551
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Major Reaction Coordinates Linking Transient Amyloid-β Oligomers to Fibrils Measured at Atomic Level. Biophys J 2017; 113:805-816. [PMID: 28834717 DOI: 10.1016/j.bpj.2017.06.068] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 06/22/2017] [Accepted: 06/22/2017] [Indexed: 11/22/2022] Open
Abstract
The structural underpinnings for the higher toxicity of the oligomeric intermediates of amyloidogenic peptides, compared to the mature fibrils, remain unknown at present. The transient nature and heterogeneity of the oligomers make it difficult to follow their structure. Here, using vibrational and solid-state nuclear magnetic resonance spectroscopy, and molecular dynamics simulations, we show that freely aggregating Aβ40 oligomers in physiological solutions have an intramolecular antiparallel configuration that is distinct from the intermolecular parallel β-sheet structure observed in mature fibrils. The intramolecular hydrogen-bonding network flips nearly 90°, and the two β-strands of each monomeric unit move apart, to give rise to the well-known intermolecular in-register parallel β-sheet structure in the mature fibrils. Solid-state nuclear magnetic resonance distance measurements capture the interstrand separation within monomer units during the transition from the oligomer to the fibril form. We further find that the D23-K28 salt-bridge, a major feature of the Aβ40 fibrils and a focal point of mutations linked to early onset Alzheimer's disease, is not detectable in the small oligomers. Molecular dynamics simulations capture the correlation between changes in the D23-K28 distance and the flipping of the monomer secondary structure between antiparallel and parallel β-sheet architectures. Overall, we propose interstrand separation and salt-bridge formation as key reaction coordinates describing the structural transition of the small Aβ40 oligomers to fibrils.
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552
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Boopathi S, Kolandaivel P. Effect of mutation on Aβ1-42-Heme complex in aggregation mechanism: Alzheimer’s disease. J Mol Graph Model 2017; 76:224-233. [DOI: 10.1016/j.jmgm.2017.06.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 06/15/2017] [Accepted: 06/19/2017] [Indexed: 10/19/2022]
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553
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Zhang J, Sandberg A, Wu X, Nyström S, Lindgren M, Konradsson P, Hammarström P. trans-Stilbenoids with Extended Fluorescence Lifetimes for the Characterization of Amyloid Fibrils. ACS OMEGA 2017; 2:4693-4704. [PMID: 31457755 PMCID: PMC6641930 DOI: 10.1021/acsomega.7b00535] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 07/13/2017] [Indexed: 05/29/2023]
Abstract
It was previously reported that two naphthyl-based trans-stilbene probes, (E)-4-(2-(naphthalen-1-yl)vinyl)benzene-1,2-diol (1) and (E)-4-(2-(naphthalen-2-yl)vinyl)benzene-1,2-diol (3), can bind to both native transthyretin (TTR) and misfolded protofibrillar TTR at physiological concentrations, displaying distinct emission maxima bound to the different conformational states (>100 nm difference). To further explore this amyloid probe scaffold to obtain extended fluorescence lifetimes, two new analogues with expanded aromatic ring systems (anthracene and pyrene), (E)-4-(2-(anthracen-2-yl)vinyl)benzene-1,2-diol (4) and (E)-4-(2-(pyren-2-yl)vinyl)benzene-1,2-diol (5), were synthesized employing the palladium-catalyzed Mizoroki-Heck reaction. (E)-4-Styrylbenzene-1,2-diol (2), 3, 4, and 5 were investigated with respect to their photophysical properties in methanol and when bound to insulin, lysozyme, and Aβ1-42 fibrils, including time-resolved fluorescence measurements. In conclusion, 4 and 5 can bind to both native and fibrillar TTR, becoming highly fluorescent. Compounds 2-5 bind specifically to insulin, lysozyme, and Aβ1-42 fibrils with an apparent fluorescence intensity increase and moderate binding affinities. The average fluorescence lifetimes of the probes bound to Aβ1-42 fibrils are 1.3 ns (2), 1.5 ns (3), 5.7 ns (4), and 29.8 ns (5). In summary, the variable aromatic moieties of the para-positioned trans-stilbenoid vinyl-benzene-1,2-diol with benzene, naphthalene, anthracene, and pyrene showed that the extended conjugated systems retained the amyloid targeting properties of the probes. Furthermore, both the anthracene and pyrene moieties extensively enhanced the fluorescence intensity and prolonged lifetimes. These attractive probe properties should improve amyloid detection and characterization by fluorescence-based techniques.
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Affiliation(s)
- Jun Zhang
- IFM-Department
of Chemistry, Linköping University, Linköping 581 83, Sweden
| | - Alexander Sandberg
- IFM-Department
of Chemistry, Linköping University, Linköping 581 83, Sweden
| | - Xiongyu Wu
- IFM-Department
of Chemistry, Linköping University, Linköping 581 83, Sweden
| | - Sofie Nyström
- IFM-Department
of Chemistry, Linköping University, Linköping 581 83, Sweden
| | - Mikael Lindgren
- Department
of Physics, The Norwegian University of
Science and Technology, 7491 Trondheim, Norway
| | - Peter Konradsson
- IFM-Department
of Chemistry, Linköping University, Linköping 581 83, Sweden
| | - Per Hammarström
- IFM-Department
of Chemistry, Linköping University, Linköping 581 83, Sweden
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554
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Membrane-Accelerated Amyloid-β Aggregation and Formation of Cross-β Sheets. MEMBRANES 2017; 7:membranes7030049. [PMID: 28858214 PMCID: PMC5618134 DOI: 10.3390/membranes7030049] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 07/26/2017] [Accepted: 08/23/2017] [Indexed: 11/17/2022]
Abstract
Amyloid- β aggregates play a causative role in Alzheimer's disease. These aggregates are a product of the physical environment provided by the basic neuronal membrane, composed of a lipid bilayer. The intrinsic properties of the lipid bilayer allow amyloid- β peptides to nucleate and form well-ordered cross- β sheets within the membrane. Here, we correlate the aggregation of the hydrophobic fragment of the amyloid- β protein, A β 25 - 35 , with the hydrophobicity, fluidity, and charge density of a lipid bilayer. We summarize recent biophysical studies of model membranes and relate these to the process of aggregation in physiological systems.
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555
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Fan Y, Wu D, Yi X, Tang H, Wu L, Xia Y, Wang Z, Liu Q, Zhou Z, Wang J. TMPyP Inhibits Amyloid-β Aggregation and Alleviates Amyloid-Induced Cytotoxicity. ACS OMEGA 2017; 2:4188-4195. [PMID: 30023716 PMCID: PMC6044923 DOI: 10.1021/acsomega.7b00877] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 07/20/2017] [Indexed: 05/27/2023]
Abstract
The aggregation or misfolding of amyloid-β (Aβ) is a major pathological hallmark of Alzheimer's disease (AD). The regulation of Aβ aggregation is thought to be an effective strategy for AD treatment. The capability of a water-soluble porphyrin, 5,10,15,20-tetrakis(N-methyl-4-pyridyl)porphyrin (TMPyP), to inhibit Aβ aggregation and to lower Aβ-induced toxicity was demonstrated. As evidenced by surface plasmon resonance and circular dichroism, TMPyP can not only disrupt Aβ aggregation but also disassemble the preformed Aβ aggregates. The atomic force microscopy imaging proves that TMPyP inhibits the formation of both oligomers and fibrils. Molecular dynamic simulations provide an insight into the interaction between TMPyP and Aβ at the molecular level. The half-maximal inhibitory concentrations of TMPyP acting on the oligomers and fibrils were determined to be 0.6 and 0.43 μM, respectively. As a member of porphyrin family, TMPyP is of rather low cytotoxicity, and the cytotoxicity of the Aβ aggregates was also relieved upon coincubation with TMPyP. The excellent performance of TMPyP thus makes it a potential drug candidate for AD therapy.
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Affiliation(s)
- Yujuan Fan
- College
of Chemistry and Chemical Engineering, Central
South University, Changsha 410083, Hunan, P. R. China
| | - Daohong Wu
- College
of Chemistry and Chemical Engineering, Central
South University, Changsha 410083, Hunan, P. R. China
| | - Xinyao Yi
- College
of Chemistry and Chemical Engineering, Central
South University, Changsha 410083, Hunan, P. R. China
| | - Hailin Tang
- State
Key Laboratory of Oncology in South China, Collaborative Innovation
Center for Cancer Medicine, Sun Yat-Sen
University Cancer Center, Guangzhou 510060, Guangdong, P. R. China
| | - Ling Wu
- College
of Chemistry and Chemical Engineering, Central
South University, Changsha 410083, Hunan, P. R. China
| | - Yonghong Xia
- College
of Chemistry and Chemical Engineering, Central
South University, Changsha 410083, Hunan, P. R. China
| | - Zixiao Wang
- College
of Chemistry and Chemical Engineering, Central
South University, Changsha 410083, Hunan, P. R. China
| | - Qiuhua Liu
- School
of Chemistry and Chemical Engineering and Key Laboratory of Theoretical
Organic Chemistry and Functional Molecule of the Ministry of Education, Hunan University of Science and Technology, Xiangtan 411201, Hunan, P. R. China
| | - Zaichun Zhou
- School
of Chemistry and Chemical Engineering and Key Laboratory of Theoretical
Organic Chemistry and Functional Molecule of the Ministry of Education, Hunan University of Science and Technology, Xiangtan 411201, Hunan, P. R. China
| | - Jianxiu Wang
- College
of Chemistry and Chemical Engineering, Central
South University, Changsha 410083, Hunan, P. R. China
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556
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Saini RK, Shuaib S, Goyal B. Molecular insights into Aβ42protofibril destabilization with a fluorinated compound D744: A molecular dynamics simulation study. J Mol Recognit 2017; 30. [DOI: 10.1002/jmr.2656] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 07/25/2017] [Accepted: 07/26/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Rajneet Kaur Saini
- Department of Chemistry, School of Basic and Applied Sciences; Sri Guru Granth Sahib World University; Fatehgarh Sahib Punjab India
| | - Suniba Shuaib
- Department of Chemistry, School of Basic and Applied Sciences; Sri Guru Granth Sahib World University; Fatehgarh Sahib Punjab India
| | - Bhupesh Goyal
- Department of Chemistry, School of Basic and Applied Sciences; Sri Guru Granth Sahib World University; Fatehgarh Sahib Punjab India
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557
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Stark T, Lieblein T, Pohland M, Kalden E, Freund P, Zangl R, Grewal R, Heilemann M, Eckert GP, Morgner N, Göbel MW. Peptidomimetics That Inhibit and Partially Reverse the Aggregation of Aβ1–42. Biochemistry 2017; 56:4840-4849. [DOI: 10.1021/acs.biochem.7b00223] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
| | | | | | | | | | | | - Rekha Grewal
- Institute
of Nutritional Sciences, Justus-Liebig-University Giessen, Wilhelmstrasse
20, D-35392 Giessen, Germany
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558
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Nanoelectrical characterization of amyloid-β42 aggregates via Kelvin probe force microscopy. Macromol Res 2017. [DOI: 10.1007/s13233-017-5155-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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559
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Monomer-dependent secondary nucleation in amyloid formation. Biophys Rev 2017; 9:329-338. [PMID: 28812278 PMCID: PMC5578932 DOI: 10.1007/s12551-017-0289-z] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 07/26/2017] [Indexed: 12/30/2022] Open
Abstract
Secondary nucleation of monomers on the surface of an already existing aggregate that is formed from the same kind of monomers may lead to autocatalytic amplification of a self-assembly process. Such monomer-dependent secondary nucleation occurs during the crystallization of small molecules or proteins and self-assembled materials, as well as in protein self-assembly into fibrous structures. Indications of secondary nucleation may come from analyses of kinetic experiments starting from pure monomers or monomers supplemented with a low concentration of pre-formed aggregates (seeds). More firm evidence requires additional experiments, for example those employing isotope labels to distinguish new aggregates arising from the monomer from those resulting from fragmentation of the seed. In cases of amyloid formation, secondary nucleation leads to the formation of toxic oligomers, and inhibitors of secondary nucleation may serve as starting points for therapeutic developments. Secondary nucleation displays a high degree of structural specificity and may be enhanced by mutations or screening of electrostatic repulsion.
