1
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Shi C, Kaffy J, Ha-Duong T, Gallard JF, Pruvost A, Mabondzo A, Ciccone L, Ongeri S, Tonali N. Proteolytically Stable Diaza-Peptide Foldamers Mimic Helical Hot Spots of Protein-Protein Interactions and Act as Natural Chaperones. J Med Chem 2023; 66:12005-12017. [PMID: 37632446 DOI: 10.1021/acs.jmedchem.3c00611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/28/2023]
Abstract
A novel class of peptidomimetic foldamers based on diaza-peptide units are reported. Circular dichroism, attenuated total reflection -Fourier transform infrared, NMR, and molecular dynamics studies demonstrate that unlike the natural parent nonapeptide, the specific incorporation of one diaza-peptide unit at the N-terminus allows helical folding in water, which is further reinforced by the introduction of a second unit at the C-terminus. The ability of these foldamers to resist proteolysis, to mimic the small helical hot spot of transthyretin-amyloid β (Aβ) cross-interaction, and to decrease pathological Aβ aggregation demonstrates that the introduction of diaza-peptide units is a valid approach for designing mimics or inhibitors of protein-protein interaction and other therapeutic peptidomimetics. This study also reveals that small peptide foldamers can play the same role as physiological chaperone proteins and opens a new way to design inhibitors of amyloid protein aggregation, a hallmark of more than 20 serious human diseases such as Alzheimer's disease.
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Affiliation(s)
- Chenghui Shi
- Université Paris-Saclay, CNRS, BioCIS, Bat. Henri Moissan, 17 av. des Sciences, 91400 Orsay, France
| | - Julia Kaffy
- Université Paris-Saclay, CNRS, BioCIS, Bat. Henri Moissan, 17 av. des Sciences, 91400 Orsay, France
| | - Tâp Ha-Duong
- Université Paris-Saclay, CNRS, BioCIS, Bat. Henri Moissan, 17 av. des Sciences, 91400 Orsay, France
| | - Jean-François Gallard
- Equipe Biologie et Chimie Structurales, Dept Chimie et Biologie Structurales et Analytiques, ICSN CNRS, Université Paris Saclay, 1 avenue de la terrasse, 91190 Gif sur Yvette, France
| | - Alain Pruvost
- CEA, INRAE, Département Médicaments et Technologies pour La Santé, Université Paris-Saclay, SPI 91191 Gif-sur-Yvette, France
| | - Aloise Mabondzo
- CEA, INRAE, Département Médicaments et Technologies pour La Santé, Université Paris-Saclay, SPI 91191 Gif-sur-Yvette, France
| | - Lidia Ciccone
- Department of Pharmacy, University of Pisa, 56126 Pisa, Italy
| | - Sandrine Ongeri
- Université Paris-Saclay, CNRS, BioCIS, Bat. Henri Moissan, 17 av. des Sciences, 91400 Orsay, France
| | - Nicolo Tonali
- Université Paris-Saclay, CNRS, BioCIS, Bat. Henri Moissan, 17 av. des Sciences, 91400 Orsay, France
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2
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IKK2/NF-κB Activation in Astrocytes Reduces amyloid β Deposition: A Process Associated with Specific Microglia Polarization. Cells 2021; 10:cells10102669. [PMID: 34685649 PMCID: PMC8534251 DOI: 10.3390/cells10102669] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/29/2021] [Accepted: 10/04/2021] [Indexed: 02/06/2023] Open
Abstract
Alzheimer's disease (AD) is a common neurodegenerative disease that is accompanied by pronounced neuroinflammatory responses mainly characterized by marked microgliosis and astrogliosis. However, it remains open as to how different aspects of astrocytic and microglial activation affect disease progression. Previously, we found that microglia expansion in the spinal cord, initiated by IKK2/NF-κB activation in astrocytes, exhibits stage-dependent beneficial effects on the progression of amyotrophic lateral sclerosis. Here, we investigated the impact of NF-κB-initiated neuroinflammation on AD pathogenesis using the APP23 mouse model of AD in combination with conditional activation of IKK2/NF-κB signaling in astrocytes. We show that NF-κB activation in astrocytes triggers a distinct neuroinflammatory response characterized by striking astrogliosis as well as prominent microglial reactivity. Immunohistochemistry and Congo red staining revealed an overall reduction in the size and number of amyloid plaques in the cerebral cortex and hippocampus. Interestingly, isolated primary astrocytes and microglia cells exhibit specific marker gene profiles which, in the case of microglia, point to an enhanced plaque clearance capacity. In contrast, direct IKK2/NF-κB activation in microglia results in a pro-inflammatory polarization program. Our findings suggest that IKK2/NF-κB signaling in astrocytes may activate paracrine mechanisms acting on microglia function but also on APP processing in neurons.
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3
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Gao L, Wang W, Wang X, Yang F, Xie L, Shen J, Brimble MA, Xiao Q, Yao SQ. Fluorescent probes for bioimaging of potential biomarkers in Parkinson's disease. Chem Soc Rev 2021; 50:1219-1250. [DOI: 10.1039/d0cs00115e] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This review comprehensively summarizes various types of fluorescent probes for PD and their applications for detection of various PD biomarkers.
