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Ziaunys M, Sulskis D, Mikalauskaite K, Sakalauskas A, Snieckute R, Smirnovas V. S100A9 inhibits and redirects prion protein 89-230 fragment amyloid aggregation. Arch Biochem Biophys 2024; 758:110087. [PMID: 38977154 DOI: 10.1016/j.abb.2024.110087] [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: 05/06/2024] [Revised: 06/22/2024] [Accepted: 07/05/2024] [Indexed: 07/10/2024]
Abstract
Protein aggregation in the form of amyloid fibrils has long been associated with the onset and development of various amyloidoses, including Alzheimer's, Parkinson's or prion diseases. Recent studies of their fibril formation process have revealed that amyloidogenic protein cross-interactions may impact aggregation pathways and kinetic parameters, as well as the structure of the resulting aggregates. Despite a growing number of reports exploring this type of interaction, they only cover just a small number of possible amyloidogenic protein pairings. One such pair is between two neurodegeneration-associated proteins: the pro-inflammatory S100A9 and prion protein, which are known to co-localize in vivo. In this study, we examined their cross-interaction in vitro and discovered that the fibrillar form of S100A9 modulated the aggregation pathway of mouse prion protein 89-230 fragment, while non-aggregated S100A9 also significantly inhibited its primary nucleation process. These results complement previous observations of the pro-inflammatory protein's role in amyloid aggregation and highlight its potential role against neurodegenerative disorders.
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Affiliation(s)
- Mantas Ziaunys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257, Vilnius, Lithuania.
| | - Darius Sulskis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257, Vilnius, Lithuania
| | - Kamile Mikalauskaite
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257, Vilnius, Lithuania
| | - Andrius Sakalauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257, Vilnius, Lithuania
| | - Ruta Snieckute
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257, Vilnius, Lithuania
| | - Vytautas Smirnovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257, Vilnius, Lithuania
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2
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Ziaunys M, Mikalauskaite K, Sakalauskas A, Smirnovas V. Investigating lysozyme amyloid fibril formation and structural variability dependence on its initial folding state under different pH conditions. Protein Sci 2024; 33:e4888. [PMID: 38151910 PMCID: PMC10804668 DOI: 10.1002/pro.4888] [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: 08/22/2023] [Revised: 11/21/2023] [Accepted: 12/26/2023] [Indexed: 12/29/2023]
Abstract
Protein fibril formation and accumulation are associated with dozens of amyloidoses, including the widespread and yet-incurable Alzheimer's and Parkinson's diseases. Currently, there are still several aspects of amyloid aggregation that are not fully understood, which negatively contributes to the development of disease-altering drugs and treatments. One factor which requires a more in-depth analysis is the effect of the environment on both the initial state of amyloidogenic proteins and their aggregation process and resulting fibril characteristics. In this work, we examine how lysozyme's folding state influences its amyloid formation kinetics and resulting aggregate structural characteristics under several different pH conditions, ranging from acidic to neutral. We demonstrate that both the initial state of the protein and the solution's pH value have a significant combined effect on the variability of the resulting aggregate secondary structures, as well as their stabilities, interactions with amyloid-specific dye molecules, and self-replication properties.
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Affiliation(s)
- Mantas Ziaunys
- Institute of Biotechnology, Life Sciences Center, Vilnius UniversityVilniusLithuania
| | - Kamile Mikalauskaite
- Institute of Biotechnology, Life Sciences Center, Vilnius UniversityVilniusLithuania
| | - Andrius Sakalauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius UniversityVilniusLithuania
| | - Vytautas Smirnovas
- Institute of Biotechnology, Life Sciences Center, Vilnius UniversityVilniusLithuania
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3
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Ziaunys M, Mikalauskaite K, Krasauskas L, Smirnovas V. Conformation-Specific Association of Prion Protein Amyloid Aggregates with Tau Protein Monomers. Int J Mol Sci 2023; 24:ijms24119277. [PMID: 37298227 DOI: 10.3390/ijms24119277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/23/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
Protein aggregation into amyloid fibrils is associated with several amyloidoses, including neurodegenerative Alzheimer's and Parkinson's diseases. Despite years of research and numerous studies, the process is still not fully understood, which significantly impedes the search for cures of amyloid-related disorders. Recently, there has been an increase in reports of amyloidogenic protein cross-interactions during the fibril formation process, which further complicates the already intricate process of amyloid aggregation. One of these reports displayed an interaction involving Tau and prion proteins, which prompted a need for further investigation into the matter. In this work, we generated five populations of conformationally distinct prion protein amyloid fibrils and examined their interaction with Tau proteins. We observed that there was a conformation-specific association between Tau monomers and prion protein fibrils, which increased the aggregate self-association and amyloidophilic dye binding capacity. We also determined that the interaction did not induce the formation of Tau protein amyloid aggregates, but rather caused their electrostatic adsorption to the prion protein fibril surface.
