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Lends A, Birlirakis N, Cai X, Daskalov A, Shenoy J, Abdul-Shukkoor MB, Berbon M, Ferrage F, Liu Y, Loquet A, Tan KO. Efficient 18.8 T MAS-DNP NMR reveals hidden side chains in amyloid fibrils. JOURNAL OF BIOMOLECULAR NMR 2023:10.1007/s10858-023-00416-5. [PMID: 37289306 DOI: 10.1007/s10858-023-00416-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 05/02/2023] [Indexed: 06/09/2023]
Abstract
Amyloid fibrils are large and insoluble protein assemblies composed of a rigid core associated with a cross-β arrangement rich in β-sheet structural elements. It has been widely observed in solid-state NMR experiments that semi-rigid protein segments or side chains do not yield easily observable NMR signals at room temperature. The reasons for the missing peaks may be due to the presence of unfavorable dynamics that interfere with NMR experiments, which result in very weak or unobservable NMR signals. Therefore, for amyloid fibrils, semi-rigid and dynamically disordered segments flanking the amyloid core are very challenging to study. Here, we show that high-field dynamic nuclear polarization (DNP), an NMR hyperpolarization technique typically performed at low temperatures, can circumvent this issue because (i) the low-temperature environment (~ 100 K) slows down the protein dynamics to escape unfavorable detection regime, (ii) DNP improves the overall NMR sensitivity including those of flexible side chains, and (iii) efficient cross-effect DNP biradicals (SNAPol-1) optimized for high-field DNP (≥ 18.8 T) are employed to offer high sensitivity and resolution suitable for biomolecular NMR applications. By combining these factors, we have successfully established an impressive enhancement factor of ε ~ 50 on amyloid fibrils using an 18.8 T/ 800 MHz magnet. We have compared the DNP efficiencies of M-TinyPol, NATriPol-3, and SNAPol-1 biradicals on amyloid fibrils. We found that SNAPol-1 (with ε ~ 50) outperformed the other two radicals. The MAS DNP experiments revealed signals of flexible side chains previously inaccessible at conventional room-temperature experiments. These results demonstrate the potential of MAS-DNP NMR as a valuable tool for structural investigations of amyloid fibrils, particularly for side chains and dynamically disordered segments otherwise hidden at room temperature.
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Affiliation(s)
- Alons Lends
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), UMR 5348, Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, 33600, Pessac, France
| | - Nicolas Birlirakis
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Xinyi Cai
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Asen Daskalov
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), UMR 5348, Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, 33600, Pessac, France
| | - Jayakrishna Shenoy
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), UMR 5348, Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, 33600, Pessac, France
| | - Muhammed Bilal Abdul-Shukkoor
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), UMR 5348, Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, 33600, Pessac, France
| | - Mélanie Berbon
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), UMR 5348, Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, 33600, Pessac, France
| | - Fabien Ferrage
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Yangping Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Antoine Loquet
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), UMR 5348, Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, 33600, Pessac, France.
| | - Kong Ooi Tan
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France.
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2
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Liu J, Wu XL, Zeng YT, Hu ZH, Lu JX. Solid-state NMR studies of amyloids. Structure 2023; 31:230-243. [PMID: 36750098 DOI: 10.1016/j.str.2023.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/10/2022] [Accepted: 01/09/2023] [Indexed: 02/08/2023]
Abstract
Amyloids have special structural properties and are involved in many aspects of biological function. In particular, amyloids are the cause or hallmarks of a group of notorious and incurable neurodegenerative diseases. The extraordinary high molecular weight and aggregation states of amyloids have posed a challenge for researchers studying them. Solid-state NMR (SSNMR) has been extensively applied to study the structures and dynamics of amyloids for the past 20 or more years and brought us tremendous progress in understanding their structure and related diseases. These studies, at the same time, helped to push SSNMR technical developments in sensitivity and resolution. In this review, some interesting research studies and important technical developments are highlighted to give the reader an overview of the current state of this field.
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Affiliation(s)
- Jing Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xia-Lian Wu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yu-Teng Zeng
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Zhi-Heng Hu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jun-Xia Lu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
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3
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Cell-free synthesis of amyloid fibrils with infectious properties and amenable to sub-milligram magic-angle spinning NMR analysis. Commun Biol 2022; 5:1202. [DOI: 10.1038/s42003-022-04175-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/26/2022] [Indexed: 11/11/2022] Open
Abstract
AbstractStructural investigations of amyloid fibrils often rely on heterologous bacterial overexpression of the protein of interest. Due to their inherent hydrophobicity and tendency to aggregate as inclusion bodies, many amyloid proteins are challenging to express in bacterial systems. Cell-free protein expression is a promising alternative to classical bacterial expression to produce hydrophobic proteins and introduce NMR-active isotopes that can improve and speed up the NMR analysis. Here we implement the cell-free synthesis of the functional amyloid prion HET-s(218-289). We present an interesting case where HET-s(218-289) directly assembles into infectious fibril in the cell-free expression mixture without the requirement of denaturation procedures and purification. By introducing tailored 13C and 15N isotopes or CF3 and 13CH2F labels at strategic amino-acid positions, we demonstrate that cell-free synthesized amyloid fibrils are readily amenable to high-resolution magic-angle spinning NMR at sub-milligram quantity.
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4
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Siemer AB. What makes functional amyloids work? Crit Rev Biochem Mol Biol 2022; 57:399-411. [PMID: 35997712 PMCID: PMC9588633 DOI: 10.1080/10409238.2022.2113030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 06/29/2022] [Accepted: 08/10/2022] [Indexed: 01/27/2023]
Abstract
Although first described in the context of disease, cross-β (amyloid) fibrils have also been found as functional entities in all kingdoms of life. However, what are the specific properties of the cross-β fibril motif that convey biological function, make them especially suited for their particular purpose, and distinguish them from other fibrils found in biology? This review approaches these questions by arguing that cross-β fibrils are highly periodic, stable, and self-templating structures whose formation is accompanied by substantial conformational change that leads to a multimerization of their core and framing sequences. A discussion of each of these properties is followed by selected examples of functional cross-β fibrils that show how function is usually achieved by leveraging many of these properties.
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Affiliation(s)
- Ansgar B Siemer
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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5
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Miller JG, Hughes SA, Modlin C, Conticello VP. Structures of synthetic helical filaments and tubes based on peptide and peptido-mimetic polymers. Q Rev Biophys 2022; 55:1-103. [PMID: 35307042 DOI: 10.1017/s0033583522000014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
AbstractSynthetic peptide and peptido-mimetic filaments and tubes represent a diverse class of nanomaterials with a broad range of potential applications, such as drug delivery, vaccine development, synthetic catalyst design, encapsulation, and energy transduction. The structures of these filaments comprise supramolecular polymers based on helical arrangements of subunits that can be derived from self-assembly of monomers based on diverse structural motifs. In recent years, structural analyses of these materials at near-atomic resolution (NAR) have yielded critical insights into the relationship between sequence, local conformation, and higher-order structure and morphology. This structural information offers the opportunity for development of new tools to facilitate the predictable and reproduciblede novodesign of synthetic helical filaments. However, these studies have also revealed several significant impediments to the latter process – most notably, the common occurrence of structural polymorphism due to the lability of helical symmetry in structural space. This article summarizes the current state of knowledge on the structures of designed peptide and peptido-mimetic filamentous assemblies, with a focus on structures that have been solved to NAR for which reliable atomic models are available.
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Affiliation(s)
- Jessalyn G Miller
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA30322
| | - Spencer A Hughes
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA30322
| | - Charles Modlin
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA30322
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Jayan P, Vahid AA, Kizhakkeduth ST, Muhammed SOH, Shibina AB, Vijayan V. Direct Observation of the Self-Aggregation of R3R4 Bi-repeat of Tau Protein. Chembiochem 2021; 22:2093-2097. [PMID: 33826208 DOI: 10.1002/cbic.202100013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/04/2021] [Indexed: 11/06/2022]
Abstract
Different cryo-EM derived atomic models of in vivo tau filaments from patients with tauopathies consisted of R3 and R4 repeats of the microtubule-binding domain. In comparison, only the R3 repeat forms the core of the heparin-induced fibrils of the three repeat tau isoforms. For developing therapeutics, it is desirable to have an in vitro tau aggregation system producing fibrils corresponding to the disease morphology. Here we report the self-aggregation of truncated tau segment R3R4 peptide without requiring heparin for aggregation induction. We used NMR spectroscopy and other biophysical methods to monitor the self-aggregation of R3R4. We identified the hexapeptide region in R3 and β-turn region in R4 as the aggregation initiating region of the protein. The solid-state NMR of self-aggregated R3R4 fibrils demonstrated that in addition to R3 residues, residues of R4 were also part of the fibril filaments. The presence of both R3 and R4 residues in the aggregation process and the core of fibril filaments suggest that the aggregation of R3R4 might resemble the in vivo aggregation process.
