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Scheidt HA, Korn A, Schwarze B, Krueger M, Huster D. Conformation of Pyroglutamated Amyloid β (3-40) and (11-40) Fibrils - Extended or Hairpin? J Phys Chem B 2024; 128:1647-1655. [PMID: 38334278 PMCID: PMC10895672 DOI: 10.1021/acs.jpcb.3c07285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/04/2024] [Accepted: 01/30/2024] [Indexed: 02/10/2024]
Abstract
Amyloid β (Aβ) is a hallmark protein of Alzheimer's disease. One physiologically important Aβ variant is formed by initial N-terminal truncation at a glutamic acid position (either E3 or E11), which is subsequently cyclized to a pyroglutamate (either pE3 or pE11). Both forms have been found in high concentrations in the core of amyloid plaques and are likely of high importance in the pathology of Alzheimer's disease. However, the molecular structure of the fibrils of these variants is not entirely clear. Solid-state NMR spectroscopy studies have reported a molecular contact between Gly25 and Ile31, which would disagree with the conventional hairpin model of wildtype (WT-)Aβ1-40 fibrils, most often described in the literature. We investigated the conformation of the monomeric unit of pE3-Aβ3-40 and pE11-Aβ11-40 (and for comparison also wildtype (WT)-Aβ1-40) fibrils to find out whether the hairpin or a newly suggested extended structure dominates the structure of the Aβ monomers in these fibrils. To this end, solid-state NMR spectroscopy was applied probing the inter-residual contacts between Phe19/Leu34, Ala21/Leu34, and especially Gly25/Ile31 using suitable isotopic labeling schemes. In the second part, the flexible turn of the Aβ40 peptides was replaced by a (3-(3-aminomethyl)phenylazo)phenylacetic acid (AMPP)-based photoswitch, which can predefine the peptide conformation to either an extended (trans) or hairpin (cis) conformation. This enables simultaneous spectroscopic assessment of the conformation of the AMPP-photoswitch, allowing in situ structural investigations during fibrillation in contrast to structural techniques such as NMR spectroscopy or cryo-EM, which can only be applied to stable conformers. Both methods confirm an extended structure for the peptidic monomers in fibrils of all investigated Aβ variants. Especially the Gly25/Ile31 contact is a decisive indicator for the extended structure along with the characteristic absorption spectra of trans-AMPP-Aβ.
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Affiliation(s)
- Holger A. Scheidt
- Institute
for Medical Physics and Biophysics, Leipzig
University Härtelstr. 16/18, D-04107 Leipzig, Germany
| | - Alexander Korn
- Institute
for Medical Physics and Biophysics, Leipzig
University Härtelstr. 16/18, D-04107 Leipzig, Germany
| | - Benedikt Schwarze
- Institute
for Medical Physics and Biophysics, Leipzig
University Härtelstr. 16/18, D-04107 Leipzig, Germany
| | - Martin Krueger
- Institute
of Anatomy, Leipzig University, Liebigstr. 13, 04103 Leipzig, Germany
| | - Daniel Huster
- Institute
for Medical Physics and Biophysics, Leipzig
University Härtelstr. 16/18, D-04107 Leipzig, Germany
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2
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Parlato R, Volarić J, Lasorsa A, Bagherpoor Helabad M, Kobauri P, Jain G, Miettinen MS, Feringa BL, Szymanski W, van der Wel PCA. Photocontrol of the β-Hairpin Polypeptide Structure through an Optimized Azobenzene-Based Amino Acid Analogue. J Am Chem Soc 2024; 146:2062-2071. [PMID: 38226790 PMCID: PMC10811659 DOI: 10.1021/jacs.3c11155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/17/2024]
Abstract
A family of neurodegenerative diseases, including Huntington's disease (HD) and spinocerebellar ataxias, are associated with an abnormal polyglutamine (polyQ) expansion in mutant proteins that become prone to form amyloid-like aggregates. Prior studies have suggested a key role for β-hairpin formation as a driver of nucleation and aggregation, but direct experimental studies have been challenging. Toward such research, we set out to enable spatiotemporal control over β-hairpin formation by the introduction of a photosensitive β-turn mimic in the polypeptide backbone, consisting of a newly designed azobenzene derivative. The reported derivative overcomes the limitations of prior approaches associated with poor photochemical properties and imperfect structural compatibility with the desired β-turn structure. A new azobenzene-based β-turn mimic was designed, synthesized, and found to display improved photochemical properties, both prior and after incorporation into the backbone of a polyQ polypeptide. The two isomers of the azobenzene-polyQ peptide showed different aggregate structures of the polyQ peptide fibrils, as demonstrated by electron microscopy and solid-state NMR (ssNMR). Notably, only peptides in which the β-turn structure was stabilized (azobenzene in the cis configuration) closely reproduced the spectral fingerprints of toxic, β-hairpin-containing fibrils formed by mutant huntingtin protein fragments implicated in HD. These approaches and findings will enable better deciphering of the roles of β-hairpin structures in protein aggregation processes in HD and other amyloid-related neurodegenerative diseases.
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Affiliation(s)
- Raffaella Parlato
- Zernike
Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Jana Volarić
- Stratingh
Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The
Netherlands
| | - Alessia Lasorsa
- Zernike
Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Mahdi Bagherpoor Helabad
- Department
of Theory and Bio-Systems, Max Planck Institute
of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Piermichele Kobauri
- Stratingh
Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The
Netherlands
| | - Greeshma Jain
- Zernike
Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Markus S. Miettinen
- Computational
Biology Unit, Departments of Chemistry and Informatics, University of Bergen, 5020 Bergen, Norway
| | - Ben L. Feringa
- Stratingh
Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The
Netherlands
| | - Wiktor Szymanski
- Stratingh
Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The
Netherlands
- Medical
Imaging Center, University Medical Center
Groningen, Hanzeplein
1, 9713 GZ Groningen, The Netherlands
| | - Patrick C. A. van der Wel
- Zernike
Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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3
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Biedenbänder T, Aladin V, Saeidpour S, Corzilius B. Dynamic Nuclear Polarization for Sensitivity Enhancement in Biomolecular Solid-State NMR. Chem Rev 2022; 122:9738-9794. [PMID: 35099939 DOI: 10.1021/acs.chemrev.1c00776] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Solid-state NMR with magic-angle spinning (MAS) is an important method in structural biology. While NMR can provide invaluable information about local geometry on an atomic scale even for large biomolecular assemblies lacking long-range order, it is often limited by low sensitivity due to small nuclear spin polarization in thermal equilibrium. Dynamic nuclear polarization (DNP) has evolved during the last decades to become a powerful method capable of increasing this sensitivity by two to three orders of magnitude, thereby reducing the valuable experimental time from weeks or months to just hours or days; in many cases, this allows experiments that would be otherwise completely unfeasible. In this review, we give an overview of the developments that have opened the field for DNP-enhanced biomolecular solid-state NMR including state-of-the-art applications at fast MAS and high magnetic field. We present DNP mechanisms, polarizing agents, and sample constitution methods suitable for biomolecules. A wide field of biomolecular NMR applications is covered including membrane proteins, amyloid fibrils, large biomolecular assemblies, and biomaterials. Finally, we present perspectives and recent developments that may shape the field of biomolecular DNP in the future.
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Affiliation(s)
- Thomas Biedenbänder
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
| | - Victoria Aladin
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
| | - Siavash Saeidpour
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
| | - Björn Corzilius
- Institute of Chemistry, University of Rostock, Albert-Einstein-Straße 3a, 18059 Rostock, Germany.,Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany
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4
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Jaroniec CP. Two decades of progress in structural and dynamic studies of amyloids by solid-state NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 306:42-47. [PMID: 31311708 PMCID: PMC6703944 DOI: 10.1016/j.jmr.2019.07.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 06/22/2019] [Accepted: 07/08/2019] [Indexed: 05/09/2023]
Abstract
In this perspective article I briefly highlight the rapid progress made over the past two decades in atomic level structural and dynamic studies of amyloids, which are representative of non-crystalline biomacromolecular assemblies, by magic-angle spinning solid-state NMR spectroscopy. Given new and continuing developments in solid-state NMR instrumentation and methodology, ongoing research in this area promises to contribute to an improved understanding of amyloid structure, polymorphism, interactions, assembly mechanisms, and biological function and toxicity.