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Affiliation(s)
- Mantas Ziaunys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Kamile Mikalauskaite
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Lukas Krasauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
| | - Vytautas Smirnovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
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4
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Sun Y, Jack K, Ercolani T, Sangar D, Hosszu L, Collinge J, Bieschke J. Direct Observation of Competing Prion Protein Fibril Populations with Distinct Structures and Kinetics. ACS NANO 2023; 17:6575-6588. [PMID: 36802500 PMCID: PMC10100569 DOI: 10.1021/acsnano.2c12009] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
In prion diseases, fibrillar assemblies of misfolded prion protein (PrP) self-propagate by incorporating PrP monomers. These assemblies can evolve to adapt to changing environments and hosts, but the mechanism of prion evolution is poorly understood. We show that PrP fibrils exist as a population of competing conformers, which are selectively amplified under different conditions and can "mutate" during elongation. Prion replication therefore possesses the steps necessary for molecular evolution analogous to the quasispecies concept of genetic organisms. We monitored structure and growth of single PrP fibrils by total internal reflection and transient amyloid binding super-resolution microscopy and detected at least two main fibril populations, which emerged from seemingly homogeneous PrP seeds. All PrP fibrils elongated in a preferred direction by an intermittent "stop-and-go" mechanism, but each population possessed distinct elongation mechanisms that incorporated either unfolded or partially folded monomers. Elongation of RML and ME7 prion rods likewise exhibited distinct kinetic features. The discovery of polymorphic fibril populations growing in competition, which were previously hidden in ensemble measurements, suggests that prions and other amyloid replicating by prion-like mechanisms may represent quasispecies of structural isomorphs that can evolve to adapt to new hosts and conceivably could evade therapeutic intervention.
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Affiliation(s)
- Yuanzi Sun
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - Kezia Jack
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - Tiziana Ercolani
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - Daljit Sangar
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - Laszlo Hosszu
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - John Collinge
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - Jan Bieschke
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
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5
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Ziaunys M, Mikalauskaite K, Veiveris D, Sakalauskas A, Smirnovas V. Superoxide dismutase-1 alters the rate of prion protein aggregation and resulting fibril conformation. Arch Biochem Biophys 2022; 715:109096. [PMID: 34848178 DOI: 10.1016/j.abb.2021.109096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/22/2021] [Accepted: 11/24/2021] [Indexed: 11/02/2022]
Abstract
The assembly of amyloidogenic proteins into highly-structured fibrillar aggregates is related to the onset and progression of several amyloidoses, including neurodegenerative Alzheimer's or Parkinson's diseases. Despite years of research and a general understanding of the process of such aggregate formation, there are currently still very few drugs and treatment modalities available. One of the factors that is relatively insufficiently understood is the cross-interaction between different amyloid-forming proteins. In recent years, it has been shown that several of these proteins or their aggregates can alter each other's fibrillization properties, however, there are still many unknowns in the amyloid interactome. In this work, we examine the interaction between amyloid disease-related prion protein and superoxide dismutase-1. We show that not only does superoxide dismutase-1 increase the lag time of prion protein fibril formation, but it also changes the conformation of the resulting aggregates.
