1
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Heerde T, Bansal A, Schmidt M, Fändrich M. Cryo-EM structure of a catalytic amyloid fibril. Sci Rep 2023; 13:4070. [PMID: 36906667 PMCID: PMC10008563 DOI: 10.1038/s41598-023-30711-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/28/2023] [Indexed: 03/13/2023] Open
Abstract
Catalytic amyloid fibrils are novel types of bioinspired, functional materials that combine the chemical and mechanical robustness of amyloids with the ability to catalyze a certain chemical reaction. In this study we used cryo-electron microcopy to analyze the amyloid fibril structure and the catalytic center of amyloid fibrils that hydrolyze ester bonds. Our findings show that catalytic amyloid fibrils are polymorphic and consist of similarly structured, zipper-like building blocks that consist of mated cross-β sheets. These building blocks define the fibril core, which is decorated by a peripheral leaflet of peptide molecules. The observed structural arrangement differs from previously described catalytic amyloid fibrils and yielded a new model of the catalytic center.
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Affiliation(s)
- Thomas Heerde
- Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany.
| | - Akanksha Bansal
- Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany
| | - Matthias Schmidt
- Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany
| | - Marcus Fändrich
- Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany
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2
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Tomiyama R, So M, Yamaguchi K, Miyanoiri Y, Sakurai K. The residual structure of acid-denatured β 2 -microglobulin is relevant to an ordered fibril morphology. Protein Sci 2023; 32:e4487. [PMID: 36321362 PMCID: PMC9793977 DOI: 10.1002/pro.4487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/15/2022] [Accepted: 10/29/2022] [Indexed: 11/09/2022]
Abstract
β2 -Microglobulin (β2m) forms amyloid fibrils in vitro under acidic conditions. Under these conditions, the residual structure of acid-denatured β2m is relevant to seeding and fibril extension processes. Disulfide (SS) bond-oxidized β2m has been shown to form rigid, ordered fibrils, whereas SS bond-reduced β2m forms curvy, less-ordered fibrils. These findings suggest that the presence of an SS bond affects the residual structure of the monomer, which subsequently influences the fibril morphology. To clarify this process, we herein performed NMR experiments. The results obtained revealed that oxidized β2m contained a residual structure throughout the molecule, including the N- and C-termini, whereas the residual structure of the reduced form was localized and other regions had a random coil structure. The range of the residual structure in the oxidized form was wider than that of the fibril core. These results indicate that acid-denatured β2m has variable conformations. Most conformations in the ensemble cannot participate in fibril formation because their core residues are hidden by residual structures. However, when hydrophobic residues are exposed, polypeptides competently form an ordered fibril. This conformational selection phase may be needed for the ordered assembly of amyloid fibrils.
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Affiliation(s)
- Ryosuke Tomiyama
- Graduate School of Biology‐oriented Science and TechnologyKindai UniversityWakayamaJapan
| | - Masatomo So
- Institute for Protein ResearchOsaka UniversityOsakaJapan,Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsUK
| | - Keiichi Yamaguchi
- Global Center for Medical Engineering and InformaticsOsaka UniversitySuitaJapan
| | | | - Kazumasa Sakurai
- Graduate School of Biology‐oriented Science and TechnologyKindai UniversityWakayamaJapan,High Pressure Protein Research Center, Institute of Advanced TechnologyKindai UniversityWakayamaJapan
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3
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Yamaguchi K, Hasuo K, So M, Ikenaka K, Mochizuki H, Goto Y. Strong acids induce amyloid fibril formation of β 2-microglobulin via an anion-binding mechanism. J Biol Chem 2021; 297:101286. [PMID: 34626645 PMCID: PMC8564678 DOI: 10.1016/j.jbc.2021.101286] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 11/28/2022] Open
Abstract
Amyloid fibrils, crystal-like fibrillar aggregates of proteins associated with various amyloidoses, have the potential to propagate via a prion-like mechanism. Among known methodologies to dissolve preformed amyloid fibrils, acid treatment has been used with the expectation that the acids will degrade amyloid fibrils similar to acid inactivation of protein functions. Contrary to our expectation, treatment with strong acids, such as HCl or H2SO4, of β2-microglobulin (β2m) or insulin actually promoted amyloid fibril formation, proportionally to the concentration of acid used. A similar promotion was observed at pH 2.0 upon the addition of salts, such as NaCl or Na2SO4. Although trichloroacetic acid, another strong acid, promoted amyloid fibril formation of β2m, formic acid, a weak acid, did not, suggesting the dominant role of anions in promoting fibril formation of this protein. Comparison of the effects of acids and salts confirmed the critical role of anions, indicating that strong acids likely induce amyloid fibril formation via an anion-binding mechanism. The results suggest that although the addition of strong acids decreases pH, it is not useful for degrading amyloid fibrils, but rather induces or stabilizes amyloid fibrils via an anion-binding mechanism.
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Affiliation(s)
- Keiichi Yamaguchi
- Global Center for Medical Engineering and Informatics, Osaka University, Suita, Osaka, Japan; Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Kenshiro Hasuo
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Masatomo So
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Kensuke Ikenaka
- Department of Neurology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Hideki Mochizuki
- Department of Neurology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Yuji Goto
- Global Center for Medical Engineering and Informatics, Osaka University, Suita, Osaka, Japan; Institute for Protein Research, Osaka University, Suita, Osaka, Japan.
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4
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Current Understanding of the Structure, Stability and Dynamic Properties of Amyloid Fibrils. Int J Mol Sci 2021; 22:ijms22094349. [PMID: 33919421 PMCID: PMC8122407 DOI: 10.3390/ijms22094349] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 04/17/2021] [Accepted: 04/18/2021] [Indexed: 02/07/2023] Open
Abstract
Amyloid fibrils are supramolecular protein assemblies represented by a cross-β structure and fibrous morphology, whose structural architecture has been previously investigated. While amyloid fibrils are basically a main-chain-dominated structure consisting of a backbone of hydrogen bonds, side-chain interactions also play an important role in determining their detailed structures and physicochemical properties. In amyloid fibrils comprising short peptide segments, a steric zipper where a pair of β-sheets with side chains interdigitate tightly is found as a fundamental motif. In amyloid fibrils comprising longer polypeptides, each polypeptide chain folds into a planar structure composed of several β-strands linked by turns or loops, and the steric zippers are formed locally to stabilize the structure. Multiple segments capable of forming steric zippers are contained within a single protein molecule in many cases, and polymorphism appears as a result of the diverse regions and counterparts of the steric zippers. Furthermore, the β-solenoid structure, where the polypeptide chain folds in a solenoid shape with side chains packed inside, is recognized as another important amyloid motif. While side-chain interactions are primarily achieved by non-polar residues in disease-related amyloid fibrils, the participation of hydrophilic and charged residues is prominent in functional amyloids, which often leads to spatiotemporally controlled fibrillation, high reversibility, and the formation of labile amyloids with kinked backbone topology. Achieving precise control of the side-chain interactions within amyloid structures will open up a new horizon for designing useful amyloid-based nanomaterials.
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5
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Sakurai K, Tomiyama R. Enhanced accessibility and hydrophobicity of amyloidogenic intermediates of the β2-microglobulin D76N mutant revealed by high-pressure experiments. J Biol Chem 2021; 296:100333. [PMID: 33508321 PMCID: PMC7950326 DOI: 10.1016/j.jbc.2021.100333] [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: 11/23/2020] [Revised: 01/16/2021] [Accepted: 01/22/2021] [Indexed: 11/05/2022] Open
Abstract
β2-Microglobulin (β2m) is the causative protein of dialysis-related amyloidosis. Its unfolding mainly proceeds along the pathway of NC →UC ⇄ UT, whereas refolding follows the UT → IT (→NT) →NC pathway, in which N, I, and U are the native, intermediate, and unfolded states, respectively, with the Pro32 peptidyl-prolyl bond in cis or trans conformation as indicated by the subscript. It is noted that the IT state is a putative amyloidogenic precursor state. Several aggregation-prone variants of β2m have been reported to date. One of these variants is D76N β2m, which is a naturally occurring amyloidogenic mutant. To elucidate the molecular mechanisms contributing to the enhanced amyloidogenicity of the mutant, we investigated the equilibrium and kinetic transitions of pressure-induced folding/unfolding equilibria in the wild type and D76N mutant by monitoring intrinsic tryptophan and 1-anilino-8-naphthalene sulfonate fluorescence. An analysis of kinetic data revealed that the different folding/unfolding behaviors of the wild type and D76N mutant were due to differences in the activation energy between the unfolded and the intermediate states as well as stability of the native state, leading to more rapid accumulation of IT state for D76N in the refolding process. In addition, the IT state was found to assume more hydrophobic nature. These changes induced the enhanced amyloidogenicity of the D76N mutant and the distinct pathogenic symptoms of patients. Our results suggest that the stabilization of the native state will be an effective approach for suppressing amyloid fibril formation of this mutant.
