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Paul S, Jeništová A, Vosough F, Berntsson E, Mörman C, Jarvet J, Gräslund A, Wärmländer SKTS, Barth A. 13C- and 15N-labeling of amyloid-β and inhibitory peptides to study their interaction via nanoscale infrared spectroscopy. Commun Chem 2023; 6:163. [PMID: 37537303 PMCID: PMC10400569 DOI: 10.1038/s42004-023-00955-w] [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: 11/22/2022] [Accepted: 07/06/2023] [Indexed: 08/05/2023] Open
Abstract
Interactions between molecules are fundamental in biology. They occur also between amyloidogenic peptides or proteins that are associated with different amyloid diseases, which makes it important to study the mutual influence of two polypeptides on each other's properties in mixed samples. However, addressing this research question with imaging techniques faces the challenge to distinguish different polypeptides without adding artificial probes for detection. Here, we show that nanoscale infrared spectroscopy in combination with 13C, 15N-labeling solves this problem. We studied aggregated amyloid-β peptide (Aβ) and its interaction with an inhibitory peptide (NCAM1-PrP) using scattering-type scanning near-field optical microscopy. Although having similar secondary structure, labeled and unlabeled peptides could be distinguished by comparing optical phase images taken at wavenumbers characteristic for either the labeled or the unlabeled peptide. NCAM1-PrP seems to be able to associate with or to dissolve existing Aβ fibrils because pure Aβ fibrils were not detected after mixing.
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Affiliation(s)
- Suman Paul
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
- attocube systems AG, Haar, Germany
| | - Adéla Jeništová
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Faraz Vosough
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Elina Berntsson
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Cecilia Mörman
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Jüri Jarvet
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
- National Institute of Chemical Physics and Biophysics, Tallinn, Estonia
| | - Astrid Gräslund
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | | | - Andreas Barth
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
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2
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Tilbury MA, Tran TQ, Shingare D, Lefevre M, Power AM, Leclère P, Wall JG. Self-assembly of a barnacle cement protein into intertwined amyloid fibres and determination of their adhesive and viscoelastic properties. J R Soc Interface 2023; 20:20230332. [PMID: 37553991 PMCID: PMC10410215 DOI: 10.1098/rsif.2023.0332] [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: 06/07/2023] [Accepted: 07/18/2023] [Indexed: 08/10/2023] Open
Abstract
The stalked barnacle Pollicipes pollicipes uses a multi-protein cement to adhere to highly varied substrates in marine environments. We investigated the morphology and adhesiveness of a component 19 kDa protein in barnacle cement gland- and seawater-like conditions, using transmission electron microscopy and state-of-the art scanning probe techniques. The protein formed amyloid fibres after 5 days in gland-like but not seawater conditions. After 7-11 days, the fibres self-assembled under gland-like conditions into large intertwined fibrils of up to 10 µm in length and 200 nm in height, with a distinctive twisting of fibrils evident after 11 days. Atomic force microscopy (AFM)-nanodynamic mechanical analysis of the protein in wet conditions determined E' (elasticity), E'' (viscosity) and tan δ values of 2.8 MPa, 1.2 MPa and 0.37, respectively, indicating that the protein is a soft and viscoelastic material, while the adhesiveness of the unassembled protein and assembled fibres, measured using peak force quantitative nanomechanical mapping, was comparable to that of the commercial adhesive Cell-Tak™. The study provides a comprehensive insight into the nanomechanical and viscoelastic properties of the barnacle cement protein and its self-assembled fibres under native-like conditions and may have application in the design of amyloid fibril-based biomaterials or bioadhesives.
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Affiliation(s)
- Maura A. Tilbury
- Microbiology, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
- SFI Centre for Medical Devices (CÚRAM), University of Galway, Galway, Ireland
| | - Thi Quynh Tran
- Laboratory for Physics of Nanomaterials and Energy, Research Institute for Materials, University of Mons, 7000 Mons, Belgium
| | - Dilip Shingare
- Microbiology, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
- SFI Centre for Medical Devices (CÚRAM), University of Galway, Galway, Ireland
| | - Mathilde Lefevre
- Laboratory for Physics of Nanomaterials and Energy, Research Institute for Materials, University of Mons, 7000 Mons, Belgium
- Laboratory of Cell Biology, Research Institute for Biosciences, University of Mons, Place du Parc 23, 7000 Mons, Belgium
| | - Anne Marie Power
- Ryan Institute, School of Natural Sciences, University of Galway, Galway, Ireland
| | - Philippe Leclère
- Laboratory for Physics of Nanomaterials and Energy, Research Institute for Materials, University of Mons, 7000 Mons, Belgium
| | - J. Gerard Wall
- Microbiology, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
- SFI Centre for Medical Devices (CÚRAM), University of Galway, Galway, Ireland
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3
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Di Rocco G, Bernini F, Battistuzzi G, Ranieri A, Bortolotti CA, Borsari M, Sola M. Hydrogen peroxide induces heme degradation and protein aggregation in human neuroglobin: roles of the disulfide bridge and hydrogen-bonding in the distal heme cavity. FEBS J 2023; 290:148-161. [PMID: 35866372 PMCID: PMC10087938 DOI: 10.1111/febs.16581] [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: 05/05/2022] [Revised: 07/05/2022] [Accepted: 07/20/2022] [Indexed: 01/14/2023]
Abstract
In the present study, human neuroglobin (hNgb) was found to undergo H2 O2 -induced breakdown of the heme center at a much slower rate than other globins, namely in the timescale of hours against minutes. We investigated how the rate of the process is affected by the Cys46/Cys55 disulfide bond and the network of non-covalent interactions in the distal heme side involving Tyr44, Lys67, the His64 heme iron axial ligand and the heme propionate-7. The rate is increased by the Tyr44 to Ala and Phe mutations; however the rate is lowered by Lys67 to Ala swapping. The absence of the disulfide bridge slows down the reaction further. Therefore, the disulfide bond-controlled accessibility of the heme site and the residues at position 44 and 67 affect the activation barrier of the reaction. Wild-type and mutated species form β-amyloid aggregates in the presence of H2 O2 producing globular structures. Furthermore, the C46A/C55A, Y44A, Y44F and Y44F/C46A/C55A variants yield potentially harmful fibrils. Finally, the nucleation and growth kinetics for the aggregation of the amyloid structures can be successfully described by the Finke-Watzky model.
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Affiliation(s)
- Giulia Di Rocco
- Department of Life Sciences, University of Modena and Reggio Emilia, Italy
| | - Fabrizio Bernini
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Italy
| | - Gianantonio Battistuzzi
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Italy
| | - Antonio Ranieri
- Department of Life Sciences, University of Modena and Reggio Emilia, Italy
| | | | - Marco Borsari
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Italy
| | - Marco Sola
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia, Italy
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4
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Kutzli I, Zhou J, Li T, Baier SK, Mezzenga R. Formation and characterization of plant-based amyloid fibrils from hemp seed protein. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2022.108307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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5
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Lam NT, McCluskey JB, Glover DJ. Harnessing the Structural and Functional Diversity of Protein Filaments as Biomaterial Scaffolds. ACS APPLIED BIO MATERIALS 2022; 5:4668-4686. [PMID: 35766918 DOI: 10.1021/acsabm.2c00275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The natural ability of many proteins to polymerize into highly structured filaments has been harnessed as scaffolds to align functional molecules in a diverse range of biomaterials. Protein-engineering methodologies also enable the structural and physical properties of filaments to be tailored for specific biomaterial applications through genetic engineering or filaments built from the ground up using advances in the computational prediction of protein folding and assembly. Using these approaches, protein filament-based biomaterials have been engineered to accelerate enzymatic catalysis, provide routes for the biomineralization of inorganic materials, facilitate energy production and transfer, and provide support for mammalian cells for tissue engineering. In this review, we describe how the unique structural and functional diversity in natural and computationally designed protein filaments can be harnessed in biomaterials. In addition, we detail applications of these protein assemblies as material scaffolds with a particular emphasis on applications that exploit unique properties of specific filaments. Through the diversity of protein filaments, the biomaterial engineer's toolbox contains many modular protein filaments that will likely be incorporated as the main structural component of future biomaterials.