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Affiliation(s)
- Mantas Ziaunys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
| | - Kamile Mikalauskaite
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Dominykas Veiveris
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Andrius Sakalauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Vytautas Smirnovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
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6
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Ziaunys M, Sakalauskas A, Mikalauskaite K, Smirnovas V. Polymorphism of Alpha-Synuclein Amyloid Fibrils Depends on Ionic Strength and Protein Concentration. Int J Mol Sci 2021; 22:12382. [PMID: 34830264 PMCID: PMC8621411 DOI: 10.3390/ijms222212382] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 12/20/2022] Open
Abstract
Protein aggregate formation is linked with multiple amyloidoses, including Alzheimer's and Parkinson's diseases. Currently, the understanding of such fibrillar structure formation and propagation is still not sufficient, the outcome of which is a lack of potent, anti-amyloid drugs. The environmental conditions used during in vitro protein aggregation assays play an important role in determining both the aggregation kinetic parameters, as well as resulting fibril structure. In the case of alpha-synuclein, ionic strength has been shown as a crucial factor in its amyloid aggregation. In this work, we examine a large sample size of alpha-synuclein aggregation reactions under thirty different ionic strength and protein concentration combinations and determine the resulting fibril structural variations using their dye-binding properties, secondary structure and morphology. We show that both ionic strength and protein concentration determine the structural variability of alpha-synuclein amyloid fibrils and that sometimes even identical conditions can result in up to four distinct types of aggregates.
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Affiliation(s)
- Mantas Ziaunys
- Institute of Biotechnology, Life Sciences Centre, Vilnius University, 10257 Vilnius, Lithuania; (A.S.); (K.M.); (V.S.)
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7
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Fridmanis J, Toleikis Z, Sneideris T, Ziaunys M, Bobrovs R, Smirnovas V, Jaudzems K. Aggregation Condition-Structure Relationship of Mouse Prion Protein Fibrils. Int J Mol Sci 2021; 22:9635. [PMID: 34502545 PMCID: PMC8431800 DOI: 10.3390/ijms22179635] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 11/16/2022] Open
Abstract
Prion diseases are associated with conformational conversion of cellular prion protein into a misfolded pathogenic form, which resembles many properties of amyloid fibrils. The same prion protein sequence can misfold into different conformations, which are responsible for variations in prion disease phenotypes (prion strains). In this work, we use atomic force microscopy, FTIR spectroscopy and magic-angle spinning NMR to devise structural models of mouse prion protein fibrils prepared in three different denaturing conditions. We find that the fibril core region as well as the structure of its N- and C-terminal parts is almost identical between the three fibrils. In contrast, the central part differs in length of β-strands and the arrangement of charged residues. We propose that the denaturant ionic strength plays a major role in determining the structure of fibrils obtained in a particular condition by stabilizing fibril core interior-facing glutamic acid residues.
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Affiliation(s)
- Jēkabs Fridmanis
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Aizkraukles 21, LV-1006 Riga, Latvia; (J.F.); (Z.T.); (R.B.)
| | - Zigmantas Toleikis
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Aizkraukles 21, LV-1006 Riga, Latvia; (J.F.); (Z.T.); (R.B.)
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania; (T.S.); (M.Z.); (V.S.)
| | - Tomas Sneideris
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania; (T.S.); (M.Z.); (V.S.)
| | - Mantas Ziaunys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania; (T.S.); (M.Z.); (V.S.)
| | - Raitis Bobrovs
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Aizkraukles 21, LV-1006 Riga, Latvia; (J.F.); (Z.T.); (R.B.)
| | - Vytautas Smirnovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania; (T.S.); (M.Z.); (V.S.)
| | - Kristaps Jaudzems
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Aizkraukles 21, LV-1006 Riga, Latvia; (J.F.); (Z.T.); (R.B.)
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8
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Temperature-Dependent Structural Variability of Prion Protein Amyloid Fibrils. Int J Mol Sci 2021; 22:ijms22105075. [PMID: 34064883 PMCID: PMC8151363 DOI: 10.3390/ijms22105075] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/07/2021] [Accepted: 05/09/2021] [Indexed: 12/20/2022] Open
Abstract
Prion protein aggregation into amyloid fibrils is associated with the onset and progression of prion diseases—a group of neurodegenerative amyloidoses. The process of such aggregate formation is still not fully understood, especially regarding their polymorphism, an event where the same type of protein forms multiple, conformationally and morphologically distinct structures. Considering that such structural variations can greatly complicate the search for potential antiamyloid compounds, either by having specific propagation properties or stability, it is important to better understand this aggregation event. We have recently reported the ability of prion protein fibrils to obtain at least two distinct conformations under identical conditions, which raised the question if this occurrence is tied to only certain environmental conditions. In this work, we examined a large sample size of prion protein aggregation reactions under a range of temperatures and analyzed the resulting fibril dye-binding, secondary structure and morphological properties. We show that all temperature conditions lead to the formation of more than one fibril type and that this variability may depend on the state of the initial prion protein molecules.