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Affiliation(s)
- Kazumasa Sakurai
- High Pressure Protein Research Center, Institute of Advanced Technology, Kindai University, Wakayama, Japan; Department of Biotechnology, Faculty of Biology-oriented Science and Technology, Kindai University, Wakayama, Japan.
| | - Ryosuke Tomiyama
- Department of Biotechnology, Faculty of Biology-oriented Science and Technology, Kindai University, Wakayama, Japan
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6
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Sakurai K, Maeno A, Lee YH, Akasaka K. Conformational Properties Relevant to the Amyloidogenicity of β 2-Microglobulin Analyzed Using Pressure- and Salt-Dependent Chemical Shift Data. J Phys Chem B 2019; 123:836-844. [PMID: 30604603 DOI: 10.1021/acs.jpcb.8b11408] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
β2-Microglobulin (β2m) is associated with dialysis-related amyloidosis. In vitro experiments have shown that β2m forms amyloid fibrils at acidic pHs in the presence of moderate concentrations of salt. Previous studies suggested that acid-denatured β2m has a hydrophobic residual structure, and the exposure of the hydrophobic residues enhances the association with seeds or other β2m monomers. However, the nature of the residual structure relevant to its amyloidogenicity remains to be investigated. To understand the structural properties of acid-denatured β2m and the role of salt, we investigated pressure- and salt concentration-dependent conformational changes by nuclear magnetic resonance spectroscopy and other methods. Here, pressure was utilized to characterize the conformers existing in a conformational equilibrium at ambient pressure. The obtained pressure- and salt concentration-dependent chemical shift data were simultaneously subjected to principal component analysis to characterize individual conformational change events. Unexpectedly, the addition of salt induced an expansion of the β2m molecule, which likely resulted from the exclusion of the N-terminal region from the hydrophobic cluster region. The dissected chemical shift patterns for the salt-induced conformational change and other experimental data indicated that this conformational change caused a rigidification in the intrinsic hydrophobic cluster, leading to the observed amyloidogenicity.
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Affiliation(s)
- Kazumasa Sakurai
- High Pressure Protein Research Center, Institute of Advanced Technology , Kindai University , 930 Nishimitani , Kinokawa, Wakayama 649-6493 , Japan.,Institute for Protein Research , Osaka University , 3-2 Yamadaoka , Suita, Osaka 565-0871 , Japan
| | - Akihiro Maeno
- Laboratory of Medical Chemistry , Kansai Medical University , 2-5-1 Shin-machi , Hirakata , Osaka 573-1010 , Japan
| | - Young-Ho Lee
- Institute for Protein Research , Osaka University , 3-2 Yamadaoka , Suita, Osaka 565-0871 , Japan.,Protein Structure Research Group, Division of Bioconvergence Analysis , Korea Basic Science Institute , Cheongju , Chungcheongbuk-do 28119 , South Korea
| | - Kazuyuki Akasaka
- Kyoto Prefectural University of Medicine , 465 Kajii-cho , Kamigyo-ku, Kyoto 602-8566 , Japan
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7
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Yamaguchi KI, Kuwata K. Formation and properties of amyloid fibrils of prion protein. Biophys Rev 2018; 10:517-525. [PMID: 29204880 PMCID: PMC5899736 DOI: 10.1007/s12551-017-0377-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 11/23/2017] [Indexed: 02/06/2023] Open
Abstract
Amyloid fibrils formed from prion protein (PrP) are associated with prion diseases. In this review we discuss a number of extrinsic and intrinsic experimental factors related to the formation of PrP amyloid fibrils in vitro. We first examined the effects of ultrasonic power on the induction of amyloid fibrillation from PrP. The most important conclusion drawn from the results is that an applied ultrasonic power of approximately 2 W enhanced the nucleation of amyloid fibrils efficiently but that more powerful ultrasonication led to retardation of growth. We also reviewed evidence on the amyloidogenic regions of PrP based on peptide screening throughout the polypeptide sequence. These results showed that helix 2 (H2) peptides of PrP were capable of both the fibrillation and propagation of straight, long fibrils. Moreover, the conformation of preformed H2 fibrils changed reversibly depending on the pH of the solution, implying that interactions between side-chains modulated the conformation of amyloid fibrils. The evidence discussed in this review relates specifically to PrP but may be relevant to other amyloidogenic proteins.
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Affiliation(s)
- Kei-ichi Yamaguchi
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 Japan
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Yanagido 1-1, Gifu, 501-1193 Japan
| | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Yanagido 1-1, Gifu, 501-1193 Japan
- Graduate School of Medicine, Gifu University, Yanagido 1-1, Gifu, 501-1193 Japan
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8
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Jansens KJA, Brijs K, Stetefeld J, Delcour JA, Scanlon MG. Ultrasonic Characterization of Amyloid-Like Ovalbumin Aggregation. ACS OMEGA 2017; 2:4612-4620. [PMID: 31457750 PMCID: PMC6641891 DOI: 10.1021/acsomega.7b00366] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 06/29/2017] [Indexed: 06/10/2023]
Abstract
Thermal processing conditions, pH, and salt content affect the formation of egg white ovalbumin amyloid, which was investigated using high-precision measurements of ultrasonic velocity and attenuation. These were related to fluorescence and particle size measurements. Fluorescence changes indicated the formation of amyloid-like aggregates that was enhanced by increasing time-temperature treatments. The ultrasonic velocity of ovalbumin after heating at neutral pH (60 min at 70 or 80 °C) was lower than that of unheated ovalbumin, whereas the attenuation was higher. The decrease in the velocity represents increased compressibility associated with a change in the compactness of the protein, whereas changes in attenuation are due to protein conformational changes. Heating ramp studies revealed transitions at approximately 58 and 73 °C. During heating at a constant temperature, the ultrasonic velocity decreased slowly with increasing heating time, indicating an increase in ovalbumin compressibility. It is suggested that the obtained amyloid-like ovalbumin aggregates contain a compact core surrounded by loosely packed protein segments.
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Affiliation(s)
- Koen J. A. Jansens
- Laboratory
of Food Chemistry and Biochemistry, Leuven
Food Science and Nutrition Research Centre (LFoRCe), KU Leuven Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Kristof Brijs
- Laboratory
of Food Chemistry and Biochemistry, Leuven
Food Science and Nutrition Research Centre (LFoRCe), KU Leuven Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Jörg Stetefeld
- Department
of Chemistry, University of Manitoba, Winnipeg, Canada R2T 2N2
| | - Jan A. Delcour
- Laboratory
of Food Chemistry and Biochemistry, Leuven
Food Science and Nutrition Research Centre (LFoRCe), KU Leuven Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Martin G. Scanlon
- Department
of Food Science, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2
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9
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Khan JM, Khan MS, Alsenaidy MA, Ahmed A, Sen P, Oves M, Al-Shabib NA, Khan RH. Sodium louroyl sarcosinate (sarkosyl) modulate amyloid fibril formation in hen egg white lysozyme (HEWL) at alkaline pH: a molecular insight study. J Biomol Struct Dyn 2017; 36:1550-1565. [DOI: 10.1080/07391102.2017.1329097] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Javed Masood Khan
- Faculty of Food and Agricultural Sciences, Department of Food Science and Nutrition, King Saud University, 2460 Riyadh 11451, Saudi Arabia
| | - Mohd Shahnawaz Khan
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | - Anwar Ahmed
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Priyankar Sen
- Centre for Bioseparation Technology, VIT University, Vellore 632014, India
| | - Mohammad Oves
- Center of Excellence in Enviromental Studies, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nasser Abdulatif Al-Shabib
- Faculty of Food and Agricultural Sciences, Department of Food Science and Nutrition, King Saud University, 2460 Riyadh 11451, Saudi Arabia
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
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10
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Jansens KJ, Brijs K, Delcour JA, Scanlon MG. Amyloid-like aggregation of ovalbumin: Effect of disulfide reduction and other egg white proteins. Food Hydrocoll 2016. [DOI: 10.1016/j.foodhyd.2016.07.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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11
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Noda S, So M, Adachi M, Kardos J, Akazawa-Ogawa Y, Hagihara Y, Goto Y. Thioflavin T-Silent Denaturation Intermediates Support the Main-Chain-Dominated Architecture of Amyloid Fibrils. Biochemistry 2016; 55:3937-48. [PMID: 27345358 DOI: 10.1021/acs.biochem.6b00231] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ultrasonication is considered one of the most effective agitations for inducing the spontaneous formation of amyloid fibrils. When we induced the ultrasonication-dependent fibrillation of β2-microglobulin and insulin monitored by amyloid-specific thioflavin T (ThT) fluorescence, both proteins showed a significant decrease in ThT fluorescence after the burst-phase increase. The decrease in ThT fluorescence was accelerated when the ultrasonic power was stronger, suggesting that this decrease was caused by the partial denaturation of preformed fibrils. The possible intermediates of denaturation retained amyloid-like morphologies, secondary structures, and seeding potentials. Similar denaturation intermediates were also observed when fibrils were denatured by guanidine hydrochloride or sodium dodecyl sulfate. The presence of these denaturation intermediates is consistent with the main-chain-dominated architecture of amyloid fibrils. Moreover, in the three types of denaturation experiments conducted, insulin fibrils were more stable than β2-microglobulin fibrils, suggesting that the relative stability of various fibrils is independent of the method of denaturation.
