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Žganec M, Taler Verčič A, Muševič I, Škarabot M, Žerovnik E. Amyloid Fibrils of Stefin B Show Anisotropic Properties. Int J Mol Sci 2023; 24:ijms24043737. [PMID: 36835149 PMCID: PMC9962164 DOI: 10.3390/ijms24043737] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/30/2023] [Accepted: 02/11/2023] [Indexed: 02/16/2023] Open
Abstract
Human stefin B, a member of the cystatin family of cysteine protease inhibitors, tends to form amyloid fibrils under relatively mild conditions, which is why it is used as a model protein to study amyloid fibrillation. Here, we show for the first time that bundles of amyloid fibrils, i.e., helically twisted ribbons, formed by human stefin B exhibit birefringence. This physical property is commonly observed in amyloid fibrils when stained with Congo red. However, we show that the fibrils arrange in regular anisotropic arrays and no staining is required. They share this property with anisotropic protein crystals, structured protein arrays such as tubulin and myosin, and other anisotropic elongated materials, such as textile fibres and liquid crystals. In certain macroscopic arrangements of amyloid fibrils, not only birefringence is observed, but also enhanced emission of intrinsic fluorescence, implying a possibility to detect amyloid fibrils with no labels by using optical microscopy. In our case, no enhancement of intrinsic tyrosine fluorescence was observed at 303 nm; instead, an additional fluorescence emission peak appeared at 425 to 430 nm. We believe that both phenomena, birefringence and fluorescence emission in the deep blue, should be further explored with this and other amyloidogenic proteins. This may allow the development of label-free detection methods for amyloid fibrils of different origins.
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Affiliation(s)
- Matjaž Žganec
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, 1000 Ljubljana, Slovenia
| | - Ajda Taler Verčič
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Jamova 39, 1000 Ljubljana, Slovenia
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
| | - Igor Muševič
- Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, 1000 Ljubljana, Slovenia
- Department of Condensed Matter Physics, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Miha Škarabot
- Department of Condensed Matter Physics, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
| | - Eva Žerovnik
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Jamova 39, 1000 Ljubljana, Slovenia
- Correspondence:
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Gowda V, Biler M, Filippov A, Mantonico MV, Ornithopoulou E, Linares M, Antzutkin ON, Lendel C. Structural characterisation of amyloid-like fibrils formed by an amyloidogenic peptide segment of β-lactoglobulin. RSC Adv 2021; 11:27868-27879. [PMID: 35480736 PMCID: PMC9037834 DOI: 10.1039/d1ra03575d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 08/09/2021] [Indexed: 12/11/2022] Open
Abstract
Protein nanofibrils (PNFs) represent a promising class of biobased nanomaterials for biomedical and materials science applications. In the design of such materials, a fundamental understanding of the structure–function relationship at both molecular and nanoscale levels is essential. Here we report investigations of the nanoscale morphology and molecular arrangement of amyloid-like PNFs of a synthetic peptide fragment consisting of residues 11–20 of the protein β-lactoglobulin (β-LG11–20), an important model system for PNF materials. Nanoscale fibril morphology was analysed by atomic force microscopy (AFM) that indicates the presence of polymorphic self-assembly of protofilaments. However, observation of a single set of 13C and 15N resonances in the solid-state NMR spectra for the β-LG11–20 fibrils suggests that the observed polymorphism originates from the assembly of protofilaments at the nanoscale but not from the molecular structure. The secondary structure and inter-residue proximities in the β-LG11–20 fibrils were probed using NMR experiments of the peptide with 13C- and 15N-labelled amino acid residues at selected positions. We can conclude that the peptides form parallel β-sheets, but the NMR data was inconclusive regarding inter-sheet packing. Molecular dynamics simulations confirm the stability of parallel β-sheets and suggest two preferred modes of packing. Comparison of molecular dynamics models with NMR data and calculated chemical shifts indicates that both packing models are possible. A 10-residue peptide segment of β-lactoglobulin (β-LG11–20) forms amyloid-like fibrils as revealed by AFM, NMR, and MD simulations.![]()