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Ziaunys M, Sakalauskas A, Mikalauskaite K, Smirnovas V. Exploring the occurrence of thioflavin-T-positive insulin amyloid aggregation intermediates. PeerJ 2021; 9:e10918. [PMID: 33614299 PMCID: PMC7881721 DOI: 10.7717/peerj.10918] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 01/18/2021] [Indexed: 12/12/2022] Open
Abstract
The aggregation of proteins is considered to be the main cause of several neurodegenerative diseases. Despite much progress in amyloid research, the process of fibrillization is still not fully understood, which is one of the main reasons why there are still very few effective treatments available. When the aggregation of insulin, a model amyloidogenic protein, is tracked using thioflavin-T (ThT), an amyloid specific dye, there is an anomalous occurrence of double-sigmoidal aggregation kinetics. Such an event is likely related to the formation of ThT-positive intermediates, which may affect the outcome of both aggregation kinetic data, as well as final fibril structure. In this work we explore insulin fibrillization under conditions, where both normal and double-sigmoidal kinetics are observed and show that, despite their dye-binding properties and random occurrence, the ThT-positive intermediates do not significantly alter the overall aggregation process.
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Affiliation(s)
- Mantas Ziaunys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Andrius Sakalauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Kamile Mikalauskaite
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Vytautas Smirnovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
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Effect of Ionic Strength on Thioflavin-T Affinity to Amyloid Fibrils and Its Fluorescence Intensity. Int J Mol Sci 2020; 21:ijms21238916. [PMID: 33255444 PMCID: PMC7727833 DOI: 10.3390/ijms21238916] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 12/12/2022] Open
Abstract
The formation of amyloid fibrils is linked to multiple neurodegenerative disorders, including Alzheimer’s and Parkinson’s disease. Despite years of research and countless studies on the topic of such aggregate formation, as well as their resulting structure, the current knowledge is still fairly limited. One of the main aspects prohibiting effective aggregation tracking is the environment’s effect on amyloid-specific dyes, namely thioflavin-T (ThT). Currently, there are only a few studies hinting at ionic strength being one of the factors that modulate the dye’s binding affinity and fluorescence intensity. In this work we explore this effect under a range of ionic strength conditions, using insulin, lysozyme, mouse prion protein, and α-synuclein fibrils. We show that ionic strength is an extremely important factor affecting both the binding affinity, as well as the fluorescence intensity of ThT.
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Rekstina VV, Sabirzyanova TA, Sabirzyanov FA, Adzhubei AA, Tkachev YV, Kudryashova IB, Snalina NE, Bykova AA, Alessenko AV, Ziganshin RH, Kuznetsov SA, Kalebina TS. The Post-Translational Modifications, Localization, and Mode of Attachment of Non-Covalently Bound Glucanosyltransglycosylases of Yeast Cell Wall as a Key to Understanding their Functioning. Int J Mol Sci 2020; 21:ijms21218304. [PMID: 33167499 PMCID: PMC7663962 DOI: 10.3390/ijms21218304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/26/2020] [Accepted: 10/30/2020] [Indexed: 01/27/2023] Open
Abstract
Glucan linked to proteins is a natural mega-glycoconjugate (mGC) playing the central role as a structural component of a yeast cell wall (CW). Regulation of functioning of non-covalently bound glucanosyltransglycosylases (ncGTGs) that have to remodel mGC to provide CW extension is poorly understood. We demonstrate that the main ncGTGs Bgl2 and Scw4 have phosphorylated and glutathionylated residues and are represented in CW as different pools of molecules having various firmness of attachment. Identified pools contain Bgl2 molecules with unmodified peptides, but differ from each other in the presence and combination of modified ones, as well as in the presence or absence of other CW proteins. Correlation of Bgl2 distribution among pools and its N-glycosylation was not found. Glutathione affects Bgl2 conformation, probably resulting in the mode of its attachment and enzymatic activity. Bgl2 from the pool of unmodified and monophosphorylated molecules demonstrates the ability to fibrillate after isolation from CW. Revealing of Bgl2 microcompartments and their mosaic arrangement summarized with the results obtained give the evidence that the functioning of ncGTGs in CW can be controlled by reversible post-translational modifications and facilitated due to their compact localization. The hypothetical scheme of distribution of Bgl2 inside CW is represented.