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Affiliation(s)
- Sayaka Noda
- Institute for Protein Research, Osaka University , Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - Masatomo So
- Institute for Protein Research, Osaka University , Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - Masayuki Adachi
- Institute for Protein Research, Osaka University , Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - József Kardos
- Department of Biochemistry and MTA-ELTE NAP B Neuroimmunology Research Group, Eötvös Loránd University , Pázmány sétány 1/C, Budapest 1117, Hungary
| | - Yoko Akazawa-Ogawa
- National Institute of Advanced Industrial Science and Technology (AIST) , 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan
| | - Yoshihisa Hagihara
- National Institute of Advanced Industrial Science and Technology (AIST) , 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan
| | - Yuji Goto
- Institute for Protein Research, Osaka University , Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
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12
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Muta H, Lee YH, Kardos J, Lin Y, Yagi H, Goto Y. Supersaturation-limited amyloid fibrillation of insulin revealed by ultrasonication. J Biol Chem 2014; 289:18228-38. [PMID: 24847058 DOI: 10.1074/jbc.m114.566950] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Amyloid fibrils form in supersaturated solutions via a nucleation and growth mechanism. We proposed that ultrasonication may be an effective agitation to trigger nucleation that would otherwise not occur under the persistent metastability of supersaturation. However, the roles of supersaturation and effects of ultrasonication have not been elucidated in detail except for limited cases. Insulin is an amyloidogenic protein that is useful for investigating the mechanisms underlying amyloid fibrillation with biological relevance. We studied the alcohol-induced amyloid fibrillation of insulin using various concentrations of 2,2,2-trifluoroethanol and 1,1,1,3,3,3-hexafluoro-2-propanol at pH 2.0 and 4.8. Ultrasonic irradiation effectively triggered fibrillation under conditions in which insulin retained persistent supersaturation. Structural analyses by circular dichroism, Fourier transform infrared spectroscopy, transmission electron microscopy, and atomic force microscopy revealed that the dominant structures of fibrils varied between parallel and antiparallel β-sheets depending on the solvent conditions. pH and alcohol concentration-dependent phase diagrams showed a marked difference before and after the ultrasonic treatment, which indicated that the persistent metastability of supersaturation determined the conformations of insulin. These results indicate the importance of an alternative view of amyloid fibrils as supersaturation-limited crystal-like aggregates formed above the solubility limit.
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Affiliation(s)
- Hiroya Muta
- From the Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan and
| | - Young-Ho Lee
- From the Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan and
| | - József Kardos
- the Department of Biochemistry, Eötvös Loránd University, Pázmány sétány 1/C, Budapest 1117, Hungary
| | - Yuxi Lin
- From the Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan and
| | - Hisashi Yagi
- From the Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan and
| | - Yuji Goto
- From the Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan and
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13
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Abstract
Fluorescence is the most widely used technique to study the effect of pressure on biochemical systems. The use of pressure as a physical variable sheds light into volumetric characteristics of reactions. Here we focus on the effect of pressure on protein solutions using a simple unfolding example in order to illustrate the applications of the methodology. Topics covered in this review include the relationships between practical aspects and technical limitations; the effect of pressure and the study of protein cavities; the interpretation of thermodynamic and relaxation kinetics; and the study of relaxation amplitudes. Finally, we discuss the insights available from the combination of fluorescence and other methods adapted to high pressure, such as SAXS or NMR. Because of the simplicity and accessibility of high-pressure fluorescence, the technique is a starting point that complements appropriately multi-methodological approaches related to understanding protein function, disfunction, and folding from the volumetric point of view.
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14
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Ikenoue T, Lee YH, Kardos J, Yagi H, Ikegami T, Naiki H, Goto Y. Heat of supersaturation-limited amyloid burst directly monitored by isothermal titration calorimetry. Proc Natl Acad Sci U S A 2014; 111:6654-9. [PMID: 24753579 PMCID: PMC4020073 DOI: 10.1073/pnas.1322602111] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Amyloid fibrils form in supersaturated solutions via a nucleation and growth mechanism. Although the structural features of amyloid fibrils have become increasingly clearer, knowledge on the thermodynamics of fibrillation is limited. Furthermore, protein aggregation is not a target of calorimetry, one of the most powerful approaches used to study proteins. Here, with β2-microglobulin, a protein responsible for dialysis-related amyloidosis, we show direct heat measurements of the formation of amyloid fibrils using isothermal titration calorimetry (ITC). The spontaneous fibrillation after a lag phase was accompanied by exothermic heat. The thermodynamic parameters of fibrillation obtained under various protein concentrations and temperatures were consistent with the main-chain dominated structural model of fibrils, in which overall packing was less than that of the native structures. We also characterized the thermodynamics of amorphous aggregation, enabling the comparison of protein folding, amyloid fibrillation, and amorphous aggregation. These results indicate that ITC will become a promising approach for clarifying comprehensively the thermodynamics of protein folding and misfolding.
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Affiliation(s)
- Tatsuya Ikenoue
- aDivision of Protein Structural Biology, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Young-Ho Lee
- aDivision of Protein Structural Biology, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - József Kardos
- bDepartment of Biochemistry, Eötvös Loránd University, 1117, Budapest, Hungary; and
| | - Hisashi Yagi
- aDivision of Protein Structural Biology, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Takahisa Ikegami
- aDivision of Protein Structural Biology, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Hironobu Naiki
- cFaculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan
| | - Yuji Goto
- aDivision of Protein Structural Biology, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
- 2To whom correspondence should be addressed. E-mail:
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15
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Sancataldo G, Vetri V, Foderà V, Di Cara G, Militello V, Leone M. Oxidation enhances human serum albumin thermal stability and changes the routes of amyloid fibril formation. PLoS One 2014; 9:e84552. [PMID: 24416244 PMCID: PMC3885593 DOI: 10.1371/journal.pone.0084552] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 11/15/2013] [Indexed: 12/22/2022] Open
Abstract
Oxidative damages are linked to several aging-related diseases and are among the chemical pathways determining protein degradation. Specifically, interplay of oxidative stress and protein aggregation is recognized to have a link to the loss of cellular function in pathologies like Alzheimer's and Parkinson's diseases. Interaction between protein and reactive oxygen species may indeed induce small changes in protein structure and lead to the inhibition/modification of protein aggregation process, potentially determining the formation of species with different inherent toxicity. Understanding the temperate relationship between these events can be of utmost importance in unraveling the molecular basis of neurodegeneration. In this work, we investigated the effect of hydrogen peroxide oxidation on Human Serum Albumin (HSA) structure, thermal stability and aggregation properties. In the selected conditions, HSA forms fibrillar aggregates, while the oxidized protein undergoes aggregation via new routes involving, in different extents, specific domains of the molecule. Minute variations due to oxidation of single residues affect HSA tertiary structure leading to protein compaction, increased thermal stability, and reduced association propensity.