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Affiliation(s)
- Vasantha Gowda
- Dept. of Chemistry, KTH Royal Institute of Technology Stockholm Sweden
| | - Michal Biler
- Dept. of Theoretical Chemistry, KTH Royal Institute of Technology Stockholm Sweden
| | - Andrei Filippov
- Chemistry of Interfaces, Luleå University of Technology Sweden.,Dept. Medical and Biological Physics, Kazan State Medical University 420012 Kazan Russia
| | | | | | - Mathieu Linares
- Dept. of Theoretical Chemistry, KTH Royal Institute of Technology Stockholm Sweden.,Laboratory of Organic Electronics and Group of Scientific Visualization, ITN, Linköping University 60174 Norrköping Sweden.,Swedish e-Science Research Centre (SeRC), Linköping University 60174 Norrköping Sweden
| | - Oleg N Antzutkin
- Chemistry of Interfaces, Luleå University of Technology Sweden.,Dept. of Physics, University of Warwick Coventry UK
| | - Christofer Lendel
- Dept. of Chemistry, KTH Royal Institute of Technology Stockholm Sweden
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3
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Žerovnik E. Viroporins vs. Other Pore-Forming Proteins: What Lessons Can We Take? Front Chem 2021; 9:626059. [PMID: 33681145 PMCID: PMC7930612 DOI: 10.3389/fchem.2021.626059] [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: 11/04/2020] [Accepted: 01/07/2021] [Indexed: 11/13/2022] Open
Abstract
Pore-forming proteins (PFPs) exist in virtually all domains of life, and by disrupting cellular membranes, depending on the pore size, they cause ion dis-balance, small substances, or even protein efflux/influx, influencing cell’s signaling routes and fate. Such pore-forming proteins exist from bacteria to viruses and also shape host defense systems, including innate immunity. There is strong evidence that amyloid toxicity is also caused by prefibrillar oligomers making “amyloid pores” into cellular membranes. For most of the PFPs, a 2-step mechanism of protein-membrane interaction takes place on the “lipid rafts,” membrane microdomains rich in gangliosides and cholesterol. In this mini-review paper, common traits of different PFPs are looked at. Possible ways for therapy of channelopathies and/or modulating immunity relevant to the new threat of SARS-CoV-2 infections could be learnt from such comparisons.
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Affiliation(s)
- Eva Žerovnik
- Department of Biochemistry and Molecular and Structural Biology, J. Stefan Institute, Ljubljana, Slovenia
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4
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Audette GF, Yaseen A, Bragagnolo N, Bawa R. Protein Nanotubes: From Bionanotech towards Medical Applications. Biomedicines 2019; 7:biomedicines7020046. [PMID: 31234611 PMCID: PMC6630890 DOI: 10.3390/biomedicines7020046] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/18/2019] [Accepted: 06/19/2019] [Indexed: 01/21/2023] Open
Abstract
Nanobiotechnology involves the study of structures found in nature to construct nanodevices for biological and medical applications with the ultimate goal of commercialization. Within a cell most biochemical processes are driven by proteins and associated macromolecular complexes. Evolution has optimized these protein-based nanosystems within living organisms over millions of years. Among these are flagellin and pilin-based systems from bacteria, viral-based capsids, and eukaryotic microtubules and amyloids. While carbon nanotubes (CNTs), and protein/peptide-CNT composites, remain one of the most researched nanosystems due to their electrical and mechanical properties, there are many concerns regarding CNT toxicity and biodegradability. Therefore, proteins have emerged as useful biotemplates for nanomaterials due to their assembly under physiologically relevant conditions and ease of manipulation via protein engineering. This review aims to highlight some of the current research employing protein nanotubes (PNTs) for the development of molecular imaging biosensors, conducting wires for microelectronics, fuel cells, and drug delivery systems. The translational potential of PNTs is highlighted.
