the physiological α-synuclein (αS) tetramer–monomer (T:M) equilibrium toward aggregation-prone monomers. A resultant increase in pSer129+ αS monomers provides a likely building block for αS aggregates. 3K αS mice, representing a neuropathological amplification of the E46K PD–causing mutation, have decreased αS T:M ratios and vesicle-rich αS+ aggregates in neurons, accompanied by a striking PD-like motor syndrome. We asked whether enhancing glucocerebrosidase (GCase) expression could benefit αS dyshomeostasis by delivering an adeno-associated virus (AAV)–human wild-type (wt) GBA1 vector into the brains of 3K neonates. Intracerebroventricular AAV-wtGBA1 at postnatal day 1 resulted in prominent forebrain neuronal GCase expression, sustained through 6 mo. GBA1 attenuated behavioral deficits both in working memory and fine motor performance tasks. Furthermore, wtGBA1 increased αS solubility and the T:M ratio in both 3K-GBA mice and control littermates and reduced pS129+ and lipid-rich aggregates in 3K-GBA. We observed GCase distribution in more finely dispersed lysosomes, in which there was increased GCase activity, lysosomal cathepsin D and B maturation, decreased perilipin-stabilized lipid droplets, and a normalized TFEB translocation to the nucleus, all indicative of improved lysosomal function and lipid turnover. Therefore, a prolonged increase of the αS T:M ratio by elevating GCase activity reduced the lipid- and vesicle-rich aggregates and ameliorated PD-like phenotypes in mice, further supporting lipid modulating therapies in PD.
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7
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D’Onofrio M, Munari F, Assfalg M. Alpha-Synuclein-Nanoparticle Interactions: Understanding, Controlling and Exploiting Conformational Plasticity. Molecules 2020; 25:E5625. [PMID: 33260436 PMCID: PMC7731430 DOI: 10.3390/molecules25235625] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/25/2020] [Accepted: 11/27/2020] [Indexed: 12/29/2022] Open
Abstract
Alpha-synuclein (αS) is an extensively studied protein due to its involvement in a group of neurodegenerative disorders, including Parkinson's disease, and its documented ability to undergo aberrant self-aggregation resulting in the formation of amyloid-like fibrils. In dilute solution, the protein is intrinsically disordered but can adopt multiple alternative conformations under given conditions, such as upon adsorption to nanoscale surfaces. The study of αS-nanoparticle interactions allows us to better understand the behavior of the protein and provides the basis for developing systems capable of mitigating the formation of toxic aggregates as well as for designing hybrid nanomaterials with novel functionalities for applications in various research areas. In this review, we summarize current progress on αS-nanoparticle interactions with an emphasis on the conformational plasticity of the biomolecule.
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Affiliation(s)
| | | | - Michael Assfalg
- Department of Biotechnology, University of Verona, 37134 Verona, Italy; (M.D.); (F.M.)
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8
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Herrera MG, Gómez Castro MF, Prieto E, Barrera E, Dodero VI, Pantano S, Chirdo F. Structural conformation and self-assembly process of p31-43 gliadin peptide in aqueous solution. Implications for celiac disease. FEBS J 2019; 287:2134-2149. [PMID: 31659864 DOI: 10.1111/febs.15109] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 09/06/2019] [Accepted: 10/25/2019] [Indexed: 12/13/2022]
Abstract
Celiac disease (CeD) is a highly prevalent chronic immune-mediated enteropathy developed in genetically predisposed individuals after ingestion of a group of wheat proteins (called gliadins and glutenins). The 13mer α-gliadin peptide, p31-43, induces proinflammatory responses, observed by in vitro assays and animal models, that may contribute to innate immune mechanisms of CeD pathogenesis. Since a cellular receptor for p31-43 has not been identified, this raises the question of whether this peptide could mediate different biological effects. In this work, we aimed to characterize the p31-43 secondary structure by different biophysical and in silico techniques. By dynamic light scattering and using an oligomer/fibril-sensitive fluorescent probe, we showed the presence of oligomers of this peptide in solution. Furthermore, atomic force microscopy analysis showed p31-43 oligomers with different height distribution. Also, peptide concentration had a very strong influence on peptide self-organization process. Oligomers gradually increased their size at lower concentration. Whereas, at higher ones, oligomers increased their complexity, forming branched structures. By CD, we observed that p31-43 self-organized in a polyproline II conformation in equilibrium with β-sheets-like structures, whose pH remained stable in the range of 3-8. In addition, these findings were supported by molecular dynamics simulation. The formation of p31-43 nanostructures with increased β-sheet structure may help to explain the molecular etiopathogenesis in the induction of proinflammatory effects and subsequent damage at the intestinal mucosa in CeD.