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Affiliation(s)
| | - Valeria Vetri
- Dipartimento di Fisica e Chimica, Universita' di Palermo, Palermo, Italy
- Consiglio Nazionale delle Ricerche-IBF u.o. Palermo, Italy
- * E-mail:
| | - Vito Foderà
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
- Sector of Biological and Soft Systems, Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, United Kingdom
| | | | - Valeria Militello
- Dipartimento di Fisica e Chimica, Universita' di Palermo, Palermo, Italy
- Consiglio Nazionale delle Ricerche-IBF u.o. Palermo, Italy
| | - Maurizio Leone
- Dipartimento di Fisica e Chimica, Universita' di Palermo, Palermo, Italy
- Consiglio Nazionale delle Ricerche-IBF u.o. Palermo, Italy
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16
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Yamaguchi KI, Kamatari YO, Fukuoka M, Miyaji R, Kuwata K. Nearly Reversible Conformational Change of Amyloid Fibrils as Revealed by pH-Jump Experiments. Biochemistry 2013; 52:6797-806. [DOI: 10.1021/bi400698u] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Kei-ichi Yamaguchi
- United Graduate School of Drug Discovery and Medical
Information
Sciences, ‡Center for Emerging Infectious Diseases, §Life Science Research Center, and ¶Supporting and Development
Center for Technology Education, Faculty of Engineering, Gifu University, Yanagido
1-1, Gifu 501-1193, Japan
| | - Yuji O. Kamatari
- United Graduate School of Drug Discovery and Medical
Information
Sciences, ‡Center for Emerging Infectious Diseases, §Life Science Research Center, and ¶Supporting and Development
Center for Technology Education, Faculty of Engineering, Gifu University, Yanagido
1-1, Gifu 501-1193, Japan
| | - Mayuko Fukuoka
- United Graduate School of Drug Discovery and Medical
Information
Sciences, ‡Center for Emerging Infectious Diseases, §Life Science Research Center, and ¶Supporting and Development
Center for Technology Education, Faculty of Engineering, Gifu University, Yanagido
1-1, Gifu 501-1193, Japan
| | - Reiji Miyaji
- United Graduate School of Drug Discovery and Medical
Information
Sciences, ‡Center for Emerging Infectious Diseases, §Life Science Research Center, and ¶Supporting and Development
Center for Technology Education, Faculty of Engineering, Gifu University, Yanagido
1-1, Gifu 501-1193, Japan
| | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical
Information
Sciences, ‡Center for Emerging Infectious Diseases, §Life Science Research Center, and ¶Supporting and Development
Center for Technology Education, Faculty of Engineering, Gifu University, Yanagido
1-1, Gifu 501-1193, Japan
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17
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Vetri V, Leone M, Morozova-Roche LA, Vestergaard B, Foderà V. Unlocked concanavalin A forms amyloid-like fibrils from coagulation of long-lived "crinkled" intermediates. PLoS One 2013; 8:e68912. [PMID: 23874809 PMCID: PMC3712988 DOI: 10.1371/journal.pone.0068912] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 06/06/2013] [Indexed: 01/14/2023] Open
Abstract
Understanding the early events during amyloid aggregation processes is crucial to single out the involved molecular mechanisms and for designing ad hoc strategies to prevent and reverse amyloidogenic disorders. Here, we show that, in conditions in which the protein is positively charged and its conformational flexibility is enhanced, Concanavalin A leads to fibril formation via a non-conventional aggregation pathway. Using a combination of light scattering, circular dichroism, small angle X-ray scattering, intrinsic (Tryptophan) and extrinsic (ANS) fluorescence and confocal and 2-photon fluorescence microscopy we characterize the aggregation process as a function of the temperature. We highlight a multi-step pathway with the formation of an on-pathway long-lived intermediate and a subsequent coagulation of such “crinkled” precursors into amyloid-like fibrils. The process results in a temperature-dependent aggregation-coagulation pathway, with the late phase of coagulation determined by the interplay between hydrophobic and electrostatic forces. Our data provide evidence for the complex aggregation pathway for a protein with a highly flexible native conformation. We demonstrate the possibility to generate a long-lived intermediate whose proportion and occurrence are easily tunable by experimental parameters (i.e. temperature). As a consequence, in the case of aggregation processes developing through well-defined energy barriers, our results can open the way to new strategies to induce more stable in vitro on-pathway intermediate species through a minute change in the initial conformational flexibility of the protein. This will allow isolating and experimentally studying such transient species, often indicated as relevant in neurodegenerative diseases, both in terms of structural and cytotoxic properties.
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Affiliation(s)
- Valeria Vetri
- Dipartimento di Fisica e Chimica, Università di Palermo, Palermo, Italy
- * E-mail: (VV); (VF)
| | - Maurizio Leone
- Dipartimento di Fisica e Chimica, Università di Palermo, Palermo, Italy
| | | | - Bente Vestergaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Vito Foderà
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
- Sector of Biological and Soft Systems, Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (VV); (VF)
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18
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Chatani E, Yagi H, Naiki H, Goto Y. Polymorphism of β2-microglobulin amyloid fibrils manifested by ultrasonication-enhanced fibril formation in trifluoroethanol. J Biol Chem 2012; 287:22827-37. [PMID: 22566695 DOI: 10.1074/jbc.m111.333310] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The polymorphic property of amyloid structures has been focused on as a molecular basis of the presence and propagation of different phenotypes of amyloid diseases, although little is known about the molecular mechanism for expressing diverse structures from only one protein sequence. Here, we have found that, in combination with an enhancing effect of ultrasonication on nucleation, β(2)-microglobulin, a protein responsible for dialysis-related amyloidosis, generates distinct fibril conformations in a concentration-dependent manner in the presence of 2,2,2-trifluoroethanol (TFE). Although the newly formed fibrils all exhibited a similar needle-like morphology with an extensive cross-β core, as suggested by Fourier transform infrared absorption spectra, they differed in thioflavin T intensity, extension kinetics, and tryptophan fluorescence spectra even in the same solvents, representing polymorphic structures. The hydrophobic residues seemed to be more exposed in the fibrils originating at higher concentrations of TFE, as indicated by the increased binding of 1-anilinonaphthalene-8-sulfonic acid, suggesting that the modulation of hydrophobic interactions is critical to the production of polymorphic amyloid structures. Interestingly, the fibrils formed at higher TFE concentrations showed significantly higher stability against guanidium hydrochloride, the perturbation of ionic strength, and, furthermore, pressurization. The cross-β structure inside the fibrils seems to have been more idealized, resulting in increased stability when nucleation occurred in the presence of the alcohol, indicating that a weaker contribution of hydrophobic interactions is intrinsically more amenable to the formation of a non-defective amyloid structure.
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Affiliation(s)
- Eri Chatani
- Department of Chemistry, Graduate School of Science, Kobe University, Hyogo 657-8501, Japan.
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19
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El Moustaine D, Perrier V, Van Ba IAT, Meersman F, Ostapchenko VG, Baskakov IV, Lange R, Torrent J. Amyloid features and neuronal toxicity of mature prion fibrils are highly sensitive to high pressure. J Biol Chem 2011; 286:13448-59. [PMID: 21357423 PMCID: PMC3075691 DOI: 10.1074/jbc.m110.192872] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 02/24/2011] [Indexed: 12/22/2022] Open
Abstract
Prion proteins (PrP) can aggregate into toxic and possibly infectious amyloid fibrils. This particular macrostructure confers on them an extreme and still unexplained stability. To provide mechanistic insights into this self-assembly process, we used high pressure as a thermodynamic tool for perturbing the structure of mature amyloid fibrils that were prepared from recombinant full-length mouse PrP. Application of high pressure led to irreversible loss of several specific amyloid features, such as thioflavin T and 8-anilino-1-naphthalene sulfonate binding, alteration of the characteristic proteinase K digestion pattern, and a significant decrease in the β-sheet structure and cytotoxicity of amyloid fibrils. Partial disaggregation of the mature fibrils into monomeric soluble PrP was observed. The remaining amyloid fibrils underwent a change in secondary structure that led to morphologically different fibrils composed of a reduced number of proto-filaments. The kinetics of these reactions was studied by recording the pressure-induced dissociation of thioflavin T from the amyloid fibrils. Analysis of the pressure and temperature dependence of the relaxation rates revealed partly unstructured and hydrated kinetic transition states and highlighted the importance of collapsing and hydrating inter- and intramolecular cavities to overcome the high free energy barrier that stabilizes amyloid fibrils.