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Affiliation(s)
- Parvathy Jayan
- School of Chemistry, IISER Thiruvananthapuram, Maruthamala P.O, Thiruvananthapuram, Kerala, India
| | - Arshad A Vahid
- School of Chemistry, IISER Thiruvananthapuram, Maruthamala P.O, Thiruvananthapuram, Kerala, India
| | - Safwa T Kizhakkeduth
- School of Chemistry, IISER Thiruvananthapuram, Maruthamala P.O, Thiruvananthapuram, Kerala, India
| | - Shafeek O H Muhammed
- School of Chemistry, IISER Thiruvananthapuram, Maruthamala P.O, Thiruvananthapuram, Kerala, India
| | - Ajmala B Shibina
- School of Chemistry, IISER Thiruvananthapuram, Maruthamala P.O, Thiruvananthapuram, Kerala, India
| | - Vinesh Vijayan
- School of Chemistry, IISER Thiruvananthapuram, Maruthamala P.O, Thiruvananthapuram, Kerala, India
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7
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Dyrka W, Coustou V, Daskalov A, Lends A, Bardin T, Berbon M, Kauffmann B, Blancard C, Salin B, Loquet A, Saupe SJ. Identification of NLR-associated Amyloid Signaling Motifs in Bacterial Genomes. J Mol Biol 2020; 432:6005-6027. [PMID: 33058872 DOI: 10.1016/j.jmb.2020.10.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 10/05/2020] [Accepted: 10/05/2020] [Indexed: 02/06/2023]
Abstract
In filamentous fungi, amyloid signaling sequences allow Nod-like receptors (NLRs) to activate downstream cell-death inducing proteins with HeLo and HeLo-like (HELL) domains and amyloid RHIM and RHIM-related motifs control immune defense pathways in mammals and flies. Herein, we show bioinformatically that analogous amyloid signaling motifs exist in bacteria. These short motifs are found at the N terminus of NLRs and at the C terminus of proteins with a domain we term BELL. The corresponding NLR and BELL proteins are encoded by adjacent genes. We identify 10 families of such bacterial amyloid signaling sequences (BASS), one of which (BASS3) is homologous to RHIM and a fungal amyloid motif termed PP. BASS motifs occur nearly exclusively in bacteria forming multicellular structures (mainly in Actinobacteria and Cyanobacteria). We analyze experimentally a subset of seven of these motifs (from the most common BASS1 family and the RHIM-related BASS3 family) and find that these sequences form fibrils in vitro. Using a fungal in vivo model, we show that all tested BASS-motifs form prions and that the NLR-side motifs seed prion-formation of the corresponding BELL-side motif. We find that BASS3 motifs show partial prion cross-seeding with mammalian RHIM and fungal PP-motifs and that proline mutations on key positions of the BASS3 core motif, conserved in RHIM and PP-motifs, abolish prion formation. This work expands the paradigm of prion amyloid signaling to multicellular prokaryotes and suggests a long-term evolutionary conservation of these motifs from bacteria, to fungi and animals.
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Affiliation(s)
- Witold Dyrka
- Politechnika Wrocławska, Wydział Podstawowych Problemów Techniki, Katedra Inżynierii Biomedycznej, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Virginie Coustou
- Non-self Recognition in Fungi, Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS, Université de Bordeaux, 1 Rue Camille Saint Saëns, 33077 Bordeaux CEDEX, France
| | - Asen Daskalov
- Institute of Chemistry & Biology of Membranes & Nanoobjects, UMR5248 CBMN, IECB, CNRS, Université de Bordeaux, Allee Geoffroy Saint-Hilaire, 33607 Pessac, France
| | - Alons Lends
- Institute of Chemistry & Biology of Membranes & Nanoobjects, UMR5248 CBMN, IECB, CNRS, Université de Bordeaux, Allee Geoffroy Saint-Hilaire, 33607 Pessac, France
| | - Thierry Bardin
- Non-self Recognition in Fungi, Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS, Université de Bordeaux, 1 Rue Camille Saint Saëns, 33077 Bordeaux CEDEX, France
| | - Mélanie Berbon
- Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS, Université de Bordeaux, 1 Rue Camille Saint Saëns, 33077 Bordeaux CEDEX, France
| | - Brice Kauffmann
- IECB, UMS 3033, US 001, CNRS, Université de Bordeaux, 2 Rue Robert Escarpit, 33607 Pessac, France
| | - Corinne Blancard
- Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS, Université de Bordeaux, 1 Rue Camille Saint Saëns, 33077 Bordeaux CEDEX, France
| | - Bénédicte Salin
- Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS, Université de Bordeaux, 1 Rue Camille Saint Saëns, 33077 Bordeaux CEDEX, France
| | - Antoine Loquet
- Institute of Chemistry & Biology of Membranes & Nanoobjects, UMR5248 CBMN, IECB, CNRS, Université de Bordeaux, Allee Geoffroy Saint-Hilaire, 33607 Pessac, France
| | - Sven J Saupe
- Non-self Recognition in Fungi, Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS, Université de Bordeaux, 1 Rue Camille Saint Saëns, 33077 Bordeaux CEDEX, France.
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8
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Terruzzi L, Spagnolli G, Boldrini A, Requena JR, Biasini E, Faccioli P. All-atom simulation of the HET-s prion replication. PLoS Comput Biol 2020; 16:e1007922. [PMID: 32946455 PMCID: PMC7526898 DOI: 10.1371/journal.pcbi.1007922] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 09/30/2020] [Accepted: 08/03/2020] [Indexed: 11/18/2022] Open
Abstract
Prions are self-replicative protein particles lacking nucleic acids. Originally discovered for causing infectious neurodegenerative disorders, they have also been found to play several physiological roles in a variety of species. Functional and pathogenic prions share a common mechanism of replication, characterized by the ability of an amyloid conformer to propagate by inducing the conversion of its physiological, soluble counterpart. Since time-resolved biophysical experiments are currently unable to provide full reconstruction of the physico-chemical mechanisms responsible for prion replication, one must rely on computer simulations. In this work, we show that a recently developed algorithm called Self-Consistent Path Sampling (SCPS) overcomes the computational limitations of plain MD and provides a viable tool to investigate prion replication processes using state-of-the-art all-atom force fields in explicit solvent. First, we validate the reliability of SCPS simulations by characterizing the folding of a class of small proteins and comparing against the results of plain MD simulations. Next, we use SCPS to investigate the replication of the prion forming domain of HET-s, a physiological fungal prion for which high-resolution structural data are available. Our atomistic reconstruction shows remarkable similarities with a previously reported mechanism of mammalian PrPSc propagation obtained using a simpler and more approximate path sampling algorithm. Together, these results suggest that the propagation of prions generated by evolutionary distant proteins may share common features. In particular, in both these cases, prions propagate their conformation through a very similar templating mechanism. Prions are proteins capable of replicating in absence of nucleic acids. By propagating the information encoded in their conformation, prions exemplify the phenomenon of protein-based inheritance. These peculiar agents are associated with neurodegenerative pathologies in mammals, but also involved in a wide variety of physiological processes occurring in various biological contexts along the evolutionary scale. In this work, we apply a recently developed computational method to study the propagation mechanism of the fungal prion HET-s, using a realistic all-atom model. We find that the replication of HET-s shares fundamental features with the templated conversion of the mammalian prion PrPSc.