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Affiliation(s)
- María Georgina Herrera
- Instituto de Química y Fisicoquímica Biológicas - IQUIFIB (UBA-CONICET), Buenos Aires, Argentina
| | | | - Eduardo Prieto
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA, UNLP-CONICET), La Plata, Argentina
| | | | | | - Sergio Pantano
- Institut Pasteur de Montevideo, Uruguay.,Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, China
| | - Fernando Chirdo
- Instituto de Estudios Inmunológicos y Fisiopatológicos (IIFP, UNLP-CONICET), La Plata, Argentina
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9
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α-Synuclein aggregation at low concentrations. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:701-709. [PMID: 31096048 DOI: 10.1016/j.bbapap.2019.05.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 05/08/2019] [Accepted: 05/10/2019] [Indexed: 11/23/2022]
Abstract
BACKGROUND Aggregation of the neuronal protein α-synuclein into amyloid fibrils is a hallmark of Parkinson's disease. The propensity of α-synuclein to aggregate increases with the protein concentration. For the development of efficient inhibitors of α-synuclein aggregation, it is important to know the critical concentration of aggregation (the concentration of monomeric protein, below which the protein does not aggregate). METHODS We performed in vitro aggregation studies of α-synuclein at low concentrations (0.11-20 μM). Aggregation kinetics was measured by ThT fluorescence. Obtained aggregates were characterized using CD-spectroscopy, fluorescent spectroscopy, dynamic light scattering and AFM imaging. RESULTS Monomeric α-synuclein at concentrations 0.45 μM and above was able to bind to fibril ends resulting in fibril growth. At the protein concentrations below 0.4 μM, monomers did not fibrillize, and fibrils disaggregated. In the absence of seeds, fibrils were formed only at monomer concentrations higher than 10 μM. At low micromolar concentrations, we observed formation of prefibrillar amyloid aggregates, which are able to induce fibril formation in α-synuclein solutions of high concentrations. CONCLUSIONS The critical concentration of α-synuclein fibril growth is ~0.4 μM. Prefibrillar amyloid aggregates appear at concentrations between 0.45 and 3 μM and are an intermediate state between monomers and fibrils. Although morphologically different from fibrils, prefibrillar aggregates have similar properties to those of fibrils. GENERAL SIGNIFICANCE We determined the critical concentration of α-synuclein fibril growth. We showed that fibrils can grow at much lower monomer concentrations than that required for de novo fibril formation. We characterized a prefibrillar intermediate species formed upon aggregation of α-synuclein at low micromolar concentration.
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10
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Lampkin BJ, Monteiro C, Powers ET, Bouc PM, Kelly JW, VanVeller B. A designed protein binding-pocket to control excited-state intramolecular proton transfer fluorescence. Org Biomol Chem 2019; 17:1076-1080. [PMID: 30534794 PMCID: PMC6549506 DOI: 10.1039/c8ob02673d] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Excited-state intramolecular proton transfer involves a photochemical isomerization and creates the opportunity for the emission of two distinct wavelengths of light from a single fluorophore. The selectivity between these two wavelengths of emission is dependent on the environment around the fluorophore and suggests the possibility for ratiometric monitoring of protein microenvironments. Unfortunately, nonspecific binding of ESIPT fluorophores does not often lead to dramatic changes in the ratio between the two wavelengths of emission. A protein binding pocket was designed to selectively discriminate between the two channels of emission available to an ESIPT fluorophore. This work is significant because it demonstrates that specific interactions between the protein and the fluorophore are essential to realize strong ratiometric differences between the two possible wavelengths of emission. The design strategies proposed here lead to an ESIPT fluorophore that can discern subtle differences in the interface between two proteins.
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Affiliation(s)
- Bryan J Lampkin
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA.
| | - Cecilia Monteiro
- Department of Chemistry, Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Evan T Powers
- Department of Chemistry, Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Paige M Bouc
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA.
| | - Jeffery W Kelly
- Department of Chemistry, Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Brett VanVeller
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA.
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11
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Fauerbach JA, Jovin TM. Pre-aggregation kinetics and intermediates of α-synuclein monitored by the ESIPT probe 7MFE. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2017; 47:345-362. [PMID: 29255947 PMCID: PMC5982440 DOI: 10.1007/s00249-017-1272-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 12/05/2017] [Accepted: 12/08/2017] [Indexed: 01/04/2023]
Abstract
The defining feature of the extensive family of amyloid diseases is the formation of networks of entangled elongated protein fibrils and amorphous aggregates exhibiting crossed β-sheet secondary structure. The time course of amyloid conversion has been studied extensively in vitro with the proteins involved in the neurodegenerative pathology of Parkinson's disease (α-synuclein), Alzheimer's disease (Tau) and Huntington's disease (Huntingtin). Although much is known about the thermodynamics and kinetics of the transition from a soluble, intrinsically disordered monomer to the fibrillar end state, the putative oligomeric intermediates, currently considered to be the major initiators of cellular toxicity, are as yet poorly defined. We have detected and characterized amyloid precursors by monitoring AS aggregation with ESIPT (excited state intramolecular protein transfer) probes, one of which, 7MFE [7-(3-maleimido-N-propanamide)-2-(4-diethyaminophenyl)-3-hydroxychromone], is introduced here and compared with a related compound, 6MFC, used previously. A series of 140 spectra for sparsely labeled AS was acquired during the course of aggregation, and resolved into the relative contributions (spectra, intensities) of discrete molecular species including the monomeric, fibrillar, and ensemble of intermediate forms. Based on these findings, a kinetic scheme was devised to simulate progress curves as a function of key parameters. An essential feature of the model, one not previously invoked in schemes of amyloid aggregation, is the catalysis of molecular fuzziness by discrete colloidal nanoparticles arising spontaneously via monomer condensation upon exposure of AS to ≥ 37 °C.