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560
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Rogawski R, McDermott AE. New NMR tools for protein structure and function: Spin tags for dynamic nuclear polarization solid state NMR. Arch Biochem Biophys 2017; 628:102-113. [PMID: 28623034 PMCID: PMC5815514 DOI: 10.1016/j.abb.2017.06.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/05/2017] [Accepted: 06/12/2017] [Indexed: 12/13/2022]
Abstract
Magic angle spinning solid state NMR studies of biological macromolecules [1-3] have enabled exciting studies of membrane proteins [4,5], amyloid fibrils [6], viruses, and large macromolecular assemblies [7]. Dynamic nuclear polarization (DNP) provides a means to enhance detection sensitivity for NMR, particularly for solid state NMR, with many recent biological applications and considerable contemporary efforts towards elaboration and optimization of the DNP experiment. This review explores precedents and innovations in biological DNP experiments, especially highlighting novel chemical biology approaches to introduce the radicals that serve as a source of polarization in DNP experiments.
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Affiliation(s)
- Rivkah Rogawski
- Department of Chemistry, Columbia University, NY, NY 10027, United States
| | - Ann E McDermott
- Department of Chemistry, Columbia University, NY, NY 10027, United States.
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561
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Chandra B, Mithu VS, Bhowmik D, Das AK, Sahoo B, Maiti S, Madhu PK. Curcumin Dictates Divergent Fates for the Central Salt Bridges in Amyloid-β 40 and Amyloid-β 42. Biophys J 2017; 112:1597-1608. [PMID: 28445751 DOI: 10.1016/j.bpj.2017.02.043] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 02/02/2017] [Accepted: 02/07/2017] [Indexed: 12/25/2022] Open
Abstract
There are three specific regions in the Amyloid beta (Aβ) peptide sequence where variations cause enhanced toxicity in Alzheimer's disease: the N-terminus, the central salt bridge, and the C-terminus. Here, we investigate if there is a close conformational connection between these three regions, which may suggest a concerted mechanism of toxicity. We measure the effects of Zn2+ and curcumin on Aβ40, and compare these with their previously reported effects on Aβ42. Aβ42 and Aβ40 differ only near the C-terminus, where curcumin interacts, while Zn2+ interacts near the N-terminus. Therefore, this comparison should help us differentiate the effect of modulating the C- and the N-termini. We find that curcumin allows fibril-like structures containing the salt bridge to emerge in the mature Aβ40 aggregates, but not in Aβ42. In contrast, we find no difference in the effects of Zn+2 on Aβ40 and Aβ42. In the presence of Zn+2, both of these fail to form proper fibrils, and the salt bridge remains disrupted. These results indicate that modulations of the Aβ termini can determine the fate of a salt bridge far away in the sequence, and this has significant consequences for Aβ toxicity. We also infer that small molecules can alter oligomer-induced toxicity by modulating the aggregation pathway, without substantially changing the final product of aggregation.
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Affiliation(s)
- Bappaditya Chandra
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai, India
| | | | - Debanjan Bhowmik
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai, India
| | - Anand Kant Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai, India
| | - Bankanidhi Sahoo
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Narsinghi, Hyderabad, India
| | - Sudipta Maiti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai, India.
| | - Perunthiruthy K Madhu
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Colaba, Mumbai, India; TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Narsinghi, Hyderabad, India.
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562
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Xue K, Sarkar R, Motz C, Asami S, Camargo DCR, Decker V, Wegner S, Tosner Z, Reif B. Limits of Resolution and Sensitivity of Proton Detected MAS Solid-State NMR Experiments at 111 kHz in Deuterated and Protonated Proteins. Sci Rep 2017; 7:7444. [PMID: 28785098 PMCID: PMC5547042 DOI: 10.1038/s41598-017-07253-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/21/2017] [Indexed: 01/23/2023] Open
Abstract
MAS solid-state NMR is capable of determining structures of protonated solid proteins using proton-detected experiments. These experiments are performed at MAS rotation frequency of around 110 kHz, employing 0.5 mg of material. Here, we compare 1H, 13C correlation spectra obtained from protonated and deuterated microcrystalline proteins at MAS rotation frequency of 111 kHz, and show that the spectral quality obtained from deuterated samples is superior to those acquired using protonated samples in terms of resolution and sensitivity. In comparison to protonated samples, spectra obtained from deuterated samples yield a gain in resolution on the order of 3 and 2 in the proton and carbon dimensions, respectively. Additionally, the spectrum from the deuterated sample yields approximately 2–3 times more sensitivity compared to the spectrum of a protonated sample. This gain could be further increased by a factor of 2 by making use of stereospecific precursors for biosynthesis. Although the overall resolution and sensitivity of 1H, 13C correlation spectra obtained using protonated solid samples with rotation frequencies on the order of 110 kHz is high, the spectral quality is still poor when compared to the deuterated samples. We believe that experiments involving large protein complexes in which sensitivity is limiting will benefit from the application of deuteration schemes.
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Affiliation(s)
- Kai Xue
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Riddhiman Sarkar
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany. .,Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany.
| | - Carina Motz
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany
| | - Sam Asami
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany
| | - Diana C Rodriguez Camargo
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany
| | - Venita Decker
- Bruker BioSpin, Silberstreifen 4, 76287, Rheinstetten, Germany
| | | | - Zdenek Tosner
- Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany.,Deptartment of chemistry, Faculty of Science, Charles University, Hlavova 8, 12842, Praha 2, Czech Republic
| | - Bernd Reif
- Helmholtz-Zentrum München (HMGU), Deutsches Forschungszentrum für Gesundheit und Umwelt, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany. .,Munich Center for Integrated Protein Science (CIPS-M) at Department Chemie, Technische Universität München (TUM), Lichtenbergstr. 4, 85747, Garching, Germany.
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563
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Abstract
Aggregation of the islet amyloid polypeptide (IAPP) to form fibrils and oligomers is important in the progression of type 2 diabetes. This article describes X-ray crystallographic and solution-state NMR studies of peptides derived from residues 11-17 of IAPP that assemble to form tetramers. Incorporation of residues 11-17 of IAPP (RLANFLV) into a macrocyclic β-sheet peptide results in a monomeric peptide that does not self-assemble to form oligomers. Mutation of Arg11 to the uncharged isostere citrulline gives peptide homologues that assemble to form tetramers in both the crystal state and in aqueous solution. The tetramers consist of hydrogen-bonded dimers that sandwich together through hydrophobic interactions. The tetramers share several features with structures reported for IAPP fibrils and demonstrate the importance of hydrogen bonding and hydrophobic interactions in the oligomerization of IAPP-derived peptides.
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Affiliation(s)
- Yilin Wang
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025
| | - Adam G. Kreutzer
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025
| | - Nicholas L. Truex
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025
| | - James S. Nowick
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025
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564
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Zinke M, Fricke P, Samson C, Hwang S, Wall JS, Lange S, Zinn‐Justin S, Lange A. Bacteriophage Tail-Tube Assembly Studied by Proton-Detected 4D Solid-State NMR. Angew Chem Int Ed Engl 2017; 56:9497-9501. [PMID: 28644511 PMCID: PMC5582604 DOI: 10.1002/anie.201706060] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Indexed: 01/03/2023]
Abstract
Obtaining unambiguous resonance assignments remains a major bottleneck in solid-state NMR studies of protein structure and dynamics. Particularly for supramolecular assemblies with large subunits (>150 residues), the analysis of crowded spectral data presents a challenge, even if three-dimensional (3D) spectra are used. Here, we present a proton-detected 4D solid-state NMR assignment procedure that is tailored for large assemblies. The key to recording 4D spectra with three indirect carbon or nitrogen dimensions with their inherently large chemical shift dispersion lies in the use of sparse non-uniform sampling (as low as 2 %). As a proof of principle, we acquired 4D (H)COCANH, (H)CACONH, and (H)CBCANH spectra of the 20 kDa bacteriophage tail-tube protein gp17.1 in a total time of two and a half weeks. These spectra were sufficient to obtain complete resonance assignments in a straightforward manner without use of previous solution NMR data.
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Affiliation(s)
- Maximilian Zinke
- Department of Molecular BiophysicsLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
| | - Pascal Fricke
- Department of Molecular BiophysicsLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
| | - Camille Samson
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRSUniversité Paris-Sud, Université Paris-SaclayGif-sur-Yvette CedexFrance
| | - Songhwan Hwang
- Department of Molecular BiophysicsLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
| | | | - Sascha Lange
- Department of Molecular BiophysicsLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
| | - Sophie Zinn‐Justin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRSUniversité Paris-Sud, Université Paris-SaclayGif-sur-Yvette CedexFrance
| | - Adam Lange
- Department of Molecular BiophysicsLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)BerlinGermany
- Institut für BiologieHumboldt-Universität zu BerlinBerlinGermany
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565
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Abstract
When assembling as fibrils Aβ40 peptides can only assume U-shaped conformations while Aβ42 can also arrange as S-shaped three-stranded chains. We show that this allows Aβ42 peptides to assemble pore-like structures that may explain their higher toxicity. For this purpose, we develop a scalable model of ring-like assemblies of S-shaped Aβ1-42 chains and study the stability and structural properties of these assemblies through atomistic molecular dynamics simulations. We find that the proposed arrangements are in size and symmetry compatible with experimentally observed Aβ assemblies. We further show that the interior pore in our models allows for water leakage as a possible mechanism of cell toxicity of Aβ42 amyloids.