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Affiliation(s)
- Gerald F Audette
- Department of Chemistry and the Centre for Research on Biomolecular Interactions, York University, Toronto, ON M3J 1P3, Canada.
| | - Ayat Yaseen
- Department of Chemistry and the Centre for Research on Biomolecular Interactions, York University, Toronto, ON M3J 1P3, Canada.
| | - Nicholas Bragagnolo
- Department of Chemistry and the Centre for Research on Biomolecular Interactions, York University, Toronto, ON M3J 1P3, Canada.
| | - Raj Bawa
- Patent Law Department, Bawa Biotech LLC, Ashburn, VA 20147, USA.
- Guanine Inc., Rensselaer, NY 12144-3463, USA.
- Pharmaceutical Research Institute of Albany College of Pharmacy and Health Sciences, Albany, NY 12208, USA.
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5
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6
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Tuning lysozyme nanofibers dimensions using deep eutectic solvents for improved reinforcement ability. Int J Biol Macromol 2018; 115:518-527. [DOI: 10.1016/j.ijbiomac.2018.03.150] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 03/14/2018] [Accepted: 03/24/2018] [Indexed: 11/18/2022]
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7
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Gravagnuolo AM, Longobardi S, Luchini A, Appavou MS, De Stefano L, Notomista E, Paduano L, Giardina P. Class I Hydrophobin Vmh2 Adopts Atypical Mechanisms to Self-Assemble into Functional Amyloid Fibrils. Biomacromolecules 2016; 17:954-64. [DOI: 10.1021/acs.biomac.5b01632] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alfredo Maria Gravagnuolo
- Department
of Chemical Sciences, University of Naples “Federico II”, Via Cintia 4, 80126 Naples, Italy
| | - Sara Longobardi
- Department
of Chemical Sciences, University of Naples “Federico II”, Via Cintia 4, 80126 Naples, Italy
| | - Alessandra Luchini
- Department
of Chemical Sciences, University of Naples “Federico II”, Via Cintia 4, 80126 Naples, Italy
| | - Marie-Sousai Appavou
- Jülich
Centre for Neutron Science JCNS, Forschungszentrum Jülich GmbH,
Outstation at MLZ, Lichtenbergstraße
1, 85747 Garching, Germany
| | - Luca De Stefano
- Unit of Naples,
Institute for Microelectronics and Microsystems, National Council
of Research, Via Pietro Castellino
111, 80131 Naples, Italy
| | - Eugenio Notomista
- Department
of Biology, University of Naples “Federico II”, Via Cintia
4, 80126 Naples, Italy
| | - Luigi Paduano
- Department
of Chemical Sciences, University of Naples “Federico II”, Via Cintia 4, 80126 Naples, Italy
| | - Paola Giardina
- Department
of Chemical Sciences, University of Naples “Federico II”, Via Cintia 4, 80126 Naples, Italy
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8
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Rubin DJ, Amini S, Zhou F, Su H, Miserez A, Joshi NS. Structural, nanomechanical, and computational characterization of D,L-cyclic peptide assemblies. ACS NANO 2015; 9:3360-3368. [PMID: 25757883 DOI: 10.1021/acsnano.5b00672] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The rigid geometry and tunable chemistry of D,L-cyclic peptides makes them an intriguing building-block for the rational design of nano- and microscale hierarchically structured materials. Herein, we utilize a combination of electron microscopy, nanomechanical characterization including depth sensing-based bending experiments, and molecular modeling methods to obtain the structural and mechanical characteristics of cyclo-[(Gln-D-Leu)4] (QL4) assemblies. QL4 monomers assemble to form large, rod-like structures with diameters up to 2 μm and lengths of tens to hundreds of micrometers. Image analysis suggests that large assemblies are hierarchically organized from individual tubes that undergo bundling to form larger structures. With an elastic modulus of 11.3 ± 3.3 GPa, hardness of 387 ± 136 MPa and strength (bending) of 98 ± 19 MPa the peptide crystals are among the most robust known proteinaceous micro- and nanofibers. The measured bending modulus of micron-scale fibrils (10.5 ± 0.9 GPa) is in the same range as the Young's modulus measured by nanoindentation indicating that the robust nanoscale network from which the assembly derives its properties is preserved at larger length-scales. Materials selection charts are used to demonstrate the particularly robust properties of QL4 including its specific flexural modulus in which it outperforms a number of biological proteinaceous and nonproteinaceous materials including collagen and enamel. The facile synthesis, high modulus, and low density of QL4 fibers indicate that they may find utility as a filler material in a variety of high efficiency, biocompatible composite materials.