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Affiliation(s)
- Nga T Lam
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Joshua B McCluskey
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Dominic J Glover
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales 2052, Australia
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6
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Diao Y, Zhang Y, Zhang W, Xu W, Hu Z, Yi Y, Wang Y. Acid‐thermal‐induced formation of rice bran protein nano‐particles: foaming properties and physicochemical characteristics. Int J Food Sci Technol 2022. [DOI: 10.1111/ijfs.15686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yunchun Diao
- Key Laboratory for Deep Processing of Major Grain and Oil Ministry of Education Wuhan Polytechnic University Wuhan 430023 China
- College of Food Science and Engineering Wuhan Polytechnic University Wuhan 430023 China
| | - Yanpeng Zhang
- Key Laboratory for Deep Processing of Major Grain and Oil Ministry of Education Wuhan Polytechnic University Wuhan 430023 China
- College of Food Science and Engineering Wuhan Polytechnic University Wuhan 430023 China
| | - Weinong Zhang
- College of Food Science and Engineering Wuhan Polytechnic University Wuhan 430023 China
| | - Wei Xu
- College of Food Science and Engineering Wuhan Polytechnic University Wuhan 430023 China
| | - Zhixiong Hu
- College of Food Science and Engineering Wuhan Polytechnic University Wuhan 430023 China
| | - Yang Yi
- College of Food Science and Engineering Wuhan Polytechnic University Wuhan 430023 China
| | - Yuehui Wang
- Key Laboratory for Deep Processing of Major Grain and Oil Ministry of Education Wuhan Polytechnic University Wuhan 430023 China
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7
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Tang CH. Nano-architectural assembly of soy proteins: A promising strategy to fabricate nutraceutical nanovehicles. Adv Colloid Interface Sci 2021; 291:102402. [PMID: 33752139 DOI: 10.1016/j.cis.2021.102402] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/11/2021] [Accepted: 03/14/2021] [Indexed: 12/15/2022]
Abstract
Use of protein-based nanovehicles has been well recognized to be one of the most effective strategies to improve water dispersibility, stability and bioavailability of nutraceuticals or bioactive ingredients. Thanks to their health-benefiting effects and unique assembly behavior, soy proteins seem to be the perfect food proteins for fabricating nanovehicles in this regard. This review presents the state-of-art knowledge about the assembly of soy proteins into nano-architectures, e. g., nanoparticles, nanocomplexes or nanogels, induced by different physicochemical strategies and approaches. The strategies to trigger the assembly of soy proteins into a variety of nano-architectures are highlighted and critically reviewed. Such strategies include heating, enzymatic hydrolysis, pH shift, urea or ethanol treatment, reduction, and static high pressure treatment. The self-assembly behavior of soy proteins (native or denatured) is also reviewed. Besides the assembly of proteins alone, soy proteins can co-assemble with polysaccharides to form versatile nano-architectures, through different processes, e.g., heating or ultrasonication. Finally, recent progress in the development of assembled soy protein nano-architectures as nanovehicles for hydrophobic nutraceuticals is briefly summarized. With the fast increasing health awareness for natural and safe functional foods, this review is of crucial relevance for providing an important strategy to develop a kind of novel soy protein-based functional foods with dual-function health effects from soy proteins and nutraceuticals.
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8
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Gaina V, Nechifor M, Gaina C, Ursache O. Maleimides – a versatile platform for polymeric materials designed/tailored for high performance applications. POLYM-PLAST TECH MAT 2020. [DOI: 10.1080/25740881.2020.1811315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- V. Gaina
- Laboratory of Poliaddition and Photochemistry, “Petru Poni” Institute of Macromolecular Chemistry, Iasi, Romania
| | - M. Nechifor
- Laboratory of Poliaddition and Photochemistry, “Petru Poni” Institute of Macromolecular Chemistry, Iasi, Romania
| | - C. Gaina
- Laboratory of Poliaddition and Photochemistry, “Petru Poni” Institute of Macromolecular Chemistry, Iasi, Romania
| | - O. Ursache
- Laboratory of Poliaddition and Photochemistry, “Petru Poni” Institute of Macromolecular Chemistry, Iasi, Romania
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9
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Seeley JP, Cotlet M, Eagleton AM, Higashiya S, Welch JT. Resonance Energy Transfer in a Genetically Engineered Polypeptide Results in Unanticipated Fluorescence Intensity. Chemistry 2019; 25:961-965. [PMID: 30414202 DOI: 10.1002/chem.201804470] [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: 09/02/2018] [Revised: 11/08/2018] [Indexed: 11/11/2022]
Abstract
The fluorescence intensity of a C-terminal acceptor chromophore, N-(7-dimethylamino-4-methyl coumarin (DACM), increased proportionally with 280 nm irradiation of an increasing number of donor tryptophan residues located on a β-sheet forming polypeptide. The fluorescence intensity of the acceptor chromophore increased even as the length of the β-sheet edge approached 256 Å, well beyond the Förster radius for the tryptophan-acceptor chromophore pair. The folding of the peptides under investigation was verified by circular dichroism (CD) and deep UV resonance Raman experiments. Control experiments showed that the enhancement of DACM fluorescence occurred concomitantly with peptide folding. In other control experiments, the DACM fluorescence intensity of the solutions of tryptophan and DACM did not show any enhancement of DACM fluorescence with increasing tryptophan concentrations. Formation of fibrillar aggregates of the substrate peptides prepared for the fluorescence studies was undetectable by thioflavin T (ThT) fluorescence.
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Affiliation(s)
- Jason P Seeley
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave., Albany, NY, 12222, USA
| | - Mircea Cotlet
- Center for Functional Nanomaterials, Brookhaven National Laboratory, 735 Brookhaven Ave., Upton, NY, 11973, USA
| | - Aileen M Eagleton
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave., Albany, NY, 12222, USA
| | - Seiichiro Higashiya
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave., Albany, NY, 12222, USA
| | - John T Welch
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Ave., Albany, NY, 12222, USA
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10
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Erskine E, MacPhee CE, Stanley-Wall NR. Functional Amyloid and Other Protein Fibers in the Biofilm Matrix. J Mol Biol 2018; 430:3642-3656. [PMID: 30098341 PMCID: PMC6173796 DOI: 10.1016/j.jmb.2018.07.026] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 07/17/2018] [Accepted: 07/24/2018] [Indexed: 02/06/2023]
Abstract
Biofilms are ubiquitous in the natural and man-made environment. They are defined as microbes that are encapsulated in an extracellular, self-produced, biofilm matrix. Growing evidence from the genetic and biochemical analysis of single species biofilms has linked the presence of fibrous proteins to a functional biofilm matrix. Some of these fibers have been described as functional amyloid or amyloid-like fibers. Here we provide an overview of the biophysical and biological data for a wide range of protein fibers found in the biofilm matrix of Gram-positive and Gram-negative bacteria.
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Affiliation(s)
- Elliot Erskine
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Cait E MacPhee
- James Clerk Maxwell Building, School of Physics, University of Edinburgh, The Kings Buildings, Mayfield Road, Edinburgh, EH9 3JZ, UK.
| | - Nicola R Stanley-Wall
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
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11
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Mason TO, Shimanovich U. Fibrous Protein Self-Assembly in Biomimetic Materials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1706462. [PMID: 29883013 DOI: 10.1002/adma.201706462] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 03/28/2018] [Indexed: 05/22/2023]
Abstract
Protein self-assembly processes, by which polypeptides interact and independently form multimeric structures, lead to a wide array of different endpoints. Structures formed range from highly ordered molecular crystals to amorphous aggregates. Order arises in the system from a balance between many low-energy processes occurring due to a set of interactions between residues in a chain, between residues in different chains, and between solute and solvent. In Nature, self-assembling protein systems have evolved over millions of years to organize into supramolecular structures, optimized for specific functions, with this propensity determined by the sequence of their constituent amino acids, of which only 20 are encoded in DNA. The structural materials that arise from biological self-assembly can display remarkable mechanical properties, often as a result of hierarchical structure on the nano- and microscales, and much research has been devoted to mimicking and exploiting these properties for a variety of end uses. This work presents a review of a range of studies in which biological functions are effectively reproduced through the design of self-assembling fibrous protein systems.