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Affiliation(s)
- Christopher P Jaroniec
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA.
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6
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Linser R. Solid-state NMR spectroscopic trends for supramolecular assemblies and protein aggregates. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2017; 87:45-53. [PMID: 28869877 DOI: 10.1016/j.ssnmr.2017.08.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 08/18/2017] [Accepted: 08/22/2017] [Indexed: 06/07/2023]
Abstract
Solid-state NMR is able to generate structural data on sample preparations that are explicitly non-crystalline. In particular, for amyloid fibril samples, which can comprise significant degrees of sample disorder, solid-state NMR has been used very successfully. But also solid-state NMR studies of other supramolecular assemblies that have resisted assessment by more standard methods are being performed with increasing ease and biological impact, many of which are briefly reviewed here. New technical trends with respect to structure calculation, protein dynamics and smaller sample amounts have reshaped the field of solid-state NMR recently. In particular, proton-detected approaches based on fast Magic-Angle Spinning (MAS) were demonstrated for crystalline systems initially. Currently, such approaches are being expanded to the above-mentioned non-crystalline targets, the characterization of which can now be pursued with sample amounts on the order of a milligram. In this Trends article, I am giving a brief overview about achievements of the last years as well as the directions that the field has been heading into and delineate some satisfactory perspectives for solid-state NMR's future striving.
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Affiliation(s)
- Rasmus Linser
- Department Chemistry, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377 Munich, Germany.
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7
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Alred EJ, Phillips M, Bhavaraju M, Hansmann UHE. Stability differences in the NMR ensembles of amyloid β fibrils. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2016. [DOI: 10.1142/s0219633616500590] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Alzheimer’s Disease is characterized by the formation of amyloid beta (A[Formula: see text] fibril plaques in the brain. These fibrils can be probed by solid state NMR (ssNMR), which leads to an ensemble of configurations that are compatible with the NMR signals. Typically, only the lowest energy conformer is considered in computer simulations that probe the stability of fibrils and their binding with drug candidates. This restriction could produce data that are not physiologically relevant if the NMR entries differ significantly in stability or binding affinities. In order to study this effect, we have investigated the variance in stability between members of NMR ensembles. Our test cases are a patient-derived A[Formula: see text]-fibril model and two in vitro A[Formula: see text]-fibril models from a previous study we performed on comparative stability. The latter two models allow us also to compare different staggering patterns. We observe significant variations in molecular flexibility, compactness and secondary structure, suggesting that the full NMR ensemble must be considered for a physiologically relevant description of A[Formula: see text] fibrils.
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Affiliation(s)
- Erik J. Alred
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK73109, USA
| | - Malachi Phillips
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK73109, USA
| | - Manikanthan Bhavaraju
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK73109, USA
| | - Ulrich H. E. Hansmann
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK73109, USA
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8
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Müller H, Brener O, Andreoletti O, Piechatzek T, Willbold D, Legname G, Heise H. Progress towards structural understanding of infectious sheep PrP-amyloid. Prion 2015; 8:344-58. [PMID: 25482596 PMCID: PMC4601355 DOI: 10.4161/19336896.2014.983754] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The still elusive structural difference of non-infectious and infectious amyloid of the mammalian prion protein (PrP) is a major pending milestone in understanding protein-mediated infectivity in neurodegenerative diseases. Preparations of PrP-amyloid proven to be infectious have never been investigated with a high-resolution technique. All available models to date have been based on low-resolution data. Here, we establish protocols for the preparation of infectious samples of full-length recombinant (rec) PrP-amyloid in NMR-sufficient amounts by spontaneous fibrillation and seeded fibril growth from brain extract. We link biological and structural data of infectious recPrP-amyloid, derived from bioassays, atomic force microscopy, and solid-state NMR spectroscopy. Our data indicate a semi-mobile N-terminus, some residues with secondary chemical shifts typical of α-helical secondary structure in the middle part between ∼115 to ∼155, and a distinct β-sheet core C-terminal of residue ∼155. These findings are not in agreement with all current models for PrP-amyloid. We also provide evidence that samples seeded from brain extract may not differ in the overall arrangement of secondary structure elements, but rather in the flexibility of protein segments outside the β-core region. Taken together, our protocols provide an essential basis for the high-resolution characterization of non-infectious and infectious PrP-amyloid in the near future.
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Affiliation(s)
- Henrik Müller
- a Institute of Complex Systems; ICS-6: Structural Biochemistry; Forschungszentrum Jülich (FZJ) ; Jülich , Germany
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9
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Tiwari V, Solanki V, Tiwari M. In-vivoandin-vitrotechniques used to investigate Alzheimer's disease. FRONTIERS IN LIFE SCIENCE 2015. [DOI: 10.1080/21553769.2015.1044129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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10
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Le NTT, Narkiewicz J, Aulić S, Salzano G, Tran HT, Scaini D, Moda F, Giachin G, Legname G. Synthetic prions and other human neurodegenerative proteinopathies. Virus Res 2014; 207:25-37. [PMID: 25449570 DOI: 10.1016/j.virusres.2014.10.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 10/02/2014] [Accepted: 10/22/2014] [Indexed: 12/13/2022]
Abstract
Transmissible spongiform encephalopathies (TSE) are a heterogeneous group of neurodegenerative disorders. The common feature of these diseases is the pathological conversion of the normal cellular prion protein (PrP(C)) into a β-structure-rich conformer-termed PrP(Sc). The latter can induce a self-perpetuating process leading to amplification and spreading of pathological protein assemblies. Much evidence suggests that PrP(Sc) itself is able to recruit and misfold PrP(C) into the pathological conformation. Recent data have shown that recombinant PrP(C) can be misfolded in vitro and the resulting synthetic conformers are able to induce the conversion of PrP(C) into PrP(Sc)in vivo. In this review we describe the state-of-the-art of the body of literature in this field. In addition, we describe a cell-based assay to test synthetic prions in cells, providing further evidence that synthetic amyloids are able to template conversion of PrP into prion inclusions. Studying prions might help to understand the pathological mechanisms governing other neurodegenerative diseases. Aggregation and deposition of misfolded proteins is a common feature of several neurodegenerative disorders, such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis and other disorders. Although the proteins implicated in each of these diseases differ, they share a common prion mechanism. Recombinant proteins are able to aggregate in vitro into β-rich amyloid fibrils, sharing some features of the aggregates found in the brain. Several studies have reported that intracerebral inoculation of synthetic aggregates lead to unique pathology, which spread progressively to distal brain regions and reduced survival time in animals. Here, we review the prion-like features of different proteins involved in neurodegenerative disorders, such as α-synuclein, superoxide dismutase-1, amyloid-β and tau.
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Affiliation(s)
- Nhat Tran Thanh Le
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Joanna Narkiewicz
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Suzana Aulić
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Giulia Salzano
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Hoa Thanh Tran
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
| | - Denis Scaini
- Life Science Department, University of Trieste, Trieste, Italy
| | - Fabio Moda
- Carlo Besta Neurological Institute, Department of Neuropathology and Neurology 5, Milan, Italy
| | - Gabriele Giachin
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy.
| | - Giuseppe Legname
- Laboratory of Prion Biology, Department of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy; Elettra-Sincrotrone Trieste S.C.p.A., Area Science Park, Basovizza, Trieste, Italy.