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Affiliation(s)
- Wenhui Xi
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Ulrich H E Hansmann
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, 73019, USA.
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566
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Aleksis R, Oleskovs F, Jaudzems K, Pahnke J, Biverstål H. Structural studies of amyloid-β peptides: Unlocking the mechanism of aggregation and the associated toxicity. Biochimie 2017; 140:176-192. [PMID: 28751216 DOI: 10.1016/j.biochi.2017.07.011] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 07/21/2017] [Indexed: 12/31/2022]
Abstract
Alzheimer's disease (AD) is one of the most prevalent neurodegenerative diseases worldwide. Formation of amyloid plaques consisting of amyloid-β peptides (Aβ) is one of the hallmarks of AD. Several lines of evidence have shown a correlation between the Aβ aggregation and the disease development. Extensive research has been conducted with the aim to reveal the structures of the neurotoxic Aβ aggregates. However, the exact structure of pathological aggregates and mechanism of the disease still remains elusive due to complexity of the occurring processes and instability of various disease-relevant Aβ species. In this article we review up-to-date structural knowledge about amyloid-β peptides, focusing on data acquired using solution and solid state NMR techniques. Furthermore, we discuss implications from these structural studies on the mechanisms of aggregation and neurotoxicity.
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Affiliation(s)
- Rihards Aleksis
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, Latvia.
| | - Filips Oleskovs
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, Latvia
| | - Kristaps Jaudzems
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, Latvia
| | - Jens Pahnke
- Department of Neuro-/Pathology, Translational Neurodegeneration Research and Neuropathology Lab, University of Oslo (UiO) & Oslo University Hospital (OUS), Norway; LIED, University of Lübeck Uzl, Germany; Leibniz-Institute of Plant Biochemistry (IPB), Halle, Germany
| | - Henrik Biverstål
- Department of Physical Organic Chemistry, Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, Latvia; Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet, Stockholm, Sweden
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567
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Wahlberg E, Rahman MM, Lindberg H, Gunneriusson E, Schmuck B, Lendel C, Sandgren M, Löfblom J, Ståhl S, Härd T. Identification of proteins that specifically recognize and bind protofibrillar aggregates of amyloid-β. Sci Rep 2017; 7:5949. [PMID: 28729665 PMCID: PMC5519597 DOI: 10.1038/s41598-017-06377-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 06/12/2017] [Indexed: 12/12/2022] Open
Abstract
Protofibrils of the 42 amino acids long amyloid-β peptide are transient pre-fibrillar intermediates in the process of peptide aggregation into amyloid plaques and are thought to play a critical role in the pathology of Alzheimer’s disease. Hence, there is a need for research reagents and potential diagnostic reagents for detection and imaging of such aggregates. Here we describe an in vitro selection of Affibody molecules that bind to protofibrils of Aβ42cc, which is a stable engineered mimic of wild type Aβ42 protofibrils. Several binders were identified that bind Aβ42cc protofibrils with low nanomolar affinities, and which also recognize wild type Aβ42 protofibrils. Dimeric head-to-tail fusion proteins with subnanomolar binding affinities, and very slow dissociation off-rates, were also constructed. A mapping of the chemical properties of the side chains onto the Affibody scaffold surface reveals three distinct adjacent surface areas of positively charged surface, nonpolar surface and a polar surface, which presumably match a corresponding surface epitope on the protofibrils. The results demonstrate that the engineered Aβ42cc is a suitable antigen for directed evolution of affinity reagents with specificity for wild type Aβ42 protofibrils.
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Affiliation(s)
- Elisabet Wahlberg
- Department of Molecular Sciences, Swedish University of Agricultural Sciences (SLU), Uppsala BioCenter, Box 7015, SE-750 07, Uppsala, Sweden.,Affibody AB, Gunnar Asplunds Allé 24, SE-171 69, Solna, Sweden
| | - M Mahafuzur Rahman
- Department of Molecular Sciences, Swedish University of Agricultural Sciences (SLU), Uppsala BioCenter, Box 7015, SE-750 07, Uppsala, Sweden
| | - Hanna Lindberg
- Division of Protein Technology, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Center, SE-106 91, Stockholm, Sweden
| | | | - Benjamin Schmuck
- Department of Molecular Sciences, Swedish University of Agricultural Sciences (SLU), Uppsala BioCenter, Box 7015, SE-750 07, Uppsala, Sweden
| | - Christofer Lendel
- Department of Molecular Sciences, Swedish University of Agricultural Sciences (SLU), Uppsala BioCenter, Box 7015, SE-750 07, Uppsala, Sweden.,Department of Chemistry, School of Chemical Science and Engineering, Royal Institute of Technology (KTH), SE-100 44, Stockholm, Sweden
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences (SLU), Uppsala BioCenter, Box 7015, SE-750 07, Uppsala, Sweden
| | - John Löfblom
- Division of Protein Technology, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Center, SE-106 91, Stockholm, Sweden
| | - Stefan Ståhl
- Division of Protein Technology, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Center, SE-106 91, Stockholm, Sweden
| | - Torleif Härd
- Department of Molecular Sciences, Swedish University of Agricultural Sciences (SLU), Uppsala BioCenter, Box 7015, SE-750 07, Uppsala, Sweden.
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568
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Dutta S, Foley AR, Warner CJA, Zhang X, Rolandi M, Abrams B, Raskatov JA. Suppression of Oligomer Formation and Formation of Non‐Toxic Fibrils upon Addition of Mirror‐Image Aβ42 to the Natural
l
‐Enantiomer. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706279] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Subrata Dutta
- Dept. of Chemistry and Biochemistry UCSC 1156 High Street Santa Cruz CA USA
| | - Alejandro R. Foley
- Dept. of Chemistry and Biochemistry UCSC 1156 High Street Santa Cruz CA USA
| | | | - Xiaolin Zhang
- Dept. of Electrical Engineering UCSC 1156 High Street Santa Cruz CA USA
- Dept. of Materials Science and Engineering University of Washington Seattle WA USA
| | - Marco Rolandi
- Dept. of Electrical Engineering UCSC 1156 High Street Santa Cruz CA USA
| | - Benjamin Abrams
- Dept. of Biomolecular Engineering Life Sciences Microscopy Center UCSC 1156 High Street Santa Cruz 95064 CA USA
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569
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Dutta S, Foley AR, Warner CJA, Zhang X, Rolandi M, Abrams B, Raskatov JA. Suppression of Oligomer Formation and Formation of Non-Toxic Fibrils upon Addition of Mirror-Image Aβ42 to the Natural l-Enantiomer. Angew Chem Int Ed Engl 2017; 56:11506-11510. [PMID: 28682473 DOI: 10.1002/anie.201706279] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Indexed: 11/11/2022]
Abstract
Racemates often have lower solubility than enantiopure compounds, and the mixing of enantiomers can enhance the aggregation propensity of peptides. Amyloid beta (Aβ) 42 is an aggregation-prone peptide that is believed to play a key role in Alzheimer's disease. Soluble Aβ42 aggregation intermediates (oligomers) have emerged as being particularly neurotoxic. We hypothesized that the addition of mirror-image d-Aβ42 should reduce the concentration of toxic oligomers formed from natural l-Aβ42. We synthesized l- and D-Aβ42 and found their equimolar mixing to lead to accelerated fibril formation. Confocal microscopy with fluorescently labeled analogues of the enantiomers showed their colocalization in racemic fibrils. Owing to the enhanced fibril formation propensity, racemic Aβ42 was less prone to form soluble oligomers. This resulted in the protection of cells from the toxicity of l-Aβ42 at concentrations up to 50 μm. The mixing of Aβ42 enantiomers thus accelerates the formation of non-toxic fibrils.
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Affiliation(s)
- Subrata Dutta
- Dept. of Chemistry and Biochemistry, UCSC, 1156 High Street, Santa Cruz, CA, USA
| | - Alejandro R Foley
- Dept. of Chemistry and Biochemistry, UCSC, 1156 High Street, Santa Cruz, CA, USA
| | | | - Xiaolin Zhang
- Dept. of Electrical Engineering, UCSC, 1156 High Street, Santa Cruz, CA, USA.,Dept. of Materials Science and Engineering, University of Washington, Seattle, WA, USA
| | - Marco Rolandi
- Dept. of Electrical Engineering, UCSC, 1156 High Street, Santa Cruz, CA, USA
| | - Benjamin Abrams
- Dept. of Biomolecular Engineering, Life Sciences Microscopy Center, UCSC, 1156 High Street, Santa Cruz, 95064, CA, USA
| | - Jevgenij A Raskatov
- Dept. of Chemistry and Biochemistry, UCSC, 1156 High Street, Santa Cruz, CA, USA
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570
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Dong M, Zhao W, Hu D, Ai H, Kang B. N-Terminus Binding Preference for Either Tanshinone or Analogue in Both Inhibition of Amyloid Aggregation and Disaggregation of Preformed Amyloid Fibrils-Toward Introducing a Kind of Novel Anti-Alzheimer Compounds. ACS Chem Neurosci 2017; 8:1577-1588. [PMID: 28406293 DOI: 10.1021/acschemneuro.7b00080] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Amyloid-β (Aβ40/Aβ42) peptide with a length of 40 or 42 residues is naturally secreted as cleavage product of the amyloid precursor protein, and formation of Aβ aggregates in a patient's brain is a hallmark of Alzheimer's disease (AD). Therefore, disaggregation and disruption provide potential therapeutic approaches to reduce, inhibit, and even reverse Aβ aggregation. The disaggregation/inhibition effect of the inhibitors applies generally to both Aβ40 and Aβ42 aggregations. Here we capture the atomic-level details of the interaction between Aβ40/Aβ42 and either natural tanshinone compound TS1 or its derivative TS0, and observe novel results by using molecular dynamics simulations. We observe that the natural TS1 indeed inhibits the monomolecular Aβ42 (mAβ42) aggregation and disaggregates Aβ42 amyloid fibrils, being in good agreement with the experimental results. TS1 is favorable to stabilize mAβ40 and even Aβ40 fibril, playing an opposite role to that in the Aβ42 counterpart, however. TS0 can inhibit the misfolding of either mAβ40 or mAβ42 and disaggregate Aβ42 fibril but stabilize the Aβ40 fibril. Using a combination of secondary structural analysis, MM-PBSA binding energy calculations, and radial distribution functions computations, we find that both TS0 and TS1, especially the former, prefer to bind at the charged residues within disordered N-terminus with a scarce positive binding energy and disappear the characteristic C-terminal bend region of Aβ42 fibril, as well as twist the Aβ42 fibril seriously. It turns out to destabilize the Aβ42 fibril and enable the conversion of U-shaped Aβ42 fibril from the onefold to the twofold morphologies. The N-terminal binding preference helps us to identify N-terminal region as the specific epitope for specific inhibitors/drugs (such as TS0 and analogues), heralding unusual inhibition/disaggregation or stabilization mechanisms, and offering an alternative direction in engineering new inhibitors to treat AD.