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Affiliation(s)
- Driss El Moustaine
- From the University of Montpellier 2 and
- INSERM, U710, Montpellier F-34095, France
- Ecole Pratique des Hautes Études, Paris F-75007, France
| | - Veronique Perrier
- From the University of Montpellier 2 and
- INSERM, U710, Montpellier F-34095, France
- Ecole Pratique des Hautes Études, Paris F-75007, France
| | - Isabelle Acquatella-Tran Van Ba
- From the University of Montpellier 2 and
- INSERM, U710, Montpellier F-34095, France
- Ecole Pratique des Hautes Études, Paris F-75007, France
| | - Filip Meersman
- the Department of Chemistry, Katholieke Universiteit Leuven, Leuven B-3001, Belgium, and
| | - Valeriy G. Ostapchenko
- the Center for Biomedical Engineering and Technology, Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Ilia V. Baskakov
- the Center for Biomedical Engineering and Technology, Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Reinhard Lange
- From the University of Montpellier 2 and
- INSERM, U710, Montpellier F-34095, France
- Ecole Pratique des Hautes Études, Paris F-75007, France
| | - Joan Torrent
- From the University of Montpellier 2 and
- INSERM, U710, Montpellier F-34095, France
- Ecole Pratique des Hautes Études, Paris F-75007, France
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20
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Vetri V, D’Amico M, Foderà V, Leone M, Ponzoni A, Sberveglieri G, Militello V. Bovine Serum Albumin protofibril-like aggregates formation: Solo but not simple mechanism. Arch Biochem Biophys 2011; 508:13-24. [DOI: 10.1016/j.abb.2011.01.024] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Revised: 01/31/2011] [Accepted: 01/31/2011] [Indexed: 11/29/2022]
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21
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Kardos J, Micsonai A, Pál-Gábor H, Petrik É, Gráf L, Kovács J, Lee YH, Naiki H, Goto Y. Reversible heat-induced dissociation of β2-microglobulin amyloid fibrils. Biochemistry 2011; 50:3211-20. [PMID: 21388222 DOI: 10.1021/bi2000017] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recent progress in the field of amyloid research indicates that the classical view of amyloid fibrils, being irreversibly formed highly stable structures resistant to perturbating conditions and proteolytic digestion, is getting more complex. We studied the thermal stability and heat-induced depolymerization of amyloid fibrils of β(2)-microglobulin (β2m), a protein responsible for dialysis-related amyloidosis. We found that freshly polymerized β2m fibrils at 0.1-0.3 mg/mL concentration completely dissociated to monomers upon 10 min incubation at 99 °C. Fibril depolymerization was followed by thioflavin-T fluorescence and circular dichroism spectroscopy at various temperatures. Dissociation of β2m fibrils was found to be a reversible and dynamic process reaching equilibrium between fibrils and monomers within minutes. Repolymerization experiments revealed that the number of extendable fibril ends increased significantly upon incubation at elevated temperatures suggesting that the mechanism of fibril unfolding involves two distinct processes: (1) dissociation of monomers from the fibril ends and (2) the breakage of fibrils. The breakage of fibrils may be an important in vivo factor multiplying the number of fibril nuclei and thus affecting the onset and progress of disease. We investigated the effects of some additives and different factors on the stability of amyloid fibrils. Sample aging increased the thermal stability of β2m fibril solution. 0.5 mM SDS completely prevented β2m fibrils from dissociation up to the applied highest temperature of 99 °C. The generality of our findings was proved on fibrils of K3 peptide and α-synuclein. Our simple method may also be beneficial for screening and developing amyloid-active compounds for therapeutic purposes.
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Affiliation(s)
- József Kardos
- Department of Biochemistry, Institute of Biology, Eötvös Loránd University, Budapest H-1117, Hungary.
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22
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Rondeau P, Navarra G, Cacciabaudo F, Leone M, Bourdon E, Militello V. Thermal aggregation of glycated bovine serum albumin. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:789-98. [PMID: 20006741 DOI: 10.1016/j.bbapap.2009.12.003] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2009] [Revised: 11/23/2009] [Accepted: 12/05/2009] [Indexed: 12/20/2022]
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23
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Ladner CL, Chen M, Smith DP, Platt GW, Radford SE, Langen R. Stacked sets of parallel, in-register beta-strands of beta2-microglobulin in amyloid fibrils revealed by site-directed spin labeling and chemical labeling. J Biol Chem 2010; 285:17137-47. [PMID: 20335170 PMCID: PMC2878032 DOI: 10.1074/jbc.m110.117234] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
β2-microglobulin (β2m) is a 99-residue protein with an immunoglobulin fold that forms β-sheet-rich amyloid fibrils in dialysis-related amyloidosis. Here the environment and accessibility of side chains within amyloid fibrils formed in vitro from β2m with a long straight morphology are probed by site-directed spin labeling and accessibility to modification with N-ethyl maleimide using 19 site-specific cysteine variants. Continuous wave electron paramagnetic resonance spectroscopy of these fibrils reveals a core predominantly organized in a parallel, in-register arrangement, by contrast with other β2m aggregates. A continuous array of parallel, in-register β-strands involving most of the polypeptide sequence is inconsistent with the cryoelectron microscopy structure, which reveals an architecture based on subunit repeats. To reconcile these data, the number of spins in close proximity required to give rise to spin exchange was determined. Systematic studies of a model protein system indicated that juxtaposition of four spin labels is sufficient to generate exchange narrowing. Combined with information about side-chain mobility and accessibility, we propose that the amyloid fibrils of β2m consist of about six β2m monomers organized in stacks with a parallel, in-register array. The results suggest an organization more complex than the accordion-like β-sandwich structure commonly proposed for amyloid fibrils.
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Affiliation(s)
- Carol L Ladner
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
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24
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Celej MS, Caarls W, Demchenko AP, Jovin TM. A triple-emission fluorescent probe reveals distinctive amyloid fibrillar polymorphism of wild-type alpha-synuclein and its familial Parkinson's disease mutants. Biochemistry 2009; 48:7465-72. [PMID: 19586054 DOI: 10.1021/bi9003843] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Intracytoplasmic neuronal deposits containing amyloid fibrils of the 140-amino acid presynaptic protein alpha-synuclein (AS) are the hallmark of Parkinson's (PD) disease and related neurodegenerative disorders. Three point mutations (A53T, A30P, and E46K) are linked to early onset PD. Compared to the wild-type (WT) protein, the mutants aggregate faster in vitro, but their fibrillar products are quite similar. Using the extrinsic multiple-emission probe 4'-(diethylamino)-3-hydroxyflavone (FE), we demonstrate unique and distinct spectroscopic signatures for the amyloid fibrils formed by the WT and mutant AS, presumably indicative of subtle differences in supramolecular structure. The two well-separated emission bands of the FE probe originate from a proton transfer reaction in the excited state. The ratiometric response constitutes a sensitive, tunable reporter of microenvironmental properties such as polarity and hydrogen bonding. The very distinctive fluorescence spectra of the FE probe bound to the four AS variants reflect different tautomeric equilibria in the excited state and the existence of at least two different binding sites in the fibrils for the dye. Deconvolution of the two-dimensional excitation-emission spectra leads to estimations of different local dielectric constants and extents of hydration characteristic of the proteins. The sensitivity of such a simple external probe to conformational alterations induced by point mutations is unprecedented and provides new insight into key phenomena related to amyloid fibrils: plasticity, polymorphism, propagation of structural features, and structure-function relationships underlying toxicity.
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Affiliation(s)
- M Soledad Celej
- Laboratory of Cellular Dynamics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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25
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Palhano FL, Rocha CB, Bernardino A, Weissmuller G, Masuda CA, Montero-Lomelí M, Gomes AM, Chien P, Fernandes PMB, Foguel D. A fluorescent mutant of the NM domain of the yeast prion Sup35 provides insight into fibril formation and stability. Biochemistry 2009; 48:6811-23. [PMID: 19530740 DOI: 10.1021/bi9000276] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Sup35 protein of Saccharomyces cerevisiae forms a prion that generates the [PSI(+)] phenotype. Its NM region governs prion status, forming self-seeding amyloid fibers in vivo and in vitro. A tryptophan mutant of Sup35 (NM(F117W)) was used to probe its aggregation. Four indicators of aggregation, Trp 117 maximum emission, Trp polarization, thio-T binding, and light scattering increase, revealed faster aggregation at 4 degrees C than at 25 degrees C, and all indicators changed in a concerted fashion at the former temperature. Curiously, at 25 degrees C the changes were not synchronized; the first two indicators, which reflect nucleation, changed more quickly than the last two, which reflect fibril formation. These results suggest that nucleation is insensitive to temperature, whereas fibril extension is temperature dependent. As expected, aggregation is accelerated when a small fraction (5%) of the nuclei produced at 4 or 25 degrees C are added to a suspension containing the soluble NM domain, although these nuclei do not seem to propagate any structural information to the growing fibrils. Fibrils grown at 4 degrees C were less stable in GdmCl than those grown at higher temperature. However, they were both resistant to high pressure; in fact, both sets of fibrils responded to high pressure by adopting an altered conformation with a higher capacity for thio-T binding. From these data, we calculated the change in volume and free energy associated with this conformational change. AFM revealed that the fibrils grown at 4 degrees C were statistically smaller than those grown at 25 degrees C. In conclusion, the introduction of Trp 117 allowed us to more carefully dissect the effects of temperature on the aggregation of the Sup35 NM domain.