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Affiliation(s)
- Jonathan A Fauerbach
- Miltenyi Biotec GmbH, Friedrich-Ebert Str. 42, 51429, Bergisch-Gladbach, Germany
| | - Thomas M Jovin
- Laboratory of Cellular Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.
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12
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Afitska K, Fucikova A, Shvadchak VV, Yushchenko DA. Modification of C Terminus Provides New Insights into the Mechanism of α-Synuclein Aggregation. Biophys J 2017; 113:2182-2191. [PMID: 28939194 DOI: 10.1016/j.bpj.2017.08.027] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 08/12/2017] [Accepted: 08/14/2017] [Indexed: 10/18/2022] Open
Abstract
Aggregation of neuronal protein α-synuclein leads to the formation of amyloid fibrils, which are associated with the development of Parkinson's disease. The mechanism of α-synuclein pathology is not fully understood and is a subject of active research in the field. To tackle this problem, the fusions of fluorescent proteins to α-synuclein C-terminus are often used in cellular and animal studies. The effects induced by such α-synuclein sequence extension on α-synuclein aggregation propensity are, however, not systematically examined despite the evidence that the negatively charged C-terminus plays a critical role in the regulation of α-synuclein aggregation. In this work, we investigated how the charge and length variations of the C-terminus affect the aggregation propensity of α-synuclein. To address these questions, we prepared mutants of α-synuclein carrying additional moieties of different charge and length at the protein C-terminus. We determined the rates of two different aggregation stages (primary nucleation and elongation) based on a thioflavin T kinetic assay. We observed that all mutants bearing neutrally charged moieties of different length fibrilized slower than wild-type α-synuclein. The primary nucleation and elongation rates strongly decreased with increase of the C-terminal extension length. Meanwhile, charge variation of the C-terminus significantly changed the rate of α-synuclein nucleation, but did not markedly affect the rate of fibril elongation. Our data demonstrate that both the charge and length of the C-terminus play an important role at the stage of initial fibril formation, but the stage of fibril elongation is affected mainly by the length of C-terminal extension. In addition, our results suggest that there are at least two steps of incorporation of α-synuclein monomers into the amyloid fibril: namely, the initial monomer binding to the fibril end (charge-dependent, relatively fast), and the subsequent conformational change of the protein (charge-independent, relatively slow, and thus the rate-limiting step).
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Affiliation(s)
- Kseniia Afitska
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Anna Fucikova
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
| | - Volodymyr V Shvadchak
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Dmytro A Yushchenko
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
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13
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Azcárate JC, Díaz SA, Fauerbach JA, Gillanders F, Rubert AA, Jares-Erijman EA, Jovin TM, Fonticelli MH. ESIPT and FRET probes for monitoring nanoparticle polymer coating stability. NANOSCALE 2017; 9:8647-8656. [PMID: 28612865 DOI: 10.1039/c7nr01787a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Coating strategies of inorganic nanoparticles (NPs) can provide properties unavailable to the NP core alone, such as targeting, specific sensing, and increased biocompatibility. Non-covalent amphiphilic NP capping polymers function via hydrophobic interactions with surface ligands and are extensively used to transfer NPs to aqueous media. For applications of coated NPs as actuators (sensors, markers, or for drug delivery) in a complex environment, such as biological systems, it is important to achieve a deep understanding of the factors affecting coating stability and behavior. We have designed a system that tests the coating stability of amphiphilic polymers through a simple fluorescent readout using either polarity sensing ESIPT (excited state intramolecular proton transfer) dyes or NP FRET (Förster resonance energy transfer). The stability of the coating was determined in response to changes in polarity, pH and ionic strength in the medium. Using the ESIPT system we observed linear changes in signal up to ∼20-25% v/v of co-solvent addition, constituting a break point. Based on such data, we propose a model for coating instability and the important adjustable parameters, such as the electrical charge distribution. FRET data provided confirmatory evidence for the model. The ESIPT dyes and FRET based methods represent new, simple tools for testing NP coating stability in complex environments.
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Affiliation(s)
- Julio C Azcárate
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Facultad de Ciencias Exactas, Universidad Nacional de La Plata - CONICET Sucursal 4, Casilla de Correo 16, 1900 La Plata, Argentina.
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14
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Gade Malmos K, Blancas-Mejia LM, Weber B, Buchner J, Ramirez-Alvarado M, Naiki H, Otzen D. ThT 101: a primer on the use of thioflavin T to investigate amyloid formation. Amyloid 2017; 24:1-16. [PMID: 28393556 DOI: 10.1080/13506129.2017.1304905] [Citation(s) in RCA: 241] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Thioflavin T (ThT) has been widely used to investigate amyloid formation since 1989. While concerns have recently been raised about its use as a probe specific for amyloid, ThT still continues to be a very valuable tool for studying kinetic aspects of fibrillation and associated inhibition mechanisms. This review aims to provide a conceptual instruction manual, covering appropriate considerations and pitfalls related to the use of ThT. We start by giving a brief introduction to amyloid formation with focus on the morphology of different aggregate species, followed by a discussion of the quality of protein needed to obtain reliable fibrillation data. After an overview of the photochemical basis for ThT's amyloid binding properties and artifacts that may arise from this, we describe how to plan and analyze ThT assays. We conclude with recommendations for complementary techniques to address shortcomings in the ThT assay.