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Affiliation(s)
- Thomas O Mason
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ulyana Shimanovich
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot, 7610001, Israel
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12
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Hilaire MR, Ding B, Mukherjee D, Chen J, Gai F. Possible Existence of α-Sheets in the Amyloid Fibrils Formed by a TTR 105-115 Mutant. J Am Chem Soc 2018; 140:629-635. [PMID: 29241000 PMCID: PMC5796419 DOI: 10.1021/jacs.7b09262] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Herein, we combine several methods to characterize the fibrils formed by a TTR105-115 mutant in which Leu111 is replaced by the unnatural amino acid aspartic acid 4-methyl ester. We find that this mutant peptide exhibits significantly different aggregation behavior than the wild-type peptide: (1) it forms fibrils with a much faster rate, (2) its fibrils lack the long-range helical twists observed in TTR105-115 fibrils, (3) its fibrils exhibit a giant far-UV circular dichroism signal, and (4) its fibrils give rise to an unusual amide I' band consisting of four distinct and sharp peaks. On the basis of these results and also several previous computational studies, we hypothesize that the fibrils formed by this TTR mutant peptide contain both β- and α-sheets.
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Affiliation(s)
- Mary Rose Hilaire
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Bei Ding
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
- The Ultrafast Optical Processes Laboratory, University of Pennsylvania, Philadelphia, PA 19104
| | | | - Jianxin Chen
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
- The Ultrafast Optical Processes Laboratory, University of Pennsylvania, Philadelphia, PA 19104
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
- The Ultrafast Optical Processes Laboratory, University of Pennsylvania, Philadelphia, PA 19104
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13
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Hanczyc P, Mikhailovsky A, Boyer DR, Sawaya MR, Heeger A, Eisenberg D. Ultrafast Time-Resolved Studies on Fluorescein for Recognition Strands Architecture in Amyloid Fibrils. J Phys Chem B 2018; 122:8-18. [DOI: 10.1021/acs.jpcb.7b07923] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - David R. Boyer
- Howard Hughes Medical Institute, UCLA-DOE Institute of Genomics and Proteomics, Los Angeles, California 90095-1570, United States
| | - Michael R. Sawaya
- Howard Hughes Medical Institute, UCLA-DOE Institute of Genomics and Proteomics, Los Angeles, California 90095-1570, United States
| | | | - David Eisenberg
- Howard Hughes Medical Institute, UCLA-DOE Institute of Genomics and Proteomics, Los Angeles, California 90095-1570, United States
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14
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Affiliation(s)
- Barbara L. DeButts
- Macromolecular Science and Engineering and Macromolecules Innovation InstituteVirginia TechBlacksburg Virginia 24061
- Biological Systems EngineeringVirginia Tech, 301 Human and Agricultural Biosciences Building 1, 1230 Washington St. SWBlacksburg Virginia 24061
| | - Laura E. Hanzly
- Biological Systems EngineeringVirginia Tech, 301 Human and Agricultural Biosciences Building 1, 1230 Washington St. SWBlacksburg Virginia 24061
| | - Justin R. Barone
- Macromolecular Science and Engineering and Macromolecules Innovation InstituteVirginia TechBlacksburg Virginia 24061
- Biological Systems EngineeringVirginia Tech, 301 Human and Agricultural Biosciences Building 1, 1230 Washington St. SWBlacksburg Virginia 24061
- Center for Soft Matter and Biological PhysicsVirginia TechBlacksburg Virginia 24061
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15
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Raynes JK, Day L, Crepin P, Horrocks MH, Carver JA. Coaggregation of κ-Casein and β-Lactoglobulin Produces Morphologically Distinct Amyloid Fibrils. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1603591. [PMID: 28146312 DOI: 10.1002/smll.201603591] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 12/20/2016] [Indexed: 06/06/2023]
Abstract
The unfolding, misfolding, and aggregation of proteins lead to a variety of structural species. One form is the amyloid fibril, a highly aligned, stable, nanofibrillar structure composed of β-sheets running perpendicular to the fibril axis. β-Lactoglobulin (β-Lg) and κ-casein (κ-CN) are two milk proteins that not only individually form amyloid fibrillar aggregates, but can also coaggregate under environmental stress conditions such as elevated temperature. The aggregation between β-Lg and κ-CN is proposed to proceed via disulfide bond formation leading to amorphous aggregates, although the exact mechanism is not known. Herein, using a range of biophysical techniques, it is shown that β-Lg and κ-CN coaggregate to form morphologically distinct co-amyloid fibrillar structures, a phenomenon previously limited to protein isoforms from different species or different peptide sequences from an individual protein. A new mechanism of aggregation is proposed whereby β-Lg and κ-CN not only form disulfide-linked aggregates, but also amyloid fibrillar coaggregates. The coaggregation of two structurally unrelated proteins into cofibrils suggests that the mechanism can be a generic feature of protein aggregation as long as the prerequisites for sequence similarity are met.
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Affiliation(s)
- Jared K Raynes
- CSIRO Agriculture and Food, Werribee, Victoria, 3031, Australia
| | - Li Day
- AgResearch Limited, Grasslands Research Centre, Tennent Drive, Palmerston North, 4442, New Zealand
| | - Pauline Crepin
- École Nationale Supérieure de Chimie, Biologie et Physique, Bordeaux, 33607, France
| | - Mathew H Horrocks
- Proteostasis and Disease Research Centre, School of Biological Sciences, University of Wollongong, Wollongong, New South Wales, 2522, Australia
| | - John A Carver
- Research School of Chemistry, The Australian National University, Acton, Australian Capital Territory, 2601, Australia
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16
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VandenAkker CC, Schleeger M, Bruinen AL, Deckert-Gaudig T, Velikov KP, Heeren RMA, Deckert V, Bonn M, Koenderink GH. Multimodal Spectroscopic Study of Amyloid Fibril Polymorphism. J Phys Chem B 2016; 120:8809-17. [DOI: 10.1021/acs.jpcb.6b05339] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Michael Schleeger
- Department
of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Anne L. Bruinen
- FOM Institute AMOLF, Science
Park 104, 1098 XG Amsterdam, The Netherlands
| | - Tanja Deckert-Gaudig
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Krassimir P. Velikov
- Soft
Condensed Matter, Debye Institute for Nanomaterials Science, Department
of Physics and Astronomy, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands
- Unilever R&D Vlaardingen, Olivier van Noortlaan 120, 3130 AC Vlaardingen, The Netherlands
| | - Ron M. A. Heeren
- FOM Institute AMOLF, Science
Park 104, 1098 XG Amsterdam, The Netherlands
| | - Volker Deckert
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, 07745 Jena, Germany
- Institute
for Physical Chemistry and Abbe Center of Photonics, University of Jena, Helmholtzweg 4, 07743 Jena, Germany
| | - Mischa Bonn
- Department
of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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17
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Knowles TPJ, Mezzenga R. Amyloid Fibrils as Building Blocks for Natural and Artificial Functional Materials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:6546-61. [PMID: 27165397 DOI: 10.1002/adma.201505961] [Citation(s) in RCA: 343] [Impact Index Per Article: 42.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/15/2016] [Indexed: 05/20/2023]
Abstract
Proteinaceous materials based on the amyloid core structure have recently been discovered at the origin of biological functionality in a remarkably diverse set of roles, and attention is increasingly turning towards such structures as the basis of artificial self-assembling materials. These roles contrast markedly with the original picture of amyloid fibrils as inherently pathological structures. Here we outline the salient features of this class of functional materials, both in the context of the functional roles that have been revealed for amyloid fibrils in nature, as well as in relation to their potential as artificial materials. We discuss how amyloid materials exemplify the emergence of function from protein self-assembly at multiple length scales. We focus on the connections between mesoscale structure and material function, and demonstrate how the natural examples of functional amyloids illuminate the potential applications for future artificial protein based materials.