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11
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Expression and purification of the aortic amyloid polypeptide medin. Protein Expr Purif 2014; 98:32-7. [DOI: 10.1016/j.pep.2014.02.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 02/12/2014] [Accepted: 02/13/2014] [Indexed: 01/18/2023]
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12
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Abelein A, Abrahams JP, Danielsson J, Gräslund A, Jarvet J, Luo J, Tiiman A, Wärmländer SKTS. The hairpin conformation of the amyloid β peptide is an important structural motif along the aggregation pathway. J Biol Inorg Chem 2014; 19:623-34. [PMID: 24737040 DOI: 10.1007/s00775-014-1131-8] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 04/02/2014] [Indexed: 12/29/2022]
Abstract
The amyloid β (Aβ) peptides are 39-42 residue-long peptides found in the senile plaques in the brains of Alzheimer's disease (AD) patients. These peptides self-aggregate in aqueous solution, going from soluble and mainly unstructured monomers to insoluble ordered fibrils. The aggregation process(es) are strongly influenced by environmental conditions. Several lines of evidence indicate that the neurotoxic species are the intermediate oligomeric states appearing along the aggregation pathways. This minireview summarizes recent findings, mainly based on solution and solid-state NMR experiments and electron microscopy, which investigate the molecular structures and characteristics of the Aβ peptides at different stages along the aggregation pathways. We conclude that a hairpin-like conformation constitutes a common motif for the Aβ peptides in most of the described structures. There are certain variations in different hairpin conformations, for example regarding H-bonding partners, which could be one reason for the molecular heterogeneity observed in the aggregated systems. Interacting hairpins are the building blocks of the insoluble fibrils, again with variations in how hairpins are organized in the cross-section of the fibril, perpendicular to the fibril axis. The secondary structure propensities can be seen already in peptide monomers in solution. Unfortunately, detailed structural information about the intermediate oligomeric states is presently not available. In the review, special attention is given to metal ion interactions, particularly the binding constants and ligand structures of Aβ complexes with Cu(II) and Zn(II), since these ions affect the aggregation process(es) and are considered to be involved in the molecular mechanisms underlying AD pathology.
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Affiliation(s)
- Axel Abelein
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, 106 91, Stockholm, Sweden
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13
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Jiang J, Golchert KJ, Kingsley CN, Brubaker WD, Martin RW, Mukamel S. Exploring the aggregation propensity of γS-crystallin protein variants using two-dimensional spectroscopic tools. J Phys Chem B 2013; 117:14294-301. [PMID: 24219230 DOI: 10.1021/jp408000k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The formation of amyloid fibrils is associated with many serious diseases as well as diverse biological functions. Despite the importance of these aggregates, predicting the aggregation propensity of a particular sequence is a major challenge. We report a joint 2D nuclear magnetic resonance (NMR) and ultraviolet (2DUV) study of fibrillization in the wild-type and two aggregation-prone mutants of the eye lens protein γS-crystallin. Simulations show that the complexity of 2DUV signals as measured by their "approximate entropy" is a good indicator for the conformational entropy and in turn is strongly correlated with its aggregation propensity. These findings are in agreement with high-resolution NMR experiments and are corroborated for amyloid fibrils. The 2DUV technique is complementary to high-resolution structural methods and has the potential to make the evaluation of the aggregation propensity for protein variant propensity of protein structure more accessible to both theory and experiment. The approximate entropy of experimental 2DUV signals can be used for fast screening, enabling identification of variants with high fibrillization propensity for the much more time-consuming NMR structural studies, potentially expediting the characterization of protein variants associated with cataract and other protein aggregation diseases.
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Affiliation(s)
- Jun Jiang
- Department of Chemical Physics, University of Science and Technology of China , Hefei, China
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Jayanthi S, Akbey Ü, Uluca B, Oschkinat H, Vega S. A Floquet description of phase alternated sequences for efficient homonuclear recoupling in solid perdeuterated systems. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 234:10-20. [PMID: 23831836 DOI: 10.1016/j.jmr.2013.05.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 05/08/2013] [Accepted: 05/21/2013] [Indexed: 06/02/2023]
Abstract
A Floquet description of a phase alternated homonuclear recoupling scheme for perdeuterated systems is presented. As a result, we demonstrate improvements in the recoupling efficiency of the DOuble Nucleus Enhanced Recoupling [DONER; J. Am. Chem. Soc. 131 (2009) 17054] technique by utilizing Phase Alternated Recoupling Irradiation Schemes [PARIS; Chem. Phys. Lett. 469 (2009) 342]. The effect of proton and deuterium radio frequency irradiation during recoupling has been systematically studied and theoretical observations have been verified experimentally using a deuterated model compound, L-Alanine, at 10 and 20 kHz magic angle spinning frequency. Experimental results are well in agreement with theoretical observations, thereby significantly increasing the recoupling efficiency of conventional DONER in perdeuterated systems.
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Affiliation(s)
- Sundaresan Jayanthi
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
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Cheng H, Huang WYC, Tsai TWT, Mou Y, Chao JCH, Chan JCC. Depletion of Water Molecules Near the End Stage of Steric Zipper Formation. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.201300073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Hsin‐Mei Cheng
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - William Y. C. Huang
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Tim W. T. Tsai
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Yun Mou
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - John Chin Hao Chao
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Jerry C. C. Chan
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
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16
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Osborne KL, Bachmann M, Strodel B. Thermodynamic analysis of structural transitions during GNNQQNY aggregation. Proteins 2013; 81:1141-55. [DOI: 10.1002/prot.24263] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 01/16/2013] [Accepted: 01/17/2013] [Indexed: 01/10/2023]
Affiliation(s)
- Kenneth L. Osborne
- Institute of Complex Systems: Structural Biochemistry; Research Centre Jülich; 52425 Jülich; Germany
| | - Michael Bachmann
- Center for Simulational Physics; The University of Georgia; Athens; Georgia 30602; USA
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Abstract
Solid-state NMR spectroscopy proved to be a versatile tool for characterization of structure and dynamics of complex biochemical systems. In particular, magic angle spinning (MAS) solid-state NMR came to maturity for application towards structural elucidation of biological macromolecules. Current challenges in applying solid-state NMR as well as progress achieved recently will be discussed in the following chapter focusing on conceptual aspects important for structural elucidation of proteins.
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Affiliation(s)
- Henrik Müller
- Institute of Physical Biology, Heinrich-Heine-University of Düsseldorf, 40225, Düsseldorf, Germany
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18
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Mou Y, Tsai TWT, Chan JCC. Constant time tensor correlation experiments by non-gamma-encoded recoupling pulse sequences. J Chem Phys 2012; 137:164201. [PMID: 23126702 DOI: 10.1063/1.4757957] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Constant-time tensor correlation under magic-angle spinning conditions is an important technique in solid-state nuclear magnetic resonance spectroscopy for the measurements of backbone or side-chain torsion angles of polypeptides and proteins. We introduce a general method for the design of constant-time tensor correlation experiments under magic-angle spinning. Our method requires that the amplitude of the average Hamiltonian must depend on all the three Euler angles bringing the principal axis system to the rotor-fixed frame, which is commonly referred to as non-gamma encoding. We abbreviate this novel approach as COrrelation of Non-Gamma-Encoded Experiment (CONGEE), which exploits the orientation-dependence of non-gamma-encoded sequences with respect to the magic-angle rotation axis. By manipulating the relative orientation of the average Hamiltonians created by two non-gamma-encoded sequences, one can obtain a modulation of the detected signal, from which the structural information can be extracted when the tensor orientations relative to the molecular frame are known. CONGEE has a prominent feature that the number of rf pulses and the total pulse sequence duration can be maintained to be constant so that for torsion angle determination the effects of systematic errors owing to the experimental imperfections and/or T(2) effects could be minimized. As a proof of concept, we illustrate the utility of CONGEE in the correlation between the C' chemical shift tensor and the C(α)-H(α) dipolar tensor for the backbone psi angle determination. In addition to a detailed theoretical analysis, numerical simulations and experiments measured for [U-(13)C, (15)N]-L-alanine and N-acetyl-[U-(13)C, (15)N]-D,L-valine are used to validate our approach at a spinning frequency of 20 kHz.