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Affiliation(s)
- Kirsten Gade Malmos
- a Interdisciplinary Nanoscience Center (iNANO) and Center for Insoluble Protein Structures (inSPIN) , Aarhus University , Aarhus C , Denmark.,b Department of Molecular Biology and Genetics , Aarhus University , Aarhus C , Denmark
| | - Luis M Blancas-Mejia
- c Department of Biochemistry and Molecular Biology , Mayo Clinic , Rochester , MN , USA
| | - Benedikt Weber
- d Center for Integrated Protein Science Munich at the Department Chemie , Technische Universität München , Garching , Germany
| | - Johannes Buchner
- d Center for Integrated Protein Science Munich at the Department Chemie , Technische Universität München , Garching , Germany
| | | | - Hironobu Naiki
- e Department of Molecular Pathology, Faculty of Medical Sciences , University of Fukui , Fukui , Japan
| | - Daniel Otzen
- a Interdisciplinary Nanoscience Center (iNANO) and Center for Insoluble Protein Structures (inSPIN) , Aarhus University , Aarhus C , Denmark
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15
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Gallea JI, Sarroukh R, Yunes-Quartino P, Ruysschaert JM, Raussens V, Celej MS. Structural remodeling during amyloidogenesis of physiological Nα-acetylated α-synuclein. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:501-10. [DOI: 10.1016/j.bbapap.2016.01.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 01/25/2016] [Accepted: 01/27/2016] [Indexed: 12/24/2022]
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16
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Herrera MG, Zamarreño F, Costabel M, Ritacco H, Hütten A, Sewald N, Dodero VI. Circular dichroism and electron microscopy studies in vitro of 33-mer gliadin peptide revealed secondary structure transition and supramolecular organization. Biopolymers 2016; 101:96-106. [PMID: 23703327 DOI: 10.1002/bip.22288] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 05/07/2013] [Accepted: 05/09/2013] [Indexed: 12/17/2022]
Abstract
Gliadin, a protein present in wheat, rye, and barley, undergoes incomplete enzymatic degradation during digestion, producing an immunogenic 33-mer peptide, LQLQPF(PQPQLPY)3 PQPQPF. The special features of 33-mer that provoke a break in its tolerance leading to gliadin sensitivity and celiac disease remains elusive. Herein, it is reported that 33-mer gliadin peptide was not only able to fold into polyproline II secondary structure but also depending on concentration resulted in conformational transition and self-assembly under aqueous condition, pH 7.0. A 33-mer dimer is presented as one initial possible step in the self-assembling process obtained by partial electrostatics charge distribution calculation and molecular dynamics. In addition, electron microscopy experiments revealed supramolecular organization of 33-mer into colloidal nanospheres. In the presence of 1 mM sodium citrate, 1 mM sodium borate, 1 mM sodium phosphate buffer, 15 mM NaCl, the nanospheres were stabilized, whereas in water, a linear organization and formation of fibrils were observed. It is hypothesized that the self-assembling process could be the result of the combination of hydrophobic effect, intramolecular hydrogen bonding, and electrostatic complementarity due to 33-mer's high content of proline and glutamine amino acids and its calculated nonionic amphiphilic character. Although, performed in vitro, these experiments have revealed new features of the 33-mer gliadin peptide that could represent an important and unprecedented event in the early stage of 33-mer interaction with the gut mucosa prior to onset of inflammation. Moreover, these findings may open new perspectives for the understanding and treatment of gliadin intolerance disorders.
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Affiliation(s)
- María G Herrera
- Department of Chemistry, INQUISUR, National University of South, CONICET, Av. Alem 1253, 8000 Bahía Blanca, Argentina
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17
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Leung CWT, Guo F, Hong Y, Zhao E, Kwok RTK, Leung NLC, Chen S, Vaikath NN, El-Agnaf OM, Tang Y, Gai WP, Tang BZ. Detection of oligomers and fibrils of α-synuclein by AIEgen with strong fluorescence. Chem Commun (Camb) 2015; 51:1866-9. [PMID: 25526628 DOI: 10.1039/c4cc07911f] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a fluorophore, TPE-TPP, with AIE characteristics which is utilized as a fluorescence probe to monitor the α-synuclein (α-Syn) fibrillation process. Compared with ThT, TPE-TPP shows a higher sensitivity in the detection of α-Syn oligomers as well as fibrils with a stronger fluorescence. The performance of TPE-TPP was evaluated using fluorescence, AFM, dot blot, and SEC.
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Affiliation(s)
- Chris Wai Tung Leung
- HKUST Shenzhen Research Institute, No. 9 Yuexing 1st RD, South Area, Hi-tech Park Nanshan, Shenzhen 518057, China.
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18
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Haldar S, Sil P, Thangamuniyandi M, Chattopadhyay K. Conversion of amyloid fibrils of cytochrome c to mature nanorods through a honeycomb morphology. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:4213-23. [PMID: 25338286 DOI: 10.1021/la5029993] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Amyloid species with various morphologies have been found for different proteins and disease systems. In this article, we aim to ask if these morphologies are unique to a particular protein or if they convert from one to another. Using a heme protein containing iron as the transition-metal activator of aggregation and a negatively charged surfactant, partial unfolding of the protein and its aggregation have been induced. In the pathway of aggregation, we have observed the formation of several morphological structures of a single protein, which were visualized directly using atomic force microscopy (AFM). These structures have been found to appear and disappear with time, and their formation could be monitored under normal buffer conditions and at room temperature without requiring any sophisticated chemical or biological methodologies. In addition, we have observed the formation of honeycomb-shaped morphology, which may serve as an intermediate. These amyloid-based nanostructures may have the potential to be explored in therapeutics delivery and other biomedical applications.