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Affiliation(s)
- Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, United Kingdom
| | - Raffaele Mezzenga
- Department of Health Sciences and Technology, ETH Zurich, Switzerland
- Department of Materials Science, ETH Zurich, Switzerland
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18
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Krieg E, Bastings MMC, Besenius P, Rybtchinski B. Supramolecular Polymers in Aqueous Media. Chem Rev 2016; 116:2414-77. [DOI: 10.1021/acs.chemrev.5b00369] [Citation(s) in RCA: 527] [Impact Index Per Article: 65.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
| | | | - Pol Besenius
- Institute
of Organic Chemistry, Johannes Gutenberg-Universität Mainz, Mainz 55128, Germany
| | - Boris Rybtchinski
- Department
of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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19
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Ida M, Ando M, Adachi M, Tanaka A, Machida K, Hongo K, Mizobata T, Yamakawa MY, Watanabe Y, Nakashima K, Kawata Y. Structural basis of Cu, Zn-superoxide dismutase amyloid fibril formation involves interaction of multiple peptide core regions. J Biochem 2015; 159:247-60. [PMID: 26319711 DOI: 10.1093/jb/mvv091] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 08/24/2015] [Indexed: 12/29/2022] Open
Abstract
Cu, Zn-superoxide dismutase (SOD1), an enzyme implicated in the progression of familial amyotrophic lateral sclerosis (fALS), forms amyloid fibrils under certain experimental conditions. As part of our efforts to understand ALS pathogenesis, in this study we found that reduction of the intramolecular disulfide bond destabilized the tertiary structure of metal free wild-type SOD1 and greatly enhanced fibril formation in vitro. We also identified fibril core peptides that are resistant to protease digestion by using mass spectroscopy and Edman degradation analyses. Three regions dispersed throughout the sequence were detected as fibril core sequences of SOD1. Interestingly, by using three synthetic peptides that correspond to these identified regions, we determined that each region was capable of fibril formation, either alone or in a mixture containing multiple peptides. It was also revealed that by reducing the disulfide bond and causing a decrease in the structural stability, the amyloid fibril formation of a familial mutant SOD1 G93A was accelerated even under physiological conditions. These results demonstrate that by destabilizing the structure of SOD1 by removing metal ions and breaking the intramolecular disulfide bridge, multiple fibril-forming core regions are exposed, which then interact with each another and form amyloid fibrils under physiological conditions.
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Affiliation(s)
- Masataka Ida
- Department of Chemistry and Biotechnology, Graduate School of Engineering
| | - Mizuho Ando
- Department of Chemistry and Biotechnology, Graduate School of Engineering
| | - Masayuki Adachi
- Department of Chemistry and Biotechnology, Graduate School of Engineering
| | - Asumi Tanaka
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science and
| | - Kodai Machida
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science and
| | - Kunihiro Hongo
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science and
| | - Tomohiro Mizobata
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science and
| | - Miho Yoshida Yamakawa
- Division of Neurology, Department of Brain and Neurosciences, Faculty of Medicine, Tottori University, Tottori, Japan
| | - Yasuhiro Watanabe
- Division of Neurology, Department of Brain and Neurosciences, Faculty of Medicine, Tottori University, Tottori, Japan
| | - Kenji Nakashima
- Division of Neurology, Department of Brain and Neurosciences, Faculty of Medicine, Tottori University, Tottori, Japan
| | - Yasushi Kawata
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science and
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20
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Sonzini S, Jones ST, Walsh Z, Scherman OA. Simple fluorinated moiety insertion on Aβ 16-23 peptide for stain-free TEM imaging. Analyst 2015; 140:2735-40. [PMID: 25705744 DOI: 10.1039/c4an02278e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Peptide aggregation and fibre formation are one of the major underlying causes of several neurodegenerative disorders such as Alzheimer's disease. During the past decades the characterisation of these fibres has been widely studied in an attempt to further understand the nature of the related diseases and in an effort to develop treatments. Transmission electron microscopy (TEM) is one of the most commonly used techniques to identify these fibres, but requires the use of a radioactive staining agent. The procedure we report overcomes this drawback through simple addition of a fluorinated moiety to a short Amyloid β sequence via solid phase peptide synthesis (SPPS). This method is synthetically straightforward, widely applicable to different aggregation-prone sequences and, above all, allows for stain-free TEM imaging with improved quality compared to standard imaging procedures. The presence of the fluorinated moiety does not cause major changes in the fibre structure or aggregation, but rather serves to dissipate the microscope's electron beam, thus allowing for high contrast and straightforward imaging by TEM.
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Affiliation(s)
- Silvia Sonzini
- Melville Laboratory for Polymer Chemistry, Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK.
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21
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Cueno ME, Nagano K, Imai K, Tamura M, Yoshimura F, Ochiai K. Ab initio modeling approach towards establishing the structure and docking orientation of the Porphyromonas gingivalis FimA. J Mol Graph Model 2015; 55:65-71. [DOI: 10.1016/j.jmgm.2014.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 10/22/2014] [Accepted: 11/07/2014] [Indexed: 01/30/2023]
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22
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Ponnumallayan P, Fee CJ. Reversible and rapid pH-regulated self-assembly of a poly(ethylene glycol)-peptide bioconjugate. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:14250-6. [PMID: 25375076 DOI: 10.1021/la502360k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The use of external triggers to manipulate the secondary structure of self-assembling peptides conjugated to flexible synthetic polymers is a challenging problem, particularly in terms of reversibility. Here, we demonstrate, for the first time, sustained rapid and reversible, pH-regulated self-assembly of the peptide ELELELELELF (EL-5F) and its conjugates with 2 and 5 kDa poly(ethylene glycol) (EL-5F-PEG-2K and EL-5F-PEG-5K). Circular dichroism indicated the formation of β-sheet structures at pH < 5.9, 5.8, and 5.4 and disassembly to random coils above those pH values for EL-5F, EL-5F-PEG-2K, and EL-5F-PEG-5K, respectively. β-sheets were confirmed by the thioflavin T assay, while transmission electron microscopy revealed the existence of extended fibrillar structures below the above pH values. pH-induced secondary structure conversion was reproducible for over 15 cycles, even at salt concentrations of up to 200 mM NaCl, and was quantitatively related to the pH. Self-supporting hydrogelation after self-assembly was observed at concentrations as low as 0.2 wt %, which is 15-fold lower than previously reported concentrations. This simple approach to mediate reversible self-assembly of EL-5F-PEG bioconjugates is expected to offer novel functionality relevant to drug delivery and bioseparation systems.
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Affiliation(s)
- Prasanna Ponnumallayan
- Department of Chemical and Process Engineering and the Biomolecular Interaction Centre, University of Canterbury , Private Bag 4800, Christchurch, New Zealand 8041
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23
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Tabbasum K, Rao CP. Zn2+, Cd2+and Cu2+mediated formation of amyloid like fibrils by the monomers of β-sheet rich peanut agglutinin. RSC Adv 2014. [DOI: 10.1039/c4ra04186k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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24
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Tycko R. Physical and structural basis for polymorphism in amyloid fibrils. Protein Sci 2014; 23:1528-39. [PMID: 25179159 DOI: 10.1002/pro.2544] [Citation(s) in RCA: 176] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 08/28/2014] [Accepted: 08/29/2014] [Indexed: 12/24/2022]
Abstract
As our understanding of the molecular structures of amyloid fibrils has matured over the past 15 years, it has become clear that, while amyloid fibrils do have well-defined molecular structures, their molecular structures are not uniquely determined by the amino acid sequences of their constituent peptides and proteins. Self-propagating molecular-level polymorphism is a common phenomenon. This article reviews current information about amyloid fibril structures, variations in molecular structures that underlie amyloid polymorphism, and physical considerations that explain the development and persistence of amyloid polymorphism. Much of this information has been obtained through solid state nuclear magnetic resonance measurements. The biological significance of amyloid polymorphism is also discussed briefly. Although this article focuses primarily on studies of fibrils formed by amyloid-β peptides, the same principles apply to many amyloid-forming peptides and proteins.