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Affiliation(s)
- Mingyan Dong
- Shandong Provincial
Key Laboratory
of Fluorine Chemistry and Chemical Materials, School of Chemistry
and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Wei Zhao
- Shandong Provincial
Key Laboratory
of Fluorine Chemistry and Chemical Materials, School of Chemistry
and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Dingkun Hu
- Shandong Provincial
Key Laboratory
of Fluorine Chemistry and Chemical Materials, School of Chemistry
and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Hongqi Ai
- Shandong Provincial
Key Laboratory
of Fluorine Chemistry and Chemical Materials, School of Chemistry
and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Baotao Kang
- Shandong Provincial
Key Laboratory
of Fluorine Chemistry and Chemical Materials, School of Chemistry
and Chemical Engineering, University of Jinan, Jinan 250022, China
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571
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Fitzpatrick AW, Falcon B, He S, Murzin AG, Murshudov G, Garringer HJ, Crowther RA, Ghetti B, Goedert M, Scheres SH. Cryo-EM structures of tau filaments from Alzheimer's disease. Nature 2017; 547:185-190. [PMID: 28678775 PMCID: PMC5552202 DOI: 10.1038/nature23002] [Citation(s) in RCA: 1293] [Impact Index Per Article: 184.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 06/05/2017] [Indexed: 12/14/2022]
Abstract
Alzheimer's disease is the most common neurodegenerative disease, and there are no mechanism-based therapies. The disease is defined by the presence of abundant neurofibrillary lesions and neuritic plaques in the cerebral cortex. Neurofibrillary lesions comprise paired helical and straight tau filaments, whereas tau filaments with different morphologies characterize other neurodegenerative diseases. No high-resolution structures of tau filaments are available. Here we present cryo-electron microscopy (cryo-EM) maps at 3.4-3.5 Å resolution and corresponding atomic models of paired helical and straight filaments from the brain of an individual with Alzheimer's disease. Filament cores are made of two identical protofilaments comprising residues 306-378 of tau protein, which adopt a combined cross-β/β-helix structure and define the seed for tau aggregation. Paired helical and straight filaments differ in their inter-protofilament packing, showing that they are ultrastructural polymorphs. These findings demonstrate that cryo-EM allows atomic characterization of amyloid filaments from patient-derived material, and pave the way for investigation of a range of neurodegenerative diseases.
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Affiliation(s)
| | - Benjamin Falcon
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Shaoda He
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Alexey G. Murzin
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Garib Murshudov
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Holly J. Garringer
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - R. Anthony Crowther
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Bernardino Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Michel Goedert
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Sjors H.W. Scheres
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
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572
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Stewart KL, Hughes E, Yates EA, Middleton DA, Radford SE. Molecular Origins of the Compatibility between Glycosaminoglycans and Aβ40 Amyloid Fibrils. J Mol Biol 2017; 429:2449-2462. [PMID: 28697887 PMCID: PMC5548265 DOI: 10.1016/j.jmb.2017.07.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/04/2017] [Accepted: 07/06/2017] [Indexed: 10/25/2022]
Abstract
The Aβ peptide forms extracellular plaques associated with Alzheimer's disease. In addition to protein fibrils, amyloid plaques also contain non-proteinaceous components, including glycosaminoglycans (GAGs). We have shown previously that the GAG low-molecular-weight heparin (LMWH) binds to Aβ40 fibrils with a three-fold-symmetric (3Q) morphology with higher affinity than Aβ40 fibrils in alternative structures, Aβ42 fibrils, or amyloid fibrils formed from other sequences. Solid-state NMR analysis of the GAG-3Q fibril complex revealed an interaction site at the corners of the 3Q fibril structure, but the origin of the binding specificity remained obscure. Here, using a library of short heparin polysaccharides modified at specific sites, we show that the N-sulfate or 6-O-sulfate of glucosamine, but not the 2-O-sulfate of iduronate within heparin is required for 3Q binding, indicating selectivity in the interactions of the GAG with the fibril that extends beyond general electrostatic complementarity. By creating 3Q fibrils containing point substitutions in the amino acid sequence, we also show that charged residues at the fibril three-fold apices provide the majority of the binding free energy, while charged residues elsewhere are less critical for binding. The results indicate, therefore, that LMWH binding to 3Q fibrils requires a precise molecular complementarity of the sulfate moieties on the GAG and charged residues displayed on the fibril surface. Differences in GAG binding to fibrils with distinct sequence and/or structure may thus contribute to the diverse etiology and progression of amyloid diseases.
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Affiliation(s)
- Katie L Stewart
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Eleri Hughes
- Department of Chemistry, University of Lancaster, Lancaster LA1 4YB, UK
| | - Edwin A Yates
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - David A Middleton
- Department of Chemistry, University of Lancaster, Lancaster LA1 4YB, UK.
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, UK.
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573
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Chen YC. Impact of a discordant helix on β-amyloid structure, aggregation ability and toxicity. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2017; 46:681-687. [DOI: 10.1007/s00249-017-1235-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 05/26/2017] [Accepted: 06/26/2017] [Indexed: 11/24/2022]
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574
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Zinke M, Fricke P, Samson C, Hwang S, Wall JS, Lange S, Zinn-Justin S, Lange A. Bacteriophage Tail-Tube Assembly Studied by Proton-Detected 4D Solid-State NMR. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706060] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Maximilian Zinke
- Department of Molecular Biophysics; Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP); Berlin Germany
| | - Pascal Fricke
- Department of Molecular Biophysics; Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP); Berlin Germany
| | - Camille Samson
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS; Université Paris-Sud, Université Paris-Saclay; Gif-sur-Yvette Cedex France
| | - Songhwan Hwang
- Department of Molecular Biophysics; Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP); Berlin Germany
| | | | - Sascha Lange
- Department of Molecular Biophysics; Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP); Berlin Germany
| | - Sophie Zinn-Justin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS; Université Paris-Sud, Université Paris-Saclay; Gif-sur-Yvette Cedex France
| | - Adam Lange
- Department of Molecular Biophysics; Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP); Berlin Germany
- Institut für Biologie; Humboldt-Universität zu Berlin; Berlin Germany
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575
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Bakou M, Hille K, Kracklauer M, Spanopoulou A, Frost CV, Malideli E, Yan LM, Caporale A, Zacharias M, Kapurniotu A. Key aromatic/hydrophobic amino acids controlling a cross-amyloid peptide interaction versus amyloid self-assembly. J Biol Chem 2017; 292:14587-14602. [PMID: 28684415 DOI: 10.1074/jbc.m117.774893] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Revised: 07/02/2017] [Indexed: 12/28/2022] Open
Abstract
The interaction of the intrinsically disordered polypeptide islet amyloid polypeptide (IAPP), which is associated with type 2 diabetes (T2D), with the Alzheimer's disease amyloid-β (Aβ) peptide modulates their self-assembly into amyloid fibrils and may link the pathogeneses of these two cell-degenerative diseases. However, the molecular determinants of this interaction remain elusive. Using a systematic alanine scan approach, fluorescence spectroscopy, and other biophysical methods, including heterocomplex pulldown assays, far-UV CD spectroscopy, the thioflavin T binding assay, transmission EM, and molecular dynamics simulations, here we identified single aromatic/hydrophobic residues within the amyloid core IAPP region as hot spots or key residues of its cross-interaction with Aβ40(42) peptide. Importantly, we also find that none of these residues in isolation plays a key role in IAPP self-assembly, whereas simultaneous substitution of four aromatic/hydrophobic residues with Ala dramatically impairs both IAPP self-assembly and hetero-assembly with Aβ40(42). Furthermore, our experiments yielded several novel IAPP analogs, whose sequences are highly similar to that of IAPP but have distinct amyloid self- or cross-interaction potentials. The identified similarities and major differences controlling IAPP cross-peptide interaction with Aβ40(42) versus its amyloid self-assembly offer a molecular basis for understanding the underlying mechanisms. We propose that these insights will aid in designing intervention strategies and novel IAPP analogs for the management of type 2 diabetes, Alzheimer's disease, or other diseases related to IAPP dysfunction or cross-amyloid interactions.
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Affiliation(s)
- Maria Bakou
- From the Division of Peptide Biochemistry, Technische Universität München, D-85354 Freising, Germany and
| | - Kathleen Hille
- From the Division of Peptide Biochemistry, Technische Universität München, D-85354 Freising, Germany and
| | - Michael Kracklauer
- From the Division of Peptide Biochemistry, Technische Universität München, D-85354 Freising, Germany and
| | - Anna Spanopoulou
- From the Division of Peptide Biochemistry, Technische Universität München, D-85354 Freising, Germany and
| | - Christina V Frost
- the Physik Department, Technische Universität München, D-85748 Garching, Germany
| | - Eleni Malideli
- From the Division of Peptide Biochemistry, Technische Universität München, D-85354 Freising, Germany and
| | - Li-Mei Yan
- From the Division of Peptide Biochemistry, Technische Universität München, D-85354 Freising, Germany and
| | - Andrea Caporale
- From the Division of Peptide Biochemistry, Technische Universität München, D-85354 Freising, Germany and
| | - Martin Zacharias
- the Physik Department, Technische Universität München, D-85748 Garching, Germany
| | - Aphrodite Kapurniotu
- From the Division of Peptide Biochemistry, Technische Universität München, D-85354 Freising, Germany and
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576
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Maity S, Viazovkina E, Gall A, Lyubchenko YL. Single-molecule probing of amyloid nano-ensembles using the polymer nanoarray approach. Phys Chem Chem Phys 2017; 19:16387-16394. [PMID: 28621364 PMCID: PMC5536842 DOI: 10.1039/c7cp02691a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Soluble amyloid-beta (Aβ) oligomers are the prime causative agents of cognitive deficits during early stages of Alzheimer's disease (AD). The transient nature of the oligomers makes them difficult to characterize by traditional techniques, suggesting that advanced approaches are necessary. Previously developed fluorescence-based tethered approach for probing intermolecular interactions (TAPIN) and AFM-based single-molecule force spectroscopy are capable of probing dimers of Aβ peptides. In this paper, a novel polymer nanoarray approach to probe trimers and tetramers formed by the Aβ(14-23) segment of Aβ protein at the single-molecule level is applied. By using this approach combined with TAPIN and AFM force spectroscopy, the impact of pH on the assembly of these oligomers was characterized. Experimental results reveal that pH affects the oligomer assembly process. At neutral pH, trimers and tetramers assemble into structures with a similar stability, while at acidic conditions (pH 3.7), the oligomers adopt a set of structures with different lifetimes and strengths. Models for the assembly of Aβ(14-23) trimers and tetramers based on the results obtained is proposed.
