1
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Ansari NK, Rais A, Naeem A. Methotrexate for Drug Repurposing as an Anti-Aggregatory Agent to Mercuric Treated α-Chymotrypsinogen-A. Protein J 2024; 43:362-374. [PMID: 38431536 DOI: 10.1007/s10930-024-10187-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2024] [Indexed: 03/05/2024]
Abstract
Protein aggregation is related to numerous pathological conditions like Alzheimer's and Parkinson's disease. In our study, we have shown that an already existing FDA-approved drug; methotrexate (MTX) can be reprofiled on preformed α-chymotrypsinogen A (α-Cgn A) aggregates. The zymogen showed formation of aggregates upon interaction with mercuric ions, with increasing concentration of Hg2Cl2 (0-150 µM). The hike in ThT and ANS fluorescence concomitant with blue shift, bathochromic shift and the hyperchromic effect in the CR absorbance, RLS and turbidity measurements, substantiate the zymogen β-rich aggregate formation. The secondary structural alterations of α- Cgn A as analyzed by CD measurements, FTIR and Raman spectra showed the transformation of native β-barrel conformation to β-inter-molecular rich aggregates. The native α- Cgn A have about 30% α-helical content which was found to be about 3% in presence of mercuric ions suggesting the formation of aggregates. The amorphous aggregates were visualized by SEM. On incubation of Hg2Cl2 treated α- Cgn A with increasing concentration of the MTX resulted in reversing aggregates to the native-like structure. These results were supported by remarkable decrease in ThT and ANS fluorescence intensities and CR absorbance and also consistent with CD, FTIR, and Raman spectroscopy data. MTX was found to increase the α-helical content of the zymogen from 3 to 15% proposing that drug is efficient in disrupting the β-inter-molecular rich aggregates and reverting it to native like structure. The SEM images are in accordance with CD data showing the disintegration of aggregates. The most effective concentration of the drug was found to be 120 µM. Molecular docking analysis showed that MTX molecule was surrounded by the hydrophobic residues including Phe39, His40, Arg145, Tyr146, Thr151, Gly193, Ser195, and Gly216 and conventional hydrogen bonds, including Gln73 (bond length: 2.67Å), Gly142 (2.59Å), Thr144 (2.81Å), Asn150 (2.73Å), Asp153 (2.71Å), and Cys191 (2.53Å). This investigation will help to find the use of already existing drugs to cure protein misfolding-related abnormalities.
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Affiliation(s)
- Neha Kausar Ansari
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, U.P, 202002, India
| | - Amaan Rais
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, U.P, 202002, India
| | - Aabgeena Naeem
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, U.P, 202002, India.
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2
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Cortez LM, Morrison AJ, Garen CR, Patterson S, Uyesugi T, Petrosyan R, Sekar RV, Harms MJ, Woodside MT, Sim VL. Probing the origin of prion protein misfolding via reconstruction of ancestral proteins. Protein Sci 2022; 31:e4477. [PMID: 36254680 PMCID: PMC9667828 DOI: 10.1002/pro.4477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/11/2022] [Accepted: 10/13/2022] [Indexed: 12/13/2022]
Abstract
Prion diseases are fatal neurodegenerative diseases caused by pathogenic misfolding of the prion protein, PrP. They are transmissible between hosts, and sometimes between different species, as with transmission of bovine spongiform encephalopathy to humans. Although PrP is found in a wide range of vertebrates, prion diseases are seen only in certain mammals, suggesting that infectious misfolding was a recent evolutionary development. To explore when PrP acquired the ability to misfold infectiously, we reconstructed the sequences of ancestral versions of PrP from the last common primate, primate-rodent, artiodactyl, placental, bird, and amniote. Recombinant ancestral PrPs were then tested for their ability to form β-sheet aggregates, either spontaneously or when seeded with infectious prion strains from human, cervid, or rodent species. The ability to aggregate developed after the oldest ancestor (last common amniote), and aggregation capabilities diverged along evolutionary pathways consistent with modern-day susceptibilities. Ancestral bird PrP could not be seeded with modern-day prions, just as modern-day birds are resistant to prion disease. Computational modeling of structures suggested that differences in helix 2 could account for the resistance of ancestral bird PrP to seeding. Interestingly, ancestral primate PrP could be converted by all prion seeds, including both human and cervid prions, raising the possibility that species descended from an ancestral primate have retained the susceptibility to conversion by cervid prions. More generally, the results suggest that susceptibility to prion disease emerged prior to ~100 million years ago, with placental mammals possibly being generally susceptible to disease.