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Affiliation(s)
- Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892-0520
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25
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Sarell CJ, Karamanos TK, White SJ, Bunka DHJ, Kalverda AP, Thompson GS, Barker AM, Stockley PG, Radford SE. Distinguishing closely related amyloid precursors using an RNA aptamer. J Biol Chem 2014; 289:26859-26871. [PMID: 25100729 PMCID: PMC4175327 DOI: 10.1074/jbc.m114.595066] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Although amyloid fibrils assembled in vitro commonly involve a single protein, fibrils formed in vivo can contain multiple protein sequences. The amyloidogenic protein human β2-microglobulin (hβ2m) can co-polymerize with its N-terminally truncated variant (ΔN6) in vitro to form hetero-polymeric fibrils that differ from their homo-polymeric counterparts. Discrimination between the different assembly precursors, for example by binding of a biomolecule to one species in a mixture of conformers, offers an opportunity to alter the course of co-assembly and the properties of the fibrils formed. Here, using hβ2m and its amyloidogenic counterpart, ΔΝ6, we describe selection of a 2'F-modified RNA aptamer able to distinguish between these very similar proteins. SELEX with a N30 RNA pool yielded an aptamer (B6) that binds hβ2m with an EC50 of ∼200 nM. NMR spectroscopy was used to assign the (1)H-(15)N HSQC spectrum of the B6-hβ2m complex, revealing that the aptamer binds to the face of hβ2m containing the A, B, E, and D β-strands. In contrast, binding of B6 to ΔN6 is weak and less specific. Kinetic analysis of the effect of B6 on co-polymerization of hβ2m and ΔN6 revealed that the aptamer alters the kinetics of co-polymerization of the two proteins. The results reveal the potential of RNA aptamers as tools for elucidating the mechanisms of co-assembly in amyloid formation and as reagents able to discriminate between very similar protein conformers with different amyloid propensity.
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Affiliation(s)
- Claire J Sarell
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Theodoros K Karamanos
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Simon J White
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - David H J Bunka
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Arnout P Kalverda
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Gary S Thompson
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Amy M Barker
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom.
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26
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Effects of additional fibrils on structural and rheological properties of rice bran albumin solution and gel. Eur Food Res Technol 2014. [DOI: 10.1007/s00217-014-2294-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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27
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Udomprasert A, Bongiovanni MN, Sha R, Sherman WB, Wang T, Arora PS, Canary JW, Gras SL, Seeman NC. Amyloid fibrils nucleated and organized by DNA origami constructions. NATURE NANOTECHNOLOGY 2014; 9:537-41. [PMID: 24880222 PMCID: PMC4082467 DOI: 10.1038/nnano.2014.102] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 04/23/2014] [Indexed: 05/24/2023]
Abstract
Amyloid fibrils are ordered, insoluble protein aggregates that are associated with neurodegenerative conditions such as Alzheimer's disease. The fibrils have a common rod-like core structure, formed from an elongated stack of β-strands, and have a rigidity similar to that of silk (Young's modulus of 0.2-14 GPa). They also exhibit high thermal and chemical stability and can be assembled in vitro from short synthetic non-disease-related peptides. As a result, they are of significant interest in the development of self-assembled materials for bionanotechnology applications. Synthetic DNA molecules have previously been used to form intricate structures and organize other materials such as metal nanoparticles and could in principle be used to nucleate and organize amyloid fibrils. Here, we show that DNA origami nanotubes can sheathe amyloid fibrils formed within them. The fibrils are built by modifying the synthetic peptide fragment corresponding to residues 105-115 of the amyloidogenic protein transthyretin and a DNA origami construct is used to form 20-helix DNA nanotubes with sufficient space for the fibrils inside. Once formed, the fibril-filled nanotubes can be organized onto predefined two-dimensional platforms via DNA-DNA hybridization interactions.
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Affiliation(s)
| | - Marie N. Bongiovanni
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - William B. Sherman
- Bard High School Early College - Queens, 30-20 Thomson Ave., Queens, NY 11101, USA
| | - Tong Wang
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Paramjit S. Arora
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - James W. Canary
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Sally L. Gras
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Nadrian C. Seeman
- Department of Chemistry, New York University, New York, NY 10003, USA
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28
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Lai J, Fu W, Zhu L, Guo R, Liang D, Li Z, Huang Y. Fibril aggregates formed by a glatiramer-mimicking random copolymer of amino acids. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:7221-7226. [PMID: 24882278 DOI: 10.1021/la501622t] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Amyloid formation is now considered a universal and intrinsic property of all proteins, irrespective of their sequences. Therefore, it is interesting to see whether random copolymers of amino acids can also form amyloid aggregates. Here we use a copolymer of 4 amino acids, mimicking the clinically used drug Glatiramer, and demonstrate that it does form amyloid-like fibrils in the aqueous solution despite its random sequence structure. The fibrillar aggregates show an alanine-rich β-sheet secondary structure, proving the high tolerance of amyloid aggregates to the sequence irregularity in poly(amino acid)s, and suggesting the potential application of random copolymers as amyloid materials.
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Affiliation(s)
- Jingjing Lai
- Key Laboratory of Advanced Materials (MOE), Department of Chemical Engineering, Tsinghua University , Beijing 100084, China
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29
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Moscarelli P, Boraldi F, Bochicchio B, Pepe A, Salvi AM, Quaglino D. Structural characterization and biological properties of the amyloidogenic elastin-like peptide (VGGVG)3. Matrix Biol 2014; 36:15-27. [DOI: 10.1016/j.matbio.2014.03.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 03/18/2014] [Accepted: 03/19/2014] [Indexed: 10/25/2022]
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30
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Thangakani AM, Kumar S, Nagarajan R, Velmurugan D, Gromiha MM. GAP: towards almost 100 percent prediction for β-strand-mediated aggregating peptides with distinct morphologies. Bioinformatics 2014; 30:1983-90. [DOI: 10.1093/bioinformatics/btu167] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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31
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Abstract
Amyloid fibrils with cross-β spine basic architectures are prevalent and stable forms of peptides and proteins. Recent research has provided significant contributions to our understanding of the mechanisms of fibril formation and to the surprising diversity and persistence of structural polymorphism in amyloid fibrils. There have also been successful demonstrations of how molecules can be engineered to inhibit unwanted amyloid formation by different mechanisms. Future research in these areas will include investigations of mechanisms for primary nucleation and the structure of oligomeric intermediates, the general role of secondary nucleation events (autocatalysis), elucidation of the mechanisms and implications of preservation of structural morphology in amyloid propagation, and research into the largely unexplored phenomenon of cross-seeding, by which amyloid fibrils of one species induce the formation of amyloid by another species.
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Affiliation(s)
- Torleif Härd
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences (SLU), Box 7015, SE-750 07 Uppsala, Sweden
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32
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Ridgley DM, Freedman BG, Lee PW, Barone JR. Genetically encoded self-assembly of large amyloid fibers. Biomater Sci 2014; 2:560-566. [DOI: 10.1039/c3bm60223k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Experimental results demonstrate that large amyloid fibers can be engineered at the DNA level, spanning four orders of magnitude.