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Affiliation(s)
- Yun Mou
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei, Taiwan
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19
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Skora L, Zweckstetter M. Determination of amyloid core structure using chemical shifts. Protein Sci 2012; 21:1948-53. [PMID: 23033250 DOI: 10.1002/pro.2170] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 09/24/2012] [Accepted: 09/25/2012] [Indexed: 12/18/2022]
Abstract
Amyloid fibrils are the pathological hallmark of a large variety of neurodegenerative disorders. The structural characterization of amyloid fibrils, however, is challenging due to their non-crystalline, heterogeneous, and often dynamic nature. Thus, the structure of amyloid fibrils of many proteins is still unknown. We here show that the structure calculation program CS-Rosetta can be used to obtain insight into the core structure of amyloid fibrils. Driven by experimental solid-state NMR chemical shifts and taking into account the polymeric nature of fibrils CS-Rosetta allows modeling of the core of amyloid fibrils. Application to the Y145X stop mutant of the human prion protein reveals a left-handed β-helix.
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Affiliation(s)
- Lukasz Skora
- Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, Göttingen, Germany
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20
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Norlin N, Hellberg M, Filippov A, Sousa AA, Gröbner G, Leapman RD, Almqvist N, Antzutkin ON. Aggregation and fibril morphology of the Arctic mutation of Alzheimer's Aβ peptide by CD, TEM, STEM and in situ AFM. J Struct Biol 2012; 180:174-89. [PMID: 22750418 PMCID: PMC3466396 DOI: 10.1016/j.jsb.2012.06.010] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Revised: 06/10/2012] [Accepted: 06/14/2012] [Indexed: 10/28/2022]
Abstract
Morphology of aggregation intermediates, polymorphism of amyloid fibrils and aggregation kinetics of the "Arctic" mutant of the Alzheimer's amyloid β-peptide, Aβ((1-40))(E22G), in a physiologically relevant Tris buffer (pH 7.4) were thoroughly explored in comparison with the human wild type Alzheimer's amyloid peptide, wt-Aβ((1-40)), using both in situ atomic force and electron microscopy, circular dichroism and thioflavin T fluorescence assays. For arc-Aβ((1-40)) at the end of the 'lag'-period of fibrillization an abrupt appearance of ≈ 3 nm size 'spherical aggregates' with a homogeneous morphology, was identified. Then, the aggregation proceeds with a rapid growth of amyloid fibrils with a variety of morphologies, while the spherical aggregates eventually disappeared during in situ measurements. Arc-Aβ((1-40)) was also shown to form fibrils at much lower concentrations than wt-Aβ((1-40)): ≤ 2.5 μM and 12.5 μM, respectively. Moreover, at the same concentration, 50 μM, the aggregation process proceeds more rapidly for arc-Aβ((1-40)): the first amyloid fibrils were observed after c.a. 72 h from the onset of incubation as compared to approximately 7 days for wt-Aβ((1-40)). Amyloid fibrils of arc-Aβ((1-40)) exhibit a large variety of polymorphs, at least five, both coiled and non-coiled distinct fibril structures were recognized by AFM, while at least four types of arc-Aβ((1-40)) fibrils were identified by TEM and STEM and their mass-per-length statistics were collected suggesting supramolecular structures with two, four and six β-sheet laminae. Our results suggest a pathway of fibrillogenesis for full-length Alzheimer's peptides with small and structurally ordered transient spherical aggregates as on-pathway immediate precursors of amyloid fibrils.
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Affiliation(s)
- Nils Norlin
- Chemistry of Interfaces, Luleå University of Technology, SE-971 87 Luleå, Sweden
| | - Magnus Hellberg
- Division of Physics, Luleå University of Technology, SE-971 87 Luleå, Sweden
| | - Andrei Filippov
- Chemistry of Interfaces, Luleå University of Technology, SE-971 87 Luleå, Sweden
- Department of Physics, Kazan State University, 420008, Kazan, Russia
| | - Alioscka A. Sousa
- Laboratory of Bioengineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892-5766, USA
| | - Gerhard Gröbner
- Department of Biological Chemistry, Institute of Chemistry, Umeå University, SE-90187, Umeå, Sweden
| | - Richard D. Leapman
- Laboratory of Bioengineering and Physical Science, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892-5766, USA
| | - Nils Almqvist
- Division of Physics, Luleå University of Technology, SE-971 87 Luleå, Sweden
| | - Oleg N. Antzutkin
- Chemistry of Interfaces, Luleå University of Technology, SE-971 87 Luleå, Sweden
- Department of Physics, Warwick University, Coventry, CV4 7AL, United Kingdom
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21
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Bowerman CJ, Nilsson BL. Self-assembly of amphipathic β-sheet peptides: insights and applications. Biopolymers 2012; 98:169-84. [PMID: 22782560 DOI: 10.1002/bip.22058] [Citation(s) in RCA: 176] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Amphipathic peptides composed of alternating polar and nonpolar residues have a strong tendency to self-assemble into one-dimensional, amyloid-like fibril structures. Fibrils derived from peptides of general (XZXZ)(n) sequence in which X is hydrophobic and Z is hydrophilic adopt a putative β-sheet bilayer. The bilayer configuration allows burial of the hydrophobic X side chain groups in the core of the fibril and leaves the polar Z side chains exposed to solvent. This architectural arrangement provides fibrils that maintain high solubility in water and has facilitated the recent exploitation of self-assembled amphipathic peptide fibrils as functional biomaterials. This article is a critical review of the development and application of self-assembling amphipathic peptides with a focus on the fundamental insight these types of peptides provide into peptide self-assembly phenomena.
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Affiliation(s)
- Charles J Bowerman
- Department of Chemistry, University of Rochester, Rochester, NY 14627, USA
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22
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Abstract
For several different proteins an apparent correlation has been observed between the propensity for dimerization by domain-swapping and the ability to aggregate into amyloid-like fibrils. Examples include the disease-related proteins β 2-microglobulin and transthyretin. This has led to proposals that the amyloid-formation pathway may feature extensive domain swapping. One possible consequence of such an aggregation pathway is that the resulting fibrils would incorporate structural elements that resemble the domain-swapped forms of the protein and, thus, reflect certain native-like structures or domain-interactions. In magic angle spinning solid-state NMR-based and other structural studies of such amyloid fibrils, it appears that many of these proteins form fibrils that are not native-like. Several fibrils, instead, have an in-register, parallel conformation, which is a common amyloid structural motif and is seen, for instance, in various prion fibrils. Such a lack of native structure in the fibrils suggests that the apparent connection between domain-swapping ability and amyloid-formation may be more subtle or complex than may be presumed at first glance.
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Affiliation(s)
- Patrick C A van der Wel
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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23
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Chou FC, Tsai TWT, Cheng HM, Chan JCC. Measurements of 13C multiple-quantum coherences in amyloid fibrils under magic-angle spinning. J Phys Chem B 2012; 116:7162-7. [PMID: 22632418 DOI: 10.1021/jp303455w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The excitation and detection of high-order multiple quantum coherences among (13)C nuclear spins are demonstrated in the samples of [1-(13)C]-L-alanine and (13)C labeled amyloid fibrils at a spinning frequency of 20 kHz. The technique is based on the double-quantum average Hamiltonian prepared by the DRAMA-XY4 pulse sequence. Empirically, we find that multiple supercycles are required to suppress the higher-order effects for real applications. Measurements for the fibril samples formed by the polypeptides of PrP(113-127) provide the first solid-state NMR evidence for the stacking of multiple β-sheet layers at the structural core of amyloid fibrils.