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Affiliation(s)
- Valentina V. Rekstina
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (V.V.R.); (T.A.S.); (F.A.S.); (I.B.K.); (A.A.B.)
| | - Tatyana A. Sabirzyanova
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (V.V.R.); (T.A.S.); (F.A.S.); (I.B.K.); (A.A.B.)
| | - Fanis A. Sabirzyanov
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (V.V.R.); (T.A.S.); (F.A.S.); (I.B.K.); (A.A.B.)
| | - Alexei A. Adzhubei
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia; (A.A.A.); (Y.V.T.)
| | - Yaroslav V. Tkachev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia; (A.A.A.); (Y.V.T.)
| | - Irina B. Kudryashova
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (V.V.R.); (T.A.S.); (F.A.S.); (I.B.K.); (A.A.B.)
| | - Natalia E. Snalina
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia; (N.E.S.); (A.V.A.)
| | - Anastasia A. Bykova
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (V.V.R.); (T.A.S.); (F.A.S.); (I.B.K.); (A.A.B.)
| | - Alice V. Alessenko
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia; (N.E.S.); (A.V.A.)
| | - Rustam H. Ziganshin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia;
| | - Sergei A. Kuznetsov
- Institute of Biological Sciences, University of Rostock, 18059 Rostock, Germany;
| | - Tatyana S. Kalebina
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia; (V.V.R.); (T.A.S.); (F.A.S.); (I.B.K.); (A.A.B.)
- Correspondence: ; Tel.: +7-(495)-939-50-75
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12
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Self-Replication of Prion Protein Fragment 89-230 Amyloid Fibrils Accelerated by Prion Protein Fragment 107-143 Aggregates. Int J Mol Sci 2020; 21:ijms21197410. [PMID: 33049945 PMCID: PMC7583978 DOI: 10.3390/ijms21197410] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/02/2020] [Accepted: 10/03/2020] [Indexed: 12/15/2022] Open
Abstract
Prion protein amyloid aggregates are associated with infectious neurodegenerative diseases, known as transmissible spongiform encephalopathies. Self-replication of amyloid structures by refolding of native protein molecules is the probable mechanism of disease transmission. Amyloid fibril formation and self-replication can be affected by many different factors, including other amyloid proteins and peptides. Mouse prion protein fragments 107-143 (PrP(107-143)) and 89-230 (PrP(89-230)) can form amyloid fibrils. β-sheet core in PrP(89-230) amyloid fibrils is limited to residues ∼160-220 with unstructured N-terminus. We employed chemical kinetics tools, atomic force microscopy and Fourier-transform infrared spectroscopy, to investigate the effects of mouse prion protein fragment 107-143 fibrils on the aggregation of PrP(89-230). The data suggest that amyloid aggregates of a short prion-derived peptide are not able to seed PrP(89-230) aggregation; however, they accelerate the self-replication of PrP(89-230) amyloid fibrils. We conclude that PrP(107-143) fibrils could facilitate the self-replication of PrP(89-230) amyloid fibrils in several possible ways, and that this process deserves more attention as it may play an important role in amyloid propagation.
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13
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Ziaunys M, Sneideris T, Smirnovas V. Formation of distinct prion protein amyloid fibrils under identical experimental conditions. Sci Rep 2020; 10:4572. [PMID: 32165692 PMCID: PMC7067779 DOI: 10.1038/s41598-020-61663-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 02/28/2020] [Indexed: 01/01/2023] Open
Abstract
Protein aggregation into amyloid fibrils is linked to multiple neurodegenerative disorders, such as Alzheimer’s, Parkinson’s or Creutzfeldt-Jakob disease. A better understanding of the way these aggregates form is vital for the development of drugs. A large detriment to amyloid research is the ability of amyloidogenic proteins to spontaneously aggregate into multiple structurally distinct fibrils (strains) with different stability and seeding properties. In this work we show that prion proteins are capable of forming more than one type of fibril under the exact same conditions by assessing their Thioflavin T (ThT) binding ability, morphology, secondary structure, stability and seeding potential.