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Affiliation(s)
- Luca Terruzzi
- Sibylla Biotech SRL, Verona, Italy.,Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Povo, Trento, Italy
| | - Giovanni Spagnolli
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Povo, Trento, Italy.,Dulbecco Telethon Institute, University of Trento, Povo, Trento, Italy
| | - Alberto Boldrini
- Sibylla Biotech SRL, Verona, Italy.,Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Povo, Trento, Italy
| | - Jesús R Requena
- CIMUS Biomedical Research Institute & Department of Medical Sciences, University of Santiago de Compostela-IDIS, Spain
| | - Emiliano Biasini
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Povo, Trento, Italy.,Dulbecco Telethon Institute, University of Trento, Povo, Trento, Italy
| | - Pietro Faccioli
- Department of Physics, University of Trento, Povo, Trento, Italy.,INFN-TIFPA, University of Trento, Povo, Trento, Italy
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9
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Spagnolli G, Requena JR, Biasini E. Understanding prion structure and conversion. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 175:19-30. [PMID: 32958233 DOI: 10.1016/bs.pmbts.2020.07.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Since their original identification, prions have represented enigmatic agents that defy the classical concept of genetic inheritance. For almost four decades, the high-resolution structure of PrPSc, the infectious and misfolded counterpart of the cellular prion protein (PrPC), has remained elusive, mostly due to technical challenges posed by its high insolubility and aggregation propensity. As a result, such a lack of information has critically hampered the search for an effective therapy against prion diseases. Nevertheless, multiple attempts to get insights into the structure of PrPSc have provided important experimental constraints that, despite being at limited resolution, are paving the way for the application of computer-aided technologies to model the three-dimensional architecture of prions and their templated replication mechanism. Here, we review the most relevant studies carried out so far to elucidate the conformation of infectious PrPSc and offer an overview of the most advanced molecular models to explain prion structure and conversion.
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Affiliation(s)
- Giovanni Spagnolli
- Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, TN, Italy; Dulbecco Telethon Institute, University of Trento, Trento, TN, Italy
| | - Jesús R Requena
- CIMUS Biomedical Research Institute & Department of Medical Sciences, University of Santiago de Compostela-IDIS, Santiago, Spain
| | - Emiliano Biasini
- Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, TN, Italy; Dulbecco Telethon Institute, University of Trento, Trento, TN, Italy.
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10
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Pang Y, Kovachev P, Sanyal S. Ribosomal RNA Modulates Aggregation of the Podospora Prion Protein HET-s. Int J Mol Sci 2020; 21:ijms21176340. [PMID: 32882892 PMCID: PMC7504336 DOI: 10.3390/ijms21176340] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 08/28/2020] [Indexed: 01/19/2023] Open
Abstract
The role of the nucleic acids in prion aggregation/disaggregation is becoming more and more evident. Here, using HET-s prion from fungi Podospora anserina (P. anserina) as a model system, we studied the role of RNA, particularly of different domains of the ribosomal RNA (rRNA), in its aggregation process. Our results using Rayleigh light scattering, Thioflavin T (ThT) binding, transmission electron microscopy (TEM) and cross-seeding assay show that rRNA, in particular the domain V of the major rRNA from the large subunit of the ribosome, substantially prevents insoluble amyloid and amorphous aggregation of the HET-s prion in a concentration-dependent manner. Instead, it facilitates the formation of the soluble oligomeric “seeds”, which are capable of promoting de novo HET-s aggregation. The sites of interactions of the HET-s prion protein on domain V rRNA were identified by primer extension analysis followed by UV-crosslinking, which overlap with the sites previously identified for the protein-folding activity of the ribosome (PFAR). This study clarifies a missing link between the rRNA-based PFAR and the mode of propagation of the fungal prions.
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11
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Siemer AB. Advances in studying protein disorder with solid-state NMR. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2020; 106:101643. [PMID: 31972419 PMCID: PMC7202078 DOI: 10.1016/j.ssnmr.2020.101643] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/06/2020] [Accepted: 01/07/2020] [Indexed: 05/26/2023]
Abstract
Solution NMR is a key tool to study intrinsically disordered proteins (IDPs), whose importance for biological function is widely accepted. However, disordered proteins are not limited to solution and are also found in non-soluble systems such as fibrils and membrane proteins. In this Trends article, I will discuss how solid-state NMR can be used to study disorder in non-soluble proteins. Techniques based on dipolar couplings can study static protein disorder which either occurs naturally as e.g. in spider silk or can be induced by freeze trapping IDPs or unfolded proteins. In this case, structural ensembles are directly reflected by a static distribution of dihedral angels that can be determined by the distribution of chemical shifts or other methods. Techniques based on J-couplings can detect dynamic protein disorder under MAS. In this case, only average chemical shifts are measured but disorder can be characterized with a variety of data including secondary chemical shifts, relaxation rates, paramagnetic relaxation enhancements, or residual dipolar couplings. I describe both technical aspects and examples of solid-state NMR on protein disorder and end the article with a discussion of challenges and opportunities of this emerging field.
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Affiliation(s)
- Ansgar B Siemer
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Univeristy of Southern California, 1501 San Pablo Street, Los Angeles, CA, 90033, USA.
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12
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Shenoy J, El Mammeri N, Dutour A, Berbon M, Saad A, Lends A, Morvan E, Grélard A, Lecomte S, Kauffmann B, Theillet FX, Habenstein B, Loquet A. Structural dissection of amyloid aggregates of TDP-43 and its C-terminal fragments TDP-35 and TDP-16. FEBS J 2019; 287:2449-2467. [PMID: 31782904 DOI: 10.1111/febs.15159] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 10/17/2019] [Accepted: 11/27/2019] [Indexed: 12/12/2022]
Abstract
The TAR DNA-binding protein (TDP-43) self-assembles into prion-like aggregates considered to be the structural hallmark of amyotrophic lateral sclerosis and frontotemporal dementia. Here, we use a combination of electron microscopy, X-ray fiber diffraction, Fourier-transform infrared spectroscopy analysis, and solid-state NMR spectroscopy to investigate the molecular organization of different TDP constructs, namely the full-length TDP-43 (1-414), two C-terminal fragments [TDP-35 (90-414) and TDP-16 (267-414)], and a C-terminal truncated fragment (TDP-43 ∆GaroS2), in their fibrillar state. Although the different protein constructs exhibit similar fibril morphology and a typical cross-β signature by X-ray diffraction, solid-state NMR indicates that TDP-43 and TDP-35 share the same polymorphic molecular structure, while TDP-16 encompasses a well-ordered amyloid core. We identified several residues in the so-called C-terminal GaroS2 (368-414) domain that participates in the rigid core of TDP-16 fibrils, underlining its importance during the aggregation process. Our findings demonstrate that C-terminal fragments can adopt a different molecular conformation in isolation or in the context of the full-length assembly, suggesting that the N-terminal domain and RRM domains play an important role in the TDP-43 amyloid transition.
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Affiliation(s)
- Jayakrishna Shenoy
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Nadia El Mammeri
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Antoine Dutour
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Mélanie Berbon
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Ahmad Saad
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Alons Lends
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Estelle Morvan
- Université de Bordeaux, CNRS, INSERM, UMS3033, Institut Européen de Chimie et Biologie (IECB), Pessac, France
| | - Axelle Grélard
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Sophie Lecomte
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Brice Kauffmann
- Université de Bordeaux, CNRS, INSERM, UMS3033, Institut Européen de Chimie et Biologie (IECB), Pessac, France
| | - François-Xavier Theillet
- Institut de Biologie Intégrative de la Cellule, CEA, CNRS, Université Paris Sud, UMR 9198, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Birgit Habenstein
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
| | - Antoine Loquet
- CBMN (UMR5248), Université de Bordeaux - CNRS - IPB, Institut Européen de Chimie et Biologie, Pessac, France
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13
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Eraña H, Charco JM, Di Bari MA, Díaz-Domínguez CM, López-Moreno R, Vidal E, González-Miranda E, Pérez-Castro MA, García-Martínez S, Bravo S, Fernández-Borges N, Geijo M, D’Agostino C, Garrido J, Bian J, König A, Uluca-Yazgi B, Sabate R, Khaychuk V, Vanni I, Telling GC, Heise H, Nonno R, Requena JR, Castilla J. Development of a new largely scalable in vitro prion propagation method for the production of infectious recombinant prions for high resolution structural studies. PLoS Pathog 2019; 15:e1008117. [PMID: 31644574 PMCID: PMC6827918 DOI: 10.1371/journal.ppat.1008117] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 11/04/2019] [Accepted: 10/01/2019] [Indexed: 12/12/2022] Open
Abstract
The resolution of the three-dimensional structure of infectious prions at the atomic level is pivotal to understand the pathobiology of Transmissible Spongiform Encephalopathies (TSE), but has been long hindered due to certain particularities of these proteinaceous pathogens. Difficulties related to their purification from brain homogenates of disease-affected animals were resolved almost a decade ago by the development of in vitro recombinant prion propagation systems giving rise to highly infectious recombinant prions. However, lack of knowledge about the molecular mechanisms of the misfolding event and the complexity of systems such as the Protein Misfolding Cyclic Amplification (PMCA), have limited generating the large amounts of homogeneous recombinant prion preparations required for high-resolution techniques such as solid state Nuclear Magnetic Resonance (ssNMR) imaging. Herein, we present a novel recombinant prion propagation system based on PMCA that substitutes sonication with shaking thereby allowing the production of unprecedented amounts of multi-labeled, infectious recombinant prions. The use of specific cofactors, such as dextran sulfate, limit the structural heterogeneity of the in vitro propagated prions and makes possible, for the first time, the generation of infectious and likely homogeneous samples in sufficient quantities for studies with high-resolution structural techniques as demonstrated by the preliminary ssNMR spectrum presented here. Overall, we consider that this new method named Protein Misfolding Shaking Amplification (PMSA), opens new avenues to finally elucidate the three-dimensional structure of infectious prions.