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Affiliation(s)
- Liqian Gao
- School of Pharmaceutical Sciences (Shenzhen)
- Sun Yat-sen University
- Shenzhen, 518107
- P. R. China
- Department of Chemistry
| | - Wei Wang
- School of Pharmaceutical Sciences (Shenzhen)
- Sun Yat-sen University
- Shenzhen, 518107
- P. R. China
- Department of Chemistry
| | - Xuan Wang
- School of Pharmaceutical Sciences (Shenzhen)
- Sun Yat-sen University
- Shenzhen, 518107
- P. R. China
| | - Fen Yang
- School of Pharmaceutical Sciences (Shenzhen)
- Sun Yat-sen University
- Shenzhen, 518107
- P. R. China
| | - Liuxing Xie
- School of Pharmaceutical Sciences (Shenzhen)
- Sun Yat-sen University
- Shenzhen, 518107
- P. R. China
| | - Jun Shen
- Department of Radiology
- Sun Yat-Sen Memorial Hospital
- Sun Yat-Sen University
- Guangzhou
- P. R. China
| | - Margaret A. Brimble
- School of Chemical Sciences
- The University of Auckland
- Auckland 1010
- New Zealand
| | - Qicai Xiao
- School of Pharmaceutical Sciences (Shenzhen)
- Sun Yat-sen University
- Shenzhen, 518107
- P. R. China
- Department of Chemistry
| | - Shao Q. Yao
- Department of Chemistry
- National University of Singapore
- Singapore
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4
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Mehringer J, Hofmann E, Touraud D, Koltzenburg S, Kellermeier M, Kunz W. Salting-in and salting-out effects of short amphiphilic molecules: a balance between specific ion effects and hydrophobicity. Phys Chem Chem Phys 2021; 23:1381-1391. [DOI: 10.1039/d0cp05491g] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Salting-in or salting-out tendencies depend on a balance between headgroup-specific ion effects and the hydrophobicity of the tail.
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Affiliation(s)
- Johannes Mehringer
- Institute of Theoretical and Physical Chemistry
- University of Regensburg
- 93053 Regensburg
- Germany
| | - Evamaria Hofmann
- Institute of Theoretical and Physical Chemistry
- University of Regensburg
- 93053 Regensburg
- Germany
| | - Didier Touraud
- Institute of Theoretical and Physical Chemistry
- University of Regensburg
- 93053 Regensburg
- Germany
| | | | | | - Werner Kunz
- Institute of Theoretical and Physical Chemistry
- University of Regensburg
- 93053 Regensburg
- Germany
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5
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Salient Features of Monomeric Alpha-Synuclein Revealed by NMR Spectroscopy. Biomolecules 2020; 10:biom10030428. [PMID: 32164323 PMCID: PMC7175124 DOI: 10.3390/biom10030428] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/09/2020] [Accepted: 03/04/2020] [Indexed: 12/17/2022] Open
Abstract
Elucidating the structural details of proteins is highly valuable and important for the proper understanding of protein function. In the case of intrinsically disordered proteins (IDPs), however, obtaining the structural details is quite challenging, as the traditional structural biology tools have only limited use. Nuclear magnetic resonance (NMR) is a unique experimental tool that provides ensemble conformations of IDPs at atomic resolution, and when studying IDPs, a slightly different experimental strategy needs to be employed than the one used for globular proteins. We address this point by reviewing many NMR investigations carried out on the α-synuclein protein, the aggregation of which is strongly correlated with Parkinson’s disease.
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6
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Ardah MT, Ghanem SS, Abdulla SA, Lv G, Emara MM, Paleologou KE, Vaikath NN, Lu JH, Li M, Vekrellis K, Eliezer D, El-Agnaf OMA. Inhibition of alpha-synuclein seeded fibril formation and toxicity by herbal medicinal extracts. BMC Complement Med Ther 2020; 20:73. [PMID: 32143619 PMCID: PMC7076823 DOI: 10.1186/s12906-020-2849-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 02/11/2020] [Indexed: 12/15/2022] Open
Abstract
Background Recent studies indicated that seeded fibril formation and toxicity of α-synuclein (α-syn) play a main role in the pathogenesis of certain diseases including Parkinson’s disease (PD), multiple system atrophy, and dementia with Lewy bodies. Therefore, examination of compounds that abolish the process of seeding is considered a key step towards therapy of several synucleinopathies. Methods Using biophysical, biochemical and cell-culture-based assays, assessment of eleven compounds, extracted from Chinese medicinal herbs, was performed in this study for their effect on α-syn fibril formation and toxicity caused by the seeding process. Results Salvianolic acid B and dihydromyricetin were the two compounds that strongly inhibited the fibril growth and neurotoxicity of α-syn. In an in-vitro cell model, these compounds decreased the insoluble phosphorylated α-syn and aggregation. Also, in primary neuronal cells, these compounds showed a reduction in α-syn aggregates. Both compounds inhibited the seeded fibril growth with dihydromyricetin having the ability to disaggregate preformed α-syn fibrils. In order to investigate the inhibitory mechanisms of these two compounds towards fibril formation, we demonstrated that salvianolic acid B binds predominantly to monomers, while dihydromyricetin binds to oligomeric species and to a lower extent to monomers. Remarkably, these two compounds stabilized the soluble non-toxic oligomers lacking β-sheet content after subjecting them to proteinase K digestion. Conclusions Eleven compounds were tested but only two showed inhibition of α-syn aggregation, seeded fibril formation and toxicity in vitro. These findings highlight an essential beginning for development of new molecules in the field of synucleinopathies treatment.
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Affiliation(s)
- Mustafa T Ardah
- Department of Biochemistry, College of Medicine and Health Science, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Simona S Ghanem
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Education City, Qatar Foundation, P.O. Box 5825, Doha, Qatar
| | - Sara A Abdulla
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Education City, Qatar Foundation, P.O. Box 5825, Doha, Qatar
| | - Guohua Lv
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, USA
| | - Mohamed M Emara
- Basic Medical Sciences Department, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Katerina E Paleologou
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Nishant N Vaikath
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Education City, Qatar Foundation, P.O. Box 5825, Doha, Qatar
| | - Jia-Hong Lu
- State Key Lab of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao, China
| | - Min Li
- School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - Konstantinos Vekrellis
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, 11527, Athens, Greece
| | - David Eliezer
- Department of Biochemistry, Weill Cornell Medical College, New York, NY, USA
| | - Omar M A El-Agnaf
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Education City, Qatar Foundation, P.O. Box 5825, Doha, Qatar.