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Affiliation(s)
- Leonardo M. Cortez
- Centre for Prions and Protein Folding DiseasesUniversity of AlbertaEdmontonAlbertaCanada
- Division of Neurology, Department of MedicineUniversity of AlbertaEdmontonAlbertaCanada
- Neuroscience and Mental Health InstituteUniversity of AlbertaEdmontonAlbertaCanada
| | - Anneliese J. Morrison
- Institute of Molecular BiologyUniversity of OregonEugeneOregonUSA
- Department of Chemistry and BiochemistryUniversity of OregonEugeneOregonUSA
| | - Craig R. Garen
- Department of PhysicsUniversity of AlbertaEdmontonAlbertaCanada
| | - Sawyer Patterson
- Centre for Prions and Protein Folding DiseasesUniversity of AlbertaEdmontonAlbertaCanada
| | - Toshi Uyesugi
- Department of PhysicsUniversity of AlbertaEdmontonAlbertaCanada
| | - Rafayel Petrosyan
- Department of PhysicsUniversity of AlbertaEdmontonAlbertaCanada
- Present address:
Zaven & Sonia Akian College of Science and EngineeringAmerican University of ArmeniaYerevanArmenia
| | | | - Michael J. Harms
- Institute of Molecular BiologyUniversity of OregonEugeneOregonUSA
- Department of Chemistry and BiochemistryUniversity of OregonEugeneOregonUSA
| | - Michael T. Woodside
- Centre for Prions and Protein Folding DiseasesUniversity of AlbertaEdmontonAlbertaCanada
- Department of PhysicsUniversity of AlbertaEdmontonAlbertaCanada
- Li Ka Shing Institute of VirologyUniversity of AlbertaEdmontonAlbertaCanada
| | - Valerie L. Sim
- Centre for Prions and Protein Folding DiseasesUniversity of AlbertaEdmontonAlbertaCanada
- Division of Neurology, Department of MedicineUniversity of AlbertaEdmontonAlbertaCanada
- Neuroscience and Mental Health InstituteUniversity of AlbertaEdmontonAlbertaCanada
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3
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Housmans JAJ, Houben B, Monge-Morera M, Asvestas D, Nguyen HH, Tsaka G, Louros N, Carpentier S, Delcour JA, Rousseau F, Schymkowitz J. Investigating the Sequence Determinants of the Curling of Amyloid Fibrils Using Ovalbumin as a Case Study. Biomacromolecules 2022; 23:3779-3797. [PMID: 36027608 DOI: 10.1021/acs.biomac.2c00660] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Highly ordered, straight amyloid fibrils readily lend themselves to structure determination techniques and have therefore been extensively characterized. However, the less ordered curly fibrils remain relatively understudied, and the structural organization underlying their specific characteristics remains poorly understood. We found that the exemplary curly fibril-forming protein ovalbumin contains multiple aggregation prone regions (APRs) that form straight fibrils when isolated as peptides or when excised from the full-length protein through hydrolysis. In the context of the intact full-length protein, however, the regions separating the APRs facilitate curly fibril formation. In fact, a meta-analysis of previously reported curly fibril-forming proteins shows that their inter-APRs are significantly longer and more hydrophobic when compared to straight fibril-forming proteins, suggesting that they may cause strain in the amyloid state. Hence, inter-APRs driving curly fibril formation may not only apply to our model protein but rather constitute a more general mechanism.
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Affiliation(s)
- Joëlle A J Housmans
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
| | - Bert Houben
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
| | - Margarita Monge-Morera
- Laboratory of Food Chemistry and Biochemistry and Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Kasteelpark Arenberg 20, 3001 Leuven, Belgium
| | - Diego Asvestas
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
| | - Hung Huy Nguyen
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
| | - Grigoria Tsaka
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
| | - Nikolaos Louros
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
| | - Sebastien Carpentier
- Facility for Systems Biology Based Mass Spectrometry, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Jan A Delcour
- Laboratory of Food Chemistry and Biochemistry and Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Kasteelpark Arenberg 20, 3001 Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
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4
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Rajan D, Rajamanikandan R, Ilanchelian M. Morphological and biophysical insights into the gold nanorods binding interaction of haemoglobin/myoglobin by hybrid spectroscopic approaches with bacterial cytotoxicity evaluation. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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5
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Bergasa-Caceres F, Rabitz HA. Identification of Two Early Folding Stage Prion Non-Local Contacts Suggested to Serve as Key Steps in Directing the Final Fold to Be Either Native or Pathogenic. Int J Mol Sci 2021; 22:ijms22168619. [PMID: 34445324 PMCID: PMC8395309 DOI: 10.3390/ijms22168619] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/30/2021] [Accepted: 08/04/2021] [Indexed: 12/16/2022] Open
Abstract
The initial steps of the folding pathway of the C-terminal domain of the murine prion protein mPrP(90–231) are predicted based on the sequential collapse model (SCM). A non-local dominant contact is found to form between the connecting region between helix 1 and β-sheet 1 and the C-terminal region of helix 3. This non-local contact nucleates the most populated molten globule-like intermediate along the folding pathway. A less stable early non-local contact between segments 120–124 and 179–183, located in the middle of helix 2, promotes the formation of a less populated molten globule-like intermediate. The formation of the dominant non-local contact constitutes an example of the postulated Nature’s Shortcut to the prion protein collapse into the native structure. The possible role of the less populated molten globule-like intermediate is explored as the potential initiation point for the folding for three pathogenic mutants (T182A, I214V, and Q211P in mouse prion numbering) of the prion protein.
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6
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Mechanism of misfolding of the human prion protein revealed by a pathological mutation. Proc Natl Acad Sci U S A 2021; 118:2019631118. [PMID: 33731477 PMCID: PMC7999870 DOI: 10.1073/pnas.2019631118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The misfolding and aggregation of the human prion protein (PrP) is associated with transmissible spongiform encephalopathies (TSEs). Intermediate conformations forming during the conversion of the cellular form of PrP into its pathological scrapie conformation are key drivers of the misfolding process. Here, we analyzed the properties of the C-terminal domain of the human PrP (huPrP) and its T183A variant, which is associated with familial forms of TSEs. We show that the mutation significantly enhances the aggregation propensity of huPrP, such as to uniquely induce amyloid formation under physiological conditions by the sole C-terminal domain of the protein. Using NMR spectroscopy, biophysics, and metadynamics simulations, we identified the structural characteristics of the misfolded intermediate promoting the aggregation of T183A huPrP and the nature of the interactions that prevent this species to be populated in the wild-type protein. In support of these conclusions, POM antibodies targeting the regions that promote PrP misfolding were shown to potently suppress the aggregation of this amyloidogenic mutant.