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Affiliation(s)
- Hasier Eraña
- CIC bioGUNE, Derio (Bizkaia), Spain
- ATLAS Molecular Pharma S. L. Derio (Bizkaia), Spain
| | | | - Michele A. Di Bari
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | | | | | - Enric Vidal
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Barcelona, Spain
| | | | | | | | - Susana Bravo
- Proteomics Lab, IDIS, Santiago de Compostela, Spain
| | | | - Mariví Geijo
- Animal Health Department, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Derio (Bizkaia), Spain
| | - Claudia D’Agostino
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | - Joseba Garrido
- Animal Health Department, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Derio (Bizkaia), Spain
| | - Jifeng Bian
- Prion Research Center (PRC), Colorado State University, Fort Collins, Colorado, United States of America
| | - Anna König
- Institute of Complex Systems (ICS-6) and Jülich Center for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
- Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Boran Uluca-Yazgi
- Institute of Complex Systems (ICS-6) and Jülich Center for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
- Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Raimon Sabate
- Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, Spain
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, Spain
| | - Vadim Khaychuk
- Prion Research Center (PRC), Colorado State University, Fort Collins, Colorado, United States of America
| | - Ilaria Vanni
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | - Glenn C. Telling
- Prion Research Center (PRC), Colorado State University, Fort Collins, Colorado, United States of America
| | - Henrike Heise
- Institute of Complex Systems (ICS-6) and Jülich Center for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
- Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Romolo Nonno
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | - Jesús R. Requena
- CIMUS Biomedical Research Institute, University of Santiago de Compostela-IDIS, Spain
| | - Joaquín Castilla
- CIC bioGUNE, Derio (Bizkaia), Spain
- IKERBasque, Basque Foundation for Science, Bilbao (Bizkaia), Spain
- * E-mail:
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14
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Gao C, Judge PT, Sesti EL, Price LE, Alaniva N, Saliba EP, Albert BJ, Soper NJ, Chen PH, Barnes AB. Four millimeter spherical rotors spinning at 28 kHz with double-saddle coils for cross polarization NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 303:1-6. [PMID: 30978570 DOI: 10.1016/j.jmr.2019.03.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/07/2019] [Accepted: 03/20/2019] [Indexed: 06/09/2023]
Abstract
Spherical rotors in magic angle spinning (MAS) experiments have significant advantages over traditional cylindrical rotors including simplified spinning implementation, easy sample exchange, more efficient microwave coupling for dynamic nuclear polarization (DNP), and feasibility of downscaling to access higher spinning frequencies. Here, we implement spherical rotors with 4 mm outside diameter (o.d.) and demonstrate spinning >28 kHz using a single aperture for spinning gas. We show a modified stator geometry to improve fiber optic detection, increase NMR filling factor, and improve alignment for sample exchange and microwave irradiation. Higher NMR Rabi frequencies were obtained using smaller radiofrequency (RF) coils on small-diameter spherical rotors, compared to our previous implementation of MAS spheres with an o.d. of 9.5 mm. We report nutation fields of 110 kHz on 13C with 820 W of input power and 100 kHz on 1H with 800 W of input power. Proton decoupling fields of 78 kHz were applied over 20 ms of signal acquisition without any sign of arcing. Compared to our initial demonstration of a split coil for 9.5 mm spheres, this current implementation of a double-saddle coil inductor for 4 mm spheres not only intensifies the RF fields, but also improves RF homogeneity. We achieve an 810°/90° nutation intensity ratio of 0.84 at 300.197 MHz (1H). We also show electromagnetic simulations predicting a nearly 3-fold improvement in electron Rabi frequency of 0.99 MHz (with 4 mm spheres) compared to 0.38 MHz (with 3.2 mm cylinders), with 5 W of incident microwave power. Further improvements in magnetic resonance spin control are expected as RF inductors and microwave coupling are optimized for spherical rotors and scaled down to the micron scale.
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Affiliation(s)
- Chukun Gao
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Patrick T Judge
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Biochemistry, Biophysics & Structural Biology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Erika L Sesti
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Lauren E Price
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Nicholas Alaniva
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Edward P Saliba
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Brice J Albert
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Nathan J Soper
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Pin-Hui Chen
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Physics, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Alexander B Barnes
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA.
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15
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Alaniva N, Saliba EP, Sesti EL, Judge PT, Barnes AB. Electron Decoupling with Chirped Microwave Pulses for Rapid Signal Acquisition and Electron Saturation Recovery. Angew Chem Int Ed Engl 2019; 58:7259-7262. [DOI: 10.1002/anie.201900139] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 03/01/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Nicholas Alaniva
- Department of Chemistry Washington University in St. Louis One Brookings Drive St. Louis MO 63130 USA
| | - Edward P. Saliba
- Department of Chemistry Washington University in St. Louis One Brookings Drive St. Louis MO 63130 USA
| | - Erika L. Sesti
- Department of Chemistry Washington University in St. Louis One Brookings Drive St. Louis MO 63130 USA
| | - Patrick T. Judge
- Department of Chemistry Washington University in St. Louis One Brookings Drive St. Louis MO 63130 USA
- Department of Biochemistry, Biophysics, and Biology Washington University in St. Louis School of Medicine 660 S. Euclid Ave St Louis MO 63110 USA
| | - Alexander B. Barnes
- Department of Chemistry Washington University in St. Louis One Brookings Drive St. Louis MO 63130 USA
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16
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Alaniva N, Saliba EP, Sesti EL, Judge PT, Barnes AB. Electron Decoupling with Chirped Microwave Pulses for Rapid Signal Acquisition and Electron Saturation Recovery. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201900139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Nicholas Alaniva
- Department of Chemistry Washington University in St. Louis One Brookings Drive St. Louis MO 63130 USA
| | - Edward P. Saliba
- Department of Chemistry Washington University in St. Louis One Brookings Drive St. Louis MO 63130 USA
| | - Erika L. Sesti
- Department of Chemistry Washington University in St. Louis One Brookings Drive St. Louis MO 63130 USA
| | - Patrick T. Judge
- Department of Chemistry Washington University in St. Louis One Brookings Drive St. Louis MO 63130 USA
- Department of Biochemistry, Biophysics, and Biology Washington University in St. Louis School of Medicine 660 S. Euclid Ave St Louis MO 63110 USA
| | - Alexander B. Barnes
- Department of Chemistry Washington University in St. Louis One Brookings Drive St. Louis MO 63130 USA
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17
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Demers JP, Fricke P, Shi C, Chevelkov V, Lange A. Structure determination of supra-molecular assemblies by solid-state NMR: Practical considerations. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 109:51-78. [PMID: 30527136 DOI: 10.1016/j.pnmrs.2018.06.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 06/15/2018] [Accepted: 06/15/2018] [Indexed: 05/26/2023]
Abstract
In the cellular environment, biomolecules assemble in large complexes which can act as molecular machines. Determining the structure of intact assemblies can reveal conformations and inter-molecular interactions that are only present in the context of the full assembly. Solid-state NMR (ssNMR) spectroscopy is a technique suitable for the study of samples with high molecular weight that allows the atomic structure determination of such large protein assemblies under nearly physiological conditions. This review provides a practical guide for the first steps of studying biological supra-molecular assemblies using ssNMR. The production of isotope-labeled samples is achievable via several means, which include recombinant expression, cell-free protein synthesis, extraction of assemblies directly from cells, or even the study of assemblies in whole cells in situ. Specialized isotope labeling schemes greatly facilitate the assignment of chemical shifts and the collection of structural data. Advanced strategies such as mixed, diluted, or segmental subunit labeling offer the possibility to study inter-molecular interfaces. Detailed and practical considerations are presented with respect to first setting up magic-angle spinning (MAS) ssNMR experiments, including the selection of the ssNMR rotor, different methods to best transfer the sample and prepare the rotor, as well as common and robust procedures for the calibration of the instrument. Diagnostic spectra to evaluate the resolution and sensitivity of the sample are presented. Possible improvements that can reduce sample heterogeneity and improve the quality of ssNMR spectra are reviewed.