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7
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Waudby CA, Ouvry M, Davis B, Christodoulou J. Two-dimensional NMR lineshape analysis of single, multiple, zero and double quantum correlation experiments. JOURNAL OF BIOMOLECULAR NMR 2020; 74:95-109. [PMID: 31915980 PMCID: PMC7015968 DOI: 10.1007/s10858-019-00297-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 12/31/2019] [Indexed: 05/05/2023]
Abstract
NMR spectroscopy provides a powerful approach for the characterisation of chemical exchange and molecular interactions by analysis of series of experiments acquired over the course of a titration measurement. The appearance of NMR resonances undergoing chemical exchange depends on the frequency difference relative to the rate of exchange, and in the case of one-dimensional experiments chemical exchange regimes are well established and well known. However, two-dimensional experiments present additional complexity, as at least one additional frequency difference must be considered. Here we provide a systematic classification of chemical exchange regimes in two-dimensional NMR spectra. We highlight important differences between exchange in HSQC and HMQC experiments, that on a practical level result in more severe exchange broadening in HMQC spectra, but show that complementary alternatives to the HMQC are available in the form of HZQC and HDQC experiments. We present the longitudinal relaxation optimised SOFAST-H(Z/D)QC experiment for the simultaneous acquisition of sensitivity-enhanced HZQC and HDQC spectra, and the longitudinal and transverse relaxation optimised BEST-ZQ-TROSY for analysis of large molecular weight systems. We describe the application of these experiments to the characterisation of the interaction between the Hsp90 N-terminal domain and a small molecule ligand, and show that the independent analysis of HSQC, HMQC, HZQC and HDQC experiments provides improved confidence in the fitted dissociation constant and dissociation rate. Joint analysis of such data may provide improved sensitivity to detect and analyse more complex multi-state interaction mechanisms such as induced fit or conformational selection.
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Affiliation(s)
- Christopher A Waudby
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London, UK.
| | - Margaux Ouvry
- Biotechnologie, Sanofi, Route d'Avignon, 30390, Aramon, France
| | - Ben Davis
- Vernalis (R&D) Limited, Granta Park, Great Abington, UK
| | - John Christodoulou
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, London, UK
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8
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Ptak CP, Akif M, Hsieh C, Devarajan A, He P, Xu Y, Oswald RE, Chang Y. Comparative screening of recombinant antigen thermostability for improved leptospirosis vaccine design. Biotechnol Bioeng 2018; 116:260-271. [DOI: 10.1002/bit.26864] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 10/29/2018] [Accepted: 11/07/2018] [Indexed: 12/29/2022]
Affiliation(s)
- Christopher P. Ptak
- Department of Population Medicine and Diagnostic SciencesCollege of Veterinary Medicine, Cornell UniversityIthaca New York
- Department of Molecular MedicineCollege of Veterinary Medicine, Cornell UniversityIthaca New York
| | - Mohd. Akif
- Department of Population Medicine and Diagnostic SciencesCollege of Veterinary Medicine, Cornell UniversityIthaca New York
- Department of BiochemistryUniversity of HyderabadHyderabad India
| | - Ching‐Lin Hsieh
- Department of Population Medicine and Diagnostic SciencesCollege of Veterinary Medicine, Cornell UniversityIthaca New York
| | - Alex Devarajan
- Department of Molecular MedicineCollege of Veterinary Medicine, Cornell UniversityIthaca New York
| | - Ping He
- Department of Microbiology and ImmunologyInstitutes of Medical Science, Shanghai Jiao Tong University School of MedicineShanghai China
| | - Yinghua Xu
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug ControlBeijing China
| | - Robert E. Oswald
- Department of Molecular MedicineCollege of Veterinary Medicine, Cornell UniversityIthaca New York
| | - Yung‐Fu Chang
- Department of Population Medicine and Diagnostic SciencesCollege of Veterinary Medicine, Cornell UniversityIthaca New York
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9
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Wójcik S, Birol M, Rhoades E, Miranker AD, Levine ZA. Targeting the Intrinsically Disordered Proteome Using Small-Molecule Ligands. Methods Enzymol 2018; 611:703-734. [DOI: 10.1016/bs.mie.2018.09.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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10
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Zheng X, Xu Z, Li H, Fu H. A sensitive probe for amyloid fibril detection with strong fluorescence and early response. RSC Adv 2018; 8:15870-15875. [PMID: 35542196 PMCID: PMC9080103 DOI: 10.1039/c8ra00751a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 03/29/2018] [Indexed: 02/05/2023] Open
Abstract
We synthesized a new probe, 4-[2-(2-naphthyl)-(E)-ethenyl]-benzyl(triphenyl)phosphonium bromide (NEB), to detect the formation of amyloid fibrils of bovine insulin. The fluorescence intensity of NEB in the presence of insulin fibrils was 30 times higher than that before fibrillation, with the fluorescence quantum yield increased from 2.5% to 78%. In comparison with the commercially available probe, thioflavin T (ThT), NEB exhibits a 10 times stronger fluorescence and a shorter identification lag phase for detecting insulin fibrillation, indicating a higher sensitivity in detection of insulin oligomers and fibrils. We synthesized a new probe, 4-[2-(2-naphthyl)-(E)-ethenyl]-benzyl(triphenyl)phosphonium bromide (NEB), to detect the formation of amyloid fibrils of bovine insulin.![]()
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Affiliation(s)
- Xiaolin Zheng
- Beijing Key Laboratory for Optical Materials and Photonic Devices
- Department of Chemistry
- Capital Normal University
- Beijing 100048
- People's Republic of China
| | - Zhenzhen Xu
- Beijing Key Laboratory for Optical Materials and Photonic Devices
- Department of Chemistry
- Capital Normal University
- Beijing 100048
- People's Republic of China
| | - Haiyang Li
- Beijing Key Laboratory for Optical Materials and Photonic Devices
- Department of Chemistry