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7
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9-N-substituted novel berberine derivative for selective and sensitive nanomolar level fluorometric detection of human hemoglobin: A synthesis, sensing and interaction study. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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8
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Hasan S, Isar M, Naeem A. Macromolecular crowding stabilises native structure of α-chymotrypsinogen-A against hexafluoropropanol-induced aggregates. Int J Biol Macromol 2020; 164:3780-3788. [PMID: 32835802 DOI: 10.1016/j.ijbiomac.2020.08.149] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 08/06/2020] [Accepted: 08/19/2020] [Indexed: 12/20/2022]
Abstract
Cell interior is extremely congested with tightly packed biological macromolecules that exerts macromolecular crowding effect, influencing biophysical properties of proteins. To have a deeper insight into it we studied consequences of crowding on aggregation susceptibility and structural stability of α-chymotrypsinogen-A, pro-enzyme of serine protease family, upon addition of co-solvent reported to exert stress on polypeptides crafting favourable conditions for aggregation. Hexafluoropropan-2-ol (HFIP), a fluorinated alcohol caused structural disruption at 5% v/v unveiled by reduced intrinsic intensity and blue shifted ANS spectra. Significantly enhanced, red-shifted ThT and Congo red spectra sustained conformational changes concomitant with aggregation. FTIR and CD results confirmed transition of native structure to non-native extended, cross-linked beta-sheets. Transmission electron micrographs visibly exhibited incidence of amorphous aggregates. Macromolecular crowding, typically mimicked by concentrated solutions of dextran 70, was noticeably witnessed to defend conformational stability under denaturing condition. The native structure was retained maximally in presence of 100 mg/ml followed by 200 and 300 mg/ml dextran indicating concentration dependent deceleration of aggregate formation. It can be established that explicit consideration of crowding effects using relevant range of inert crowding agents must be a requisite for presumptions on intracellular conformational behaviour of proteins deduced from in vitro experiments.
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Affiliation(s)
- Samra Hasan
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, U.P., India
| | - Mohd Isar
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, U.P., India
| | - Aabgeena Naeem
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, U.P., India.
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9
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Thivya P, Wilson J. Electron rays irradiated polyaniline anchored over bovine serum albumin for simultaneous detection of epinephrine and uric acid. Microchem J 2019. [DOI: 10.1016/j.microc.2018.12.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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10
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Shen HCH, Chen YH, Lin YS, Chu BKY, Liang CS, Yang CC, Chen RPY. Segments in the Amyloid Core that Distinguish Hamster from Mouse Prion Fibrils. Neurochem Res 2019; 44:1399-1409. [PMID: 30603982 DOI: 10.1007/s11064-018-02709-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/29/2018] [Accepted: 12/23/2018] [Indexed: 10/27/2022]
Abstract
Prion diseases are transmissible fatal neurodegenerative disorders affecting humans and other mammals. The disease transmission can occur between different species but is limited by the sequence homology between host and inoculum. The crucial molecular event in the progression of this disease is prion formation, starting from the conformational conversion of the normal, membrane-anchored prion protein (PrPC) into the misfolded, β-sheet-rich and aggregation-prone isoform (PrPSc), which then self-associates into the infectious amyloid form called prion. Amyloid is the aggregate formed from one-dimensional protein association. As amyloid formation is a key hallmark in prion pathogenesis, studying which segments in prion protein are involved in the amyloid formation can provide molecular details in the cross-species transmission barrier of prion diseases. However, due to the difficulties of studying protein aggregates, very limited knowledge about prion structure or prion formation was disclosed by now. In this study, cross-seeding assay was used to identify the segments involved in the amyloid fibril formation of full-length hamster prion protein, SHaPrP(23-231). Our results showed that the residues in the segments 108-127, 172-194 (helix 2 in PrPC) and 200-227 (helix 3 in PrPC) are in the amyloid core of hamster prion fibrils. The segment 127-143, but not 107-126 (which corresponds to hamster sequence 108-127), was previously reported to be involved in the amyloid core of full-length mouse prion fibrils. Our results indicate that hamster prion protein and mouse prion protein use different segments to form the amyloid core in amyloidogenesis. The sequence-dependent core formation can be used to explain the seeding barrier between mouse and hamster.
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Affiliation(s)
- Howard C-H Shen
- Institute of Biological Chemistry, Academia Sinica, No. 128, Sec. 2, Academia Rd, Nankang, Taipei, 11529, Taiwan.,Institute of Biochemical Sciences, National Taiwan University, Taipei, 10617, Taiwan
| | - Yung-Han Chen
- Institute of Biological Chemistry, Academia Sinica, No. 128, Sec. 2, Academia Rd, Nankang, Taipei, 11529, Taiwan
| | - Yu-Sheng Lin
- Institute of Biological Chemistry, Academia Sinica, No. 128, Sec. 2, Academia Rd, Nankang, Taipei, 11529, Taiwan.,Department of Biochemical Science and Technology, National Taiwan University, Taipei, 10617, Taiwan
| | - Brett K-Y Chu
- Institute of Biological Chemistry, Academia Sinica, No. 128, Sec. 2, Academia Rd, Nankang, Taipei, 11529, Taiwan.,Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan
| | - Ching-Shin Liang
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, 10617, Taiwan
| | - Chien-Chih Yang
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, 10617, Taiwan
| | - Rita P-Y Chen
- Institute of Biological Chemistry, Academia Sinica, No. 128, Sec. 2, Academia Rd, Nankang, Taipei, 11529, Taiwan. .,Institute of Biochemical Sciences, National Taiwan University, Taipei, 10617, Taiwan.
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11
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Green synthesis of silver nanoparticles, its characterization, and chaperone-like activity in the aggregation inhibition of α-chymotrypsinogen A. Int J Biol Macromol 2018; 120:2381-2389. [DOI: 10.1016/j.ijbiomac.2018.09.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 08/25/2018] [Accepted: 09/03/2018] [Indexed: 02/01/2023]
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12
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Honda R, Yamaguchi KI, Elhelaly AE, Fuji M, Kuwata K. Poly-L-histidine inhibits prion propagation in a prion-infected cell line. Prion 2018; 12:226-233. [PMID: 30074430 DOI: 10.1080/19336896.2018.1505395] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Transmissible spongiform encephalopathies (TSEs) are a group of lethal neurodegenerative diseases involving the structural conversion of cellular prion protein (PrPC) into the pathogenic isoform (PrPSc) for which no effective treatment is currently available. Previous studies have implicated that a polymeric molecule with a repeating unit, such as pentosane polysulfate and polyamidoamide dendrimers, exhibits a potent anti-prion activity, suggesting that poly-(amino acid)s could be a candidate molecule for inhibiting prion propagation. Here, by screening a series of poly-(amino acid)s in a prion-infected neuroblastoma cell line (GTFK), we identified poly-L-His as a novel anti-prion compound with an IC50 value of 1.8 µg/mL (0.18 µM). This potent anti-prion activity was specific to a high-molecular-weight poly-L-His and absent in monomeric histidine or low-molecular-weight poly-L-His. Solution NMR data indicated that poly-L-His directly binds to the loop region connecting Helix 2 and Helix 3 of PrPC and sterically blocks the structural conversion toward PrPSc. Poly-L-His, however, did not inhibit prion propagation in a prion-infected mouse when administered intraperitoneally, suggesting that the penetration of blood-brain barrier and/or the chemical stability of this polypeptide must be addressed before its application in vivo. Taken together, this study revealed the potential use of poly-L-His as a novel treatment against TSEs. (203 words).