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Affiliation(s)
- Jean-Philippe Demers
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Laboratory of Cell Biology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Pascal Fricke
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Chaowei Shi
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Veniamin Chevelkov
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Adam Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
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18
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Chen P, Albert BJ, Gao C, Alaniva N, Price LE, Scott FJ, Saliba EP, Sesti EL, Judge PT, Fisher EW, Barnes AB. Magic angle spinning spheres. SCIENCE ADVANCES 2018; 4:eaau1540. [PMID: 30255153 PMCID: PMC6155130 DOI: 10.1126/sciadv.aau1540] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/10/2018] [Indexed: 05/18/2023]
Abstract
Magic angle spinning (MAS) is commonly used in nuclear magnetic resonance of solids to improve spectral resolution. Rather than using cylindrical rotors for MAS, we demonstrate that spherical rotors can be spun stably at the magic angle. Spherical rotors conserve valuable space in the probe head and simplify sample exchange and microwave coupling for dynamic nuclear polarization. In this current implementation of spherical rotors, a single gas stream provides bearing gas to reduce friction, drive propulsion to generate and maintain angular momentum, and variable temperature control for thermostating. Grooves are machined directly into zirconia spheres, thereby converting the rotor body into a robust turbine with high torque. We demonstrate that 9.5-mm-outside diameter spherical rotors can be spun at frequencies up to 4.6 kHz with N2(g) and 10.6 kHz with He(g). Angular stability of the spinning axis is demonstrated by observation of 79Br rotational echoes out to 10 ms from KBr packed within spherical rotors. Spinning frequency stability of ±1 Hz is achieved with resistive heating feedback control. A sample size of 36 μl can be accommodated in 9.5-mm-diameter spheres with a cylindrical hole machined along the spinning axis. We further show that spheres can be more extensively hollowed out to accommodate 161 μl of the sample, which provides superior signal-to-noise ratio compared to traditional 3.2-mm-diameter cylindrical rotors.
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Affiliation(s)
- Pinhui Chen
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
- Department of Physics, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Brice J. Albert
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Chukun Gao
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Nicholas Alaniva
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Lauren E. Price
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Faith J. Scott
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Edward P. Saliba
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Erika L. Sesti
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Patrick T. Judge
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
- Department of Biochemistry, Biophysics and Structural Biology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Edward W. Fisher
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
- Department of Biochemistry, Biophysics and Structural Biology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Alexander B. Barnes
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
- Corresponding author.
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19
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Methods to Characterize the Nanostructure and Molecular Organization of Amphiphilic Peptide Assemblies. Methods Mol Biol 2018; 1777:3-21. [PMID: 29744826 DOI: 10.1007/978-1-4939-7811-3_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Methods to characterize the nanostructure and molecular organization of aggregates of peptides such as amyloid or amphiphilic peptide assemblies are reviewed. We discuss techniques to characterize conformation and secondary structure including circular and linear dichroism and FTIR and Raman spectroscopies, as well as fluorescence methods to detect aggregation. NMR spectroscopy methods, especially solid-state NMR measurements to probe beta-sheet packing motifs, are also briefly outlined. Also discussed are scattering methods including X-ray diffraction and small-angle scattering techniques including SAXS (small-angle X-ray scattering) and SANS (small-angle neutron scattering) and dynamic light scattering. Imaging methods are direct methods to uncover features of peptide nanostructures, and we provide a summary of electron microscopy and atomic force microscopy techniques. Selected examples are highlighted showing data obtained using these techniques, which provide a powerful suite of methods to probe ordering from the molecular scale to the aggregate superstructure.
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20
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Seuring C, Verasdonck J, Ringler P, Cadalbert R, Stahlberg H, Böckmann A, Meier BH, Riek R. Amyloid Fibril Polymorphism: Almost Identical on the Atomic Level, Mesoscopically Very Different. J Phys Chem B 2017; 121:1783-1792. [PMID: 28075583 DOI: 10.1021/acs.jpcb.6b10624] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Amyloid polymorphism of twisted and straight β-endorphin fibrils was studied by negative-stain transmission electron microscopy, scanning transmission electron microscopy, and solid-state nuclear magnetic resonance spectroscopy. Whereas fibrils assembled in the presence of salt formed flat, striated ribbons, in the absence of salt they formed mainly twisted filaments. To get insights into their structural differences at the atomic level, 3D solid-state NMR spectra of both fibril types were acquired, allowing the detection of the differences in chemical shifts of 13C and 15N atoms in both preparations. The spectral fingerprints and therefore the chemical shifts are very similar for both fibril types. This indicates that the monomer structure and the molecular interfaces are almost the same but that these small differences do propagate to produce flat and twisted morphologies at the mesoscopic scale. This finding is in agreement with both experimental and theoretical considerations on the assembly of polymers (including amyloids) under different salt conditions, which attribute the mesoscopic difference of flat versus twisted fibrils to electrostatic intermolecular repulsions.
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Affiliation(s)
- Carolin Seuring
- Laboratory of Physical Chemistry, ETH Zürich , Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Joeri Verasdonck
- Laboratory of Physical Chemistry, ETH Zürich , Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Philippe Ringler
- Center for Cellular Imaging and Nano Analytics (C-CINA), Biozentrum University of Basel , 4085 Basel, Switzerland
| | - Riccardo Cadalbert
- Laboratory of Physical Chemistry, ETH Zürich , Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Henning Stahlberg
- Center for Cellular Imaging and Nano Analytics (C-CINA), Biozentrum University of Basel , 4085 Basel, Switzerland
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS, Université de Lyon 1 , 7 passage du Vercors, 69367 Lyon, France
| | - Beat H Meier
- Laboratory of Physical Chemistry, ETH Zürich , Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, ETH Zürich , Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland.,Structural Biology Laboratory, The Salk Institute , 10010 N Torrey Pines Road, 92037 La Jolla, California, United States
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21
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Smith AA, Ravotti F, Testori E, Cadalbert R, Ernst M, Böckmann A, Meier BH. Partially-deuterated samples of HET-s(218-289) fibrils: assignment and deuterium isotope effect. JOURNAL OF BIOMOLECULAR NMR 2017; 67:109-119. [PMID: 28074361 DOI: 10.1007/s10858-016-0087-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 12/25/2016] [Indexed: 05/26/2023]
Abstract
Fast magic-angle spinning and partial sample deuteration allows direct detection of 1H in solid-state NMR, yielding significant gains in mass sensitivity. In order to further analyze the spectra, 1H detection requires assignment of the 1H resonances. In this work, resonance assignments of backbone HN and Hα are presented for HET-s(218-289) fibrils, based on the existing assignment of Cα, Cβ, C', and N resonances. The samples used are partially deuterated for higher spectral resolution, and the shifts in resonance frequencies of Cα and Cβ due to the deuterium isotope effect are investigated. It is shown that the deuterium isotope effect can be estimated and used for assigning resonances of deuterated samples in solid-state NMR, based on known resonances of the protonated protein.
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Affiliation(s)
- Albert A Smith
- ETH Zürich, Physical Chemistry, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Francesco Ravotti
- ETH Zürich, Physical Chemistry, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Emilie Testori
- ETH Zürich, Physical Chemistry, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Riccardo Cadalbert
- ETH Zürich, Physical Chemistry, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Matthias Ernst
- ETH Zürich, Physical Chemistry, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland.
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, Labex Ecofect, UMR 5086 CNRS, Université de Lyon, 7 passage du Vercors, 69367, Lyon, France.
| | - Beat H Meier
- ETH Zürich, Physical Chemistry, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland.
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22
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Seuring C, Gath J, Verasdonck J, Cadalbert R, Rivier J, Böckmann A, Meier BH, Riek R. Solid-state NMR sequential assignment of the β-endorphin peptide in its amyloid form. BIOMOLECULAR NMR ASSIGNMENTS 2016; 10:259-268. [PMID: 27165576 DOI: 10.1007/s12104-016-9681-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 04/12/2016] [Indexed: 06/05/2023]
Abstract
Insights into the three-dimensional structure of hormone fibrils are crucial for a detailed understanding of how an amyloid structure allows the storage of hormones in secretory vesicles prior to hormone secretion into the blood stream. As an example for various hormone amyloids, we have studied the endogenous opioid neuropeptide β-endorphin in one of its fibril forms. We have achieved the sequential assignment of the chemical shifts of the backbone and side-chain heavy atoms of the fibril. The secondary chemical shift analysis revealed that the β-endorphin peptide adopts three β-strands in its fibril state. This finding fosters the amyloid nature of a hormone at the atomic level.