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Affiliation(s)
- Sibaprasad Maity
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA.
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577
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Chiti F, Dobson CM. Protein Misfolding, Amyloid Formation, and Human Disease: A Summary of Progress Over the Last Decade. Annu Rev Biochem 2017; 86:27-68. [DOI: 10.1146/annurev-biochem-061516-045115] [Citation(s) in RCA: 1664] [Impact Index Per Article: 237.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
Peptides and proteins have been found to possess an inherent tendency to convert from their native functional states into intractable amyloid aggregates. This phenomenon is associated with a range of increasingly common human disorders, including Alzheimer and Parkinson diseases, type II diabetes, and a number of systemic amyloidoses. In this review, we describe this field of science with particular reference to the advances that have been made over the last decade in our understanding of its fundamental nature and consequences. We list the proteins that are known to be deposited as amyloid or other types of aggregates in human tissues and the disorders with which they are associated, as well as the proteins that exploit the amyloid motif to play specific functional roles in humans. In addition, we summarize the genetic factors that have provided insight into the mechanisms of disease onset. We describe recent advances in our knowledge of the structures of amyloid fibrils and their oligomeric precursors and of the mechanisms by which they are formed and proliferate to generate cellular dysfunction. We show evidence that a complex proteostasis network actively combats protein aggregation and that such an efficient system can fail in some circumstances and give rise to disease. Finally, we anticipate the development of novel therapeutic strategies with which to prevent or treat these highly debilitating and currently incurable conditions.
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Affiliation(s)
- Fabrizio Chiti
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio,” Section of Biochemistry, Università di Firenze, 50134 Firenze, Italy
| | - Christopher M. Dobson
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge CB2 1EW, United Kingdom
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578
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Abstract
Curli are functional amyloids produced by proteobacteria like Escherichia coli as part of the extracellular matrix that holds cells together into biofilms. The molecular events that occur during curli nucleation and fiber extension remain largely unknown. Combining observations from curli amyloidogenesis in bulk solutions with real-time in situ nanoscopic imaging at the single-fiber level, we show that curli display polar growth, and we detect two kinetic regimes of fiber elongation. Single fibers exhibit stop-and-go dynamics characterized by bursts of steady-state growth alternated with periods of stagnation. At high subunit concentrations, fibers show constant, unperturbed burst growth. Curli follow a one-step nucleation process in which monomers contemporaneously fold and oligomerize into minimal fiber units that have growth characteristics identical to those of the mature fibrils. Kinetic data and interaction studies of curli fibrillation in the presence of the natural inhibitor CsgC show that the inhibitor binds curli fibers and predominantly acts at the level of fiber elongation.
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579
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Phage display and kinetic selection of antibodies that specifically inhibit amyloid self-replication. Proc Natl Acad Sci U S A 2017; 114:6444-6449. [PMID: 28584111 DOI: 10.1073/pnas.1700407114] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The aggregation of the amyloid β peptide (Aβ) into amyloid fibrils is a defining characteristic of Alzheimer's disease. Because of the complexity of this aggregation process, effective therapeutic inhibitors will need to target the specific microscopic steps that lead to the production of neurotoxic species. We introduce a strategy for generating fibril-specific antibodies that selectively suppress fibril-dependent secondary nucleation of the 42-residue form of Aβ (Aβ42). We target this step because it has been shown to produce the majority of neurotoxic species during aggregation of Aβ42. Starting from large phage display libraries of single-chain antibody fragments (scFvs), the three-stage approach that we describe includes (i) selection of scFvs with high affinity for Aβ42 fibrils after removal of scFvs that bind Aβ42 in its monomeric form; (ii) ranking, by surface plasmon resonance affinity measurements, of the resulting candidate scFvs that bind to the Aβ42 fibrils; and (iii) kinetic screening and analysis to find the scFvs that inhibit selectively the fibril-catalyzed secondary nucleation process in Aβ42 aggregation. By applying this approach, we have identified four scFvs that inhibit specifically the fibril-dependent secondary nucleation process. Our method also makes it possible to discard antibodies that inhibit elongation, an important factor because the suppression of elongation does not target directly the production of toxic oligomers and may even lead to its increase. On the basis of our results, we suggest that the method described here could form the basis for rationally designed immunotherapy strategies to combat Alzheimer's and related neurodegenerative diseases.
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580
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Aprile FA, Sormanni P, Perni M, Arosio P, Linse S, Knowles TPJ, Dobson CM, Vendruscolo M. Selective targeting of primary and secondary nucleation pathways in Aβ42 aggregation using a rational antibody scanning method. SCIENCE ADVANCES 2017; 3:e1700488. [PMID: 28691099 PMCID: PMC5479649 DOI: 10.1126/sciadv.1700488] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 04/26/2017] [Indexed: 05/19/2023]
Abstract
Antibodies targeting Aβ42 are under intense scrutiny because of their therapeutic potential for Alzheimer's disease. To enable systematic searches, we present an "antibody scanning" strategy for the generation of a panel of antibodies against Aβ42. Each antibody in the panel is rationally designed to target a specific linear epitope, with the selected epitopes scanning the Aβ42 sequence. By screening in vitro the panel to identify the specific microscopic steps in the Aβ42 aggregation process influenced by each antibody, we identify two antibodies that target specifically the primary and the secondary nucleation steps, which are key for the production of Aβ42 oligomers. These two antibodies act, respectively, to delay the onset of aggregation and to block the proliferation of aggregates, and correspondingly reduce the toxicity in a Caenorhabditis elegans model overexpressing Aβ42. These results illustrate how the antibody scanning method described here can be used to readily obtain very small antibody libraries with extensive coverage of the sequences of target proteins.
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Affiliation(s)
- Francesco A. Aprile
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Michele Perni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Sara Linse
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, 221 00 Lund, Sweden
| | - Tuomas P. J. Knowles
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Christopher M. Dobson
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
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581
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Quittot N, Sebastiao M, Bourgault S. Modulation of amyloid assembly by glycosaminoglycans: from mechanism to biological significance. Biochem Cell Biol 2017; 95:329-337. [DOI: 10.1139/bcb-2016-0236] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Glycosaminoglycans (GAGs) are long and unbranched polysaccharides that are abundant in the extracellular matrix and basement membrane of multicellular organisms. These linear polyanionic macromolecules are involved in many physiological functions from cell adhesion to cellular signaling. Interestingly, amyloid fibrils extracted from patients afflicted with protein misfolding diseases are virtually always associated with GAGs. Amyloid fibrils are highly organized nanostructures that have been historically associated with pathological states, such as Alzheimer’s disease and systemic amyloidoses. However, recent studies have identified functional amyloids that accomplish crucial physiological roles in almost all living organisms, from bacteria to insects and mammals. Over the last 2 decades, numerous reports have revealed that sulfated GAGs accelerate and (or) promote the self-assembly of a large diversity of proteins, both inherently amyloidogenic and non-aggregation prone. Despite the fact that many studies have investigated the molecular mechanism(s) by which GAGs induce amyloid assembly, the mechanistic elucidation of GAG-mediated amyloidogenesis still remains the subject of active research. In this review, we expose the contribution of GAGs in amyloid assembly, and we discuss the pathophysiological and functional significance of GAG-mediated fibrillization. Finally, we propose mechanistic models of the unique and potent ability of sulfated GAGs to hasten amyloid fibril formation.
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Affiliation(s)
- Noé Quittot
- Department of Chemistry, Pharmaqam, C.P. 8888, Succursale Centre-Ville, Université du Québec à Montréal (UQAM), Montreal, QC H3C 3P8, Canada
- Department of Chemistry, Pharmaqam, C.P. 8888, Succursale Centre-Ville, Université du Québec à Montréal (UQAM), Montreal, QC H3C 3P8, Canada
| | - Mathew Sebastiao
- Department of Chemistry, Pharmaqam, C.P. 8888, Succursale Centre-Ville, Université du Québec à Montréal (UQAM), Montreal, QC H3C 3P8, Canada
- Department of Chemistry, Pharmaqam, C.P. 8888, Succursale Centre-Ville, Université du Québec à Montréal (UQAM), Montreal, QC H3C 3P8, Canada
| | - Steve Bourgault
- Department of Chemistry, Pharmaqam, C.P. 8888, Succursale Centre-Ville, Université du Québec à Montréal (UQAM), Montreal, QC H3C 3P8, Canada
- Department of Chemistry, Pharmaqam, C.P. 8888, Succursale Centre-Ville, Université du Québec à Montréal (UQAM), Montreal, QC H3C 3P8, Canada
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582
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Jain MG, Lalli D, Stanek J, Gowda C, Prakash S, Schwarzer TS, Schubeis T, Castiglione K, Andreas LB, Madhu PK, Pintacuda G, Agarwal V. Selective 1H- 1H Distance Restraints in Fully Protonated Proteins by Very Fast Magic-Angle Spinning Solid-State NMR. J Phys Chem Lett 2017; 8:2399-2405. [PMID: 28492324 DOI: 10.1021/acs.jpclett.7b00983] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Very fast magic-angle spinning (MAS > 80 kHz) NMR combined with high-field magnets has enabled the acquisition of proton-detected spectra in fully protonated solid samples with sufficient resolution and sensitivity. One of the primary challenges in structure determination of protein is observing long-range 1H-1H contacts. Here we use band-selective spin-lock pulses to obtain selective 1H-1H contacts (e.g., HN-HN) on the order of 5-6 Å in fully protonated proteins at 111 kHz MAS. This approach is a major advancement in structural characterization of proteins given that magnetization can be selectively transferred between protons that are 5-6 Å apart despite the presence of other protons at shorter distance. The observed contacts are similar to those previously observed only in perdeuterated proteins with selective protonation. Simulations and experiments show the proposed method has performance that is superior to that of the currently used methods. The method is demonstrated on GB1 and a β-barrel membrane protein, AlkL.