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Affiliation(s)
- Ryo Honda
- a United Graduate School of Drug Discovery and Medical Information Sciences , Gifu University , Gifu , Japan
| | | | - Abdelazim Elsayed Elhelaly
- a United Graduate School of Drug Discovery and Medical Information Sciences , Gifu University , Gifu , Japan
| | - Mitsuhiko Fuji
- a United Graduate School of Drug Discovery and Medical Information Sciences , Gifu University , Gifu , Japan
| | - Kazuo Kuwata
- a United Graduate School of Drug Discovery and Medical Information Sciences , Gifu University , Gifu , Japan.,c Department of Gene and Development , Graduate School of Medicine, Gifu University , Gifu , Japan
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13
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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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14
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Honda R, Kuwata K. Evidence for a central role of PrP helix 2 in the nucleation of amyloid fibrils. FASEB J 2018; 32:3641-3652. [PMID: 29401635 DOI: 10.1096/fj.201701183rr] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Amyloid fibrils are filamentous protein aggregates associated with the pathogenesis of a wide variety of human diseases. The formation of such aggregates typically follows nucleation-dependent kinetics, wherein the assembly and structural conversion of amyloidogenic proteins into oligomeric aggregates (nuclei) is the rate-limiting step of the overall reaction. In this study, we sought to gain structural insights into the oligomeric nuclei of the human prion protein (PrP) by preparing a series of deletion mutants lacking 14-44 of the C-terminal 107 residues of PrP and examined the kinetics and thermodynamics of these mutants in amyloid formation. An analysis of the experimental data using the concepts of the Φ-value analysis indicated that the helix 2 region (residues 168-196) acquires an amyloid-like β-sheet during nucleation, whereas the other regions preserves a relatively disordered structure in the nuclei. This finding suggests that the helix 2 region serves as the nucleation site for the assembly of amyloid fibrils.-Honda, R., Kuwata, K. Evidence for a central role of PrP helix 2 in the nucleation of amyloid fibrils.
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Affiliation(s)
- Ryo Honda
- Department of Molecular Pathobiochemistry, Graduate School of Medicine, Gifu University, Gifu, Japan.,United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan
| | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan.,Department of Gene and Development, Graduate School of Medicine, Gifu University, Gifu, Japan
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15
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Heier JL, Mikolajczak DJ, Böttcher C, Koksch B. Substrate specificity of an actively assembling amyloid catalyst. Biopolymers 2017; 108. [PMID: 27858968 DOI: 10.1002/bip.23003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 10/01/2016] [Accepted: 10/12/2016] [Indexed: 01/20/2023]
Abstract
In the presence of Zn2+ , the catalytic, amyloid-forming peptide Ac-IHIHIQI-NH2 , was found to exhibit enhanced selectivity for hydrophobic p-nitrophenyl ester substrates while in the process of self-assembly. As opposed to the substrate p-nitrophenyl acetate, which was more effectively hydrolyzed with Ac-IHIHIQI-NH2 in its fully fibrillar state, the hydrophobic substrate Z-L-Phe-ONp was converted with a second-order rate constant more than 11-times greater when the catalyst was actively assembling. Under such conditions, Z-L-Phe-ONp hydrolysis proceeded at a greater velocity than the more hydrophilic and otherwise more labile ester Boc-L-Asn-ONp. When assembling, the catalyst also showed increased selectivity for the L-enantiomer of Z-Phe-ONp. These findings suggest the occurrence of increased interactions of hydrophobic moieties of the substrate with exposed hydrophobic surfaces of the assembling peptides and present valuable features for future de novo design consideration.
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Affiliation(s)
- Jason L Heier
- Freie Universität Berlin Department of Biology, Chemistry, Pharmacy Institute of Chemistry and Biochemistry Berlin, Germany
| | - Dorian J Mikolajczak
- Freie Universität Berlin Department of Biology, Chemistry, Pharmacy Institute of Chemistry and Biochemistry Berlin, Germany
| | - Christoph Böttcher
- Freie Universität Berlin Department of Biology, Chemistry, Pharmacy Institute of Chemistry and Biochemistry Research Center for Electron Microscopy Berlin, Germany
| | - Beate Koksch
- Freie Universität Berlin Department of Biology, Chemistry, Pharmacy Institute of Chemistry and Biochemistry Berlin, Germany
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16
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The role of the unusual threonine string in the conversion of prion protein. Sci Rep 2016; 6:38877. [PMID: 27982059 PMCID: PMC5159806 DOI: 10.1038/srep38877] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 11/15/2016] [Indexed: 01/24/2023] Open
Abstract
The conversion of normal prion protein (PrP) into pathogenic PrP conformers is central to prion disease, but the mechanism remains unclear. The α-helix 2 of PrP contains a string of four threonines, which is unusual due to the high propensity of threonine to form β-sheets. This structural feature was proposed as the basis for initiating PrP conversion, but experimental results have been conflicting. We studied the role of the threonine string on PrP conversion by analyzing mouse Prnpa and Prnpb polymorphism that contains a polymorphic residue at the beginning of the threonine string, and PrP mutants in which threonine 191 was replaced by valine, alanine, or proline. The PMCA (protein misfolding cyclic amplification) assay was able to recapitulate the in vivo transmission barrier between PrPa and PrPb. Relative to PMCA, the amyloid fibril growth assay is less restrictive, but it did reflect certain properties of in vivo prion transmission. Our results suggest a plausible theory explaining the apparently contradictory results in the role of the threonine string in PrP conversion and provide novel insights into the complicated relationship among PrP stability, seeded conformational change, and prion structure, which is critical for understanding the molecular basis of prion infectivity.