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Affiliation(s)
- D. M. Ridgley
- Biological Systems Engineering
- Virginia Tech
- Blacksburg, USA
| | - B. G. Freedman
- Biological Systems Engineering
- Virginia Tech
- Blacksburg, USA
| | - P. W. Lee
- Biological Systems Engineering
- Virginia Tech
- Blacksburg, USA
| | - J. R. Barone
- Biological Systems Engineering
- Virginia Tech
- Blacksburg, USA
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33
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Ridgley DM, Claunch EC, Barone JR. Characterization of large amyloid fibers and tapes with Fourier transform infrared (FT-IR) and Raman spectroscopy. APPLIED SPECTROSCOPY 2013; 67:1417-1426. [PMID: 24359656 DOI: 10.1366/13-07059] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Amyloids are self-assembled protein structures implicated in a host of neurodegenerative diseases. Organisms can also produce "functional amyloids" to perpetuate life, and these materials serve as models for robust biomaterials. Amyloids are typically studied using fluorescent dyes, Fourier transform infrared (FT-IR), or Raman spectroscopy analysis of the protein amide I region, and X-ray diffraction (XRD) because the self-assembled β-sheet secondary structure of the amyloid can be easily identified with these techniques. Here, FT-IR and Raman spectroscopy analyses are described to characterize amyloid structures beyond just identification of the β-sheet structure. It has been shown that peptide mixtures can self-assemble into nanometer-sized amyloid structures that then continue to self-assemble to the micrometer scale. The resulting structures are flat tapes of low rigidity or cylinders of high rigidity depending on the peptides in the mixture. By monitoring the aggregation of peptides in solution using FT-IR spectroscopy, it is possible to identify specific amino acids implicated in β-sheet formation and higher order self-assembly. It is also possible to predict the final tape or cylinder morphology and gain insight into the structure's physical properties based on observed intermolecular interactions during the self-assembly process. Tapes and cylinders are shown to both have a similar core self-assembled β-sheet structure. Soft tapes also have weak hydrophobic interactions between alanine, isoleucine, leucine, and valine that facilitate self-assembly. Rigid cylinders have similar hydrophobic interactions that facilitate self-assembly and also have extensive hydrogen bonding between glutamines. Raman spectroscopy performed on the dried tapes and fibers shows the persistence of these interactions. The spectroscopic analyses described could be generalized to other self-assembling amyloid systems to explain property and morphological differences.
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Affiliation(s)
- Devin M Ridgley
- Biological Systems Engineering Department, Virginia Tech, 303 Seitz Hall, Blacksburg, VA 24061 USA
| | - Elizabeth C Claunch
- Biological Systems Engineering Department, Virginia Tech, 303 Seitz Hall, Blacksburg, VA 24061 USA
| | - Justin R Barone
- Biological Systems Engineering Department, Virginia Tech, 303 Seitz Hall, Blacksburg, VA 24061 USA
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34
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Sarell CJ, Stockley PG, Radford SE. Assessing the causes and consequences of co-polymerization in amyloid formation. Prion 2013; 7:359-68. [PMID: 24025483 PMCID: PMC4134340 DOI: 10.4161/pri.26415] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
How, and why, different proteins form amyloid fibrils is most often studied in vitro using a single purified protein sequence. However, many amyloid diseases involve co-aggregation of different protein species, including proteins with/without post-translational modifications (e.g., different strains of PrP), proteins of different length (e.g., β₂-microglobulin and ΔN6, Aβ40, and Aβ42), sequence variants (e.g., Aβ and Aβ(ARC)), and proteins from different organisms (e.g., bovine PrP and human PrP). The consequences of co-aggregation of different proteins upon the structure, stability, species transmission and toxicity of the resulting amyloid aggregates is discussed here, including the role of co-aggregation in expanding the repertoire of oligomeric and fibrillar structures and how this can affect their biological and biophysical properties.
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Affiliation(s)
- Claire J Sarell
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology; University of Leeds; Leeds, UK
| | - Peter G Stockley
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology; University of Leeds; Leeds, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology; University of Leeds; Leeds, UK
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35
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Liu J, Tang CH. Heat-induced fibril assembly of vicilin at pH2.0: Reaction kinetics, influence of ionic strength and protein concentration, and molecular mechanism. Food Res Int 2013. [DOI: 10.1016/j.foodres.2012.12.049] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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36
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Morriss-Andrews A, Bellesia G, Shea JE. β-sheet propensity controls the kinetic pathways and morphologies of seeded peptide aggregation. J Chem Phys 2013; 137:145104. [PMID: 23061868 DOI: 10.1063/1.4755748] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The effect of seeds in templating the morphology of peptide aggregates is examined using molecular dynamics simulations and a coarse-grained peptide representation. Varying the nature of the aggregate seed between β-sheet, amorphous, and β-barrel seeds leads to different aggregation pathways and to morphologically different aggregates. Similar effects are seen by varying the β-sheet propensity of the free peptides. For a fibrillar seed and free peptides of high β-sheet propensity, fibrillar growth occurred by means of direct attachment (without structural rearrangement) of free individual peptides and small ordered oligomers onto the seed. For a fibrillar seed and free peptides of low β-sheet propensity, fibrillar growth occurred through a dock-lock mechanism, in which the free peptides first docked onto the seed, and then locked on, extending and aligning to join the fibril. Amorphous seeds absorbed free peptides into themselves indiscriminately, with any fibrillar rearrangement subsequent to this absorption by means of a condensation-ordering transition. Although the mechanisms observed by varying peptide β-sheet propensity are diverse, the initial pathways can always be broken down into the following steps: (i) the free peptides diffuse in the bulk and attach individually to the seed; (ii) the free peptides diffuse and aggregate among themselves; (iii) the free peptide oligomers collide with the seed; and (iv) the free oligomers merge with the seed and rearrange in a manner dependent on the backbone flexibility of both the free and seed peptides. Our simulations indicate that it is possible to sequester peptides from amorphous aggregates into fibrils, and also that aggregate morphology (and thus cytoxicity) can be controlled by introducing seeds of aggregate-compatible peptides with differing β-sheet propensities into the system.
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Affiliation(s)
- Alex Morriss-Andrews
- Department of Physics, University of California Santa Barbara, Santa Barbara, California 93106, USA
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37
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Ridgley DM, Barone JR. Evolution of the amyloid fiber over multiple length scales. ACS NANO 2013; 7:1006-1015. [PMID: 23268732 DOI: 10.1021/nn303489a] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The amyloid is a natural self-assembled peptide material comparable in specific stiffness to spider silk and steel. Throughout the literature there are many studies of the nanometer-sized amyloid fibril; however, peptide mixtures are capable of self-assembling beyond the nanometer scale into micrometer-sized fibers. Here, atomic force microscopy (AFM) and scanning electron microscopy (SEM) are used to observe the self-assembly of the peptide mixtures in solution for 20 days and the fibers upon drying. Beyond the nanometer scale, self-assembling fibers differentiate into two morphologies, cylindrical or rectangular cross-section, depending on peptide properties. Microscopic observations delineate a four stage self-assembly mechanism: (1) protofibril (2-4 nm high and 15-30 nm wide) formation; (2) protofibril aggregation into fibrils 6-10 nm high and 60-120 nm wide; (3) fibril aggregation into large fibrils and morphological differentiation where large fibrils begin to resemble the final fiber morphology of cylinders (WG peptides) or tapes (Gd:My peptides). WG large fibrils are 50 nm high and 480 nm wide and Gd:My large fibrils are 10 nm high and 150 nm wide; (4) micrometer-sized fiber formation upon drying at 480 h resulting in 18.0 μm diameter cylindrical fibers (WG peptides) and 14.0 μm wide and 6.0 μm thick flat tapes (Gd:My peptides). Evolution of the large fiber morphology can be rationalized on the basis of the peptide properties.