- Capital Normal University
- Beijing 100048
- People's Republic of China
| | - Hongbing Fu
- Beijing Key Laboratory for Optical Materials and Photonic Devices
- Department of Chemistry
- Capital Normal University
- Beijing 100048
- People's Republic of China
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11
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Fonseca-Ornelas L, Schmidt C, Camacho-Zarco AR, Fernandez CO, Becker S, Zweckstetter M. Small-Molecule-Induced Soluble Oligomers of α-Synuclein with Helical Structure. Chemistry 2017; 23:13010-13014. [PMID: 28763125 DOI: 10.1002/chem.201703001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Indexed: 11/08/2022]
Abstract
Accumulation of α-synuclein (αSyn) aggregates constitutes the hallmark of synucleinopathies including Parkinson's disease. However, many steps from the innocuous, monomeric αSyn toward misfolded oligomers and fibrillar species remain unclear. Here, we show that αSyn can form in solution α-helical oligomers, which are off-pathway to fibrillization, through interaction with the tetrapyrrole phthalocyanine tetrasulfonate. Chemical cross-linking combined with mass spectrometry reveals a large number of intermolecular cross-links along the entire αSyn sequence in the phthalocyanine tetrasulfonate-stabilized αSyn oligomers. Our study suggests that stabilization of structured oligomers by small molecules provides a viable strategy to interfere with αSyn fibrillization.
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Affiliation(s)
- Luis Fonseca-Ornelas
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Carla Schmidt
- Interdisciplinary Research Center HALOmem, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle/ Saale, Germany
| | - Aldo R Camacho-Zarco
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075, Göttingen, Germany
| | - Claudio O Fernandez
- Max Planck Laboratory for Structural Biology, Chemistry and Molecular Biophysics of Rosario (MPLbioR), Universidad Nacional de Rosario, S2002LRK- Rosario, Argentina, Instituto de Investigaciones para el Descubrimiento de Farmacos de Rosario-IIDEFAR (CONICET-UNR), S2002LRK-, Rosario, Argentina
| | - Stefan Becker
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Markus Zweckstetter
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075, Göttingen, Germany.,Department of Neurology, University Medical Center, University of Göttingen, Waldweg 33, 37073, Göttingen, Germany
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12
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Donaldson L, Vaidya A. Visualising recalcitrance by colocalisation of cellulase, lignin and cellulose in pretreated pine biomass using fluorescence microscopy. Sci Rep 2017; 7:44386. [PMID: 28281670 PMCID: PMC5345003 DOI: 10.1038/srep44386] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 02/07/2017] [Indexed: 11/08/2022] Open
Abstract
Mapping the location of bound cellulase enzymes provides information on the micro-scale distribution of amenable and recalcitrant sites in pretreated woody biomass for biofuel applications. The interaction of a fluorescently labelled cellulase enzyme cocktail with steam-exploded pine (SEW) was quantified using confocal microscopy. The spatial distribution of Dylight labelled cellulase was quantified relative to lignin (autofluorescence) and cellulose (Congo red staining) by measuring their colocalisation using Pearson correlations. Correlations were greater in cellulose-rich secondary cell walls compared to lignin-rich middle lamella but with significant variations among individual biomass particles. The distribution of cellulose in the pretreated biomass accounted for 30% of the variation in the distribution of enzyme after correcting for the correlation between lignin and cellulose. For the first time, colocalisation analysis was able to quantify the spatial distribution of amenable and recalcitrant sites in relation to the histochemistry of cellulose and lignin. This study will contribute to understanding the role of pretreatment in enzymatic hydrolysis of recalcitrant softwood biomass.
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Affiliation(s)
- Lloyd Donaldson
- Scion, 49 Sala Street, Private Bag 3020, Rotorua 3010, New Zealand
| | - Alankar Vaidya
- Scion, 49 Sala Street, Private Bag 3020, Rotorua 3010, New Zealand
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13
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Roche J, Shen Y, Lee JH, Ying J, Bax A. Monomeric Aβ(1-40) and Aβ(1-42) Peptides in Solution Adopt Very Similar Ramachandran Map Distributions That Closely Resemble Random Coil. Biochemistry 2016; 55:762-75. [PMID: 26780756 PMCID: PMC4750080 DOI: 10.1021/acs.biochem.5b01259] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
The
pathogenesis of Alzheimer’s disease is characterized
by the aggregation and fibrillation of amyloid peptides Aβ1–40 and Aβ1–42 into amyloid
plaques. Despite strong potential therapeutic interest, the structural
pathways associated with the conversion of monomeric Aβ peptides
into oligomeric species remain largely unknown. In particular, the
higher aggregation propensity and associated toxicity of Aβ1–42 compared to that of Aβ1–40 are poorly understood. To explore in detail the structural propensity
of the monomeric Aβ1–40 and Aβ1–42 peptides in solution, we recorded a large set of nuclear magnetic
resonance (NMR) parameters, including chemical shifts, nuclear Overhauser
effects (NOEs), and J couplings. Systematic comparisons
show that at neutral pH the Aβ1–40 and Aβ1–42 peptides populate almost indistinguishable coil-like
conformations. Nuclear Overhauser effect spectra collected at very
high resolution remove assignment ambiguities and show no long-range
NOE contacts. Six sets of backbone J couplings (3JHNHα, 3JC′C′, 3JC′Hα, 1JHαCα, 2JNCα, and 1JNCα) recorded
for Aβ1–40 were used as input for the recently
developed MERA Ramachandran map analysis, yielding residue-specific
backbone ϕ/ψ torsion angle distributions that closely
resemble random coil distributions, the absence of a significantly
elevated propensity for β-conformations in the C-terminal region
of the peptide, and a small but distinct propensity for αL at K28. Our results suggest that the self-association of
Aβ peptides into toxic oligomers is not driven by elevated propensities
of the monomeric species to adopt β-strand-like conformations.