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Affiliation(s)
- Mukul G Jain
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research , 21 Brundavan Colony, Narsingi, Hyderabad 500 075, India
| | - Daniela Lalli
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon , 5 rue de la Doua, 69100 Villeurbanne, France
| | - Jan Stanek
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon , 5 rue de la Doua, 69100 Villeurbanne, France
| | - Chandrakala Gowda
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research , 21 Brundavan Colony, Narsingi, Hyderabad 500 075, India
| | - Satya Prakash
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research , 21 Brundavan Colony, Narsingi, Hyderabad 500 075, India
| | - Tom S Schwarzer
- Institute of Biochemical Engineering, Technical University of Munich , Boltzmannstraße 15, D-85748 Garching, Germany
| | - Tobias Schubeis
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon , 5 rue de la Doua, 69100 Villeurbanne, France
| | - Kathrin Castiglione
- Institute of Biochemical Engineering, Technical University of Munich , Boltzmannstraße 15, D-85748 Garching, Germany
| | - Loren B Andreas
- Max Planck Institute for Biophysical Chemistry , Am Fassberg 11, D-37077 Göttingen, Germany
| | - P K Madhu
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research , 21 Brundavan Colony, Narsingi, Hyderabad 500 075, India
- Department of Chemical Sciences, Tata Institute of Fundamental Research , Homi Bhabha Road, Colaba, Mumbai 400 005, India
| | - Guido Pintacuda
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon , 5 rue de la Doua, 69100 Villeurbanne, France
| | - Vipin Agarwal
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research , 21 Brundavan Colony, Narsingi, Hyderabad 500 075, India
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583
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Abstract
Throughout biology, amyloids are key structures in both functional proteins and the end product of pathologic protein misfolding. Amyloids might also represent an early precursor in the evolution of life because of their small molecular size and their ability to self-purify and catalyze chemical reactions. They also provide attractive backbones for advanced materials. When β-strands of an amyloid are arranged parallel and in register, side chains from the same position of each chain align, facilitating metal chelation when the residues are good ligands such as histidine. High-resolution structures of metalloamyloids are needed to understand the molecular bases of metal-amyloid interactions. Here we combine solid-state NMR and structural bioinformatics to determine the structure of a zinc-bound metalloamyloid that catalyzes ester hydrolysis. The peptide forms amphiphilic parallel β-sheets that assemble into stacked bilayers with alternating hydrophobic and polar interfaces. The hydrophobic interface is stabilized by apolar side chains from adjacent sheets, whereas the hydrated polar interface houses the Zn2+-binding histidines with binding geometries unusual in proteins. Each Zn2+ has two bis-coordinated histidine ligands, which bridge adjacent strands to form an infinite metal-ligand chain along the fibril axis. A third histidine completes the protein ligand environment, leaving a free site on the Zn2+ for water activation. This structure defines a class of materials, which we call metal-peptide frameworks. The structure reveals a delicate interplay through which metal ions stabilize the amyloid structure, which in turn shapes the ligand geometry and catalytic reactivity of Zn2.
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584
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Cheng Q, Qiang W. Solid-State-NMR-Structure-Based Inhibitor Design to Achieve Selective Inhibition of the Parallel-in-Register β-Sheet versus Antiparallel Iowa Mutant β-Amyloid Fibrils. J Phys Chem B 2017; 121:5544-5552. [DOI: 10.1021/acs.jpcb.7b02953] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Qinghui Cheng
- Department of Chemistry, The State University of New York at Binghamton, Binghamton, New York 13902, United States
| | - Wei Qiang
- Department of Chemistry, The State University of New York at Binghamton, Binghamton, New York 13902, United States
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585
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Nano-assembly of amyloid β peptide: role of the hairpin fold. Sci Rep 2017; 7:2344. [PMID: 28539626 PMCID: PMC5443804 DOI: 10.1038/s41598-017-02454-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 04/10/2017] [Indexed: 12/12/2022] Open
Abstract
Structural investigations have revealed that β hairpin structures are common features in amyloid fibrils, suggesting that these motifs play an important role in amyloid assembly. To test this hypothesis, we characterized the effect of the hairpin fold on the aggregation process using a model β hairpin structure, consisting of two Aβ(14–23) monomers connected by a turn forming YNGK peptide. AFM studies of the assembled aggregates revealed that the hairpin forms spherical structures whereas linear Aβ(14–23) monomers form fibrils. Additionally, an equimolar mixture of the monomer and the hairpin assembles into non-fibrillar aggregates, demonstrating that the hairpin fold dramatically changes the morphology of assembled amyloid aggregates. To understand the molecular mechanism underlying the role of the hairpin fold on amyloid assembly, we performed single-molecule probing experiments to measure interactions between hairpin and monomer and two hairpin complexes. The studies reveal that the stability of hairpin-monomer complexes is much higher than hairpin-hairpin complexes. Molecular dynamics simulations revealed a novel intercalated complex for the hairpin and monomer and Monte Carlo modeling further demonstrated that such nano-assemblies have elevated stability compared with stability of the dimer formed by Aβ(14–23) hairpin. The role of such folding on the amyloid assembly is also discussed.
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586
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Ni QZ, Markhasin E, Can TV, Corzilius B, Tan KO, Barnes AB, Daviso E, Su Y, Herzfeld J, Griffin RG. Peptide and Protein Dynamics and Low-Temperature/DNP Magic Angle Spinning NMR. J Phys Chem B 2017; 121:4997-5006. [PMID: 28437077 DOI: 10.1021/acs.jpcb.7b02066] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In DNP MAS NMR experiments at ∼80-110 K, the structurally important -13CH3 and -15NH3+ signals in MAS spectra of biological samples disappear due to the interference of the molecular motions with the 1H decoupling. Here we investigate the effect of these dynamic processes on the NMR line shapes and signal intensities in several typical systems: (1) microcrystalline APG, (2) membrane protein bR, (3) amyloid fibrils PI3-SH3, (4) monomeric alanine-CD3, and (5) the protonated and deuterated dipeptide N-Ac-VL over 78-300 K. In APG, the three-site hopping of the Ala-Cβ peak disappears completely at 112 K, concomitant with the attenuation of CP signals from other 13C's and 15N's. Similarly, the 15N signal from Ala-NH3+ disappears at ∼173 K, concurrent with the attenuation in CP experiments of other 15N's as well as 13C's. In bR and PI3-SH3, the methyl groups are attenuated at ∼95 K, while all other 13C's remain unaffected. However, both systems exhibit substantial losses of intensity at ∼243 K. Finally, with spectra of Ala and N-Ac-VL, we show that it is possible to extract site specific dynamic data from the temperature dependence of the intensity losses. Furthermore, 2H labeling can assist with recovering the spectral intensity. Thus, our study provides insight into the dynamic behavior of biological systems over a wide range of temperatures, and serves as a guide to optimizing the sensitivity and resolution of structural data in low temperature DNP MAS NMR spectra.
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Affiliation(s)
- Qing Zhe Ni
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Evgeny Markhasin
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Thach V Can
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Björn Corzilius
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Kong Ooi Tan
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Alexander B Barnes
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Eugenio Daviso
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.,Department of Chemistry, Brandeis University , Waltham, Massachusetts 02454, United States
| | - Yongchao Su
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Judith Herzfeld
- Department of Chemistry, Brandeis University , Waltham, Massachusetts 02454, United States
| | - Robert G Griffin
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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587
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Donovan KJ, Silvers R, Linse S, Griffin RG. 3D MAS NMR Experiment Utilizing Through-Space 15N- 15N Correlations. J Am Chem Soc 2017; 139:6518-6521. [PMID: 28447786 DOI: 10.1021/jacs.7b01159] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We demonstrate a novel 3D NNC magic angle spinning NMR experiment that generates 15N-15N internuclear contacts in protein systems using an optimized 15N-15N proton assisted recoupling (PAR) mixing period and a 13C dimension for improved resolution. The optimized PAR condition permits the acquisition of high signal-to-noise 3D data that enables backbone chemical shift assignments using a strategy that is complementary to current schemes. The spectra can also provide distance constraints. The utility of the experiment is demonstrated on an M0Aβ1-42 fibril sample that yields high-quality data that is readily assigned and interpreted. The 3D NNC experiment therefore provides a powerful platform for solid-state protein studies and is broadly applicable to a variety of systems and experimental conditions.
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Affiliation(s)
- Kevin J Donovan
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Robert Silvers
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Sara Linse
- Department of Biochemistry and Structural Biology, Lund University , Lund 221 00, Sweden
| | - Robert G Griffin
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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588
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Wang T, Jo H, DeGrado WF, Hong M. Water Distribution, Dynamics, and Interactions with Alzheimer's β-Amyloid Fibrils Investigated by Solid-State NMR. J Am Chem Soc 2017; 139:6242-6252. [PMID: 28406028 PMCID: PMC5808936 DOI: 10.1021/jacs.7b02089] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Water is essential for protein folding and assembly of amyloid fibrils. Internal water cavities have been proposed for several amyloid fibrils, but no direct structural and dynamical data have been reported on the water dynamics and site-specific interactions of water with the fibrils. Here we use solid-state NMR spectroscopy to investigate the water interactions of several Aβ40 fibrils. 1H spectral lineshapes, T2 relaxation times, and two-dimensional (2D) 1H-13C correlation spectra show that there are five distinct water pools: three are peptide-bound water, while two are highly dynamic water that can be assigned to interfibrillar water and bulk-like matrix water. All these water pools are associated with the fibrils on the nanometer scale. Water-transferred 2D correlation spectra allow us to map out residue-specific hydration and give evidence for the presence of a water pore in the center of the three-fold symmetric wild-type Aβ40 fibril. In comparison, the loop residues and the intramolecular strand-strand interface have low hydration, excluding the presence of significant water cavities in these regions. The Osaka Aβ40 mutant shows lower hydration and more immobilized water than wild-type Aβ40, indicating the influence of peptide structure on the dynamics and distribution of hydration water. Finally, the highly mobile interfibrillar and matrix water exchange with each other on the time scale of seconds, suggesting that fibril bundling separates these two water pools, and water molecules must diffuse along the fibril axis before exchanging between these two environments. These results provide insights and experimental constraints on the spatial distribution and dynamics of water pools in these amyloid fibrils.
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Affiliation(s)
- Tuo Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Hyunil Jo
- Department of Pharmaceutical Chemistry and Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, California 94143, United States
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry and Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, California 94143, United States
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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589
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Irie Y, Murakami K, Hanaki M, Hanaki Y, Suzuki T, Monobe Y, Takai T, Akagi KI, Kawase T, Hirose K, Irie K. Synthetic Models of Quasi-Stable Amyloid β40 Oligomers with Significant Neurotoxicity. ACS Chem Neurosci 2017; 8:807-816. [PMID: 28026168 DOI: 10.1021/acschemneuro.6b00390] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The formation of soluble oligomers of amyloid β42 and 40 (Aβ42, Aβ40) is the initial event in the pathogenesis of Alzheimer's disease (AD). Based on previous systematic proline replacement and solid-state NMR, we proposed a toxic dimer structure of Aβ42, a highly aggregative alloform, with a turn at positions 22 and 23, and a hydrophobic core in the C-terminal region. However, in addition to Aβ42, Aβ40 dimers can also contribute to AD progression because of the more abundance of Aβ40 monomer in biological fluids. Here, we describe the synthesis and characterization of three dimer models of the toxic-conformation constrained E22P-Aβ40 using l,l-2,6-diaminopimeric acid (DAP) or l,l-2,8-diaminoazelaic acid (DAZ) linker at position 30, which is incorporated into the intermolecular parallel β-sheet region, and DAP at position 38 in the C-terminal hydrophobic core. E22P-A30DAP-Aβ40 dimer (1) and E22P-A30DAZ-Aβ40 dimer (2) existed mainly in oligomeric states even after 2 weeks incubation without forming fibrils, unlike the corresponding monomer. Their neurotoxicity toward SH-SY5Y neuroblastoma cells was very weak. In contrast, E22P-G38DAP-Aβ40 dimer (3) formed β-sheet-rich oligomeric aggregates, and exhibited more potent neurotoxicity than the corresponding monomer. Ion mobility-mass spectrometry suggested that high molecular-weight oligomers (12-24-mer) of 3 form, but not for 1 and 2 after 4 h incubation. These findings indicate that formation of the hydrophobic core at the C-terminus, rather than intermolecular parallel β-sheet, triggers the formation of toxic Aβ oligomers. Compound 3 may be a suitable model for studying the etiology of Alzheimer's disease.