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Affiliation(s)
- Fernando L Palhano
- Instituto de Bioquimica Medica, Programa de Biologia Estrutural e Programa de Biologia Molecular e Biotecnologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-590, Brazil
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26
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Sasahara K, Yagi H, Naiki H, Goto Y. Thermal Response with Exothermic Effects of β2-Microglobulin Amyloid Fibrils and Fibrillation. J Mol Biol 2009; 389:584-94. [DOI: 10.1016/j.jmb.2009.04.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2008] [Revised: 04/01/2009] [Accepted: 04/14/2009] [Indexed: 10/20/2022]
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27
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White HE, Hodgkinson JL, Jahn TR, Cohen-Krausz S, Gosal WS, Müller S, Orlova EV, Radford SE, Saibil HR. Globular tetramers of beta(2)-microglobulin assemble into elaborate amyloid fibrils. J Mol Biol 2009; 389:48-57. [PMID: 19345691 PMCID: PMC2726924 DOI: 10.1016/j.jmb.2009.03.066] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2009] [Revised: 03/27/2009] [Accepted: 03/30/2009] [Indexed: 11/24/2022]
Abstract
Amyloid fibrils are ordered polymers in which constituent polypeptides adopt a non-native fold. Despite their importance in degenerative human diseases, the overall structure of amyloid fibrils remains unknown. High-resolution studies of model peptide assemblies have identified residues forming cross-β-strands and have revealed some details of local β-strand packing. However, little is known about the assembly contacts that define the fibril architecture. Here we present a set of three-dimensional structures of amyloid fibrils formed from full-length β2-microglobulin, a 99-residue protein involved in clinical amyloidosis. Our cryo-electron microscopy maps reveal a hierarchical fibril structure built from tetrameric units of globular density, with at least three different subunit interfaces in this homopolymeric assembly. These findings suggest a more complex superstructure for amyloid than hitherto suspected and prompt a re-evaluation of the defining features of the amyloid fold.
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Affiliation(s)
- Helen E White
- Department of Crystallography and Institute of Structural and Molecular Biology, Birkbeck College, London, UK
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28
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Silva JL, Foguel D. Hydration, cavities and volume in protein folding, aggregation and amyloid assembly. Phys Biol 2009; 6:015002. [DOI: 10.1088/1478-3975/6/1/015002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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29
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Abstract
beta(2)-microglobulin (beta(2)m) is capable of forming amyloid in osteoarticular structures in kidney failure patients that undergo chronic hemodialysis treatment. Although sophisticated analytical methods have yielded comprehensive data about the conformation of the native protein both as a monomer and as the light chain of the type I major histocompatibility complex, the cause and mechanisms leading to the transformation of beta(2)m into amyloid deposits in patients with dialysis-related amyloidosis are unsettled. The impact on conformational stability of various truncations, cleavages, amino acid substitutions, and divalent cations, especially Cu(2+), however, are highly relevant for understanding beta(2)m unfolding pathways leading to amyloid formation. This review describes the current knowledge about such conformationally destabilizing and amyloidogenic factors and links these to the structure and function of beta(2)m in normal physiology and pathology. Tables listing modifications of beta(2)m found in amyloid from patients and a systematic overview of laboratory conditions conducive to beta(2)m-fibrillogenesis are also included.
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30
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Mishra R, Winter R. Cold- and Pressure-Induced Dissociation of Protein Aggregates and Amyloid Fibrils. Angew Chem Int Ed Engl 2008; 47:6518-21. [DOI: 10.1002/anie.200802027] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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31
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Mishra R, Winter R. Kälte- und druckinduzierte Dissoziation von Proteinaggregaten und Amyloidfibrillen. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200802027] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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32
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Radovan D, Smirnovas V, Winter R. Effect of pressure on islet amyloid polypeptide aggregation: revealing the polymorphic nature of the fibrillation process. Biochemistry 2008; 47:6352-60. [PMID: 18498175 DOI: 10.1021/bi800503j] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Type II diabetes mellitus is a disease which is characterized by peripheral insulin resistance coupled with a progressive loss of insulin secretion that is associated with a decrease in pancreatic islet beta-cell mass and the deposition of amyloid in the extracellular matrix of beta-cells, which lead to islet cell death. The principal component of the islet amyloid is a pancreatic hormone called islet amyloid polypeptide (IAPP). High-pressure coupled with FT-IR spectroscopic and AFM studies were carried out to elucidate further information about the aggregation pathway as well as the aggregate structures of IAPP. To this end, a comparative fibrillation study of IAPP fragments was carried out as well. As high hydrostatic pressure (HHP) is acting to weaken or even prevent hydrophobic self-organization and electrostatic interactions, application of HHP has been used as a measure to reveal the importance of these interactions in the fibrillation process of IAPP and its fragments. IAPP preformed fibrils exhibit a strong polymorphism with heterogeneous structures, a large population of which are rather sensitive to high hydrostatic pressure, thus indicating a high percentage of ionic and hydrophobic interactions and loose packing of these species. Conversely, fragments 1-19 and 1-29 are resistant to pressure treatment, suggesting more densely packed aggregate structures with less void volume and strong cooperative hydrogen bonding. Furthermore, the FT-IR data indicate that fragment 1-29 has intermolecular beta-sheet conformational properties different from those of fragment 1-19, the latter exhibiting polymorphic behavior with more disordered structures and less strongly hydrogen bonded fibrillar assemblies. The data also suggest that hydrophobic interactions and/or less efficient packing of amino acids 30-37 region leads to the marked pressure sensitivity observed for full-length IAPP.
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Affiliation(s)
- Diana Radovan
- Department of Chemistry, Physical Chemistry I-Biophysical Chemistry, Dortmund University of Technology, D-44227 Dortmund, Germany
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33
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Boldyreva EV. High-pressure diffraction studies of molecular organic solids. A personal view. Acta Crystallogr A 2007; 64:218-31. [DOI: 10.1107/s0108767307065786] [Citation(s) in RCA: 146] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2007] [Accepted: 12/05/2007] [Indexed: 11/10/2022] Open
Abstract
This paper discusses the trends in the experimental studies of molecular organic solids at high pressures by diffraction techniques. Crystallization of liquids, crystallization from solutions and solid-state transformations are considered. Special attention is paid to the high-pressure studies of pharmaceuticals and of biomimetics.
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34
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Akasaka K, Latif ARA, Nakamura A, Matsuo K, Tachibana H, Gekko K. Amyloid Protofibril is Highly Voluminous and Compressible. Biochemistry 2007; 46:10444-50. [PMID: 17715944 DOI: 10.1021/bi700648b] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report here results of the first direct measurement of partial volume and compressibility changes of a protein as it forms an amyloid protofibril. We use a high precision density meter and an ultrasonic velocity meter on a solution of intrinsically denatured, disulfide-deficient variant of hen lysozyme, and follow the time-dependent changes in volume and compressibility, as the protein spontaneously forms a protofibril. We have found a large increase in partial specific volume with time from 0.684 to 0.724 mL x g-1 (Deltanu = 0.040 mL x g-1 corresponding to 570 mL x (mol monomer)-1) and in partial specific adiabatic compressibility coefficient from -7.48 x 10(-12) to +1.35 x 10(-12) cm2 x dyn-1 (Deltabetas = 8.83 x 10(-12) x cm2 x dyn-1) as the monomer transforms into a protofibril. The results demonstrate that the protofibril is a highly voluminous and compressible entity, disclosing a cavity-rich, fluctuating nature for the amyloid protofibril. The volume and compressibility changes occur in two phases, the faster one preceding the major development of the beta-structure in the protofibril as monitored by CD.
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Affiliation(s)
- Kazuyuki Akasaka
- Department of Biotechnological Science, School of Biology-Oriented Science and Technology, Kinki University, 930 Nishimitani, Kinokawa, Wakayama 649-6493, Japan.