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Affiliation(s)
- Fang-Chieh Chou
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei, Taiwan
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24
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Morag O, Abramov G, Goldbourt A. Similarities and Differences within Members of the Ff Family of Filamentous Bacteriophage Viruses. J Phys Chem B 2011; 115:15370-9. [DOI: 10.1021/jp2079742] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Omry Morag
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel
| | - Gili Abramov
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel
| | - Amir Goldbourt
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel
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25
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Abstract
Many, perhaps most, proteins, are capable of forming self-propagating, β-sheet (amyloid) aggregates. Amyloid-like aggregates are found in a wide range of diseases and underlie prion-based inheritance. Despite intense interest in amyloids, structural details have only recently begun to be revealed as advances in biophysical approaches, such as hydrogen-deuterium exchange, X-ray crystallography, solid-state nuclear magnetic resonance (SSNMR), and cryoelectron microscopy (cryoEM), have enabled high-resolution insights into their molecular organization. Initial studies found that despite the highly divergent primary structure of different amyloid-forming proteins, amyloids from different sources share many structural similarities. With higher-resolution information, however, it has become clear that, on the molecular level, amyloids comprise a wide diversity of structures. Particularly surprising has been the finding that identical polypeptides can fold into multiple, distinct amyloid conformations and that this structural diversity can lead to distinct heritable prion states or strains.
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Affiliation(s)
- Brandon H Toyama
- Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco and California Institute for Quantitative Biomedical Research, San Francisco, California 94158-2542, USA.
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26
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Lewandowski JR, van der Wel PC, Rigney M, Grigorieff N, Griffin RG. Structural complexity of a composite amyloid fibril. J Am Chem Soc 2011; 133:14686-98. [PMID: 21766841 PMCID: PMC3190136 DOI: 10.1021/ja203736z] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The molecular structure of amyloid fibrils and the mechanism of their formation are of substantial medical and biological importance, but present an ongoing experimental and computational challenge. An early high-resolution view of amyloid-like structure was obtained on amyloid-like crystals of a small fragment of the yeast prion protein Sup35p: the peptide GNNQQNY. As GNNQQNY also forms amyloid-like fibrils under similar conditions, it has been theorized that the crystal's structural features are shared by the fibrils. Here we apply magic-angle-spinning (MAS) NMR to examine the structure and dynamics of these fibrils. Previously multiple NMR signals were observed for such samples, seemingly consistent with the presence of polymorphic fibrils. Here we demonstrate that peptides with these three distinct conformations instead assemble together into composite protofilaments. Electron microscopy (EM) of the ribbon-like fibrils indicates that these protofilaments combine in differing ways to form striations of variable widths, presenting another level of structural complexity. Structural and dynamic NMR data reveal the presence of highly restricted side-chain conformations involved in interfaces between differently structured peptides, likely comprising interdigitated steric zippers. We outline molecular interfaces that are consistent with the observed EM and NMR data. The rigid and uniform structure of the GNNQQNY crystals is found to contrast distinctly with the more complex structural and dynamic nature of these "composite" amyloid fibrils. These results provide insight into the fibril-crystal distinction and also indicate a necessary caution with respect to the extrapolation of crystal structures to the study of fibril structure and formation.
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Affiliation(s)
- Józef R. Lewandowski
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Patrick C.A. van der Wel
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Mike Rigney
- Howard Hughes Medical Institute, Brandeis University, Waltham, MA 02464, USA
| | - Nikolaus Grigorieff
- Howard Hughes Medical Institute, Brandeis University, Waltham, MA 02464, USA
| | - Robert G. Griffin
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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27
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Abstract
The technique of solid-state NMR, as applied to pharmaceutical analysis, has evolved from a sparingly used technique into an integrated, information-rich technique that uses a variety of sophisticated 1D and 2D experiments. In this article, several key developments in the field are reviewed, highlighting the increasing sophistication of the analyses being utilized and the detailed results obtained, in addition to future directions and developments.
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28
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Cheng HM, Tsai TWT, Huang WYC, Lee HK, Lian HY, Chou FC, Mou Y, Chan JCC. Steric zipper formed by hydrophobic peptide fragment of Syrian hamster prion protein. Biochemistry 2011; 50:6815-23. [PMID: 21749158 DOI: 10.1021/bi200712z] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Steric zippers, where the residues of two neighboring β-sheet layers are tightly interdigitated, have been proposed as fundamental structural units of amyloid fibrils by Eisenberg and co-workers. The steric zipper formed by polypeptides containing the palindromic sequence AGAAAAGA has a distinctive feature that the distance between two interdigitated β-sheet layers is comparable to the interstrand distance of the individual β-sheet. This structural motif is of great interest in the study of prion disease because the AGAAAAGA sequence is highly conserved in prion proteins of different species. In this work, the amyloid fibrils formed by the polypeptides of PrP(113-127), viz. Ac-AGAAAAGAVVGGLGG-NH(2), are taken as the model compound to investigate the biophysical principles governing the steric zipper formation. The target fibrils adopt the structural motif of class 7 steric zipper, which is formed by stacking of antiparallel β-sheet layers with residue 117 + k forming backbone hydrogen bonds to residue 120 - k. Implication of our results in the infectivity of scrapie prion is briefly discussed.
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Affiliation(s)
- Hsin-Mei Cheng
- Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
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29
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Structural characterization of polyglutamine fibrils by solid-state NMR spectroscopy. J Mol Biol 2011; 412:121-36. [PMID: 21763317 DOI: 10.1016/j.jmb.2011.06.045] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 06/21/2011] [Accepted: 06/27/2011] [Indexed: 01/21/2023]
Abstract
Protein aggregation via polyglutamine stretches occurs in a number of severe neurodegenerative diseases such as Huntington's disease. We have investigated fibrillar aggregates of polyglutamine peptides below, at, and above the toxicity limit of around 37 glutamine residues using solid-state NMR and electron microscopy. Experimental data are consistent with a dry fibril core of at least 70-80 Å in width for all constructs. Solid-state NMR dipolar correlation experiments reveal a largely β-strand character of all samples and point to tight interdigitation of hydrogen-bonded glutamine side chains from different sheets. Two approximately equally frequent populations of glutamine residues with distinct sets of chemical shifts are found, consistent with local backbone dihedral angles compensating for β-strand twist or with two distinct sets of side-chain conformations. Peptides comprising 15 glutamine residues are present as single extended β-strands. Data obtained for longer constructs are most compatible with a superpleated arrangement with individual molecules contributing β-strands to more than one sheet and an antiparallel assembly of strands within β-sheets.