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Affiliation(s)
- Daniel J Rubin
- †Harvard University, School of Engineering and Applied Sciences, Cambridge, Massachusetts 02138, United States
- ‡Wyss Institute for Biologically Inspired Engineering, Cambridge, Massachusetts 02138, United States
| | - Shahrouz Amini
- §School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
- ∥Center for Biomimetic Sensor Science, Nanyang Technological University, Singapore 637553, Singapore
| | - Feng Zhou
- §School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Haibin Su
- §School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Ali Miserez
- §School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
- ∥Center for Biomimetic Sensor Science, Nanyang Technological University, Singapore 637553, Singapore
- ⊥School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Neel S Joshi
- †Harvard University, School of Engineering and Applied Sciences, Cambridge, Massachusetts 02138, United States
- ‡Wyss Institute for Biologically Inspired Engineering, Cambridge, Massachusetts 02138, United States
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9
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Liu Y, Liu Y, Wang S, Dong S, Chang P, Jiang Z. Structural characteristics of (−)-epigallocatechin-3-gallate inhibiting amyloid Aβ42 aggregation and remodeling amyloid fibers. RSC Adv 2015. [DOI: 10.1039/c5ra09608a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
To elucidate the structural requirements of EGCG analogs inhibiting Aβ42 protein aggregation and remodeling amyloid fibers, the interactions mechanism between Aβ42 and four EGCG analogs, EGCG, GCG, ECG and EGC, were investigated in this work.
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Affiliation(s)
- Yun Liu
- Beijing Key Laboratory of Bioprocess
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Yang Liu
- Beijing Key Laboratory of Bioprocess
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Shihui Wang
- Beijing Key Laboratory of Bioprocess
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Shengzhao Dong
- Beijing Key Laboratory of Bioprocess
- College of Life Science and Technology
- Beijing University of Chemical Technology
- Beijing 100029
- China
| | - Ping Chang
- College of Applied Arts and Science
- Beijing Union University
- Beijing 100101
- China
| | - Zhaofeng Jiang
- College of Applied Arts and Science
- Beijing Union University
- Beijing 100101
- China
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10
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Kaur M, Healy J, Vasudevamurthy M, Lassé M, Puskar L, Tobin MJ, Valery C, Gerrard JA, Sasso L. Stability and cytotoxicity of crystallin amyloid nanofibrils. NANOSCALE 2014; 6:13169-78. [PMID: 25255060 DOI: 10.1039/c4nr04624b] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Previous work has identified crystallin proteins extracted from fish eye lenses as a cheap and readily available source for the self-assembly of amyloid nanofibrils. However, before exploring potential applications, the biophysical aspects and safety of this bionanomaterial need to be assessed so as to ensure that it can be effectively and safely used. In this study, crude crystallin amyloid fibrils are shown to be stable across a wide pH range, in a number of industrially relevant solvents, at both low and high temperatures, and in the presence of proteases. Crystallin nanofibrils were compared to well characterised insulin and whey protein fibrils using Thioflavin T assays and TEM imaging. Cell cytotoxicity assays suggest no adverse impact of both mature and fragmented crystallin fibrils on cell viability of Hec-1a endometrial cells. An IR microspectroscopy study supports long-term structural integrity of crystallin nanofibrils.
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Affiliation(s)
- Manmeet Kaur
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand.
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