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Affiliation(s)
- Shubhasis Haldar
- Protein Folding and Dynamics Laboratory, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, India
| | - Pallabi Sil
- Protein Folding and Dynamics Laboratory, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, India
| | - Muruganandan Thangamuniyandi
- Protein Folding and Dynamics Laboratory, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, India
| | - Krishnananda Chattopadhyay
- Protein Folding and Dynamics Laboratory, Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, India
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19
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Shvadchak VV, Claessens MMAE, Subramaniam V. Fibril Breaking Accelerates α-Synuclein Fibrillization. J Phys Chem B 2015; 119:1912-8. [DOI: 10.1021/jp5111604] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Volodymyr V. Shvadchak
- FOM Institute AMOLF, Science
Park 104, 1098 XG Amsterdam, The Netherlands
- Nanobiophysics, MESA+ Institute for Nanotechnology & MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, P. O. Box 217, 7500 AE Enschede, The Netherlands
| | - Mireille M. A. E. Claessens
- Nanobiophysics, MESA+ Institute for Nanotechnology & MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, P. O. Box 217, 7500 AE Enschede, The Netherlands
| | - Vinod Subramaniam
- FOM Institute AMOLF, Science
Park 104, 1098 XG Amsterdam, The Netherlands
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20
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Blancas-Mejía LM, Hammernik J, Marin-Argany M, Ramirez-Alvarado M. Differential effects on light chain amyloid formation depend on mutations and type of glycosaminoglycans. J Biol Chem 2014; 290:4953-4965. [PMID: 25538238 DOI: 10.1074/jbc.m114.615401] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Amyloid light chain (AL) amyloidosis is a protein misfolding disease where immunoglobulin light chains sample partially folded states that lead to misfolding and amyloid formation, resulting in organ dysfunction and death. In vivo, amyloid deposits are found in the extracellular space and involve a variety of accessory molecules, such as glycosaminoglycans, one of the main components of the extracellular matrix. Glycosaminoglycans are a group of negatively charged heteropolysaccharides composed of repeating disaccharide units. In this study, we investigated the effect of glycosaminoglycans on the kinetics of amyloid fibril formation of three AL cardiac amyloidosis light chains. These proteins have similar thermodynamic stability but exhibit different kinetics of fibril formation. We also studied single restorative and reciprocal mutants and wild type germ line control protein. We found that the type of glycosaminoglycan has a different effect on the kinetics of fibril formation, and this effect seems to be associated with the natural propensity of each AL protein to form fibrils. Heparan sulfate accelerated AL-12, AL-09, κI Y87H, and AL-103 H92D fibril formation; delayed fibril formation for AL-103; and did not promote any fibril formation for AL-12 R65S, AL-103 delP95aIns, or κI O18/O8. Chondroitin sulfate A, on the other hand, showed a strong fibril formation inhibition for all proteins. We propose that heparan sulfate facilitates the formation of transient amyloidogenic conformations of AL light chains, thereby promoting amyloid formation, whereas chondroitin sulfate A kinetically traps partially unfolded intermediates, and further fibril elongation into fibrils is inhibited, resulting in formation/accumulation of oligomeric/protofibrillar aggregates.
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Affiliation(s)
| | - Jared Hammernik
- School of Molecular and Cellular Biology, University of Illinois, Urbana, Illinois 61801
| | | | - Marina Ramirez-Alvarado
- Departments of Biochemistry and Molecular Biology and; Immunology, Mayo Clinic, Rochester, Minnesota 55905 and.