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35
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Okuno A, Kato M, Taniguchi Y. Pressure effects on the heat-induced aggregation of equine serum albumin by FT-IR spectroscopic study: Secondary structure, kinetic and thermodynamic properties. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:652-60. [PMID: 17452032 DOI: 10.1016/j.bbapap.2007.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2006] [Revised: 03/07/2007] [Accepted: 03/08/2007] [Indexed: 10/23/2022]
Abstract
Pressure can restrain the heat-induced aggregation and dissociate the heat-induced aggregates. We investigated the aggregation-preventing pressure effect and the aggregates-dissociating pressure effect to characterize the heat-induced aggregation of equine serum albumin (ESA) by Fourier transform infrared spectroscopy. The results suggest that the alpha-helical structure collapses at the beginning of heat-induced aggregation, then the rearrangement of structure from partially unfolded structure to the intermolecular beta-sheet takes place through the activated state. We determined the activation volume for the heat-induced aggregation (DeltaV( not equal)=+92+/-8 ml mol(-1)) and the partial molar volume difference between native state and heat-induced aggregates (DeltaV(N-->HA)=+32 ml mol(-1)). This positive partial molar volume difference suggests that the heat-induced aggregates have larger internal voids than the native structure. Moreover, the positive volume change implies that the formation of the intermolecular beta-sheet is unfavorable under high pressure. We also determined the free energy profile of ESA. This energy profile explains the restriction of the formation of heat-induced aggregates by pressure. These results explain the structural differences between heat-induced aggregates with intermolecular beta-sheet and pressure-induced aggregates without intermolecular beta-sheet.
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Affiliation(s)
- Akira Okuno
- Department of Applied Chemistry, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
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36
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Iwata K, Fujiwara T, Matsuki Y, Akutsu H, Takahashi S, Naiki H, Goto Y. 3D structure of amyloid protofilaments of beta2-microglobulin fragment probed by solid-state NMR. Proc Natl Acad Sci U S A 2006; 103:18119-24. [PMID: 17108084 PMCID: PMC1838716 DOI: 10.1073/pnas.0607180103] [Citation(s) in RCA: 202] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2006] [Indexed: 11/18/2022] Open
Abstract
Understanding the structure and formation of amyloid fibrils, the filamentous aggregates of proteins and peptides, is crucial in preventing diseases caused by their deposition and, moreover, for obtaining further insight into the mechanism of protein folding and misfolding. We have combined solid-state NMR, x-ray fiber diffraction, and atomic force microscopy to reveal the 3D structure of amyloid protofilament-like fibrils formed by a 22-residue K3 peptide (Ser(20)-Lys(41)) of beta(2)-microglobulin, a protein responsible for dialysis-related amyloidosis. Although a uniformly (13)C,(15)N-labeled sample was used for the NMR measurements, we could obtain the 3D structure of the fibrils on the basis of a large number of structural constraints. The conformation of K3 fibrils was found to be a beta-strand-loop-beta-strand with each K3 molecule stacked in a parallel and staggered manner. It is suggested that the fibrillar conformation is stabilized by intermolecular interactions, rather than by intramolecular hydrophobic packing as seen in globular proteins. Together with thermodynamic studies of the full-length protein, formation of the fibrils is likely to require side chains on the intermolecular surface to pack tightly against those of adjacent monomers. By revealing the structure of beta(2)-microglobulin protofilament-like fibrils, this work represents technical progress in analyzing amyloid fibrils in general through solid-state NMR.
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Affiliation(s)
- Kentaro Iwata
- *Institute for Protein Research, Osaka University and Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Suita, Osaka 565-0871, Japan; and
| | - Toshimichi Fujiwara
- *Institute for Protein Research, Osaka University and Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Suita, Osaka 565-0871, Japan; and
| | - Yoh Matsuki
- *Institute for Protein Research, Osaka University and Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Suita, Osaka 565-0871, Japan; and
| | - Hideo Akutsu
- *Institute for Protein Research, Osaka University and Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Suita, Osaka 565-0871, Japan; and
| | - Satoshi Takahashi
- *Institute for Protein Research, Osaka University and Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Suita, Osaka 565-0871, Japan; and
| | - Hironobu Naiki
- Faculty of Medical Sciences, University of Fukui and Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Matsuoka, Fukui 910-1193, Japan
| | - Yuji Goto
- *Institute for Protein Research, Osaka University and Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Suita, Osaka 565-0871, Japan; and
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37
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Kihara M, Chatani E, Iwata K, Yamamoto K, Matsuura T, Nakagawa A, Naiki H, Goto Y. Conformation of Amyloid Fibrils of β2-Microglobulin Probed by Tryptophan Mutagenesis. J Biol Chem 2006; 281:31061-9. [PMID: 16901902 DOI: 10.1074/jbc.m605358200] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Beta2-microglobulin (beta2-m), a protein responsible for dialysis-related amyloidosis, adopts an immunoglobulin domain fold in its native state. Although beta2-m has Trp residues at positions 60 and 95, both are located near the surface of the domain. Hence, beta2-m does not have a conserved Trp common to other immunoglobulin domains, which is buried in close proximity to the disulfide bond. To study the structure of amyloid fibrils in relation to their native fold, we prepared a series of Trp mutants. Trp60 and Trp95 were both replaced with Phe, and a single Trp was introduced at various positions. Among various mutants, W39-beta2-m, in which a Trp was introduced at the position corresponding to the conserved Trp, exhibited a remarkable quenching of fluorescence in the native state, as observed for other immunoglobulin domains. An x-ray structural analysis revealed that W39-beta2-m assumes the native fold with Trp39 located in the vicinity of the disulfide bond. Comparison of the fluorescence spectra of various mutants for the native and fibrillar forms indicated that, while the Trp residues introduced in the middle of the beta2-m sequence tend to be buried in the fibrils, those located in the C-terminal region are more exposed. In addition, the fluorescence spectra of fibrils prepared at pH 2.5 and 7.0 revealed a large difference in the fluorescence intensity for W60-beta2-m, implying a major structural difference between them.
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Affiliation(s)
- Miho Kihara
- Institute for Protein Research, Osaka University, and CREST, Japan Science and Technology Agency, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
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38
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Chatani E, Naiki H, Goto Y. Seeding-dependent Propagation and Maturation of β2-Microglobulin Amyloid Fibrils Under High Pressure. J Mol Biol 2006; 359:1086-96. [PMID: 16697008 DOI: 10.1016/j.jmb.2006.04.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2006] [Revised: 03/30/2006] [Accepted: 04/06/2006] [Indexed: 11/29/2022]
Abstract
High hydrostatic pressure reversibly transforms the amyloid fibrils of beta2-microglobulin (beta2-m) into a more tightly packed, reorganized structure, which has provided insight into the polymorphic properties of amyloid fibrils. Here, to further investigate the molecular mechanism that controls fibril structure, seed-dependent fibril growth from an acid-unfolded monomeric form under high pressure was studied. At all pressures up to 400 MPa, the fibril growth could be approximated by a single-exponential kinetics, although pressure above 300 MPa decreased the growth rate significantly. The fibrils formed at high pressure were similar to the reorganized fibrils formed initially at ambient pressure and then pressurized, suggesting that the reorganized fibrils were formed directly at high pressure. A systematic investigation of the extension rate under various pressures indicated that the activation free energies for the original and reorganized fibrils are significantly different, suggesting that different amino acid contacts are involved in these two types of fibrils. On the other hand, for the seed-dependent extension reactions of both types of fibrils, the activation volume was much smaller than the change in reaction volume, implying that only small numbers of side-chain interactions are achieved in the transition state. Importantly, we observed a marked acceleration of fibril growth, i.e., maturation, on repeated self-seeding above 300 MPa, revealing the coexistence of another type of fibril with a similar structure but with an increased growth-rate under high pressure.
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Affiliation(s)
- Eri Chatani
- Institute for Protein Research, Osaka University and CREST, Japan Science and Technology Agency, Suita, Osaka 565-0871, Japan
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39
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Meersman F, Smeller L, Heremans K. Protein stability and dynamics in the pressure–temperature plane. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:346-54. [PMID: 16414316 DOI: 10.1016/j.bbapap.2005.11.019] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2005] [Revised: 11/23/2005] [Accepted: 11/28/2005] [Indexed: 10/25/2022]
Abstract
The pressure-temperature stability diagram of proteins and the underlying assumptions of the elliptical shape of the diagram are discussed. Possible extensions, such as aggregation and fibril formation, are considered. An important experimental observation is the extreme pressure stability of the mature fibrils. Molecular origins of the diagram in terms of models of the partial molar volume of a protein focus on cavities and hydration. Changes in thermal expansivity, compressibility and heat capacity in terms of fluctuations of the enthalpy and volume change of the unfolding should also focus on these parameters. It is argued that the study of water-soluble polymers might further our understanding of the stability diagram. Whereas the role of water in protein behaviour is unquestioned, the role of cavities is less clear.