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17
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Wu EL, Qi Y, Park S, Mallajosyula SS, MacKerell AD, Klauda JB, Im W. Insight into Early-Stage Unfolding of GPI-Anchored Human Prion Protein. Biophys J 2016; 109:2090-100. [PMID: 26588568 DOI: 10.1016/j.bpj.2015.10.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 10/04/2015] [Accepted: 10/08/2015] [Indexed: 11/29/2022] Open
Abstract
Prion diseases are fatal neurodegenerative disorders, which are characterized by the accumulation of misfolded prion protein (PrPSc) converted from a normal host cellular prion protein (PrPC). Experimental studies suggest that PrPC is enriched with α-helical structure, whereas PrPSc contains a high proportion of β-sheet. In this study, we report the impact of N-glycosylation and the membrane on the secondary structure stability utilizing extensive microsecond molecular dynamics simulations. Our results reveal that the HB (residues 173 to 194) C-terminal fragment undergoes conformational changes and helix unfolding in the absence of membrane environments because of the competition between protein backbone intramolecular and protein-water intermolecular hydrogen bonds as well as its intrinsic instability originated from the amino acid sequence. This initiation of the unfolding process of PrPC leads to a subsequent increase in the length of the HB-HC loop (residues 195 to 199) that may trigger larger rigid body motions or further unfolding around this region. Continuous interactions between prion protein and the membrane not only constrain the protein conformation but also decrease the solvent accessibility of the backbone atoms, thereby stabilizing the secondary structure, which is enhanced by N-glycosylation via additional interactions between the N-glycans and the membrane surface.
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Affiliation(s)
- Emilia L Wu
- Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, Lawrence, Kansas
| | - Yifei Qi
- Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, Lawrence, Kansas
| | - Soohyung Park
- Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, Lawrence, Kansas
| | - Sairam S Mallajosyula
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland; Department of Chemistry, Indian Institute of Technology Gandhinagar, Chandkheda, Ahmedabad, Gujarat, India
| | - Alexander D MacKerell
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Chandkheda, Ahmedabad, Gujarat, India
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering and the Biophysics Program, The University of Maryland, College Park, Maryland
| | - Wonpil Im
- Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, Lawrence, Kansas.
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18
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Yamamoto N. Hot Spot of Structural Ambivalence in Prion Protein Revealed by Secondary Structure Principal Component Analysis. J Phys Chem B 2014; 118:9826-33. [DOI: 10.1021/jp5034245] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Norifumi Yamamoto
- Department of Life and Environmental
Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino 275-0016, Japan
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19
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Rufo CM, Moroz YS, Moroz OV, Stöhr J, Smith TA, Hu X, DeGrado WF, Korendovych IV. Short peptides self-assemble to produce catalytic amyloids. Nat Chem 2014; 6:303-9. [PMID: 24651196 PMCID: PMC3996680 DOI: 10.1038/nchem.1894] [Citation(s) in RCA: 461] [Impact Index Per Article: 46.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 02/12/2014] [Indexed: 12/22/2022]
Abstract
Enzymes fold into unique three-dimensional structures, which underlie their remarkable catalytic properties. The requirement to adopt a stable, folded conformation is likely to contribute to their relatively large size (>10,000 Da). However, much shorter peptides can achieve well-defined conformations through the formation of amyloid fibrils. To test whether short amyloid-forming peptides might in fact be capable of enzyme-like catalysis, we designed a series of seven-residue peptides that act as Zn(2+)-dependent esterases. Zn(2+) helps stabilize the fibril formation, while also acting as a cofactor to catalyse acyl ester hydrolysis. These results indicate that prion-like fibrils are able to not only catalyse their own formation, but they can also catalyse chemical reactions. Thus, they might have served as intermediates in the evolution of modern-day enzymes. These results also have implications for the design of self-assembling nanostructured catalysts including ones containing a variety of biological and non-biological metal ions.
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Affiliation(s)
- Caroline M. Rufo
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, USA
| | - Yurii S. Moroz
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, USA
| | - Olesia V. Moroz
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, USA
| | - Jan Stöhr
- Institute for Neurodegenerative Diseases and Department of Neurology, University of California – San Francisco, San Francisco, CA 94143, USA
| | - Tyler A. Smith
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, USA
| | - Xiaozhen Hu
- Department of Pharmaceutical Chemistry, University of California – San Francisco, San Francisco, CA 94158, USA
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry, University of California – San Francisco, San Francisco, CA 94158, USA
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20
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A common mechanism underlying amyloid fibrillation and protein crystallization revealed by the effects of ultrasonication. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:2640-6. [DOI: 10.1016/j.bbapap.2013.09.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 09/20/2013] [Accepted: 09/23/2013] [Indexed: 11/17/2022]
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21
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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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22
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Chatterjee B, Lee CY, Lin C, Chen EHL, Huang CL, Yang CC, Chen RPY. Amyloid core formed of full-length recombinant mouse prion protein involves sequence 127-143 but not sequence 107-126. PLoS One 2013; 8:e67967. [PMID: 23844138 PMCID: PMC3700907 DOI: 10.1371/journal.pone.0067967] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 05/23/2013] [Indexed: 12/23/2022] Open
Abstract
The principal event underlying the development of prion disease is the conversion of soluble cellular prion protein (PrP(C)) into its disease-causing isoform, PrP(Sc). This conversion is associated with a marked change in secondary structure from predominantly α-helical to a high β-sheet content, ultimately leading to the formation of aggregates consisting of ordered fibrillar assemblies referred to as amyloid. In vitro, recombinant prion proteins and short prion peptides from various species have been shown to form amyloid under various conditions and it has been proposed that, theoretically, any protein and peptide could form amyloid under appropriate conditions. To identify the peptide segment involved in the amyloid core formed from recombinant full-length mouse prion protein mPrP(23-230), we carried out seed-induced amyloid formation from recombinant prion protein in the presence of seeds generated from the short prion peptides mPrP(107-143), mPrP(107-126), and mPrP(127-143). Our results showed that the amyloid fibrils formed from mPrP(107-143) and mPrP(127-143), but not those formed from mPrP(107-126), were able to seed the amyloidogenesis of mPrP(23-230), showing that the segment residing in sequence 127-143 was used to form the amyloid core in the fibrillization of mPrP(23-230).