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Affiliation(s)
- Devin M Ridgley
- Biological Systems Engineering Department, Virginia Tech, 303 Seitz Hall, Blacksburg, Virginia 24061, USA
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38
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Hartman K, Brender JR, Monde K, Ono A, Evans M, Popovych N, Chapman MR, Ramamoorthy A. Bacterial curli protein promotes the conversion of PAP248-286 into the amyloid SEVI: cross-seeding of dissimilar amyloid sequences. PeerJ 2013; 1:e5. [PMID: 23638387 PMCID: PMC3629062 DOI: 10.7717/peerj.5] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 12/05/2012] [Indexed: 01/02/2023] Open
Abstract
Fragments of prostatic acid phosphatase (PAP248-286) in human semen dramatically increase HIV infection efficiency by increasing virus adhesion to target cells. PAP248-286 only enhances HIV infection in the form of amyloid aggregates termed SEVI (Semen Enhancer of Viral Infection), however monomeric PAP248-286 aggregates very slowly in isolation. It has therefore been suggested that SEVI fiber formation in vivo may be promoted by exogenous factors. We show here that a bacterially-produced extracellular amyloid (curli or Csg) acts as a catalytic agent for SEVI formation from PAP248-286 at low concentrations in vitro, producing fibers that retain the ability to enhance HIV (Human Immunodeficiency Virus) infection. Kinetic analysis of the cross-seeding effect shows an unusual pattern. Cross-seeding PAP248-286 with curli only moderately affects the nucleation rate while significantly enhancing the growth of fibers from existing nuclei. This pattern is in contrast to most previous observations of cross-seeding, which show cross-seeding partially bypasses the nucleation step but has little effect on fiber elongation. Seeding other amyloidogenic proteins (IAPP (islet amyloid polypeptide) and Aβ1-40) with curli showed varied results. Curli cross-seeding decreased the lag-time of IAPP amyloid formation but strongly inhibited IAPP elongation. Curli cross-seeding exerted a complicated concentration dependent effect on Aβ1-40 fibrillogenesis kinetics. Combined, these results suggest that the interaction of amyloidogenic proteins with preformed fibers of a different type can take a variety of forms and is not limited to epitaxial nucleation between proteins of similar sequence. The ability of curli fibers to interact with proteins of dissimilar sequences suggests cross-seeding may be a more general phenomenon than previously supposed.
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Affiliation(s)
- Kevin Hartman
- Department of Chemistry, University of Michigan, USA
- Department of Biophysics, University of Michigan, USA
| | - Jeffrey R. Brender
- Department of Chemistry, University of Michigan, USA
- Department of Biophysics, University of Michigan, USA
| | - Kazuaki Monde
- Department of Microbiology and Immunology, University of Michigan Medical School, USA
| | - Akira Ono
- Department of Microbiology and Immunology, University of Michigan Medical School, USA
| | - Margery L. Evans
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, USA
| | - Nataliya Popovych
- Department of Chemistry, University of Michigan, USA
- Department of Biophysics, University of Michigan, USA
| | - Matthew R. Chapman
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, USA
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry, University of Michigan, USA
- Department of Biophysics, University of Michigan, USA
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39
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Sarell CJ, Woods LA, Su Y, Debelouchina GT, Ashcroft AE, Griffin RG, Stockley PG, Radford SE. Expanding the repertoire of amyloid polymorphs by co-polymerization of related protein precursors. J Biol Chem 2013; 288:7327-37. [PMID: 23329840 PMCID: PMC3591641 DOI: 10.1074/jbc.m112.447524] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Amyloid fibrils can be generated from proteins with diverse sequences and folds. Although amyloid fibrils assembled in vitro commonly involve a single protein precursor, fibrils formed in vivo can contain more than one protein sequence. How fibril structure and stability differ in fibrils composed of single proteins (homopolymeric fibrils) from those generated by co-polymerization of more than one protein sequence (heteropolymeric fibrils) is poorly understood. Here we compare the structure and stability of homo and heteropolymeric fibrils formed from human β2-microglobulin and its truncated variant ΔN6. We use an array of approaches (limited proteolysis, magic angle spinning NMR, Fourier transform infrared spectroscopy, and fluorescence) combined with measurements of thermodynamic stability to characterize the different fibril types. The results reveal fibrils with different structural properties, different side-chain packing, and strikingly different stabilities. These findings demonstrate how co-polymerization of related precursor sequences can expand the repertoire of structural and thermodynamic polymorphism in amyloid fibrils to an extent that is greater than that obtained by polymerization of a single precursor alone.
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Affiliation(s)
- Claire J Sarell
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
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40
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Frustration in the energy landscapes of multidomain protein misfolding. Proc Natl Acad Sci U S A 2013; 110:1680-5. [PMID: 23319605 DOI: 10.1073/pnas.1222130110] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Frustration from strong interdomain interactions can make misfolding a more severe problem in multidomain proteins than in single-domain proteins. On the basis of bioinformatic surveys, it has been suggested that lowering the sequence identity between neighboring domains is one of nature's solutions to the multidomain misfolding problem. We investigate folding of multidomain proteins using the associative-memory, water-mediated, structure and energy model (AWSEM), a predictive coarse-grained protein force field. We find that reducing sequence identity not only decreases the formation of domain-swapped contacts but also decreases the formation of strong self-recognition contacts between β-strands with high hydrophobic content. The ensembles of misfolded structures that result from forming these amyloid-like interactions are energetically disfavored compared with the native state, but entropically favored. Therefore, these ensembles are more stable than the native ensemble under denaturing conditions, such as high temperature. Domain-swapped contacts compete with self-recognition contacts in forming various trapped states, and point mutations can shift the balance between the two types of interaction. We predict that multidomain proteins that lack these specific strong interdomain interactions should fold reliably.
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41
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Abstract
Many bacteria produce protein fibrils that are structurally analogous to those associated with protein misfolding diseases such as Alzheimer's disease. However, unlike fibrils associated with disease, bacterial amyloids have beneficial functions including conferring stability to biofilms, regulating development or imparting virulence. In the present review, we consider what makes amyloid fibrils so suitable for these roles and discuss recent developments in the study of bacterial amyloids, in particular the chaplins from Streptomyces coelicolor. We also consider the broader impact of the study of bacterial amyloids on our understanding of infection and disease and on developments in nanotechnology.
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42
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Brandenburg E, Berlepsch HV, Leiterer J, Emmerling F, Koksch B. Formation of α-helical nanofibers by mixing β-structured and α-helical coiled coil peptides. Biomacromolecules 2012; 13:3542-51. [PMID: 22946440 DOI: 10.1021/bm300882d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The helical coiled coil is a well-studied folding motif that can be used for the design of nanometer-sized bioinspired fibrous structures with potential applications as functional materials. A two-component system of coiled coil based model peptides is investigated, which forms, under acidic conditions, uniform, hundreds of nanometers long, and ~2.6 nm thick trimeric α-helical fibers. In the absence of the other component and under the same solvent conditions, one model peptide forms β-sheet-rich amyloid fibrils and the other forms stable trimeric α-helical coiled coils, respectively. These observations reveal that the complementary interactions driving helical folding are much stronger here than those promoting the intermolecular β-sheet formation. The results of this study are important in the context of amyloid inhibition but also open up new avenues for the design of novel fibrous peptidic materials.
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Affiliation(s)
- Enrico Brandenburg
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
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43
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Solar M, Buehler MJ. Comparative analysis of nanomechanics of protein filaments under lateral loading. NANOSCALE 2012; 4:1177-1183. [PMID: 22193831 DOI: 10.1039/c1nr11260k] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Using a combination of explicit solvent atomistic simulation and continuum theory, here we study the lateral deformation mechanics of three distinct protein structures: an amyloid fibril, a beta helix, and an alpha helix. We find that the two β-sheet rich structures - amyloid fibril and beta helix, with persistence lengths on the order of μm - are well described by continuum mechanical theory, but differ in the degree to which shear deformation affects the overall bending behavior. The alpha helical protein structure, however, with a persistence length on the order of one nanometer, does not conform to the continuum theory and its deformation is dominated by entropic elasticity due to significant fluctuations. This study provides fundamental insight into the nanomechanics of widely found protein motifs and insight into molecular-scale deformation mechanisms, as well as quantitative estimates of Young's modulus and shear modulus in agreement with experimental results.
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Affiliation(s)
- Max Solar
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA, USA
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44
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Fändrich M. Oligomeric intermediates in amyloid formation: structure determination and mechanisms of toxicity. J Mol Biol 2012; 421:427-40. [PMID: 22248587 DOI: 10.1016/j.jmb.2012.01.006] [Citation(s) in RCA: 281] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 01/03/2012] [Accepted: 01/05/2012] [Indexed: 11/30/2022]
Abstract
Oligomeric intermediates are non-fibrillar polypeptide assemblies that occur during amyloid fibril formation and that are thought to underlie the aetiology of amyloid diseases, such as Alzheimer's disease, Parkinson's disease and Huntington's disease. Focusing primarily on the oligomeric states formed from Alzheimer's disease β-amyloid (Aβ) peptide, this review will make references to other polypeptide systems, highlighting common principles or sequence-specific differences. The covered topics include the structural properties and polymorphism of oligomers, the biophysical mechanism of peptide self-assembly and its role for pathogenicity in amyloid disease. Oligomer-dependent toxicity mechanisms will be explained along with recently emerging possibilities of interference.