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30
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Mukherjee S, Pondaven SP, Jaroniec CP. Conformational Flexibility of a Human Immunoglobulin Light Chain Variable Domain by Relaxation Dispersion Nuclear Magnetic Resonance Spectroscopy: Implications for Protein Misfolding and Amyloid Assembly. Biochemistry 2011; 50:5845-57. [DOI: 10.1021/bi200410c] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sujoy Mukherjee
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Simon P. Pondaven
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210, United States
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31
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Bowerman CJ, Liyanage W, Federation AJ, Nilsson BL. Tuning β-sheet peptide self-assembly and hydrogelation behavior by modification of sequence hydrophobicity and aromaticity. Biomacromolecules 2011; 12:2735-45. [PMID: 21568346 DOI: 10.1021/bm200510k] [Citation(s) in RCA: 145] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Peptide self-assembly leading to cross-β amyloid structures is a widely studied phenomenon because of its role in amyloid pathology and the exploitation of amyloid as a functional biomaterial. The self-assembly process is governed by hydrogen bonding, hydrophobic, aromatic π-π, and electrostatic Coulombic interactions. A role for aromatic π-π interactions in peptide self-assembly leading to amyloid has been proposed, but the relative contributions of π-π versus general hydrophobic interactions in these processes are poorly understood. The Ac-(XKXK)(2)-NH(2) peptide was used to study the contributions of aromatic and hydrophobic interactions to peptide self-assembly. Position X was globally replaced by valine (Val), isoleucine (Ile), phenylalanine (Phe), pentafluorophenylalanine (F(5)-Phe), and cyclohexylalanine (Cha). At low pH, these peptides remain monomeric because of repulsion of charged lysine (Lys) residues. Increasing the solvent ionic strength to shield repulsive charge-charge interactions between protonated Lys residues facilitated cross-β fibril formation. It was generally found that as peptide hydrophobicity increased, the required ionic strength to induce self-assembly decreased. At [NaCl] ranging from 0 to 1000 mM, the Val sequence failed to assemble. Assembly of the Phe sequence commenced at 700 mM NaCl and at 300 mM NaCl for the less hydrophobic Ile variant, even though it displayed a mixture of random coil and β-sheet secondary structures over all NaCl concentrations. β-Sheet formation for F(5)-Phe and Cha sequences was observed at only 20 and 60 mM NaCl, respectively. Whereas self-assembly propensity generally correlated to peptide hydrophobicity and not aromatic character the presence of aromatic amino acids imparted unique properties to fibrils derived from these peptides. Nonaromatic peptides formed fibrils of 3-15 nm in diameter, whereas aromatic peptides formed nanotape or nanoribbon architectures of 3-7 nm widths. In addition, all peptides formed fibrillar hydrogels at sufficient peptide concentrations, but nonaromatic peptides formed weak gels, whereas aromatic peptides formed rigid gels. These findings clarify the influence of aromatic amino acids on peptide self-assembly processes and illuminate design principles for the inclusion of aromatic amino acids in amyloid-derived biomaterials.
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Affiliation(s)
- Charles J Bowerman
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, USA
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32
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Brubaker WD, Freites JA, Golchert KJ, Shapiro RA, Morikis V, Tobias DJ, Martin RW. Separating instability from aggregation propensity in γS-crystallin variants. Biophys J 2011; 100:498-506. [PMID: 21244846 DOI: 10.1016/j.bpj.2010.12.3691] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Revised: 12/01/2010] [Accepted: 12/06/2010] [Indexed: 02/02/2023] Open
Abstract
Molecular dynamics (MD) simulations, circular dichroism (CD), and dynamic light scattering (DLS) measurements were used to investigate the aggregation propensity of the eye-lens protein γS-crystallin. The wild-type protein was investigated along with the cataract-related G18V variant and the symmetry-related G106V variant. The MD simulations suggest that local sequence differences result in dramatic differences in dynamics and hydration between these two apparently similar point mutations. This finding is supported by the experimental measurements, which show that although both variants appear to be mostly folded at room temperature, both display increased aggregation propensity. Although the disease-related G18V variant is not the most strongly destabilized, it aggregates more readily than either the wild-type or the G106V variant. These results indicate that γS-crystallin provides an excellent model system for investigating the role of dynamics and hydration in aggregation by locally unfolded proteins.
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Affiliation(s)
- William D Brubaker
- Department of Molecular Biology and Biochemistry, University of California, Irvine, USA
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33
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Leskes M, Akbey U, Oschkinat H, van Rossum BJ, Vega S. Radio frequency assisted homonuclear recoupling - a Floquet description of homonuclear recoupling via surrounding heteronuclei in fully protonated to fully deuterated systems. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2011; 209:207-219. [PMID: 21316279 DOI: 10.1016/j.jmr.2011.01.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2010] [Revised: 01/09/2011] [Accepted: 01/10/2011] [Indexed: 05/30/2023]
Abstract
We present a Floquet theory approach for the analysis of homonuclear recoupling assisted by radio frequency (RF) irradiation of surrounding heteronuclear spins. This description covers a broad range of systems from fully protonated to deuterated proteins, focusing in detail on recoupling via protons and deuterons separately as well as simultaneously by the double nucleus enhanced recoupling (DONER) scheme. The theoretical description, supported by numerical simulations and compared to experimental results from a partially deuterated model compound, indicates that in perdeuterated systems setting the RF amplitude equal to the magic angle spinning (MAS) frequency is not necessarily optimal for recoupling via (1)H and/or (2)H nuclei and modified recoupling conditions are identified.
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Affiliation(s)
- Michal Leskes
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
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34
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Kaminski Schierle GS, Bertoncini CW, Chan FTS, van der Goot AT, Schwedler S, Skepper J, Schlachter S, van Ham T, Esposito A, Kumita JR, Nollen EAA, Dobson CM, Kaminski CF. A FRET sensor for non-invasive imaging of amyloid formation in vivo. Chemphyschem 2011; 12:673-680. [PMID: 21308945 PMCID: PMC5402868 DOI: 10.1002/cphc.201000996] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Indexed: 11/10/2022]
Abstract
Misfolding and aggregation of amyloidogenic polypeptides lie at the root of many neurodegenerative diseases. Whilst protein aggregation can be readily studied in vitro by established biophysical techniques, direct observation of the nature and kinetics of aggregation processes taking place in vivo is much more challenging. We describe here, however, a Förster resonance energy transfer sensor that permits the aggregation kinetics of amyloidogenic proteins to be quantified in living systems by exploiting our observation that amyloid assemblies can act as energy acceptors for variants of fluorescent proteins. The observed lifetime reduction can be attributed to fluorescence energy transfer to intrinsic energy states associated with the growing amyloid species. Indeed, for a-synuclein, a protein whose aggregation is linked to Parkinson's disease, we have used this sensor to follow the kinetics of the self-association reactions taking place in vitro and in vivo and to reveal the nature of the ensuing aggregated species. Experiments were conducted in vitro, in cells in culture and in living Caenorhabditis elegans. For the latter the readout correlates directly with the appearance of a toxic phenotype. The ability to measure the appearance and development of pathogenic amyloid species in a living animal and the ability to relate such data to similar processes observed in vitro provides a powerful new tool in the study of the pathology of the family of misfolding disorders. Our study confirms the importance of the molecular environment in which aggregation reactions take place, highlighting similarities as well as differences between the processes occurring in vitro and in vivo, and their significance for defining the molecular physiology of the diseases with which they are associated.
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Affiliation(s)
- Gabriele S. Kaminski Schierle
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Pembroke Street, Cambridge CB2 3RA (U.K.)
| | - Carlos W. Bertoncini
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW (U.K.)
- Laboratory of Molecular Biophysics, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028, Barcelona (Spain)
| | - Fiona T. S. Chan
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Pembroke Street, Cambridge CB2 3RA (U.K.)
| | - Annemieke T. van der Goot
- Department of Genetics, University Medical Centre Groningen and University of Groningen 9700 RB Groningen (The Netherlands)
| | - Stefanie Schwedler
- Physikalische Chemie I, Fakultät für Chemie Universität Bielefeld, Universitätsstr. 25, 33615, Bielefeld (Germany)
| | - Jeremy Skepper
- Department of Physiology, Development and Neuroscience University of Cambridge, Downing Street, Cambridge CB2 3DY (U.K.)
| | - Simon Schlachter
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Pembroke Street, Cambridge CB2 3RA (U.K.)
| | - Tjakko van Ham
- Department of Genetics, University Medical Centre Groningen and University of Groningen 9700 RB Groningen (The Netherlands)
| | - Alessandro Esposito
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Pembroke Street, Cambridge CB2 3RA (U.K.)
| | - Janet R. Kumita
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW (U.K.)
| | - Ellen A. A. Nollen
- Department of Genetics, University Medical Centre Groningen and University of Groningen 9700 RB Groningen (The Netherlands)
| | - Christopher M. Dobson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW (U.K.)
| | - Clemens F. Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Pembroke Street, Cambridge CB2 3RA (U.K.)