Instead, the accelerated disappearance of Aβ NMR signals in
D2O over H2O, particularly pronounced for Aβ1–42, suggests that intermolecular interactions between
the hydrophobic regions of the peptide dominate the aggregation process.
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Affiliation(s)
- Julien Roche
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0510, United States
| | - Yang Shen
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0510, United States
| | - Jung Ho Lee
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0510, United States
| | - Jinfa Ying
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0510, United States
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0510, United States
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14
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Leung CWT, Guo F, Hong Y, Zhao E, Kwok RTK, Leung NLC, Chen S, Vaikath NN, El-Agnaf OM, Tang Y, Gai WP, Tang BZ. Detection of oligomers and fibrils of α-synuclein by AIEgen with strong fluorescence. Chem Commun (Camb) 2015; 51:1866-9. [PMID: 25526628 DOI: 10.1039/c4cc07911f] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a fluorophore, TPE-TPP, with AIE characteristics which is utilized as a fluorescence probe to monitor the α-synuclein (α-Syn) fibrillation process. Compared with ThT, TPE-TPP shows a higher sensitivity in the detection of α-Syn oligomers as well as fibrils with a stronger fluorescence. The performance of TPE-TPP was evaluated using fluorescence, AFM, dot blot, and SEC.
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Affiliation(s)
- Chris Wai Tung Leung
- HKUST Shenzhen Research Institute, No. 9 Yuexing 1st RD, South Area, Hi-tech Park Nanshan, Shenzhen 518057, China.
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15
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Zinc as chaperone-mimicking agent for retardation of amyloid β peptide fibril formation. Proc Natl Acad Sci U S A 2015; 112:5407-12. [PMID: 25825723 DOI: 10.1073/pnas.1421961112] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Metal ions have emerged to play a key role in the aggregation process of amyloid β (Aβ) peptide that is closely related to the pathogenesis of Alzheimer's disease. A detailed understanding of the underlying mechanistic process of peptide-metal interactions, however, has been challenging to obtain. By applying a combination of NMR relaxation dispersion and fluorescence kinetics methods we have investigated quantitatively the thermodynamic Aβ-Zn(2+) binding features as well as how Zn(2+) modulates the nucleation mechanism of the aggregation process. Our results show that, under near-physiological conditions, substoichiometric amounts of Zn(2+) effectively retard the generation of amyloid fibrils. A global kinetic profile analysis reveals that in the absence of zinc Aβ40 aggregation is driven by a monomer-dependent secondary nucleation process in addition to fibril-end elongation. In the presence of Zn(2+), the elongation rate is reduced, resulting in reduction of the aggregation rate, but not a complete inhibition of amyloid formation. We show that Zn(2+) transiently binds to residues in the N terminus of the monomeric peptide. A thermodynamic analysis supports a model where the N terminus is folded around the Zn(2+) ion, forming a marginally stable, short-lived folded Aβ40 species. This conformation is highly dynamic and only a few percent of the peptide molecules adopt this structure at any given time point. Our findings suggest that the folded Aβ40-Zn(2+) complex modulates the fibril ends, where elongation takes place, which efficiently retards fibril formation. In this conceptual framework we propose that zinc adopts the role of a minimal antiaggregation chaperone for Aβ40.
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16
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Key T, Sarker M, de Antueno R, Rainey JK, Duncan R. The p10 FAST protein fusion peptide functions as a cystine noose to induce cholesterol-dependent liposome fusion without liposome tubulation. BIOCHIMICA ET BIOPHYSICA ACTA 2015; 1848:408-16. [PMID: 25450808 DOI: 10.1016/j.bbamem.2014.10.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Revised: 10/05/2014] [Accepted: 10/15/2014] [Indexed: 11/27/2022]
Abstract
The reovirus p10 fusion-associated small transmembrane (FAST) proteins are the smallest known membrane fusion proteins, and evolved specifically to mediate cell-cell, rather than virus-cell, membrane fusion. The 36-40-residue ectodomains of avian reovirus (ARV) and Nelson Bay reovirus (NBV) p10 contain an essential intramolecular disulfide bond required for both cell-cell fusion and lipid mixing between liposomes. To more clearly define the functional, biochemical and biophysical features of this novel fusion peptide, synthetic peptides representing the p10 ectodomains of ARV and NBV were analyzed by solution-state NMR spectroscopy, circular dichroism spectroscopy, fluorescence spectroscopy-based hydrophobicity analysis, and liposome binding and fusion assays. Results indicate that disulfide bond formation promotes exposure of hydrophobic residues, as indicated by bis-ANS binding and time-dependent peptide aggregation under aqueous conditions, implying the disulfide bond creates a small, geometrically constrained, cystine noose. Noose formation is required for peptide partitioning into liposome membranes and liposome lipid mixing, and electron microscopy revealed that liposome-liposome fusion occurs in the absence of liposome tubulation. In addition, p10 fusion peptide activity, but not membrane partitioning, is dependent on membrane cholesterol.