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Affiliation(s)
| | - Chung-Yu Lee
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Chen Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Eric H.-L. Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chao-Li Huang
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Chien-Chih Yang
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Rita P.-Y. Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- * E-mail:
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23
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Zhou X, Gao Q, Feng W, Pan K. Immobilization of Yarrowia lipolyticaLipase on Bamboo Charcoal to Resolve ( R, S)-Phenylethanol in Organic Medium. Chem Eng Technol 2013. [DOI: 10.1002/ceat.201200672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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24
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Chuang CC, Liao TY, Chen EHL, Chen RPY. How do amino acid substitutions affect the amyloidogenic properties and seeding efficiency of prion peptides. Amino Acids 2013; 45:785-96. [PMID: 23736988 PMCID: PMC3776267 DOI: 10.1007/s00726-013-1522-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Accepted: 05/22/2013] [Indexed: 11/28/2022]
Abstract
The amino acid sequences in the amyloidogenic region (amino acids 108–144) of several mammalian prion proteins were compared and variations were found to occur at residues 109 (M or L), 112 (M or V), 129 (M, V, or L), 135 (N or S), 138 (M, L, or I), 139 (M or I), and 143 (N or S). Using the bovine PrP peptide (residues 108–144 based on the numbering of the human prion protein sequence) as a control peptide, several peptides with one amino acid differing from that of the bovine PrP peptide at residues 109, 112, 135, 138, 139, or 143 and several mammalian PrP peptides were synthesized, and the effects of these amino acid substitutions on the amyloidogenic properties of these peptides were compared and discussed on the basis of the chemical and structural properties of amino acids. Our results showed that the V112M substitution accelerated nucleation of amyloidogenesis, while the N143S and I139M substitutions retarded nucleation. These effects tended to cancel each other out when two substitutions with opposite effects were present on the same peptide. Moreover, acceleration or inhibition of nucleation was not necessarily correlated with effect on seeding efficiency. Using amyloid fibrils prepared from the bovine PrP peptide as seeds, the seeding efficiency for the monomer peptides with the M129L, S135N, N143S, or I139M substitution was decreased compared to that for bPrP peptide. Of all the mammalian peptides used in this study, the dog, mule deer, and pig PrP peptides had the lowest seeding efficiencies.
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Affiliation(s)
- Chi-Chen Chuang
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, 106, Taiwan, ROC
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25
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Distinguishing crystal-like amyloid fibrils and glass-like amorphous aggregates from their kinetics of formation. Proc Natl Acad Sci U S A 2012; 109:14446-51. [PMID: 22908252 DOI: 10.1073/pnas.1208228109] [Citation(s) in RCA: 220] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Amyloid fibrils and amorphous aggregates are two types of aberrant aggregates associated with protein misfolding diseases. Although they differ in morphology, the two forms are often treated indiscriminately. β(2)-microglobulin (β2m), a protein responsible for dialysis-related amyloidosis, forms amyloid fibrils or amorphous aggregates depending on the NaCl concentration at pH 2.5. We compared the kinetics of their formation, which was monitored by measuring thioflavin T fluorescence, light scattering, and 8-anilino-1-naphthalenesulfonate fluorescence. Thioflavin T fluorescence specifically monitors amyloid fibrillation, whereas light scattering and 8-anilino-1-naphthalenesulfonate fluorescence monitor both amyloid fibrillation and amorphous aggregation. The amyloid fibrils formed via a nucleation-dependent mechanism in a supersaturated solution, analogous to crystallization. The lag phase of fibrillation was reduced upon agitation with stirring or ultrasonic irradiation, and disappeared by seeding with preformed fibrils. In contrast, the glass-like amorphous aggregates formed rapidly without a lag phase. Neither agitation nor seeding accelerated the amorphous aggregation. Thus, by monitoring the kinetics, we can distinguish between crystal-like amyloid fibrils and glass-like amorphous aggregates. Solubility and supersaturation will be key factors for further understanding the aberrant aggregation of proteins.
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26
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Yamaguchi KI, Matsumoto T, Kuwata K. Proper calibration of ultrasonic power enabled the quantitative analysis of the ultrasonication-induced amyloid formation process. Protein Sci 2011; 21:38-49. [PMID: 22095682 DOI: 10.1002/pro.755] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 10/02/2011] [Accepted: 10/07/2011] [Indexed: 12/12/2022]
Abstract
To elucidate the mechanisms of ultrasonication on the amyloid fibril formation, we quantitatively determined the ultrasonic power using both calorimetry and potassium iodide (KI) oxidation, and under the properly calibrated ultrasonic power, we investigated the ultasonication-induced amyloid formation process of the mouse prion protein (mPrP(23-231)). These methods revealed that the ultrasonic power in our system ranged from 0.3 to 2.7 W but entirely dependent on the positions of the ultrasonic stage. Intriguingly, the nucleation time of the amyloid fibrils was found to be shortened almost proportionally to the ultrasonic power, indicating that the probability of the occurrence of nucleus formation increases proportionally to the ultrasonic power. Moreover, mPrP(23-231) formed two types of aggregates: rigid fibrils and short fibrils with disordered aggregates, depending on the ultrasonic power. The nucleation of rigid fibrils required an ultrasonic power larger than 1.5 W. While at the strong ultrasonic power larger than 2.6 W, amyloid fibrils were formed early, but simultaneously fine fragmentation of fibrils occurred. Thus, an ultrasonic power of approximately 2.0 W would be suitable for the formation of rigid mPrP(23-231) fibrils under the conditions utilized (ultrasonication applied for 30 s every 9 min). As ultrasonication has been widely used to amplify the scrapie form of the prion protein, or other amyloids in vitro, the calorimetry and KI oxidation methods proposed here might help determining the adequate ultrasonic powers necessary to amplify them efficiently.