- Friedrich-Alexander University of Erlangen Nürnberg 91052 Erlangen (Germany)
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35
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Chan JCC. Solid-state NMR techniques for the structural determination of amyloid fibrils. Top Curr Chem (Cham) 2011; 306:47-88. [PMID: 21630137 DOI: 10.1007/128_2011_154] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
This review discusses the solid-state NMR techniques developed for the study of amyloid fibrils. Literature up to the end of 2010 has been surveyed and the materials are organized according to five categories, viz. homonuclear dipolar recoupling and polarization transfer via J-coupling, heteronuclear dipolar recoupling, correlation spectroscopy, recoupling of chemical shift anisotropy, and tensor correlation. Our emphasis is on the NMR techniques and their practical aspects. The biological implications of the results obtained for amyloid fibrils are only briefly discussed. Our main objective is to showcase the power of NMR in the study of biological unoriented solids.
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Affiliation(s)
- Jerry C C Chan
- Department of Chemistry, National Taiwan University, Taipei, Taiwan.
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36
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van der Wel PC, Lewandowski JR, Griffin RG. Structural characterization of GNNQQNY amyloid fibrils by magic angle spinning NMR. Biochemistry 2010; 49:9457-69. [PMID: 20695483 PMCID: PMC3026921 DOI: 10.1021/bi100077x] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Several human diseases are associated with the formation of amyloid aggregates, but experimental characterization of these amyloid fibrils and their oligomeric precursors has remained challenging. Experimental and computational analysis of simpler model systems has therefore been necessary, for instance, on the peptide fragment GNNQQNY7−13 of yeast prion protein Sup35p. Expanding on a previous publication, we report here a detailed structural characterization of GNNQQNY fibrils using magic angle spinning (MAS) NMR. On the basis of additional chemical shift assignments we confirm the coexistence of three distinct peptide conformations within the fibrillar samples, as reflected in substantial chemical shift differences. Backbone torsion angle measurements indicate that the basic structure of these coexisting conformers is an extended β-sheet. We structurally characterize a previously identified localized distortion of the β-strand backbone specific to one of the conformers. Intermolecular contacts are consistent with each of the conformers being present in its own parallel and in-register sheet. Overall the MAS NMR data indicate a substantial difference between the structure of the fibrillar and crystalline forms of these peptides, with a clearly increased complexity in the GNNQQNY fibril structure. These experimental data can provide guidance for future work, both experimental and theoretical, and provide insights into the distinction between fibril growth and crystal formation.
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Affiliation(s)
| | | | - Robert G. Griffin
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
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Barbet-Massin E, Ricagno S, Lewandowski JR, Giorgetti S, Bellotti V, Bolognesi M, Emsley L, Pintacuda G. Fibrillar vs crystalline full-length beta-2-microglobulin studied by high-resolution solid-state NMR spectroscopy. J Am Chem Soc 2010; 132:5556-7. [PMID: 20356307 DOI: 10.1021/ja1002839] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Elucidating the fine structure of amyloid fibrils as well as understanding their processes of nucleation and growth remains a difficult yet essential challenge, directly linked to our current poor insight into protein misfolding and aggregation diseases. Here we consider beta-2-microglobulin (beta2m), the MHC-1 light chain component responsible for dialysis-related amyloidosis, which can give rise to amyloid fibrils in vitro under various experimental conditions, including low and neutral pH. We have used solid-state NMR to probe the structural features of fibrils formed by full-length beta2m (99 residues) at pH 2.5 and pH 7.4. A close comparison of 2D (13)C-(13)C and (15)N-(13)C correlation experiments performed on beta2m, in both the crystalline and fibrillar states, suggests that, in spite of structural changes affecting the protein loops linking the protein beta-strands, the protein chain retains a substantial share of its native secondary structure in the fibril assembly. Moreover, variations in the chemical shifts of the key Pro32 residue suggest the involvement of a cis-trans isomerization in the process of beta2m fibril formation. Lastly, the analogy of the spectra recorded on beta2m fibrils grown at different pH values hints at a conserved architecture of the amyloid species thus obtained.
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Affiliation(s)
- Emeline Barbet-Massin
- Centre de RMN à Très Hauts Champs, Université de Lyon (CNRS/ENS Lyon/UCB Lyon 1), 69100 Villeurbanne, France
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38
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Affiliation(s)
- Shi Bai
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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39
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Abdine A, Verhoeven MA, Park KH, Ghazi A, Guittet E, Berrier C, Van Heijenoort C, Warschawski DE. Structural study of the membrane protein MscL using cell-free expression and solid-state NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2010; 204:155-159. [PMID: 20194040 DOI: 10.1016/j.jmr.2010.02.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2009] [Revised: 02/01/2010] [Accepted: 02/08/2010] [Indexed: 05/28/2023]
Abstract
High-resolution structures of membrane proteins have so far been obtained mostly by X-ray crystallography, on samples where the protein is surrounded by detergent. Recent developments of solid-state NMR have opened the way to a new approach for the study of integral membrane proteins inside a membrane. At the same time, the extension of cell-free expression to the production of membrane proteins allows for the production of proteins tailor made for NMR. We present here an in situ solid-state NMR study of a membrane protein selectively labeled through the use of cell-free expression. The sample consists of MscL (mechano-sensitive channel of large conductance), a 75kDa pentameric alpha-helical ion channel from Escherichia coli, reconstituted in a hydrated lipid bilayer. Compared to a uniformly labeled protein sample, the spectral crowding is greatly reduced in the cell-free expressed protein sample. This approach may be a decisive step required for spectral assignment and structure determination of membrane proteins by solid-state NMR.
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Affiliation(s)
- Alaa Abdine
- UMR 7099, CNRS and Université Paris Diderot, IBPC, 13 rue Pierre et Marie Curie, F-75005 Paris, France
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40
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Morel B, Varela L, Conejero-Lara F. The Thermodynamic Stability of Amyloid Fibrils Studied by Differential Scanning Calorimetry. J Phys Chem B 2010; 114:4010-9. [DOI: 10.1021/jp9102993] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bertrand Morel
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Lorena Varela
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Francisco Conejero-Lara
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
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41
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Vitagliano L, Stanzione F, De Simone A, Esposito L. Dynamics and stability of amyloid-like steric zipper assemblies with hydrophobic dry interfaces. Biopolymers 2010; 91:1161-71. [PMID: 19280623 DOI: 10.1002/bip.21182] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Recent seminal investigations have suggested that the basic structural motif of amyloid fibers may be constituted by a tight association of two facing beta-sheets (steric zipper). Although this model has been derived from crystal structures of small peptide models, several theoretical investigations, essentially focused on steric zipper interface containing large polar and/or aromatic side chains, have confirmed the stability of this motif in a crystal-free context. To analyze the general validity of these findings, we carried out molecular dynamics (MD) simulations on aggregates stabilized by steric zipper interfaces made also of small or hydrophobic residues. In particular, we here characterized assemblies formed by the peptides SSTSAA and VQIVYK, whose structures have been recently solved at high resolution. In contrast to previous results obtained for polar/aromatic aggregates of the same size and with similar interface area, steric zipper assemblies composed of a pair of 10-stranded beta-sheets show high fluctuations and significant distortions in the simulation timescales (40-60 ns). Taking into account the crystal packing, the effect of the addition of an extra sheet to the assemblies was also evaluated. The MD results indicate that this addition does not provide extra-stabilization to the pair of sheet models. Although present data do not preclude the possibility that the steric zipper association identified in the crystal structure is the basic motif of SSTSAA and VQIVYK fibers, our findings highlight the importance of the nature of residues directly involved in the motif. Indeed, polar and aromatic residues that may form intrasheet and intersheet interactions likely provide a strong contribution to the steric zipper motif stability. Along this line, assemblies endowed with hydrophobic residues presumably require larger interfaces. In line with this suggestion, MD analysis of the HET-s(218-289) prion models composed of a similar number of strands shows that the assembly is endowed with a remarkable stability.