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21
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22
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Theillet FX, Binolfi A, Frembgen-Kesner T, Hingorani K, Sarkar M, Kyne C, Li C, Crowley PB, Gierasch L, Pielak GJ, Elcock AH, Gershenson A, Selenko P. Physicochemical properties of cells and their effects on intrinsically disordered proteins (IDPs). Chem Rev 2014; 114:6661-714. [PMID: 24901537 PMCID: PMC4095937 DOI: 10.1021/cr400695p] [Citation(s) in RCA: 338] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Francois-Xavier Theillet
- Department
of NMR-supported Structural Biology, In-cell NMR Laboratory, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Andres Binolfi
- Department
of NMR-supported Structural Biology, In-cell NMR Laboratory, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Tamara Frembgen-Kesner
- Department
of Biochemistry, University of Iowa, Bowen Science Building, 51 Newton
Road, Iowa City, Iowa 52242, United States
| | - Karan Hingorani
- Departments
of Biochemistry & Molecular Biology and Chemistry, Program in
Molecular & Cellular Biology, University
of Massachusetts, Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
| | - Mohona Sarkar
- Department
of Chemistry, Department of Biochemistry and Biophysics and Lineberger
Comprehensive Cancer Center, University
of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Ciara Kyne
- School
of Chemistry, National University of Ireland,
Galway, University Road, Galway, Ireland
| | - Conggang Li
- Key Laboratory
of Magnetic Resonance in Biological Systems, State Key Laboratory
of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center
for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, P.R. China
| | - Peter B. Crowley
- School
of Chemistry, National University of Ireland,
Galway, University Road, Galway, Ireland
| | - Lila Gierasch
- Departments
of Biochemistry & Molecular Biology and Chemistry, Program in
Molecular & Cellular Biology, University
of Massachusetts, Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
| | - Gary J. Pielak
- Department
of Chemistry, Department of Biochemistry and Biophysics and Lineberger
Comprehensive Cancer Center, University
of North Carolina, Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Adrian H. Elcock
- Department
of Biochemistry, University of Iowa, Bowen Science Building, 51 Newton
Road, Iowa City, Iowa 52242, United States
| | - Anne Gershenson
- Departments
of Biochemistry & Molecular Biology and Chemistry, Program in
Molecular & Cellular Biology, University
of Massachusetts, Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
| | - Philipp Selenko
- Department
of NMR-supported Structural Biology, In-cell NMR Laboratory, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Roessle Strasse 10, 13125 Berlin, Germany
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23
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Semerdzhiev SA, Dekker DR, Subramaniam V, Claessens MMAE. Self-assembly of protein fibrils into suprafibrillar aggregates: bridging the nano- and mesoscale. ACS NANO 2014; 8:5543-5551. [PMID: 24805840 DOI: 10.1021/nn406309c] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We report on in vitro self-assembly of nanometer-sized α-synuclein amyloid fibrils into well-defined micrometer-sized suprafibrillar aggregates with sheet-like or cylindrical morphology depending on the ionic strength of the solution. The cylindrical suprafibrillar structures are heavily hydrated, suggesting swollen gel-like particles. In contrast to higher order structures formed by other negatively charged biopolymers, multivalent ions are not required for the suprafibrillar aggregates to form. Their formation is induced by both mono- and divalent counterions. The self-assembly process is not mediated by protein-specific interactions but rather by the cooperative action of long-range electrostatic repulsion and short-range attraction. Understanding the mechanism driving the self-assembly might give us valuable insight into the pathological formation of fibrillar superstructures such as Lewy bodies and neurites-distinct signatures of Parkinson's disease-and will open the possibility to utilize the self-assembly process for the design of novel fibril-based smart nanostructured materials.
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Affiliation(s)
- Slav A Semerdzhiev
- Nanobiophysics, MESA+ Institute for Nanotechnology, Faculty of Science and Technology, University of Twente , PO Box 217, 7500 AE Enschede, The Netherlands
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24
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Neupane K, Solanki A, Sosova I, Belov M, Woodside MT. Diverse metastable structures formed by small oligomers of α-synuclein probed by force spectroscopy. PLoS One 2014; 9:e86495. [PMID: 24475132 PMCID: PMC3901707 DOI: 10.1371/journal.pone.0086495] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 12/12/2013] [Indexed: 11/18/2022] Open
Abstract
Oligomeric aggregates are widely suspected as toxic agents in diseases caused by protein aggregation, yet they remain poorly characterized, partly because they are challenging to isolate from a heterogeneous mixture of species. We developed an assay for characterizing structure, stability, and kinetics of individual oligomers at high resolution and sensitivity using single-molecule force spectroscopy, and applied it to observe the formation of transient structured aggregates within single oligomers of α-synuclein, an intrinsically-disordered protein linked to Parkinson's disease. Measurements of the molecular extension as the proteins unfolded under tension in optical tweezers revealed that even small oligomers could form numerous metastable structures, with a surprisingly broad range of sizes. Comparing the structures formed in monomers, dimers and tetramers, we found that the average mechanical stability increased with oligomer size. Most structures formed within a minute, with size-dependent rates. These results provide a new window onto the complex α-synuclein aggregation landscape, characterizing the microscopic structural heterogeneity and kinetics of different pathways.
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Affiliation(s)
- Krishna Neupane
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Allison Solanki
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
| | - Iveta Sosova
- National Institute for Nanotechnology, National Research Council Canada, Edmonton, Alberta, Canada
| | - Miro Belov
- National Institute for Nanotechnology, National Research Council Canada, Edmonton, Alberta, Canada
| | - Michael T. Woodside
- Department of Physics, University of Alberta, Edmonton, Alberta, Canada
- National Institute for Nanotechnology, National Research Council Canada, Edmonton, Alberta, Canada
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25
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Blancas-Mejía LM, Tischer A, Thompson JR, Tai J, Wang L, Auton M, Ramirez-Alvarado M. Kinetic control in protein folding for light chain amyloidosis and the differential effects of somatic mutations. J Mol Biol 2013; 426:347-61. [PMID: 24157440 DOI: 10.1016/j.jmb.2013.10.016] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 08/30/2013] [Accepted: 10/07/2013] [Indexed: 10/26/2022]
Abstract
Light chain amyloidosis is a devastating disease where immunoglobulin light chains form amyloid fibrils, resulting in organ dysfunction and death. Previous studies have shown a direct correlation between the protein thermodynamic stability and the propensity for amyloid formation for some proteins involved in light chain amyloidosis. Here we investigate the effect of somatic mutations on protein stability and in vitro fibril formation of single and double restorative mutants of the protein AL-103 compared to the wild-type germline control protein. A scan rate dependence and hysteresis in the thermal unfolding and refolding was observed for all proteins. This indicates that the unfolding/refolding reaction is kinetically determined with different kinetic constants for unfolding and refolding even though the process remains experimentally reversible. Our structural analysis of AL-103 and AL-103 delP95aIns suggests a kinetic coupling of the unfolding/refolding process with cis-trans prolyl isomerization. Our data reveal that the deletion of proline 95a (AL-103 delP95aIns), which removes the trans-cis di-proline motif present in the patient protein AL-103, results in a dramatic increment in the thermodynamic stability and a significant delay in fibril formation kinetics with respect to AL-103. Fibril formation is pH dependent; all proteins form fibrils at pH2; reactions become slower and more stochastic as the pH increases up to pH7. Based on these results, we propose that, in addition to thermodynamic stability, kinetic stability (possibly influenced by the presence of cis proline 95a) plays a major role in the AL-103 amyloid fibril formation process.