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Affiliation(s)
- Carolin Seuring
- Laboratory of Physical Chemistry, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093, Zurich, Switzerland
| | - Julia Gath
- Laboratory of Physical Chemistry, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093, Zurich, Switzerland
| | - Joeri Verasdonck
- Laboratory of Physical Chemistry, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093, Zurich, Switzerland
| | - Riccardo Cadalbert
- Laboratory of Physical Chemistry, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093, Zurich, Switzerland
| | - Jean Rivier
- Structural Biology Laboratory, The Salk Institute, 10010 N Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Anja Böckmann
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS, Université de Lyon 1, 7 passage du Vercors, 69367, Lyon, France
| | - Beat H Meier
- Laboratory of Physical Chemistry, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093, Zurich, Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093, Zurich, Switzerland.
- Structural Biology Laboratory, The Salk Institute, 10010 N Torrey Pines Road, La Jolla, CA, 92037, USA.
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23
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Colvin MT, Silvers R, Ni QZ, Can TV, Sergeyev I, Rosay M, Donovan KJ, Michael B, Wall J, Linse S, Griffin RG. Atomic Resolution Structure of Monomorphic Aβ42 Amyloid Fibrils. J Am Chem Soc 2016; 138:9663-74. [PMID: 27355699 PMCID: PMC5389415 DOI: 10.1021/jacs.6b05129] [Citation(s) in RCA: 610] [Impact Index Per Article: 76.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Amyloid-β (Aβ) is a 39-42 residue protein produced by the cleavage of the amyloid precursor protein (APP), which subsequently aggregates to form cross-β amyloid fibrils that are a hallmark of Alzheimer's disease (AD). The most prominent forms of Aβ are Aβ1-40 and Aβ1-42, which differ by two amino acids (I and A) at the C-terminus. However, Aβ42 is more neurotoxic and essential to the etiology of AD. Here, we present an atomic resolution structure of a monomorphic form of AβM01-42 amyloid fibrils derived from over 500 (13)C-(13)C, (13)C-(15)N distance and backbone angle structural constraints obtained from high field magic angle spinning NMR spectra. The structure (PDB ID: 5KK3 ) shows that the fibril core consists of a dimer of Aβ42 molecules, each containing four β-strands in a S-shaped amyloid fold, and arranged in a manner that generates two hydrophobic cores that are capped at the end of the chain by a salt bridge. The outer surface of the monomers presents hydrophilic side chains to the solvent. The interface between the monomers of the dimer shows clear contacts between M35 of one molecule and L17 and Q15 of the second. Intermolecular (13)C-(15)N constraints demonstrate that the amyloid fibrils are parallel in register. The RMSD of the backbone structure (Q15-A42) is 0.71 ± 0.12 Å and of all heavy atoms is 1.07 ± 0.08 Å. The structure provides a point of departure for the design of drugs that bind to the fibril surface and therefore interfere with secondary nucleation and for other therapeutic approaches to mitigate Aβ42 aggregation.
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Affiliation(s)
- Michael T. Colvin
- 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
| | - Qing Zhe Ni
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Thach V. Can
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ivan Sergeyev
- Bruker BioSpin, 15 Fortune Drive, Billerica, Massachusetts 01821, United States
| | - Melanie Rosay
- Bruker BioSpin, 15 Fortune Drive, Billerica, Massachusetts 01821, United States
| | - Kevin J. Donovan
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Brian Michael
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Joseph Wall
- Brookhaven National Laboratory, 50 Bell Avenue, Building 463, Upton, New York 11973-5000, United States
| | - Sara Linse
- Department of Biochemistry and Structural Biology, Lund University, SE22100 Lund, 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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Habenstein B, Loquet A. Solid-state NMR: An emerging technique in structural biology of self-assemblies. Biophys Chem 2016; 210:14-26. [DOI: 10.1016/j.bpc.2015.07.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 07/08/2015] [Indexed: 12/13/2022]
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Espargaró A, Busquets MA, Estelrich J, Sabate R. Amyloids in solid-state nuclear magnetic resonance: potential causes of the usually low resolution. Int J Nanomedicine 2015; 10:6975-83. [PMID: 26635473 PMCID: PMC4646584 DOI: 10.2147/ijn.s89385] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Amyloids are non-crystalline and insoluble, which imply that the classical structural biology tools, ie, X-ray crystallography and solution nuclear magnetic resonance (NMR), are not suitable for their analysis. In the last years, solid-state NMR (ssNMR) has emerged as an alternative tool to decrypt the structural signatures of amyloid fibrils, providing major contributions to our understanding of molecular structures of amyloids such as β-amyloid peptide associated with Alzheimer’s disease or fungal prions, among others. Despite this, the wide majority of amyloid fibrils display low resolution by ssNMR. Usually, this low resolution has been attributed to a high disorder or polymorphism of the fibrils, suggesting the existence of diverse elementary β-sheet structures. Here, we propose that a single β-sheet structure could be responsible for the broadening of the line widths in the ssNMR spectra. Although the fibrils and fibers consist of a single elementary structure, the angle of twist of each individual fibril in the mature fiber depends on the number of individual fibrils as well as the fibril arrangement in the final mature fiber. Thus, a wide range of angles of twist could be observed in the same amyloid sample. These twist variations involve changes in amino acid alignments that could be enough to limit the ssNMR resolution.
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Affiliation(s)
- Alba Espargaró
- Department of Physical Chemistry, School of Pharmacy, Institute of Nanoscience and Nanotechnology (IN UB), University of Barcelona, Barcelona, Spain
| | - Maria Antònia Busquets
- Department of Physical Chemistry, School of Pharmacy, Institute of Nanoscience and Nanotechnology (IN UB), University of Barcelona, Barcelona, Spain
| | - Joan Estelrich
- Department of Physical Chemistry, School of Pharmacy, Institute of Nanoscience and Nanotechnology (IN UB), University of Barcelona, Barcelona, Spain
| | - Raimon Sabate
- Department of Physical Chemistry, School of Pharmacy, Institute of Nanoscience and Nanotechnology (IN UB), University of Barcelona, Barcelona, Spain
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Schubeis T, Yuan P, Ahmed M, Nagaraj M, van Rossum B, Ritter C. Untangling a Repetitive Amyloid Sequence: Correlating Biofilm‐Derived and Segmentally Labeled Curli Fimbriae by Solid‐State NMR Spectroscopy. Angew Chem Int Ed Engl 2015; 54:14669-72. [DOI: 10.1002/anie.201506772] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Tobias Schubeis
- Laboratory of Macromolecular Interactions, Helmholtz‐Zentrum für Infektionsforschung, Inhoffenstrasse 7, 38124 Braunschweig (Germany)
| | - Puwei Yuan
- Laboratory of Macromolecular Interactions, Helmholtz‐Zentrum für Infektionsforschung, Inhoffenstrasse 7, 38124 Braunschweig (Germany)
| | - Mumdooh Ahmed
- Laboratory of Macromolecular Interactions, Helmholtz‐Zentrum für Infektionsforschung, Inhoffenstrasse 7, 38124 Braunschweig (Germany)
- Department of Physics, Faculty of Science, Suez University, Suez, 43533 (Egypt)
| | - Madhu Nagaraj
- Laboratory of Macromolecular Interactions, Helmholtz‐Zentrum für Infektionsforschung, Inhoffenstrasse 7, 38124 Braunschweig (Germany)
- NMR‐Supported Structural Biology, Leibniz‐Institut für Molekulare Pharmakologie (FMP), Robert‐Rössle‐Strasse 10, 13125 Berlin (Germany)