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Affiliation(s)
- Tim Key
- Department of Microbiology & Immunology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Muzaddid Sarker
- Department of Microbiology & Immunology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada; Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Roberto de Antueno
- Department of Microbiology & Immunology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Jan K Rainey
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada; Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada.
| | - Roy Duncan
- Department of Microbiology & Immunology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada; Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada; Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada.
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17
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Tavassoly O, Nokhrin S, Dmitriev OY, Lee JS. Cu(II) and dopamine bind to α-synuclein and cause large conformational changes. FEBS J 2014; 281:2738-53. [PMID: 24725464 DOI: 10.1111/febs.12817] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 04/04/2014] [Accepted: 04/09/2014] [Indexed: 01/06/2023]
Abstract
α-Synuclein (AS) is an intrinsically disordered protein that can misfold and aggregate to form Lewy bodies in dopaminergic neurons, a classic hallmark of Parkinson's disease. The binding of Cu(II) and dopamine to AS was evaluated by nanopore analysis with α-hemolysin. In the absence of Cu(II), wild-type AS (1 μM) readily translocated through the pore with a blockade current of--85 pA, but mostly bumping events were observed in the presence of 25 μM Cu(II). A binding site in the N-terminus was confirmed, because Cu(II) had no effect on the event profile of a peptide consisting of the C-terminal 96-140 residues. In the presence of dopamine (25 μM), the translocation events at--85 pA shifted to--80 pA, which also represents translocation events, because the event time decreases with increasing voltage. Events at--80 pA were also observed for the mutant A30P AS in the presence of dopamine. Event profiles for an N-terminal 1-60-residue peptide and a C-terminal 96-140-residue peptide were both altered in the presence of 25 μM dopamine. In contrast, dopamine had little effect on the CD spectrum of AS, and a single binding site with a Ka of 3.5 × 10(3) m(-1) was estimated by isothermal titration calorimetry. Thus, dopamine can interact with both the N-terminus and the C-terminus. Two-dimensional NMR spectroscopy of AS in the presence of dopamine showed that there were significant changes in the spectra in all regions of the protein. According to these findings, a model is presented in which dopamine induces folding between the N-terminus and C-terminus of AS. Partially folding conformations such as this may represent important intermediates in the misfolding of AS that leads to fibrillization.
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Affiliation(s)
- Omid Tavassoly
- Department of Biochemistry, University of Saskatchewan, Saskatoon, SK, Canada
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18
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Pitfalls associated with the use of Thioflavin-T to monitor anti-fibrillogenic activity. Bioorg Med Chem Lett 2014; 24:3194-8. [PMID: 24835632 DOI: 10.1016/j.bmcl.2014.04.072] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 04/13/2014] [Accepted: 04/18/2014] [Indexed: 01/02/2023]
Abstract
Thioflavin-T (ThT) is a cationic benzothiazole dye that displays enhanced fluorescence upon binding to amyloid fibrils. This property makes ThT the current reagent of choice for the quantification of amyloid fibrils. Herein, we investigate the main pitfalls associated with the use of ThT-based assays to monitor the fibrillation of α-synuclein (α-syn), a protein linked to Parkinson's disease and other α-synucleinopathies. We demonstrated for the first time that ThT interacts with α-syn disordered monomer and accelerates the protein fibrillation in vitro. As a consequence, misleading conclusions may arise from the use of ThT-based real-time assays in the evaluation of anti-fibrillogenic compounds. Interestingly, NMR experiments indicated that C-terminal domain of α-syn is the main region perturbed by ThT interaction, similarly to that found for the pesticide paraquat, a well-documented accelerator of α-syn fibrillation. Moreover, we demonstrated that certain potent inhibitors of α-syn fibrillation, such as oxidized catecholamines and polyphenols, undergo spontaneous oxidation in aqueous solution, generating compounds that strongly quench ThT fluorescence. In light of these findings, we alert for possible artifacts associated to the measure of the anti-fibrillogenic activity based only on ThT fluorescence approach.
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19
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Ying J, Roche J, Bax A. Homonuclear decoupling for enhancing resolution and sensitivity in NOE and RDC measurements of peptides and proteins. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 241:97-102. [PMID: 24360766 PMCID: PMC3965638 DOI: 10.1016/j.jmr.2013.11.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 11/11/2013] [Accepted: 11/12/2013] [Indexed: 05/23/2023]
Abstract
Application of band-selective homonuclear (BASH) (1)H decoupling pulses during acquisition of the (1)H free induction decay is shown to be an efficient procedure for removal of scalar and residual dipolar couplings between amide and aliphatic protons. BASH decoupling can be applied in both dimensions of a homonuclear 2D NMR experiment and is particularly useful for enhancing spectral resolution in the H(N)-H(α) region of NOESY spectra of peptides and proteins, which contain important information on the backbone torsion angles. The method then also prevents generation of zero quantum and Hz(N)-Hz(α) terms, thereby facilitating analysis of intraresidue interactions. Application to the NOESY spectrum of a hexapeptide fragment of the intrinsically disordered protein α-synuclein highlights the considerable diffusion anisotropy present in linear peptides. Removal of residual dipolar couplings between H(N) and aliphatic protons in weakly aligned proteins increases resolution in the (1)H-(15)N HSQC region of the spectrum and allows measurement of RDCs in samples that are relatively strongly aligned. The approach is demonstrated for measurement of RDCs in protonated (15)N/(13)C-enriched ubiquitin, aligned in Pf1, yielding improved fitting to the ubiquitin structure.