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Affiliation(s)
- Luis M Blancas-Mejía
- Department of Biochemistry and Molecular Biology, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA
| | - Alexander Tischer
- Department of Biochemistry and Molecular Biology, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA; Division of Hematology, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA
| | - James R Thompson
- Department of Physiology and Biomedical Engineering, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA
| | - Jonathan Tai
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
| | - Lin Wang
- Department of Biochemistry and Molecular Biology, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA
| | - Matthew Auton
- Department of Biochemistry and Molecular Biology, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA; Division of Hematology, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA
| | - Marina Ramirez-Alvarado
- Department of Biochemistry and Molecular Biology, Mayo Clinic, 200 First Street Southwest, Rochester, MN 55905, USA.
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26
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Pedersen JT, Heegaard NHH. Analysis of Protein Aggregation in Neurodegenerative Disease. Anal Chem 2013; 85:4215-27. [DOI: 10.1021/ac400023c] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Jeppe T. Pedersen
- Department of Chemistry, Faculty of Science, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen
Ø, Denmark
| | - Niels H. H. Heegaard
- Analytical Protein Chemistry, Department of Clinical Biochemistry, Immunology & Genetics, Statens Serum Institut, DK-2300 Copenhagen S, Denmark
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27
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Dias V, Junn E, Mouradian MM. The role of oxidative stress in Parkinson's disease. JOURNAL OF PARKINSON'S DISEASE 2013; 3:461-91. [PMID: 24252804 PMCID: PMC4135313 DOI: 10.3233/jpd-130230] [Citation(s) in RCA: 1067] [Impact Index Per Article: 97.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Oxidative stress plays an important role in the degeneration of dopaminergic neurons in Parkinson's disease (PD). Disruptions in the physiologic maintenance of the redox potential in neurons interfere with several biological processes, ultimately leading to cell death. Evidence has been developed for oxidative and nitrative damage to key cellular components in the PD substantia nigra. A number of sources and mechanisms for the generation of reactive oxygen species (ROS) are recognized including the metabolism of dopamine itself, mitochondrial dysfunction, iron, neuroinflammatory cells, calcium, and aging. PD causing gene products including DJ-1, PINK1, parkin, alpha-synuclein and LRRK2 also impact in complex ways mitochondrial function leading to exacerbation of ROS generation and susceptibility to oxidative stress. Additionally, cellular homeostatic processes including the ubiquitin-proteasome system and mitophagy are impacted by oxidative stress. It is apparent that the interplay between these various mechanisms contributes to neurodegeneration in PD as a feed forward scenario where primary insults lead to oxidative stress, which damages key cellular pathogenetic proteins that in turn cause more ROS production. Animal models of PD have yielded some insights into the molecular pathways of neuronal degeneration and highlighted previously unknown mechanisms by which oxidative stress contributes to PD. However, therapeutic attempts to target the general state of oxidative stress in clinical trials have failed to demonstrate an impact on disease progression. Recent knowledge gained about the specific mechanisms related to PD gene products that modulate ROS production and the response of neurons to stress may provide targeted new approaches towards neuroprotection.
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Affiliation(s)
- Vera Dias
- Center for Neurodegenerative and Neuroimmunologic Diseases, Department of Neurology, Rutgers - Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Eunsung Junn
- Center for Neurodegenerative and Neuroimmunologic Diseases, Department of Neurology, Rutgers - Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - M. Maral Mouradian
- Center for Neurodegenerative and Neuroimmunologic Diseases, Department of Neurology, Rutgers - Robert Wood Johnson Medical School, Piscataway, NJ, USA
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28
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Alvarez YD, Fauerbach JA, Pellegrotti JV, Jovin TM, Jares-Erijman EA, Stefani FD. Influence of gold nanoparticles on the kinetics of α-synuclein aggregation. NANO LETTERS 2013; 13:6156-63. [PMID: 24219503 DOI: 10.1021/nl403490e] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
α-synuclein (AS) is a small (140 amino acids), abundant presynaptic protein, which lacks a unique secondary structure in aqueous solution. Amyloid aggregates of AS in dopaminergic neurons of the midbrain are the hallmark of Parkinson's disease (PD). The process of aggregation involves a series of complex structural transitions from innocuous monomeric AS to oligomeric, presumably neurotoxic, forms and finally to fibril formation. Despite its potential importance for understanding PD pathobiology and devising rational, targeted therapeutic strategies, the details of the aggregation process remain largely unknown. Methodologies and reagents capable of controlling the aggregation kinetics are essential tools for the investigation of the molecular mechanisms of amyloid diseases. In this work, we investigated the influence of citrate-capped gold nanoparticles on the aggregation kinetics of AS using a fluorescent probe (MFC) sensitive to the polarity of the molecular microenvironment via excited state intramolecular proton transfer (ESIPT). The particular effects on the half time, nucleation time, and growth rate were ascertained. Gold nanoparticles produced a strong acceleration of protein aggregation with an influence on both the nucleation and growth phases of the overall mechanism. The effects were dependent on the size and concentration of the nanoparticles, being strongest for nanoparticles 10 nm in diameter, which produced a 3-fold increase in the overall aggregation rate at concentrations as low as 20 nM.