| | - Barth‐Jan van Rossum
- NMR‐Supported Structural Biology, Leibniz‐Institut für Molekulare Pharmakologie (FMP), Robert‐Rössle‐Strasse 10, 13125 Berlin (Germany)
| | - Christiane Ritter
- Laboratory of Macromolecular Interactions, Helmholtz‐Zentrum für Infektionsforschung, Inhoffenstrasse 7, 38124 Braunschweig (Germany)
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27
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Schubeis T, Yuan P, Ahmed M, Nagaraj M, van Rossum B, Ritter C. Entschlüsselung einer repetitiven Amyloidsequenz: Korrelation von Biofilm‐extrahierten und segmental markierten Curli‐Fimbrien mittels Festkörper‐NMR‐Spektroskopie. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506772] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Tobias Schubeis
- Laboratorium für makromolekulare Interaktionen, Helmholtz‐Zentrum für Infektionsforschung, Inhoffenstraße 7, 38124 Braunschweig (Deutschland)
| | - Puwei Yuan
- Laboratorium für makromolekulare Interaktionen, Helmholtz‐Zentrum für Infektionsforschung, Inhoffenstraße 7, 38124 Braunschweig (Deutschland)
| | - Mumdooh Ahmed
- Laboratorium für makromolekulare Interaktionen, Helmholtz‐Zentrum für Infektionsforschung, Inhoffenstraße 7, 38124 Braunschweig (Deutschland)
- Department of Physics, Faculty of Science, Suez University, Suez, 43533 (Ägypten)
| | - Madhu Nagaraj
- Laboratorium für makromolekulare Interaktionen, Helmholtz‐Zentrum für Infektionsforschung, Inhoffenstraße 7, 38124 Braunschweig (Deutschland)
- NMR‐Supported Structural Biology, Leibniz‐Institut für Molekulare Pharmakologie (FMP), Robert‐Rössle‐Straße 10, 13125 Berlin (Deutschland)
| | - Barth‐Jan van Rossum
- NMR‐Supported Structural Biology, Leibniz‐Institut für Molekulare Pharmakologie (FMP), Robert‐Rössle‐Straße 10, 13125 Berlin (Deutschland)
| | - Christiane Ritter
- Laboratorium für makromolekulare Interaktionen, Helmholtz‐Zentrum für Infektionsforschung, Inhoffenstraße 7, 38124 Braunschweig (Deutschland)
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28
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Colvin MT, Silvers R, Frohm B, Su Y, Linse S, Griffin RG. High resolution structural characterization of Aβ42 amyloid fibrils by magic angle spinning NMR. J Am Chem Soc 2015; 137:7509-18. [PMID: 26001057 PMCID: PMC4623963 DOI: 10.1021/jacs.5b03997] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
![]()
The presence of amyloid plaques composed
of amyloid beta (Aβ)
fibrils is a hallmark of Alzheimer’s disease (AD). The Aβ
peptide is present as several length variants with two common alloforms
consisting of 40 and 42 amino acids, denoted Aβ1–40 and Aβ1–42, respectively. While there have
been numerous reports that structurally characterize fibrils of Aβ1–40, very little is known about the structure of amyloid
fibrils of Aβ1–42, which are considered the
more toxic alloform involved in AD. We have prepared isotopically 13C/15N labeled AβM01–42 fibrils in vitro from recombinant protein and examined their 13C–13C and 13C–15N magic angle spinning (MAS) NMR spectra. In contrast to several
other studies of Aβ fibrils, we observe spectra with excellent
resolution and a single set of chemical shifts, suggesting the presence
of a single fibril morphology. We report the initial structural characterization
of AβM01–42 fibrils utilizing 13C and 15N shift assignments of 38 of the 43 residues,
including the backbone and side chains, obtained through a series
of cross-polarization based 2D and 3D 13C–13C, 13C–15N MAS NMR experiments for rigid
residues along with J-based 2D TOBSY experiments for dynamic residues.
We find that the first ∼5 residues are dynamic and most efficiently
detected in a J-based TOBSY spectrum. In contrast, residues 16–42
are easily observed in cross-polarization experiments and most likely
form the amyloid core. Calculation of ψ and φ dihedral
angles from the chemical shift assignments indicate that 4 β-strands
are present in the fibril’s secondary structure.
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Affiliation(s)
- Michael T Colvin
- †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
| | - Birgitta Frohm
- ‡Department of Biochemistry and Structural Biology, Lund University, SE22100 Lund, Sweden
| | - Yongchao Su
- †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, SE22100 Lund, 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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Daskalov A, Habenstein B, Martinez D, Debets AJM, Sabaté R, Loquet A, Saupe SJ. Signal transduction by a fungal NOD-like receptor based on propagation of a prion amyloid fold. PLoS Biol 2015; 13:e1002059. [PMID: 25671553 PMCID: PMC4344463 DOI: 10.1371/journal.pbio.1002059] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 12/29/2014] [Indexed: 01/09/2023] Open
Abstract
In the fungus Podospora anserina, the [Het-s] prion induces programmed cell death by activating the HET-S pore-forming protein. The HET-s β-solenoid prion fold serves as a template for converting the HET-S prion-forming domain into the same fold. This conversion, in turn, activates the HET-S pore-forming domain. The gene immediately adjacent to het-S encodes NWD2, a Nod-like receptor (NLR) with an N-terminal motif similar to the elementary repeat unit of the β-solenoid fold. NLRs are immune receptors controlling cell death and host defense processes in animals, plants and fungi. We have proposed that, analogously to [Het-s], NWD2 can activate the HET-S pore-forming protein by converting its prion-forming region into the β-solenoid fold. Here, we analyze the ability of NWD2 to induce formation of the β-solenoid prion fold. We show that artificial NWD2 variants induce formation of the [Het-s] prion, specifically in presence of their cognate ligands. The N-terminal motif is responsible for this prion induction, and mutations predicted to affect the β-solenoid fold abolish templating activity. In vitro, the N-terminal motif assembles into infectious prion amyloids that display a structure resembling the β-solenoid fold. In vivo, the assembled form of the NWD2 N-terminal region activates the HET-S pore-forming protein. This study documenting the role of the β-solenoid fold in fungal NLR function further highlights the general importance of amyloid and prion-like signaling in immunity-related cell fate pathways. The fungus Podospora anserina uses a prion amyloid fold as a signal transduction device between a Nod-like receptor and a downstream cell death execution protein. Although amyloids are best known as protein aggregates that are responsible for fatal neurodegenerative diseases, amyloid structures can also fulfill functional roles in cells. In particular, the controlled formation of amyloid structures appears to be involved in different signaling processes in the context of programmed cell death and host defense. The [Het-s] prion of the filamentous fungus Podospora anserina is a model system in which the 3-D structure of the prion form has been solved. The [Het-s] prion works as an activation switch for a second protein termed HET-S. HET-S is a pore-forming protein that is activated when the [Het-s] prion causes its C-terminal domain to adopt an amyloid-like fold. The protein encoded by the gene adjacent to het-S is a Nod-like receptor (NLR) called NWD2. NLRs are immune receptors that control host defense and cell death processes in plants, animals, and fungi. We show that NWD2 can template the formation of the [Het-s] prion fold in a ligand-controlled manner. NWD2 has an N-terminal motif homologous to the HET-S/s prion-forming region; we find that this region is both necessary and sufficient for its prion-inducing activity, and our functional and structural approaches reveal that the N-terminal region of NWD2 adopts a fold closely related to that of the HET-S/s prion. This study illustrates how the controlled formation of a prion amyloid fold can be used in a signaling process whereby a Nod-like receptor protein activates a downstream cell death execution domain.