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Affiliation(s)
- Mantas Ziaunys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Tomas Sneideris
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Vytautas Smirnovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
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Ziaunys M, Sneideris T, Smirnovas V. Exploring the potential of deep-blue autofluorescence for monitoring amyloid fibril formation and dissociation. PeerJ 2019; 7:e7554. [PMID: 31440437 PMCID: PMC6699583 DOI: 10.7717/peerj.7554] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 07/25/2019] [Indexed: 02/03/2023] Open
Abstract
Protein aggregation into amyloid fibrils has been linked to multiple neurodegenerative disorders. Determining the kinetics of fibril formation, as well as their structural stability are important for the mechanistic understanding of amyloid aggregation. Tracking both fibril association and dissociation is usually performed by measuring light scattering of the solution or fluorescence of amyloid specific dyes, such as thioflavin-T. A possible addition to these methods is the recently discovered deep-blue autofluorescence (dbAF), which is linked to amyloid formation. In this work we explore the potential of this phenomenon to monitor amyloid fibril formation and dissociation, as well as show its possible relation to fibril size rather than amyloid structure.
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Affiliation(s)
- Mantas Ziaunys
- Vilnius University, Life Sciences Center, Institute of Biotechnology, Vilnius, Lithuania
| | - Tomas Sneideris
- Vilnius University, Life Sciences Center, Institute of Biotechnology, Vilnius, Lithuania
| | - Vytautas Smirnovas
- Vilnius University, Life Sciences Center, Institute of Biotechnology, Vilnius, Lithuania
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15
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Honda R. Role of the Disulfide Bond in Prion Protein Amyloid Formation: A Thermodynamic and Kinetic Analysis. Biophys J 2019; 114:885-892. [PMID: 29490248 DOI: 10.1016/j.bpj.2017.12.031] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 12/15/2017] [Accepted: 12/27/2017] [Indexed: 01/19/2023] Open
Abstract
Prion diseases are associated with the structural conversion of prion protein (PrP) to a β-sheet-rich aggregate, PrPSc. Previous studies have indicated that a reduction of the disulfide bond linking C179 and C214 of PrP yields an amyloidlike β-rich aggregate in vitro. To gain mechanistic insights into the reduction-induced aggregation, here I characterized how disulfide bond reduction modulates the protein folding/misfolding landscape of PrP, by examining 1) the equilibrium stabilities of the native (N) and aggregated states relative to the unfolded (U) state, 2) the transition barrier separating the U and aggregated states, and 3) the final structure of amyloidlike misfolded aggregates. Kinetic and thermodynamic experiments revealed that disulfide bond reduction decreases the equilibrium stabilities of both the N and aggregated states by ∼3 kcal/mol, without changing either the amyloidlike aggregate structure, at least at the secondary structural level, or the transition barrier of aggregation. Therefore, disulfide bond reduction modulates the protein folding/misfolding landscape by entropically stabilizing disordered states, including the U and transition state of aggregation. This also indicates that the equilibrium stability of the N state, but not the transition barrier of aggregation, is the dominant factor determining the reduction-induced aggregation of PrP.
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Affiliation(s)
- Ryo Honda
- The United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan; Department of Molecular Pathobiochemistry, Graduate School of Medicine, Gifu University, Gifu, Japan.