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Affiliation(s)
- Yumi Irie
- Division
of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Kazuma Murakami
- Division
of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Mizuho Hanaki
- Division
of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Yusuke Hanaki
- Division
of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Takashi Suzuki
- Division
of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Yoko Monobe
- National Institute of Biomedical Innovation, Health and Nutrition, Osaka 567-0085, Japan
| | - Tomoyo Takai
- National Institute of Biomedical Innovation, Health and Nutrition, Osaka 567-0085, Japan
| | - Ken-ichi Akagi
- National Institute of Biomedical Innovation, Health and Nutrition, Osaka 567-0085, Japan
| | | | | | - Kazuhiro Irie
- Division
of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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590
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Xu L, Ma B, Nussinov R, Thompson D. Familial Mutations May Switch Conformational Preferences in α-Synuclein Fibrils. ACS Chem Neurosci 2017; 8:837-849. [PMID: 28075555 PMCID: PMC7900905 DOI: 10.1021/acschemneuro.6b00406] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The pathogenesis of Parkinson's disease is closely associated with the aggregation of the α-synuclein protein. Several familial mutants have been identified and shown to affect the aggregation kinetics of α-synuclein through distinct molecular mechanisms. Quantitative evaluation of the relative stabilities of the wild type and mutant fibrils is crucial for understanding the aggregation process and identifying the key component steps. In this work, we examined two topologically different α-synuclein fibril structures that are either determined by solid-state NMR method or modeled based on solid-state NMR data, and characterized their conformational properties and thermodynamic stabilities using molecular dynamics simulations. We show that the two fibril morphologies have comparable size, solvent exposure, secondary structures, and similar molecule/peptide binding modes; but different stabilities. Familial mutations do not significantly alter the overall fibril structures but shift their relative stabilities. Distinct mutations display altered fibril conformational behavior, suggesting different propagation preferences, reminiscent of cross-seeding among prion strains and tau deletion mutants. The simulations quantify the hydrophobic and electrostatic interactions, as well as N-terminal dynamics, that may contribute to the divergent aggregation kinetics that has been observed experimentally. Our results indicate that small molecule and peptide inhibitors may share the same binding region, providing molecular recognition that is independent of fibril conformation.
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Affiliation(s)
- Liang Xu
- Department of Physics, Bernal Institute, University of Limerick, Limerick, Ireland
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Ruth Nussinov
- Sackler Inst. of Molecular Medicine Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Damien Thompson
- Department of Physics, Bernal Institute, University of Limerick, Limerick, Ireland
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591
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Tomaselli S, Pagano K, D’Arrigo C, Molinari H, Ragona L. Evidence of Molecular Interactions of Aβ1-42 with N-Terminal Truncated Beta Amyloids by NMR. ACS Chem Neurosci 2017; 8:759-765. [PMID: 28135060 DOI: 10.1021/acschemneuro.6b00456] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Aβ peptides, the main protein components of Alzheimer's disease (AD) plaques, derive from a proteolytic cleavage of the amyloid precursor protein. Due to heterogeneous cleavage sites, a series of Aβ peptides, including the major and widely studied species Aβ1-40 (Aβ40) and Aβ1-42 (Aβ42), are produced. In addition to the C-terminal heterogeneity of Aβ peptides, significant amounts of N-terminal truncated (Aβ3-42) and pyroglutamate-modified amyloid-β peptides (AβpE3-42) have been identified in AD affected brains and shown to be more cytotoxic than unmodified Aβ peptides. Little is known about the properties of their mixtures with Aβ42. Nuclear Magnetic Resonance spectroscopy is here employed to investigate the interaction of N-truncated peptides with Aβ42 at different molar ratios. We highlight the critical concentration of N-truncated forms influencing the aggregation kinetics of Aβ42. We provide evidence, at residue level, that the C-terminal region of Aβ42 is the locus of transient specific interactions with highly aggregation prone N-truncated alloforms.
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Affiliation(s)
- Simona Tomaselli
- Istituto per lo Studio delle Macromolecole, CNR, Via Corti 12, 20133 Milan, Italy
| | - Katiuscia Pagano
- Istituto per lo Studio delle Macromolecole, CNR, Via Corti 12, 20133 Milan, Italy
| | - Cristina D’Arrigo
- Istituto per lo Studio delle Macromolecole, CNR, Via De Marini 6, 16149 Genoa, Italy
| | - Henriette Molinari
- Istituto per lo Studio delle Macromolecole, CNR, Via Corti 12, 20133 Milan, Italy
| | - Laura Ragona
- Istituto per lo Studio delle Macromolecole, CNR, Via Corti 12, 20133 Milan, Italy
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592
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Rodriguez RA, Chen LY, Plascencia-Villa G, Perry G. Elongation affinity, activation barrier, and stability of Aβ42 oligomers/fibrils in physiological saline. Biochem Biophys Res Commun 2017; 487:444-449. [PMID: 28427941 DOI: 10.1016/j.bbrc.2017.04.084] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 04/16/2017] [Indexed: 11/26/2022]
Abstract
Amyloid-beta (Aβ) peptides, Aβ40 and the more neurotoxic Aβ42, have been the subject of many research efforts for Alzheimer's disease. In two recent independent investigations, the atomistic structure of Aβ42 fibril has been clearly established in the S-shaped conformation consisting of three β-sheets stabilized by salt bridges formed between the Lys28 sidechain and the C-terminus of Ala42. This structure distinctively differs from the long-known structure of Aβ40 in the β-hairpin shaped conformation consisting of two β-sheets. Recent in silico investigations based on all-atom models have reached closer agreement with the in vitro measurements of Aβ40 thermodynamics. In this study, we present an in silico investigation of Aβ42 thermodynamics. Using the established force field parameters in seven sets of all-atom simulations, we examined the stability of small Aβ42 oligomers in physiological saline. We computed the elongation affinity of the S-shaped Aβ42 fibril, reaching agreement with the experimental data. We also estimated the Arrhenius activation barrier along the elongation pathway (from the disordered conformation of a free Aβ42 peptide to its S-shaped conformation on a fibril) that amounts to about 16 kcal/mol, which is consistent with the experimental data. Based on these quantitative agreements, we conclude that aggregation of Aβ42 peptides into fibrils is thermodynamically slow without precipitation by extrinsic factors such as heparan sulfate proteoglycan and highlight the possibility to prevent Aβ42 aggregation by eliminating some precipitation factors or by increasing competitive agents to capture and transport free Aβ42 peptides from the cerebrospinal fluid.
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Affiliation(s)
- Roberto A Rodriguez
- Department of Physics, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Liao Y Chen
- Department of Physics, University of Texas at San Antonio, San Antonio, TX 78249, USA.
| | | | - George Perry
- Department of Biology and Neurosciences Institute, University of Texas at San Antonio, San Antonio, TX 78249, USA
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593
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Shankar R, Ernst M, Madhu PK, Vosegaard T, Nielsen NC, Nielsen AB. A general theoretical description of the influence of isotropic chemical shift in dipolar recoupling experiments for solid-state NMR. J Chem Phys 2017; 146:134105. [DOI: 10.1063/1.4979123] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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594
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Man VH, Nguyen PH, Derreumaux P. Conformational Ensembles of the Wild-Type and S8C Aβ1-42 Dimers. J Phys Chem B 2017; 121:2434-2442. [PMID: 28245647 PMCID: PMC5944329 DOI: 10.1021/acs.jpcb.7b00267] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We characterized the dimer of the amyloid-β wild-type (WT) peptide, Aβ, of 42 residues and its disulfide-bond-locked double mutant (S8C) by replica exchange molecular dynamics simulations. Aβ dimers are known to be the smallest toxic species in Alzheimer's disease, and the S8C mutant has been shown experimentally to form an exclusive homogeneous and neurotoxic dimer. Our 50 μs all-atom simulations reveal similar secondary structures and collision cross-sections but very different intramolecular and intermolecular conformations upon double S8C mutation. Both dimers are very dynamic with hundreds of free-energy minima that differ from the U-shape and S-shape conformations of the peptides in the fibrils. The only common structural feature, shared by both species with a probability of 4% in WT and 12% in S8C-S8C, is a three-stranded β-sheet spanning the 17-23, 29-36, and 39-41 residues, which does not exist in the Aβ40 WT dimers.
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Affiliation(s)
- Viet Hoang Man
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202, United States
| | - Phuong H. Nguyen
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 Rue Pierre et Marie Curie, 75005 Paris, France
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595
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Lucato CM, Lupton CJ, Halls ML, Ellisdon AM. Amyloidogenicity at a Distance: How Distal Protein Regions Modulate Aggregation in Disease. J Mol Biol 2017; 429:1289-1304. [PMID: 28342736 DOI: 10.1016/j.jmb.2017.03.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/12/2017] [Accepted: 03/14/2017] [Indexed: 12/14/2022]
Abstract
The misfolding of proteins to form amyloid is a key pathological feature of several progressive, and currently incurable, diseases. A mechanistic understanding of the pathway from soluble, native protein to insoluble amyloid is crucial for therapeutic design, and recent efforts have helped to elucidate the key molecular events that trigger protein misfolding. Generally, either global or local structural perturbations occur early in amyloidogenesis to expose aggregation-prone regions of the protein that can then self-associate to form toxic oligomers. Surprisingly, these initiating structural changes are often caused or influenced by protein regions distal to the classically amyloidogenic sequences. Understanding the importance of these distal regions in the pathogenic process has highlighted many remaining knowledge gaps regarding the precise molecular events that occur in classic aggregation pathways. In this review, we discuss how these distal regions can influence aggregation in disease and the recent technical and conceptual advances that have allowed this insight.
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Affiliation(s)
- Christina M Lucato
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Christopher J Lupton
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Michelle L Halls
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Andrew M Ellisdon
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia.