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Affiliation(s)
- Yanina D Alvarez
- Departamento de Física, Facultad de Ciencias Exactas y Naturales (FCEN), Universidad de Buenos Aires (UBA) , Buenos Aires, Argentina
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Borsarelli CD, Falomir-Lockhart LJ, Ostatná V, Fauerbach JA, Hsiao HH, Urlaub H, Paleček E, Jares-Erijman EA, Jovin TM. Biophysical properties and cellular toxicity of covalent crosslinked oligomers of α-synuclein formed by photoinduced side-chain tyrosyl radicals. Free Radic Biol Med 2012; 53:1004-15. [PMID: 22771470 DOI: 10.1016/j.freeradbiomed.2012.06.035] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Revised: 06/20/2012] [Accepted: 06/25/2012] [Indexed: 12/30/2022]
Abstract
Alpha-synuclein (αS), a 140 amino acid presynaptic protein, is the major component of the fibrillar aggregates (Lewy bodies) observed in dopaminergic neurons of patients affected by Parkinson's disease. It is currently believed that noncovalent oligomeric forms of αS, arising as intermediates in its aggregation, may constitute the major neurotoxic species. However, attempts to isolate and characterize such oligomers in vitro, and even more so in living cells, have been hampered by their transient nature, low concentration, polymorphism, and inherent instability. In this work, we describe the preparation and characterization of low molecular weight covalently bound oligomeric species of αS obtained by crosslinking via tyrosyl radicals generated by blue-light photosensitization of the metal coordination complex ruthenium (II) tris-bipyridine in the presence of ammonium persulfate. Numerous analytical techniques were used to characterize the αS oligomers: biochemical (anion-exchange chromatography, SDS-PAGE, and Western blotting); spectroscopic (optical: UV/Vis absorption, steady state, dynamic fluorescence, and dynamic light scattering); mass spectrometry; and electrochemical. Light-controlled protein oligomerization was mediated by formation of Tyr-Tyr (dityrosine) dimers through -C-C- bonds acting as covalent bridges, with a predominant involvement of residue Y39. The diverse oligomeric species exhibited a direct effect on the in vitro aggregation behavior of wild-type monomeric αS, decreasing the total yield of amyloid fibrils in aggregation assays monitored by thioflavin T (ThioT) fluorescence and light scattering, and by atomic force microscopy (AFM). Compared to the unmodified monomer, the photoinduced covalent oligomeric species demonstrated increased toxic effects on differentiated neuronal-like SH-SY5Y cells. The results highlight the importance of protein modification induced by oxidative stress in the initial molecular events leading to Parkinson's disease.
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Affiliation(s)
- Claudio D Borsarelli
- Laboratorio de Cinética y Fotoquímica, Centro de Investigaciones y Transferencia de Santiago del Estero (CITSE-CONICET), Universidad Nacional de Santiago del Estero, RN 9 Km 1125, 4206 Santiago del Estero, Argentina.
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Roberti MJ, Fölling J, Celej MS, Bossi M, Jovin TM, Jares-Erijman EA. Imaging nanometer-sized α-synuclein aggregates by superresolution fluorescence localization microscopy. Biophys J 2012; 102:1598-607. [PMID: 22500760 DOI: 10.1016/j.bpj.2012.03.010] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 02/27/2012] [Accepted: 03/02/2012] [Indexed: 02/04/2023] Open
Abstract
The morphological features of α-synuclein (AS) amyloid aggregation in vitro and in cells were elucidated at the nanoscale by far-field subdiffraction fluorescence localization microscopy. Labeling AS with rhodamine spiroamide probes allowed us to image AS fibrillar structures by fluorescence stochastic nanoscopy with an enhanced resolution at least 10-fold higher than that achieved with conventional, diffraction-limited techniques. The implementation of dual-color detection, combined with atomic force microscopy, revealed the propagation of individual fibrils in vitro. In cells, labeled protein appeared as amyloid aggregates of spheroidal morphology and subdiffraction sizes compatible with in vitro supramolecular intermediates perceived independently by atomic force microscopy and cryo-electron tomography. We estimated the number of monomeric protein units present in these minute structures. This approach is ideally suited for the investigation of the molecular mechanisms of amyloid formation both in vitro and in the cellular milieu.
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Affiliation(s)
- M Julia Roberti
- Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina
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