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Affiliation(s)
- Kei-ichi Yamaguchi
- Center for Emerging Infectious Diseases, Gifu University, Yanagido 1-1, Gifu, Japan
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27
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Liao TY, Lee LYL, Chen RPY. Leu138 in bovine prion peptide fibrils is involved in seeding discrimination related to codon 129 M/V polymorphism in the prion peptide seeding experiment. FEBS J 2011; 278:4351-61. [DOI: 10.1111/j.1742-4658.2011.08353.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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28
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So M, Yagi H, Sakurai K, Ogi H, Naiki H, Goto Y. Ultrasonication-Dependent Acceleration of Amyloid Fibril Formation. J Mol Biol 2011; 412:568-77. [DOI: 10.1016/j.jmb.2011.07.069] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2011] [Revised: 06/09/2011] [Accepted: 07/29/2011] [Indexed: 11/16/2022]
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29
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Pal P, Mahato M, Kamilya T, Tah B, Sarkar R, Talapatra GB. Fibrillation of Egg White Ovalbumin: A Pathway via Biomineralization. J Phys Chem B 2011; 115:4259-65. [DOI: 10.1021/jp200607x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Prabir Pal
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700 032, India
| | - Mrityunjoy Mahato
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700 032, India
| | | | - Bidisha Tah
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700 032, India
| | | | - G. B. Talapatra
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700 032, India
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30
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Li L, Feng W, Ji P. Protein adsorption on functionalized multiwalled carbon nanotubes with amino-cyclodextrin. AIChE J 2011. [DOI: 10.1002/aic.12543] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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31
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Pal P, Mahato M, Kamilya T, Talapatra GB. Interaction of glucose with hemoglobin: a study in aqueous solution and at the air–water interface using the Langmuir–Blodgett technique. Phys Chem Chem Phys 2011; 13:9385-96. [DOI: 10.1039/c0cp02277b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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32
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Johansson J, Nerelius C, Willander H, Presto J. Conformational preferences of non-polar amino acid residues: an additional factor in amyloid formation. Biochem Biophys Res Commun 2010; 402:515-8. [PMID: 20971069 DOI: 10.1016/j.bbrc.2010.10.062] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Accepted: 10/18/2010] [Indexed: 11/18/2022]
Abstract
Amyloid consists of β-sheet polymers and is associated with disease and with functional assemblies. Amyloid-forming proteins differ widely in native structures and sequences. We describe here how conformational preferences of non-polar amino acid residues can affect amyloid formation. The most non-polar residues promote either β-strands (Val, Ile, Phe, and Cys, VIFC) or α-helices (Leu, Ala, and Met, LAM), while the most polar residues promote only α-helices. For 12 proteins associated with disease, the localizations of the amyloid core regions are known. Eleven of these contain segments that are biased for VIFC, but essentially lack segments that are biased for LAM. For the amyloid β-peptide associated with Alzheimer's disease and an amyloidogenic fragment of the prion protein, observed effects of mutations support that VIFC bias favors formation of β-sheet aggregates and amyloid, while LAM bias prevents it. VIFC and LAM profiles combine information on secondary structure propensities and polarity, and add a simple criterion to the prediction of amyloidogenic regions.
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Affiliation(s)
- Jan Johansson
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, The Biomedical Centre, 751 23 Uppsala, Sweden.
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33
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Hosszu LLP, Tattum MH, Jones S, Trevitt CR, Wells MA, Waltho JP, Collinge J, Jackson GS, Clarke AR. The H187R mutation of the human prion protein induces conversion of recombinant prion protein to the PrP(Sc)-like form. Biochemistry 2010; 49:8729-38. [PMID: 20718410 DOI: 10.1021/bi100572j] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Prion diseases are associated with a conformational switch in the prion protein (PrP) from its normal cellular form (denoted PrP(C)) to a disease-associated "scrapie" form (PrP(Sc)). A number of PrP(Sc)-like conformations can be generated by incubating recombinant PrP(C) at low pH, indicating that protonation of key residues is likely to destabilize PrP(C), facilitating its conversion to PrP(Sc). Here, we examine the stability of human PrP(C) with pH and find that PrP(C) fold stability is significantly reduced by the protonation of two histidine residues, His187 and His155. Mutation of His187 to an arginine, which imposes a permanently positively charged residue in this region of the protein, has a dramatic effect on the folding of PrP(C), resulting in a molecule that displays a markedly increased propensity to oligomerize. The oligomeric form is characterized by an increased β-sheet content, loss of fixed side chain interactions, and partial proteinase resistance. Hence, the protonation state of H187 appears to be crucial in determining the conformation of PrP; the unprotonated form favors native PrP(C), while the protonated form favors PrP(Sc)-like conformations. These results are relevant to the pathogenic H187R mutation found in humans, which is associated with an inherited prion disease [also termed Gerstmann-Sträussler-Scheinker (GSS) syndrome] with unusual features such as childhood neuropsychiatric illness. Our data imply that the intrinsic instability of the PrP(C) conformation in this variant is caused by a positive charge at this site in the protein. This mutation is distinct from all those associated with GSS, which have much more subtle physical consequences. The degree of instability might be the cause of the unusually early onset of mental disturbance in affected individuals.