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16
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Honda RP, Kuwata K. The native state of prion protein (PrP) directly inhibits formation of PrP-amyloid fibrils in vitro. Sci Rep 2017; 7:562. [PMID: 28373719 PMCID: PMC5429628 DOI: 10.1038/s41598-017-00710-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 03/08/2017] [Indexed: 11/25/2022] Open
Abstract
The conversion of globular proteins into amyloid fibrils is associated with a wide variety of human diseases. One example is the prion protein (PrP), which adopts an α-helical structure in the native state but its amyloid form is implicated in the pathogenesis of prion diseases. Previous evidence has suggested that destabilization of the native state promotes amyloid formation, but the underlying mechanism remains unknown. In this study, we report that the native state of PrP serves as a potent inhibitor in the formation of PrP amyloid fibrils. By monitoring the time courses of thioflavin T fluorescence, the kinetics of amyloid formation was studied in vitro under various concentrations of pre-formed amyloid, monomer, and denaturant. Quantitative analysis of the kinetic data using various models of enzyme kinetics suggested that the native state of PrP is either an uncompetitive or noncompetitive inhibitor of amyloid formation. This study highlights the significant role of the native state in inhibiting amyloid formation, which provides new insights into the pathogenesis of misfolding diseases.
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Affiliation(s)
- Ryo P Honda
- Department of Molecular Pathobiochemistry, Graduate School of Medicine, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan.
| | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan. .,Department of Gene and Development, Graduate School of Medicine, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan.
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17
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Kinetics of protein fibril formation: Methods and mechanisms. Int J Biol Macromol 2016; 100:3-10. [PMID: 27327908 DOI: 10.1016/j.ijbiomac.2016.06.052] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 06/14/2016] [Accepted: 06/16/2016] [Indexed: 11/23/2022]
Abstract
Amyloid fibril formation is a self-assembly reaction induced by favourable conformational changes of proteins leading to a stable, structurally organized aggregates. The deposition of stable protein fibrils in organs and tissues results in many diseases which are generally referred as amyloidosis. Though different disease conditions originate from sequentially and structurally different proteins, their fibrillar forms share common structural features. In vitro, fibril structure and kinetic pathway are investigated by using spectroscopic (fluorescence, circular dichroism, crystallography and solid state-NMR) and microscopic techniques. The kinetics of fibril formation is analysed using different mechanisms to understand the microscopic processes involved in the fibrillation reaction. This review discusses the assumptions, mechanisms, and limitations of some of the widely applied kinetic equations. Understanding of these equations would help to quantify the effect of the different microscopic process on the overall fibrillation kinetics which could aid in designing appropriate molecules to intervene in the aggregation process at different stages.
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18
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Sneideris T, Milto K, Smirnovas V. Polymorphism of amyloid-like fibrils can be defined by the concentration of seeds. PeerJ 2015; 3:e1207. [PMID: 26355941 PMCID: PMC4563235 DOI: 10.7717/peerj.1207] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 08/01/2015] [Indexed: 12/11/2022] Open
Abstract
Prions are infectious proteins where the same protein may express distinct strains. The strains are enciphered by different misfolded conformations. Strain-like phenomena have also been reported in a number of other amyloid-forming proteins. One of the features of amyloid strains is the ability to self-propagate, maintaining a constant set of physical properties despite being propagated under conditions different from those that allowed initial formation of the strain. Here we report a cross-seeding experiment using strains formed under different conditions. Using high concentrations of seeds results in rapid elongation and new fibrils preserve the properties of the seeding fibrils. At low seed concentrations, secondary nucleation plays the major role and new fibrils gain properties predicted by the environment rather than the structure of the seeds. Our findings could explain conformational switching between amyloid strains observed in a wide variety of in vivo and in vitro experiments.