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Affiliation(s)
- Luigi Vitagliano
- Istituto di Biostrutture e Bioimmagini, CNR via Mezzocannone 16, I-80134 Napoli, Italy.
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42
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van der Wel PCA, Eddy MT, Ramachandran R, Griffin RG. Targeted 13C-13C distance measurements in a microcrystalline protein via J-decoupled rotational resonance width measurements. Chemphyschem 2009; 10:1656-63. [PMID: 19565580 DOI: 10.1002/cphc.200900102] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Rotational resonance width (R(2)W) magic-angle spinning (MAS) NMR experiments are performed to measure (13)C-(13)C distances in the hydrophobic core of the microcrystalline model protein G(Beta1). Such inter-residue distances are of particular value in NMR structure determinations. The experiments are done at a Larmor frequency of 750 MHz (1)H where the contribution of (13)C chemical shift anisotropy (CSA) to the R(2) transfer mechanism is significant. To minimize line broadening in the 2D spectra, we employ a combination of even/odd isotopic labeling with [1,3-(13)C] glycerol, and J-decoupling in the indirect dimension. This results in high-precision distance measurements between aromatic side chains of three tyrosine residues and distant methyl groups in the hydrophobic core of the protein. Even in the absence of information on the relative orientation of the shift tensors, we obtain relatively high precision data, which can be further improved by additional constraints on the tensor orientations.
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Affiliation(s)
- Patrick C A van der Wel
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Langkilde AE, Vestergaard B. Methods for structural characterization of prefibrillar intermediates and amyloid fibrils. FEBS Lett 2009; 583:2600-9. [PMID: 19481541 DOI: 10.1016/j.febslet.2009.05.040] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Revised: 05/20/2009] [Accepted: 05/22/2009] [Indexed: 11/15/2022]
Abstract
Protein fibrillation is first and foremost a structural phenomenon. Adequate structural investigation of the central conformational individuals of the fibrillation process is however exceedingly difficult. This is due to the nature of the process, which may be described as a dynamically evolving equilibrium between a large number of structural species. These are furthermore of highly diverging sizes and present in very uneven amounts and timeframes. Different structural methods have different strengths and limitations. These, and in particular recent advances within solution analysis of the undisturbed equilibrium using small angle X-ray scattering, are reviewed here.
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Affiliation(s)
- Annette Eva Langkilde
- Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Copenhagen, Denmark
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Madine J, Copland A, Serpell LC, Middleton DA. Cross-β Spine Architecture of Fibrils Formed by the Amyloidogenic Segment NFGSVQFV of Medin from Solid-State NMR and X-ray Fiber Diffraction Measurements. Biochemistry 2009; 48:3089-99. [DOI: 10.1021/bi802164e] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jillian Madine
- School of Biological Sciences, University of Liverpool,
Crown Street, Liverpool L69 7ZB, United Kingdom, and Department of
Biochemistry, School of Life Sciences, University of Sussex, Falmer,
Brighton BN1 9QG, United Kingdom
| | - Alastair Copland
- School of Biological Sciences, University of Liverpool,
Crown Street, Liverpool L69 7ZB, United Kingdom, and Department of
Biochemistry, School of Life Sciences, University of Sussex, Falmer,
Brighton BN1 9QG, United Kingdom
| | - Louise C. Serpell
- School of Biological Sciences, University of Liverpool,
Crown Street, Liverpool L69 7ZB, United Kingdom, and Department of
Biochemistry, School of Life Sciences, University of Sussex, Falmer,
Brighton BN1 9QG, United Kingdom
| | - David A. Middleton
- School of Biological Sciences, University of Liverpool,
Crown Street, Liverpool L69 7ZB, United Kingdom, and Department of
Biochemistry, School of Life Sciences, University of Sussex, Falmer,
Brighton BN1 9QG, United Kingdom
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45
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Madine J, Clayton JC, Yates EA, Middleton DA. Exploiting a 13C-labelled heparin analogue for in situ solid-state NMR investigations of peptide-glycan interactions within amyloid fibrils. Org Biomol Chem 2009; 7:2414-20. [DOI: 10.1039/b820808e] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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46
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Bowerman CJ, Ryan DM, Nissan DA, Nilsson BL. The effect of increasing hydrophobicity on the self-assembly of amphipathic β-sheet peptides. MOLECULAR BIOSYSTEMS 2009; 5:1058-69. [DOI: 10.1039/b904439f] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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47
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Heise H, Celej MS, Becker S, Riedel D, Pelah A, Kumar A, Jovin TM, Baldus M. Solid-state NMR reveals structural differences between fibrils of wild-type and disease-related A53T mutant alpha-synuclein. J Mol Biol 2008; 380:444-50. [PMID: 18539297 DOI: 10.1016/j.jmb.2008.05.026] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Revised: 05/07/2008] [Accepted: 05/13/2008] [Indexed: 11/30/2022]
Abstract
Fibrils from the Parkinson's-disease-related A53T mutant of alpha-synuclein were investigated by solid-state NMR spectroscopy, electron microscopy, and atomic force microscopy. Sequential solid-state NMR resonance assignments were obtained for a large fraction of the fibril core. Experiments conducted above and below the freezing point suggest that the fibrils contain regions with increased mobility and structural elements different from beta-strand character, in addition to the rigid beta-sheet-rich core region. As in earlier studies on wild-type alpha-synuclein, the C-terminus was found to be flexible and unfolded, whereas the main core region was highly rigid and rich in beta-sheets. Compared to fibrils from wild-type alpha-synuclein, the well-ordered beta-sheet region extends to at least L38 and L100. These results demonstrate that a disease-related mutant of alpha-synuclein differs in both aggregation kinetics and fibril structure.
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Affiliation(s)
- Henrike Heise
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Solid-State NMR Group, Am Fassberg 11, D-37077 Göttingen, Germany.
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48
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Rana A, Gupta TP, Bansal S, Kundu B. Formation of amyloid fibrils by bovine carbonic anhydrase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:930-5. [PMID: 18395531 DOI: 10.1016/j.bbapap.2008.02.020] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2007] [Revised: 02/25/2008] [Accepted: 02/26/2008] [Indexed: 11/17/2022]
Abstract
Amyloids are typically characterized by extensive aggregation of proteins where the participating polypeptides are involved in formation of intermolecular cross beta-sheet structures. Alternate structure attainment and amyloid formation has been hypothesized to be a generic property of a polypeptide, the propensities of which vary widely depending on the polypeptide involved and the physicochemical conditions it encounters. Many proteins that exist in the normal form in-vivo have been shown to form amyloid when incubated in partially denaturing conditions. The protein bovine carbonic anhydrase II (BCA II) when incubated in mildly denaturing conditions showed that the partially unfolded conformers assemble together and form ordered amyloid aggregates. The properties of these aggregates were tested using the traditional Congo-Red (CR) and Thioflavin-T (ThT) assays along with fluorescence microscopy, transmission electron microscopy (TEM), and circular dichroism (CD) spectroscopy. The aggregates were found to possess most of the characteristics ascribed to amyloid fibers. Thus, we report here that the single-domain globular protein, BCA II, is capable of forming amyloid fibrils. The primary sequence of BCA II was also analyzed using recurrence quantification analysis in order to suggest the probable residues responsible for amyloid formation.
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Affiliation(s)
- Anshul Rana
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas. New Delhi 110016, India
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