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Affiliation(s)
- Filip Meersman
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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40
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Silva JL, Cordeiro Y, Foguel D. Protein folding and aggregation: Two sides of the same coin in the condensation of proteins revealed by pressure studies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:443-51. [PMID: 16480935 DOI: 10.1016/j.bbapap.2005.11.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2005] [Accepted: 11/14/2005] [Indexed: 11/12/2022]
Abstract
Hydrostatic pressure can be considered as "thermodynamic tweezers" to approach the protein folding problem and to study the cases when folding goes wrong leading to the protein folding disorders. The main outcome of the use of high pressure in this field is the stabilization of folding intermediates such as partially folded conformations, thus allowing us to characterize their structural properties. Because partially folded intermediates are usually at the intersection between productive and off-pathway folding, they may give rise to misfolded proteins, aggregates and amyloids that are involved in many neurodegenerative diseases, such as transmissible spongiform encephalopathies, Alzheimer's disease, Parkinson's disease and Huntington's disease. Of particular interest is the use of hydrostatic pressure to unveil the structural transitions in prion conversion and to populate possible intermediates in the folding/unfolding pathway of the prion protein. The main hypothesis for prion diseases proposes that the cellular protein (PrP(C)) can be altered into a misfolded, beta-sheet-rich isoform, the PrP(Sc) (from scrapie). It has been demonstrated that hydrostatic pressure affects the balance between the different prion species. The last findings on the application of high pressure on amyloidogenic proteins will be discussed here as regards to their energetic and volumetric properties. The use of high pressure promises to contribute to the identification of the underlying mechanisms of these neurodegenerative diseases and to develop new therapeutic approaches.
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Affiliation(s)
- Jerson L Silva
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica, and Centro Nacional de Ressonância Magnética Nuclear de Macromoléculas, Universidade Federal do Rio de Janeiro, 21941-590 Rio de Janeiro, RJ, Brazil.
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41
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Bocharova OV, Makarava N, Breydo L, Anderson M, Salnikov VV, Baskakov IV. Annealing prion protein amyloid fibrils at high temperature results in extension of a proteinase K-resistant core. J Biol Chem 2005; 281:2373-9. [PMID: 16314415 DOI: 10.1074/jbc.m510840200] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Amyloids are highly ordered, rigid beta-sheet-rich structures that appear to have minimal dynamic flexibility in individual polypeptide chains. Here, we demonstrate that substantial conformational rearrangements occur within mature amyloid fibrils produced from full-length mammalian prion protein. The rearrangement results in a substantial extension of a proteinase K-resistant core and is accompanied by an increase in the beta-sheet-rich conformation. The conformational rearrangement was induced in the presence of low concentrations of Triton X-100 either by brief exposure to 80 degrees C or, with less efficacy, by prolonged incubation at 37 degrees C at pH 7.5 and is referred to here as "annealing." Upon annealing, amyloid fibrils acquired a proteinase K-resistant core identical to that found in bovine spongiform encephalopathy-specific scrapie-associated prion protein. Annealing was also observed when amyloid fibrils were exposed to high temperatures in the absence of detergent but in the presence of brain homogenate. These findings suggest that the amyloid fibrils exist in two conformationally distinct states that are separated by a high energy barrier and that yet unknown cellular cofactors may facilitate transition of the fibrils into thermodynamically more stable state. Our studies provide new insight into the complex behavior of prion polymerization and highlight the annealing process, a previously unknown step in the evolution of amyloid structures.
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Affiliation(s)
- Olga V Bocharova
- Medical Biotechnology Center, Biotechnology Institute, University of Maryland School of Medicine, 725 W. Lombard Street, Baltimore, MD 21201, USA
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42
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Meersman F, Dobson CM. Probing the pressure-temperature stability of amyloid fibrils provides new insights into their molecular properties. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2005; 1764:452-60. [PMID: 16337233 DOI: 10.1016/j.bbapap.2005.10.021] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2005] [Accepted: 10/27/2005] [Indexed: 10/25/2022]
Abstract
A number of medical disorders, including Alzheimer's disease and type II diabetes, is characterised by the deposition of amyloid fibrils in tissue. The insolubility and size of the fibrils has largely precluded the determination of their structures at high resolution. Studies probing the stability of amyloid fibrils can reveal which non-covalent interactions are important in the formation and maintenance of the fibril structure. In particular, we review here the use of high hydrostatic pressure and high temperature as perturbation techniques. In general, small aggregates formed early in the assembly process can be dissociated by high pressure, but mature amyloid fibrils are highly pressure stable. This finding suggests that a temporal transition occurs during which side chain packing and hydrogen bond formation are optimised, whereas the hydrophobic effect and electrostatic interactions play a dominant role in the early stages of the aggregation. High temperatures, however, can disrupt most aggregates. Though the observed stability of amyloid fibrils is not unique to these structures, the notion that amyloid fibrils can represent the global minimum in free energy is supported by this type of investigations. Some implications regarding the nature of toxic species, associated with at least many of the amyloid disorders, and recently proposed structural models are discussed.
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Affiliation(s)
- Filip Meersman
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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43
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Yagi H, Kusaka E, Hongo K, Mizobata T, Kawata Y. Amyloid Fibril Formation of α-Synuclein Is Accelerated by Preformed Amyloid Seeds of Other Proteins. J Biol Chem 2005; 280:38609-16. [PMID: 16162499 DOI: 10.1074/jbc.m508623200] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Alpha-synuclein is one of the causative proteins of familial Parkinson disease, which is characterized by neuronal inclusions named Lewy bodies. Lewy bodies include not only alpha-synuclein but also aggregates of other proteins. This fact raises a question as to whether the formation of alpha-synuclein amyloid fibrils in Lewy bodies may occur via interaction with fibrils derived from different proteins. To probe this hypothesis, we investigated in vitro fibril formation of human alpha-synuclein in the presence of preformed fibril seeds of various different proteins. We used three proteins, Escherichia coli chaperonin GroES, hen lysozyme, and bovine insulin, all of which have been shown to form amyloid fibrils. Very surprisingly, the formation of alpha-synuclein amyloid fibril was accelerated markedly in the presence of preformed seeds of GroES, lysozyme, and insulin fibrils. The structural characteristics of the natively unfolded state of alpha-synuclein may allow binding to various protein particles, which in turn triggers the formation (extension) of alpha-synuclein amyloid fibrils. This finding is very important for understanding the molecular mechanism of Parkinson disease and also provides interesting implications into the mechanism of transmissible conformational diseases.
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Affiliation(s)
- Hisashi Yagi
- Department of Biotechnology, Faculty of Engineering, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Koyama-Minami, Tottori 680-8552, Japan
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44
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Chatani E, Goto Y. Structural stability of amyloid fibrils of beta(2)-microglobulin in comparison with its native fold. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2005; 1753:64-75. [PMID: 16213801 DOI: 10.1016/j.bbapap.2005.08.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2005] [Revised: 08/01/2005] [Accepted: 08/03/2005] [Indexed: 11/20/2022]
Abstract
Among various amyloidogenic proteins, beta(2)-microglobulin (beta2-m) responsible for dialysis-related amyloidosis is a target of extensive study because of its clinical importance and suitable size for examining the formation of amyloid fibrils in comparison with protein folding to the native state. The structure and stability of amyloid fibrils have been studied with various physicochemical methods, including H/D exchange of amyloid fibrils combined with dissolution of fibrils by dimethylsulfoxide and NMR analysis, thermodynamic analysis of amyloid fibril formation by isothermal calorimetry, and analysis of the effects of pressure on the structure of amyloid fibrils. The results are consistent with the view that amyloid fibrils are a main-chain-dominated structure with larger numbers of hydrogen bonds and pressure-accessible cavities in the interior, in contrast to the side-chain-dominated native structure with the optimal packing of amino acid residues. We consider that a main-chain dominated structure provides the structural basis for various conformational states even with one protein. When this feature is combined with another unique feature, template-dependent growth, propagation and maturation of the amyloid conformation, which cannot be predicted with Anfinsen's dogma, take place.
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Affiliation(s)
- Eri Chatani
- Institute for Protein Research, Osaka University and CREST, Japan Science and Technology Agency, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
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