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Affiliation(s)
- Marcus Fändrich
- Max-Planck Research Unit for Enzymology of Protein Folding and Martin Luther University Halle-Wittenberg, Weinbergweg 22, 01620 Halle (Saale), Germany.
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45
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Lassé M, Gerrard JA, Pearce FG. Aggregation and fibrillogenesis of proteins not associated with disease: a few case studies. Subcell Biochem 2012; 65:253-270. [PMID: 23225007 DOI: 10.1007/978-94-007-5416-4_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
While amyloid structures have been well characterised in a medical context, there is increasing interest in studying amyloid-like aggregates in other areas, such as food science and nanomaterials. Several proteins relevant to food processing, including serum albumen, lactoglobulin, lysozyme, ovalbumin, casein, and soy protein isolate have been shown to form fibrillar structures under both physiological and non-physiological conditions. These structures are likely to contribute to the structural characteristics of the final food product. In a biotechnological context, proteins such as insulin and eye lens crystallins can be induced to form amyloid structures which can subsequently be used in biotechnology. One example of this is the use of amyloid fibrils as a scaffold for the immobilisation of enzymes. Another current interest in amyloid fibrils is as a storage form for peptide hormones, including insulin, glucagon and calcitonin. Here, we give an overview of a selection of well characterised proteins that have been studied outside the context of disease.
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Affiliation(s)
- Moritz Lassé
- Biomolecular Interaction Center and School of Biological Sciences, University of Canterbury, Private Bag 4800, 8020, Christchurch, New Zealand,
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46
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Topping TB, Gloss LM. The impact of solubility and electrostatics on fibril formation by the H3 and H4 histones. Protein Sci 2011; 20:2060-73. [PMID: 21953551 DOI: 10.1002/pro.743] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Revised: 09/01/2011] [Accepted: 09/08/2011] [Indexed: 12/15/2022]
Abstract
The goal of this study was to examine fibril formation by the heterodimeric eukaryotic histones (H2A-H2B and H3-H4) and homodimeric archaeal histones (hMfB and hPyA1). The histone fold dimerization motif is an obligatorily domain-swapped structure comprised of two fused helix:β-loop:helix motifs. Domain swapping has been proposed as a mechanism for the evolution of protein oligomers as well as a means to form precursors in the formation of amyloid-like fibrils. Despite sharing a common fold, the eukaryotic histones of the core nucleosome and archaeal histones fold by kinetic mechanisms of differing complexity with transient population of partially folded monomeric and/or dimeric species. No relationship was apparent between fibrillation propensity and equilibrium stability or population of kinetic intermediates. Only H3 and H4, as isolated monomers and as a heterodimer, readily formed fibrils at room temperature, and this propensity correlates with the significantly lower solubility of these polypeptides. The fibrils were characterized by ThT fluorescence, FTIR, and far-UV CD spectroscopies and electron microscopy. The helical histone fold comprises the protease-resistant core of the fibrils, with little or no protease protection of the poorly structured N-terminal tails. The highly charged tails inhibit fibrillation through electrostatic repulsion. Kinetic studies indicate that H3 and H4 form a co-fibril, with simultaneous incorporation of both histones. The potential impact of H3 and H4 fibrillation on the cytotoxicity of extracellular histones and α-synuclein-mediated neurotoxicity and fibrillation is considered.
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Affiliation(s)
- Traci B Topping
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-7520, USA
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47
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Castro CE, Dong J, Boyce MC, Lindquist S, Lang MJ. Physical properties of polymorphic yeast prion amyloid fibers. Biophys J 2011; 101:439-48. [PMID: 21767497 DOI: 10.1016/j.bpj.2011.06.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 05/17/2011] [Accepted: 06/06/2011] [Indexed: 10/18/2022] Open
Abstract
Amyloid fibers play important roles in many human diseases and natural biological processes and have immense potential as novel nanomaterials. We explore the physical properties of polymorphic amyloid fibers formed by yeast prion protein Sup35. Amyloid fibers that conferred distinct prion phenotypes ([PSI(+)]), strong (S) versus weak (W) nonsense suppression, displayed different physical properties. Both S[PSI(+)] and W[PSI(+)] fibers contained structural inhomogeneities, specifically local regions of static curvature in S[PSI(+)] fibers and kinks and self-cross-linking in W[PSI(+)] fibers. Force-extension experiments with optical tweezers revealed persistence lengths of 1.5 μm and 3.3 μm and axial stiffness of 5600 pN and 9100 pN for S[PSI(+)] and W[PSI(+)] fibers, respectively. Thermal fluctuation analysis confirmed the twofold difference in persistence length between S[PSI(+)] and W[PSI(+)] fibers and revealed a torsional stiffness of kinks and cross-links of ~100-200 pN·nm/rad.
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Affiliation(s)
- Carlos E Castro
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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48
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Wang JM, Yang XQ, Yin SW, Yuan DB, Xia N, Qi JR. Growth kinetics of amyloid-like fibrils derived from individual subunits of soy β-conglycinin. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2011; 59:11270-7. [PMID: 21919519 DOI: 10.1021/jf202541m] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The amyloid-like fibrillation of soy β-conglycinin subunits (α, α', and β) upon heating (0-20 h) at 85 °C and pH 2.0 was characterized using dynamic light scattering, circular dichroism (CD), binding to amyloid dyes (Thioflavin T and Congo red), and atomic force microscopy. The fibrillation of all three subunits was accompanied by progressive polypeptide hydrolysis. The hydrolysis behaviors, fibrillation kinetics, and morphologies of amyloid-like fibrils considerably varied among α, α', and β subunits. Faster hydrolysis rates and special fragments were observed for the α and α' subunits compared to the β subunit. However, the order of the fibrillation rate and capacity to form β-sheets was α' > β > α, as evidenced by CD and Thioflavin T data. Moreover, sequential growth of twisted screw-structure fibrils, leading to macroscopic fibrils with distinct morphological characteristics, was observed for β-conglycinin and individual subunits. The different fibrillation kinetics and morphologies of α, α', and β subunits appear to be associated with the differences in the amino acid composition and typical sequence of peptides. Besides, the disruption of ordered structure of fibrils occurred upon further heating (6-20 h) due to extensive hydrolysis. These results would suggest that all subunits are involved in the fibrillation of β-conglycinin, following multiple steps including polypeptide hydrolysis, assembly to amyloid structure, and growth into macroscopic fibrils with a fibril shaving process.
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Affiliation(s)
- Jin-Mei Wang
- Department of Food Science and Technology, South China University of Technology, Guangzhou 510640, People's Republic of China
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49
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Rao SP, Meade SJ, Healy JP, Sutton KH, Larsen NG, Staiger MP, Gerrard JA. Amyloid fibrils as functionalizable components of nanocomposite materials. Biotechnol Prog 2011; 28:248-56. [DOI: 10.1002/btpr.726] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Revised: 08/15/2011] [Indexed: 11/11/2022]
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50
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Ridgley DM, Ebanks KC, Barone JR. Peptide Mixtures Can Self-Assemble into Large Amyloid Fibers of Varying Size and Morphology. Biomacromolecules 2011; 12:3770-9. [DOI: 10.1021/bm201005k] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Devin M. Ridgley
- Biological Systems Engineering Department, Virginia Tech, 303 Seitz Hall, Blacksburg, Virginia
24061, United States
| | - Keira C. Ebanks
- Biological Systems Engineering Department, Virginia Tech, 303 Seitz Hall, Blacksburg, Virginia
24061, United States
| | - Justin R. Barone
- Biological Systems Engineering Department, Virginia Tech, 303 Seitz Hall, Blacksburg, Virginia
24061, United States
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