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Affiliation(s)
- Jinfa Ying
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Julien Roche
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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20
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Herva ME, Zibaee S, Fraser G, Barker RA, Goedert M, Spillantini MG. Anti-amyloid compounds inhibit α-synuclein aggregation induced by protein misfolding cyclic amplification (PMCA). J Biol Chem 2014; 289:11897-11905. [PMID: 24584936 PMCID: PMC4002097 DOI: 10.1074/jbc.m113.542340] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Filaments made of α-synuclein form the characteristic Lewy pathology in Parkinson and other diseases. The formation of α-synuclein filaments can be reproduced in vitro by incubation of recombinant protein, but the filament growth is very slow and highly variable and so unsuitable for fast high throughput anti-aggregation drug screening. To overcome this obstacle we have investigated whether the protein misfolding cyclic amplification (PMCA) technique, used for fast amplification of prion protein aggregates, could be adapted for growing α-synuclein aggregates and thus suitable for screening of drugs to affect α-synuclein aggregation for the treatment of the yet incurable α-synucleinopathies. Circular dichroism, electron microscopy, and native and SDS-polyacrylamide gels were used to demonstrate α-synuclein aggregate formation by PMCA, and the strain imprint of the α-synuclein fibrils was studied by proteinase K digestion. We also demonstrated that α-synuclein fibrils are able to seed new α-synuclein PMCA reactions and to enter and aggregate in cells in culture. In particular, we have generated a line of “chronically infected” cells, which transmit α-synuclein aggregates even after multiple passages. To evaluate the sensitivity of the PMCA system as an α-synuclein anti-aggregating drug screening assay a panel of 10 drugs was tested. Anti-amyloid compounds proved efficient in inhibiting α-synuclein fibril formation induced by PMCA. Our results show that α-synuclein PMCA is a fast and reproducible system that could be used as a high throughput screening method for finding new α-synuclein anti-aggregating compounds.
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Affiliation(s)
- Maria Eugenia Herva
- John Van Geest Centre for Brain Repair, E. D. Adrian Building, Robinson Way, Cambridge CB2 0PY, United Kingdom.
| | - Shahin Zibaee
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Graham Fraser
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Roger A Barker
- John Van Geest Centre for Brain Repair, E. D. Adrian Building, Robinson Way, Cambridge CB2 0PY, United Kingdom
| | - Michel Goedert
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Maria Grazia Spillantini
- John Van Geest Centre for Brain Repair, E. D. Adrian Building, Robinson Way, Cambridge CB2 0PY, United Kingdom.
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21
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Abelein A, Kaspersen JD, Nielsen SB, Jensen GV, Christiansen G, Pedersen JS, Danielsson J, Otzen DE, Gräslund A. Formation of dynamic soluble surfactant-induced amyloid β peptide aggregation intermediates. J Biol Chem 2013; 288:23518-28. [PMID: 23775077 DOI: 10.1074/jbc.m113.470450] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Intermediate amyloidogenic states along the amyloid β peptide (Aβ) aggregation pathway have been shown to be linked to neurotoxicity. To shed more light on the different structures that may arise during Aβ aggregation, we here investigate surfactant-induced Aβ aggregation. This process leads to co-aggregates featuring a β-structure motif that is characteristic for mature amyloid-like structures. Surfactants induce secondary structure in Aβ in a concentration-dependent manner, from predominantly random coil at low surfactant concentration, via β-structure to the fully formed α-helical state at high surfactant concentration. The β-rich state is the most aggregation-prone as monitored by thioflavin T fluorescence. Small angle x-ray scattering reveals initial globular structures of surfactant-Aβ co-aggregated oligomers and formation of elongated fibrils during a slow aggregation process. Alongside this slow (minutes to hours time scale) fibrillation process, much faster dynamic exchange (k(ex) ∼1100 s(-1)) takes place between free and co-aggregate-bound peptide. The two hydrophobic segments of the peptide are directly involved in the chemical exchange and interact with the hydrophobic part of the co-aggregates. Our findings suggest a model for surfactant-induced aggregation where free peptide and surfactant initially co-aggregate to dynamic globular oligomers and eventually form elongated fibrils. When interacting with β-structure promoting substances, such as surfactants, Aβ is kinetically driven toward an aggregation-prone state.
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Affiliation(s)
- Axel Abelein
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius Väg 16, SE-106 91 Stockholm, Sweden
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22
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Lai C, Liu X, Tian C, Wu F. Integrin α1 has a long helix, extending from the transmembrane region to the cytoplasmic tail in detergent micelles. PLoS One 2013; 8:e62954. [PMID: 23646163 PMCID: PMC3639902 DOI: 10.1371/journal.pone.0062954] [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: 11/29/2012] [Accepted: 03/26/2013] [Indexed: 12/12/2022] Open
Abstract
Integrin proteins are very important adhesion receptors that mediate cell-cell and cell-extracellular matrix interactions. They play essential roles in cell signaling and the regulation of cellular shape, motility, and the cell cycle. Here, the transmembrane and cytoplasmic (TMC) domains of integrin α1 and β1 were over-expressed and purified in detergent micelles. The structure and backbone relaxations of α1-TMC in LDAO micelles were determined and analyzed using solution NMR. A long helix, extending from the transmembrane region to the cytoplasmic tail, was observed in α1-TMC. Structural comparisons of α1-TMC with reported αIIb-TMC domains indicated different conformations in the transmembrane regions and cytoplasmic tails. An NMR titration experiment indicated weak interactions between α1-TMC and β1-TMC through several α1-TMC residues located at its N-terminal juxta-transmembrane region and C-terminal extended helix region.