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596
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Wälti MA, Orts J, Riek R. Quenched hydrogen-deuterium exchange NMR of a disease-relevant Aβ(1-42) amyloid polymorph. PLoS One 2017; 12:e0172862. [PMID: 28319116 PMCID: PMC5358797 DOI: 10.1371/journal.pone.0172862] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 02/12/2017] [Indexed: 11/21/2022] Open
Abstract
Alzheimer’s disease is associated with the aggregation into amyloid fibrils of Aβ(1–42) and Aβ(1–40) peptides. Interestingly, these fibrils often do not obtain one single structure but rather show different morphologies, so-called polymorphs. Here, we compare quenched hydrogen-deuterium (H/D) exchange of a disease-relevant Aβ(1–42) fibril for which the 3D structure has been determined by solid-state NMR with H/D exchange previously determined on another structural polymorph. This comparison reveals secondary structural differences between the two polymorphs suggesting that the two polymorphisms can be classified as segmental polymorphs.
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Affiliation(s)
| | - Julien Orts
- Laboratorium für Physikalische Chemie, ETH Zürich, Zürich, Switzerland
| | - Roland Riek
- Laboratorium für Physikalische Chemie, ETH Zürich, Zürich, Switzerland
- * E-mail:
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597
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Nucleobindin 1 binds to multiple types of pre-fibrillar amyloid and inhibits fibrillization. Sci Rep 2017; 7:42880. [PMID: 28220836 PMCID: PMC5318909 DOI: 10.1038/srep42880] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 01/16/2017] [Indexed: 11/08/2022] Open
Abstract
During amyloid fibril formation, amyloidogenic polypeptides misfold and self assemble into soluble pre-fibrillar aggregates, i.e., protofibrils, which elongate and mature into insoluble fibrillar aggregates. An emerging class of chaperones, chaperone-like amyloid binding proteins (CLABPs), has been shown to interfere with aggregation of particular misfolded amyloid peptides or proteins. We have discovered that the calcium-binding protein nuclebindin-1 (NUCB1) is a novel CLABP. We show that NUCB1 inhibits aggregation of islet-amyloid polypeptide associated with type 2 diabetes mellitus, a-synuclein associated with Parkinson’s disease, transthyretin V30M mutant associated with familial amyloid polyneuropathy, and Aβ42 associated with Alzheimer’s disease by stabilizing their respective protofibril intermediates. Kinetic studies employing the modeling software AmyloFit show that NUCB1 affects both primary nucleation and secondary nucleation. We hypothesize that NUCB1 binds to the common cross-β-sheet structure of protofibril aggregates to “cap” and stabilize soluble macromolecular complexes. Transmission electron microscopy and atomic force microscopy were employed to characterize the size, shape and volume distribution of multiple sources of NUCB1-capped protofibrils. Interestingly, NUCB1 prevents Aβ42 protofibril toxicity in a cellular assay. NUCB1-stabilized amyloid protofibrils could be used as immunogens to prepare conformation-specific antibodies and as novel tools to develop screens for anti-protofibril diagnostics and therapeutics.
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598
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Chandra B, Korn A, Maity BK, Adler J, Rawat A, Krueger M, Huster D, Maiti S. Stereoisomers Probe Steric Zippers in Amyloid-β. J Phys Chem B 2017; 121:1835-1842. [PMID: 28140589 DOI: 10.1021/acs.jpcb.6b12332] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Shape complementarity between close-packed residues plays a critical role in the amyloid aggregation process. Here, we probe such "steric zipper" interactions in amyloid-β (Aβ40), whose aggregation is linked to Alzheimer's disease, by replacing natural residues by their stereoisomers. Such mutations are expected to specifically destabilize the shape sensitive "packing" interactions, which may potentially increase their solubility and change other properties. We study the stereomutants DF19 and DL34 and also the DA2/DF4/DH6/DS8 mutant of Aβ40. F19-L34 is a critical contact in a tightly packed region of Aβ, while residues 1-9 are known to be disordered. While both DF19 and DL34 slow down the kinetics of aggregation and form amyloid fibrils efficiently, only DL34 increases the final solubility. DF19 gives rise to additional off-pathway aggregation which results in large, kinetically stable aggregates, and has lower net solubility. DA2/DF4/DH6/DS8 does not have an effect on the kinetics or the solubility. Notably, both DF19 and DL34 oligomers have a significantly lower level of interactions with lipid vesicles and live cells. We conclude that stereoisomers can cause complex site dependent changes in amyloid properties, and provide an effective tool to determine the role of individual residues in shaping the packed interiors of amyloid aggregates.
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Affiliation(s)
- Bappaditya Chandra
- Department of Chemical Science, Tata Institute of Fundamental Research , Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Alexander Korn
- Institut für Medizinische Physik und Biophysik, Universität Leipzig , Härtelstrasse 16-18, D-04107 Leipzig, Germany
| | - Barun Kumar Maity
- Department of Chemical Science, Tata Institute of Fundamental Research , Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Juliane Adler
- Institut für Medizinische Physik und Biophysik, Universität Leipzig , Härtelstrasse 16-18, D-04107 Leipzig, Germany
| | - Anoop Rawat
- Department of Chemical Science, Tata Institute of Fundamental Research , Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Martin Krueger
- Institut für Medizinische Physik und Biophysik, Universität Leipzig , Härtelstrasse 16-18, D-04107 Leipzig, Germany.,Institut für Anatomie, Universität Leipzig , Liebigstr. 13, D-04103 Leipzig, Germany
| | - Daniel Huster
- Institut für Medizinische Physik und Biophysik, Universität Leipzig , Härtelstrasse 16-18, D-04107 Leipzig, Germany
| | - Sudipta Maiti
- Department of Chemical Science, Tata Institute of Fundamental Research , Homi Bhabha Road, Colaba, Mumbai 400005, India
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599
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Bertolani A, Pizzi A, Pirrie L, Gazzera L, Morra G, Meli M, Colombo G, Genoni A, Cavallo G, Terraneo G, Metrangolo P. Crystal Structure of the DFNKF Segment of Human Calcitonin Unveils Aromatic Interactions between Phenylalanines. Chemistry 2017; 23:2051-2058. [PMID: 27806188 PMCID: PMC5573999 DOI: 10.1002/chem.201604639] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Indexed: 12/24/2022]
Abstract
Although intensively studied, the high-resolution crystal structure of the peptide DFNKF, the core-segment of human calcitonin, has never been described. Here we report how the use of iodination as a strategy to promote crystallisation and facilitate phase determination, allowed us to solve, for the first time, the single-crystal X-ray structure of a DFNKF derivative. Computational studies suggest that both the iodinated and the wild-type peptides populate very similar conformations. Furthermore, the conformer found in the solid-state structure is one of the most populated in solution, making the crystal structure a reliable model for the peptide in solution. The crystal structure of DFNKF(I) confirms the overall features of the amyloid cross-β spine and highlights how aromatic-aromatic interactions are important structural factors in the self-assembly of this peptide. A detailed analysis of such interactions is reported.
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Affiliation(s)
- Arianna Bertolani
- Laboratory of Nanostructured Fluorinated Materials (NFMLab)Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”Politecnico di MilanoVia L. Mancinelli 720131MilanoItaly
| | - Andrea Pizzi
- Laboratory of Nanostructured Fluorinated Materials (NFMLab)Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”Politecnico di MilanoVia L. Mancinelli 720131MilanoItaly
| | - Lisa Pirrie
- Laboratory of Nanostructured Fluorinated Materials (NFMLab)Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”Politecnico di MilanoVia L. Mancinelli 720131MilanoItaly
| | - Lara Gazzera
- Laboratory of Nanostructured Fluorinated Materials (NFMLab)Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”Politecnico di MilanoVia L. Mancinelli 720131MilanoItaly
| | - Giulia Morra
- Istituto di Chimica del Riconoscimento MolecolareCNRVia Mario Bianco 920131MilanoItaly
| | - Massimiliano Meli
- Istituto di Chimica del Riconoscimento MolecolareCNRVia Mario Bianco 920131MilanoItaly
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento MolecolareCNRVia Mario Bianco 920131MilanoItaly
| | - Alessandro Genoni
- Laboratoire SRSMC, UMR 7565CNRSVandoeuvre-lès-Nancy54506France
- Laboratoire SRSMC, UMR 7565Université de LorraineVandoeuvre-lès-Nancy54506France
| | - Gabriella Cavallo
- Laboratory of Nanostructured Fluorinated Materials (NFMLab)Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”Politecnico di MilanoVia L. Mancinelli 720131MilanoItaly
| | - Giancarlo Terraneo
- Laboratory of Nanostructured Fluorinated Materials (NFMLab)Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”Politecnico di MilanoVia L. Mancinelli 720131MilanoItaly
| | - Pierangelo Metrangolo
- Laboratory of Nanostructured Fluorinated Materials (NFMLab)Department of Chemistry, Materials, and Chemical Engineering “Giulio Natta”Politecnico di MilanoVia L. Mancinelli 720131MilanoItaly
- Istituto di Chimica del Riconoscimento MolecolareCNRVia Mario Bianco 920131MilanoItaly
- HYBER Centre of ExcellenceDepartment of Applied PhysicsAalto University, P.O. Box 1510002150EspooFinland
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600
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Bellucci L, Bussi G, Di Felice R, Corni S. Fibrillation-prone conformations of the amyloid-β-42 peptide at the gold/water interface. NANOSCALE 2017; 9:2279-2290. [PMID: 28124697 DOI: 10.1039/c6nr06010b] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Proteins in the proximity of inorganic surfaces and nanoparticles may undergo profound adjustments that trigger biomedically relevant processes, such as protein fibrillation. The mechanisms that govern protein-surface interactions at the molecular level are still poorly understood. In this work, we investigate the adsorption onto a gold surface, in water, of an amyloid-β (Aβ) peptide, which is the amyloidogenic peptide involved in Alzheimer's disease. The entire adsorption process, from the peptide in bulk water to its conformational relaxation on the surface, is explored by large-scale atomistic molecular dynamics (MD) simulations. We start by providing a description of the conformational ensemble of Aβ in solution by a 22 μs temperature replica exchange MD simulation, which is consistent with previous results. Then, we obtain a statistical description of how the peptide approaches the gold surface by multiple MD simulations, identifying the preferential gold-binding sites and giving a kinetic picture of the association process. Finally, relaxation of the Aβ conformations at the gold/water interface is performed by a 19 μs Hamiltonian-temperature replica exchange MD simulation. We find that the conformational ensemble of Aβ is strongly perturbed by the presence of the surface. In particular, at the gold/water interface the population of the conformers akin to amyloid fibrils is significantly enriched, suggesting that this extended contact geometry may promote fibrillation.
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Affiliation(s)
- Luca Bellucci
- Center S3, CNR Institute of Nanoscience, via Campi 213/A, 41125 Modena, Italy.
| | - Giovanni Bussi
- SISSA-Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, 34136 Trieste, Italy
| | - Rosa Di Felice
- Center S3, CNR Institute of Nanoscience, via Campi 213/A, 41125 Modena, Italy. and Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA
| | - Stefano Corni
- Center S3, CNR Institute of Nanoscience, via Campi 213/A, 41125 Modena, Italy.
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