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Affiliation(s)
- Tomas Sneideris
- Department of Biothermodynamics and Drug Design, Vilnius University, Institute of Biotechnology, Vilnius, Lithuania
| | - Katažyna Milto
- Department of Biothermodynamics and Drug Design, Vilnius University, Institute of Biotechnology, Vilnius, Lithuania
| | - Vytautas Smirnovas
- Department of Biothermodynamics and Drug Design, Vilnius University, Institute of Biotechnology, Vilnius, Lithuania
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19
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Malisauskas R, Botyriute A, Cannon JG, Smirnovas V. Flavone derivatives as inhibitors of insulin amyloid-like fibril formation. PLoS One 2015; 10:e0121231. [PMID: 25799281 PMCID: PMC4370379 DOI: 10.1371/journal.pone.0121231] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 01/12/2015] [Indexed: 11/18/2022] Open
Abstract
Several natural and synthetic flavone derivatives have been reported to inhibit formation of amyloid fibrils or to remodel existing fibrils. These studies suggest that the numbers and positions of hydroxyl groups on the flavone rings determine their effectiveness as amyloid inhibitors. In many studies the primary method for determining the effectiveness of inhibition is measuring Thioflavin T (ThT) fluorescence. This method demonstrably results in a number of false positives for inhibition. We studied the effects of 265 commercially available flavone derivatives on insulin fibril formation. We enhanced the effectiveness of ThT fluorescence measurements by fitting kinetic curves to obtain halftime of aggregation (t50). Maximal values of ThT fluorescence varied two fold or more in one third of all cases, but this did not correlate with changes in t50. Changes in t50 values were more accurate measures of inhibition of amyloid formation. We showed that without a change in an assay, but just by observing complete kinetic curves it is possible to eliminate numbers of false positive and sometimes even false negative results. Examining the data from all 265 flavones we confirmed previous observations that identified the importance of hydroxyl groups for inhibition. Our evidence suggests the importance of hydroxyl groups at locations 5, 6, 7, and 4', and the absence of a hydroxyl group at location 3, for inhibiting amyloid formation. However, the main conclusion is that the positions are not additive. The structures and their effects must be thought of in the context of the whole molecule.
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Affiliation(s)
- Ricardas Malisauskas
- Department of Biothermodynamics and Drug Design, Vilnius University Institute of Biotechnology, Vilnius, Lithuania
- Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, Vilnius, Lithuania
| | - Akvile Botyriute
- Department of Biothermodynamics and Drug Design, Vilnius University Institute of Biotechnology, Vilnius, Lithuania
| | - Jonathan G. Cannon
- Department of Natural Sciences and Engineering, Middle Georgia State College, Cochran, Georgia, USA
| | - Vytautas Smirnovas
- Department of Biothermodynamics and Drug Design, Vilnius University Institute of Biotechnology, Vilnius, Lithuania
- * E-mail:
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Lu B, Zhang B, Qi W, Zhu Y, Zhao Y, Zhou N, Sun R, Bao J, Wu C. Conformational study reveals amino acid residues essential for hemagglutinating and anti-proliferative activities of Clematis montana lectin. Acta Biochim Biophys Sin (Shanghai) 2014; 46:923-34. [PMID: 25239139 DOI: 10.1093/abbs/gmu085] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Clematis montana lectin (CML), a novel mannose-binding lectin purified from C. montana Buch.-Ham stem (Ranunculaceae), has been proved to have hemagglutinating activity in rabbit erythrocytes and apoptosis-inducing activity in tumor cells. However, the biochemical properties of CML have not revealed and its structural information still needs to be elucidated. In this study, it was found that CML possessed quite good thermostability and alkaline resistance, and its hemagglutinating activity was bivalent metal cation dependent. In addition, hemagglutination test and fluorescence spectroscopy proved that GuHCl, urea, and sodium dodecyl sulfate could change the conformation of CML and further caused the loss of hemagglutination activity. Moreover, the changes of fluorescence spectrum indicated that the tryptophan (Trp) microenvironment conversion might be related to the conformation and bioactivities of CML. In addition, it was also found that Trp residues, arginine (Arg) residues, and sulfhydryl were important for the hemagglutinating activity of CML, but only Trp was proved to be crucial for the CML conformation. Furthermore, the Trp, Arg, and sulfhydryl-modified CML exhibited 97.17%, 76.99%, and 49.64% loss of its anti-proliferative activity, respectively, which was consistent with the alterations of its hemagglutinating activity. Given these findings, Trp residues on the surface of CML are essential for the active center to form substrate-accessible conformation and suitable environment for carbohydrate binding.
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Affiliation(s)
- Bangmin Lu
- School of Life Sciences and Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610064, China
| | - Bin Zhang
- School of Life Sciences and Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610064, China
| | - Wei Qi
- School of Life Sciences and Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610064, China
| | - Yanan Zhu
- School of Life Sciences and Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610064, China
| | - Yan Zhao
- School of Life Sciences and Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610064, China
| | - Nan Zhou
- School of Life Sciences and Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610064, China
| | - Rong Sun
- School of Life Sciences and Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610064, China
| | - Jinku Bao
- School of Life Sciences and Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610064, China
| | - Chuanfang Wu
- School of Life Sciences and Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610064, China
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