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Affiliation(s)
- Chaohua Lai
- Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Xiaoxi Liu
- Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Changlin Tian
- Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, Anhui, China
- * E-mail: (CT); (FW)
| | - Fangming Wu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, Anhui, China
- * E-mail: (CT); (FW)
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23
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Abelein A, Lang L, Lendel C, Gräslund A, Danielsson J. Transient small molecule interactions kinetically modulate amyloid β peptide self-assembly. FEBS Lett 2012; 586:3991-5. [PMID: 23058290 DOI: 10.1016/j.febslet.2012.09.035] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 09/11/2012] [Indexed: 01/06/2023]
Abstract
Small organic molecules, like Congo red and lacmoid, have been shown to modulate the self-assembly of the amyloid β peptide (Aβ). Here, we show that Aβ forms NMR invisible non-toxic co-aggregates together with lacmoid as well as Congo red. We find that the interaction involves two distinct kinetic processes and at every given time point only a small fraction of Aβ is in the co-aggregate. These weak transient interactions kinetically redirect the aggregation prone Aβ from self-assembling into amyloid fibrils. These findings suggest that even such weak binders might be effective as therapeutics against pathogenic protein aggregation.
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Affiliation(s)
- Axel Abelein
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
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24
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Maltsev AS, Ying J, Bax A. Deuterium isotope shifts for backbone ¹H, ¹⁵N and ¹³C nuclei in intrinsically disordered protein α-synuclein. JOURNAL OF BIOMOLECULAR NMR 2012; 54:181-91. [PMID: 22960996 PMCID: PMC3457063 DOI: 10.1007/s10858-012-9666-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 08/13/2012] [Indexed: 05/09/2023]
Abstract
Intrinsically disordered proteins (IDPs) are abundant in nature and characterization of their potential structural propensities remains a widely pursued but challenging task. Analysis of NMR secondary chemical shifts plays an important role in such studies, but the output of such analyses depends on the accuracy of reference random coil chemical shifts. Although uniform perdeuteration of IDPs can dramatically increase spectral resolution, a feature particularly important for the poorly dispersed IDP spectra, the impact of deuterium isotope shifts on random coil values has not yet been fully characterized. Very precise (2)H isotope shift measurements for (13)C(α), (13)C(β), (13)C', (15)N, and (1)H(N) have been obtained by using a mixed sample of protonated and uniformly perdeuterated α-synuclein, a protein with chemical shifts exceptionally close to random coil values. Decomposition of these isotope shifts into one-bond, two-bond and three-bond effects as well as intra- and sequential residue contributions shows that such an analysis, which ignores conformational dependence, is meaningful but does not fully describe the total isotope shift to within the precision of the measurements. Random coil (2)H isotope shifts provide an important starting point for analysis of such shifts in structural terms in folded proteins, where they are known to depend strongly on local geometry.
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Affiliation(s)
- Alexander S Maltsev
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 5 Memorial Drive, Bethesda, MD 20892-0520, USA
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25
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Maltsev AS, Ying J, Bax A. Impact of N-terminal acetylation of α-synuclein on its random coil and lipid binding properties. Biochemistry 2012; 51:5004-13. [PMID: 22694188 PMCID: PMC3383124 DOI: 10.1021/bi300642h] [Citation(s) in RCA: 167] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
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N-Terminal acetylation of α-synuclein (aS), a protein
implicated
in the etiology of Parkinson’s disease, is common in mammals.
The impact of this modification on the protein’s structure
and dynamics in free solution and on its membrane binding properties
has been evaluated by high-resolution nuclear magnetic resonance and
circular dichroism (CD) spectroscopy. While no tetrameric form of
acetylated aS could be isolated, N-terminal acetylation resulted in
chemical shift perturbations of the first 12 residues of the protein
that progressively decreased with the distance from the N-terminus.
The directions of the chemical shift changes and small changes in
backbone 3JHH couplings are
consistent with an increase in the α-helicity of the first six
residues of aS, although a high degree of dynamic conformational disorder
remains and the helical structure is sampled <20% of the time.
Chemical shift and 3JHH data
for the intact protein are virtually indistinguishable from those
recorded for the corresponding N-terminally acetylated and nonacetylated
15-residue synthetic peptides. An increase in α-helicity at
the N-terminus of aS is supported by CD data on the acetylated peptide
and by weak medium-range nuclear Overhauser effect contacts indicative
of α-helical character. The remainder of the protein has chemical
shift values that are very close to random coil values and indistinguishable
between the two forms of the protein. No significant differences in
the fibrillation kinetics were observed between acetylated and nonacetylated
aS. However, the lipid binding properties of aS are strongly impacted
by acetylation and exhibit distinct behavior for the first 12 residues,
indicative of an initiation role for the N-terminal residues in an
“initiation–elongation” process of binding to
the membrane.
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Affiliation(s)
- Alexander S Maltsev
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
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26
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Collins KD. Why continuum electrostatics theories cannot explain biological structure, polyelectrolytes or ionic strength effects in ion–protein interactions. Biophys Chem 2012; 167:43-59. [DOI: 10.1016/j.bpc.2012.04.002] [Citation(s) in RCA: 169] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Revised: 04/10/2012] [Accepted: 04/10/2012] [Indexed: 01/13/2023]
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27
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Rezaei-Ghaleh N, Blackledge M, Zweckstetter M. Intrinsically Disordered Proteins: From Sequence and Conformational Properties toward Drug Discovery. Chembiochem 2012; 13:930-50. [DOI: 10.1002/cbic.201200093] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Indexed: 01/31/2023]
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