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Affiliation(s)
- Laszlo L P Hosszu
- MRC Prion Unit, UCL Department of Neurodegenerative Disease, Institute of Neurology, Queen Square, London WC1N 3BG, UK
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34
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Zhang J. Optimal molecular structures of prion AGAAAAGA amyloid fibrils formatted by simulated annealing. J Mol Model 2010; 17:173-9. [PMID: 20411399 DOI: 10.1007/s00894-010-0691-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Accepted: 02/11/2010] [Indexed: 02/04/2023]
Abstract
To date, there is little structural data available on the AGAAAAGA palindrome in the hydrophobic region (113-120) of prion proteins, although many experimental studies have shown that this region has amyloid fibril forming properties. This region belongs to the N-terminal unstructured region (1-123) of prions, the structure of which has proved hard to determine using NMR or X-ray crystallography. This paper reports the successful construction of three amyloid fibril models for this region. The models were formatted by standard simulated annealing using suitable templates from the Protein Data Bank, and were refined using several traditional optimization methods within AMBER. Because the NMR or X-ray structure of the hydrophobic region AGAAAAGA of prion proteins has not yet been determined, these models can be used as a reference for experimental studies on this region. The results presented here confirm standard simulated annealing as an effective tool in molecular modeling. The three constructed models for amyloid fibrils may be useful in furthering the goals of medicinal chemistry in this field.
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Affiliation(s)
- Jiapu Zhang
- Victorian Life Sciences Computation Initiative, The University of Melbourne, 1-3 Hull Road, Croydon, Victoria, VIC 3136, Australia.
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35
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Ji P, Tan H, Xu X, Feng W. Lipase covalently attached to multiwalled carbon nanotubes as an efficient catalyst in organic solvent. AIChE J 2010. [DOI: 10.1002/aic.12180] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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36
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Ji HF, Zhang HY. beta-sheet constitution of prion proteins. Trends Biochem Sci 2010; 35:129-34. [PMID: 20060302 DOI: 10.1016/j.tibs.2009.12.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2009] [Revised: 12/07/2009] [Accepted: 12/09/2009] [Indexed: 11/19/2022]
Abstract
Structural information regarding normal prion protein (PrP(C)) and the scrapie isoform (PrP(Sc)) is of vital importance for elucidating the pathogenesis of prion diseases (PDs). Despite successful determination of the three-dimensional structures of PrP(C), the structural details of PrP(Sc) remain elusive. Nevertheless, accumulated evidence indicates that beta-sheets comprise the basic building blocks of PrP(Sc). Consensus has been reached about the beta-sheet constitution of the N-terminus of PrP, but the constitution of C-terminal beta-sheets is heavily debated. By evaluating the most recent observations regarding the dynamics and structures of PrP, we propose that helix 2 is more likely than helices 1 and 3 to participate in beta-sheet formation. This hypothesis also provides clues to explaining an intriguing phenomenon in prion biology-the lack of PDs in non-mammals.
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Affiliation(s)
- Hong-Fang Ji
- Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Center for Advanced Study, Shandong University of Technology, Zibo 255049, PR China.
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Mahato M, Pal P, Kamilya T, Sarkar R, Chaudhuri A, Talapatra GB. Influence of KCl on the interfacial activity and conformation of hemoglobin studied by Langmuir–Blodgett technique. Phys Chem Chem Phys 2010; 12:12997-3006. [DOI: 10.1039/c0cp00344a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Mahato M, Pal P, Kamilya T, Sarkar R, Talapatra GB. pH Induced Structural Modulation and Interfacial Activity of Hemoglobin at the Air/Water Interface. J Phys Chem B 2009; 114:495-502. [DOI: 10.1021/jp908081r] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Mrityunjoy Mahato
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India, and Department of Physics, Narajole Raj College, Narajole, Paschim Medinipur-721211, India
| | - Prabir Pal
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India, and Department of Physics, Narajole Raj College, Narajole, Paschim Medinipur-721211, India
| | - Tapanendu Kamilya
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India, and Department of Physics, Narajole Raj College, Narajole, Paschim Medinipur-721211, India
| | - Ratan Sarkar
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India, and Department of Physics, Narajole Raj College, Narajole, Paschim Medinipur-721211, India
| | - G. B. Talapatra
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India, and Department of Physics, Narajole Raj College, Narajole, Paschim Medinipur-721211, India
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Yamamoto N, Kuwata K. Regulating the Conformation of Prion Protein through Ligand Binding. J Phys Chem B 2009; 113:12853-6. [DOI: 10.1021/jp905572w] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Norifumi Yamamoto
- Division of Prion Research, Center for Emerging Infectious Diseases, Gifu University, 1-1 Yanagido, Gifu 501-1194, Japan, and CREST Project, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Kazuo Kuwata
- Division of Prion Research, Center for Emerging Infectious Diseases, Gifu University, 1-1 Yanagido, Gifu 501-1194, Japan, and CREST Project, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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Ultrasonication-dependent production and breakdown lead to minimum-sized amyloid fibrils. Proc Natl Acad Sci U S A 2009; 106:11119-24. [PMID: 19564620 DOI: 10.1073/pnas.0901422106] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Because of the insolubility and polymeric properties of amyloid fibrils, techniques used conventionally to analyze protein structure and dynamics have often been hampered. Ultrasonication can induce the monomeric solution of amyloidogenic proteins to form amyloid fibrils. However, ultrasonication can break down preformed fibrils into shorter fibrils. Here, combining these 2 opposing effects on beta(2)-microglobulin (beta2-m), a protein responsible for dialysis-related amyloidosis, we present that ultrasonication pulses are useful for preparing monodispersed amyloid fibrils of minimal size with an average molecular weight of approximately 1,660,000 (140-mer). The production of minimal and monodispersed fibrils is achieved by the free energy minimum under competition between fibril production and breakdown. The small homogeneous fibrils will be of use for characterizing the structure and dynamics of amyloid fibrils, advancing molecular understanding of amyloidosis.
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Chebaro Y, Derreumaux P. The Conversion of Helix H2 to β-Sheet Is Accelerated in the Monomer and Dimer of the Prion Protein upon T183A Mutation. J Phys Chem B 2009; 113:6942-8. [DOI: 10.1021/jp900334s] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Yassmine Chebaro
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico Chimique et Université Paris Diderot-Paris 7, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico Chimique et Université Paris Diderot-Paris 7, 13 rue Pierre et Marie Curie, 75005 Paris, France
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Palladino P, Ronga L, Benedetti E, Rossi F, Ragone R. Peptide Fragment Approach to Prion Misfolding: The Alpha-2 Domain. Int J Pept Res Ther 2009. [DOI: 10.1007/s10989-009-9171-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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