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Affiliation(s)
- Asen Daskalov
- Non-self recognition in Fungi, Institut de Biochimie et de Génétique Cellulaire, UMR 5095, CNRS—Université de Bordeaux, Bordeaux, France
| | - Birgit Habenstein
- Institute of Chemistry & Biology of Membranes & Nanoobjects, CNRS, CBMN, UMR 5248, Pessac, France
| | - Denis Martinez
- Institute of Chemistry & Biology of Membranes & Nanoobjects, CNRS, CBMN, UMR 5248, Pessac, France
| | - Alfons J. M. Debets
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg, Wageningen, The Netherlands
| | - Raimon Sabaté
- Institut de Nanociència i nanotecnologia, Departament Fisicoquímica, Universitat de Barcelona, Joan XXIII s/n, Barcelona, Spain
| | - Antoine Loquet
- Institute of Chemistry & Biology of Membranes & Nanoobjects, CNRS, CBMN, UMR 5248, Pessac, France
| | - Sven J. Saupe
- Non-self recognition in Fungi, Institut de Biochimie et de Génétique Cellulaire, UMR 5095, CNRS—Université de Bordeaux, Bordeaux, France
- * E-mail:
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30
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Daskalov A, Gantner M, Wälti MA, Schmidlin T, Chi CN, Wasmer C, Schütz A, Ceschin J, Clavé C, Cescau S, Meier B, Riek R, Saupe SJ. Contribution of specific residues of the β-solenoid fold to HET-s prion function, amyloid structure and stability. PLoS Pathog 2014; 10:e1004158. [PMID: 24945274 PMCID: PMC4055769 DOI: 10.1371/journal.ppat.1004158] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 04/15/2014] [Indexed: 01/12/2023] Open
Abstract
The [Het-s] prion of the fungus Podospora anserina represents a good model system for studying the structure-function relationship in amyloid proteins because a high resolution solid-state NMR structure of the amyloid prion form of the HET-s prion forming domain (PFD) is available. The HET-s PFD adopts a specific β-solenoid fold with two rungs of β-strands delimiting a triangular hydrophobic core. A C-terminal loop folds back onto the rigid core region and forms a more dynamic semi-hydrophobic pocket extending the hydrophobic core. Herein, an alanine scanning mutagenesis of the HET-s PFD was conducted. Different structural elements identified in the prion fold such as the triangular hydrophobic core, the salt bridges, the asparagines ladders and the C-terminal loop were altered and the effect of these mutations on prion function, fibril structure and stability was assayed. Prion activity and structure were found to be very robust; only a few key mutations were able to corrupt structure and function. While some mutations strongly destabilize the fold, many substitutions in fact increase stability of the fold. This increase in structural stability did not influence prion formation propensity in vivo. However, if an Ala replacement did alter the structure of the core or did influence the shape of the denaturation curve, the corresponding variant showed a decreased prion efficacy. It is also the finding that in addition to the structural elements of the rigid core region, the aromatic residues in the C-terminal semi-hydrophobic pocket are critical for prion propagation. Mutations in the latter region either positively or negatively affected prion formation. We thus identify a region that modulates prion formation although it is not part of the rigid cross-β core, an observation that might be relevant to other amyloid models.
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Affiliation(s)
- Asen Daskalov
- Institut de Biochimie et de Génétique Cellulaire, Unité Mixte de Recherche 5095, Centre National de la Recherche Scientifique Université de Bordeaux, Bordeaux, France
| | - Matthias Gantner
- Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Marielle Aulikki Wälti
- Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Thierry Schmidlin
- Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Celestine N. Chi
- Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Christian Wasmer
- Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Anne Schütz
- Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Johanna Ceschin
- Institut de Biochimie et de Génétique Cellulaire, Unité Mixte de Recherche 5095, Centre National de la Recherche Scientifique Université de Bordeaux, Bordeaux, France
| | - Corinne Clavé
- Institut de Biochimie et de Génétique Cellulaire, Unité Mixte de Recherche 5095, Centre National de la Recherche Scientifique Université de Bordeaux, Bordeaux, France
| | - Sandra Cescau
- Institut de Biochimie et de Génétique Cellulaire, Unité Mixte de Recherche 5095, Centre National de la Recherche Scientifique Université de Bordeaux, Bordeaux, France
| | - Beat Meier
- Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Sven J. Saupe
- Institut de Biochimie et de Génétique Cellulaire, Unité Mixte de Recherche 5095, Centre National de la Recherche Scientifique Université de Bordeaux, Bordeaux, France
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31
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Goobes G. Past and Future Solid-State NMR Spectroscopy Studies at the Convergence Point between Biology and Materials Research. Isr J Chem 2014. [DOI: 10.1002/ijch.201300113] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Hou G, Yan S, Trebosc J, Amoureux JP, Polenova T. Broadband homonuclear correlation spectroscopy driven by combined R2(n)(v) sequences under fast magic angle spinning for NMR structural analysis of organic and biological solids. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 232:18-30. [PMID: 23685715 PMCID: PMC3703537 DOI: 10.1016/j.jmr.2013.04.009] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 03/30/2013] [Accepted: 04/15/2013] [Indexed: 05/08/2023]
Abstract
We recently described a family of experiments for R2n(v) Driven Spin Diffusion (RDSD) spectroscopy suitable for homonuclear correlation experiments under fast MAS conditions [G. Hou, S. Yan, S.J. Sun, Y. Han, I.J. Byeon, J. Ahn, J. Concel, A. Samoson, A.M. Gronenborn, T. Polenova, Spin diffusion drive by R-symmetry sequencs: applications to homonuclear correlation spectroscopy in MAS NMR of biological and organic solids, J. Am. Chem. Soc. 133 (2011) 3943-3953]. In these RDSD experiments, since the broadened second-order rotational resonance conditions are dominated by the radio frequency field strength and the phase shifts, as well as the size of reintroduced dipolar couplings, the different R2n(v) sequences display unique polarization transfer behaviors and different recoupling frequency bandwidths. Herein, we present a series of modified R2n(v) sequences, dubbed COmbined R2n(v)-Driven (CORD), that yield broadband homonuclear dipolar recoupling and give rise to uniform distribution of cross peak intensities across the entire correlation spectrum. We report NMR experiments and numerical simulations demonstrating that these CORD spin diffusion sequences are suitable for broadband recoupling at a wide range of magnetic fields and MAS frequencies, including fast-MAS conditions (νr=40 kHz and above). Since these CORD sequences are largely insensitive to dipolar truncation, they are well suited for the determination of long-range distance constraints, which are indispensable for the structural characterization of a broad range of systems. Using U-(13)C,(15)N-alanine and U-(13)C,(15)N-histidine, we show that under fast-MAS conditions, the CORD sequences display polarization transfer efficiencies within broadband frequency regions that are generally higher than those offered by other existing spin diffusion pulse schemes. A 89-residue U-(13)C,(15)N-dynein light chain (LC8) protein has also been used to demonstrate that the CORD sequences exhibit uniformly high cross peak intensities across the entire chemical shift range.
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Affiliation(s)
- Guangjin Hou
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- , Tel. (302) 831-1968, FAX (302) 831-6335;
| | - Si Yan
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Julien Trebosc
- Unit of Catalysis and Chemistry of Solids (UCCS), CNRS-8181, University Lille Nord de France, 59652 Villeneuve d’Ascq, France
| | - Jean-Paul Amoureux
- Unit of Catalysis and Chemistry of Solids (UCCS), CNRS-8181, University Lille Nord de France, 59652 Villeneuve d’Ascq, France
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- , Tel. (302) 831-1968, FAX (302) 831-6335;
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33
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Comellas G, Rienstra CM. Protein Structure Determination by Magic-Angle Spinning Solid-State NMR, and Insights into the Formation, Structure, and Stability of Amyloid Fibrils. Annu Rev Biophys 2013; 42:515-36. [DOI: 10.1146/annurev-biophys-083012-130356] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Chad M. Rienstra
- Center for Biophysics and Computational Biology,
- Department of Chemistry, and
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801; ,
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34
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Fowler DM, Kelly JW. Functional amyloidogenesis and cytotoxicity-insights into biology and pathology. PLoS Biol 2012; 10:e1001459. [PMID: 23300381 PMCID: PMC3531510 DOI: 10.1371/journal.pbio.1001459] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 11/13/2012] [Indexed: 12/22/2022] Open
Abstract
Prions are self-templating protein structures that can be transferred from organism to organism. The [Het-s] prion propagates as a functional amyloid aggregate in the filamentous fungi Podospora anserina, and is involved in mediating heterokaryon incompatibility. Fusion of a P. anserina strain harboring the [Het-s] prion with another strain expressing the soluble Het-S protein results in cell death. The mechanism of Het-s/Het-S-mediated cell death has now been revealed in a paper just published in PLOS Biology. The study shows that Het-s and Het-S C-terminal domain co-amyloidogenesis induces a profound conformational rearrangement in the N-terminal Het-S HeLo domain, resulting in the exposure of a nascent transmembrane helix. Oligomerization of these helices leads to pore formation, leakage of the cytosolic contents, and subsequent cell death. Thus, Het-s amyloid plays a major role in the life cycle of P. anserina by orchestrating a complex conformational change in the Het-S protein, resulting in cytotoxicity by compromising membrane integrity. This ability of Het-s functional amyloid to initiate programmed cytotoxicity by mediating a conformational change in another protein significantly expands the functional repertoire of amyloid. Moreover, the mechanism of Het-S cell killing may be similar to the mechanism by which some pathological amyloid proteins lead to the demise of post-mitotic tissue.
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Affiliation(s)
- Douglas M. Fowler
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- * E-mail: (DMF); (JWK)
| | - Jeffery W. Kelly
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, United States of America
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail: (DMF); (JWK)
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Allison JR. Assessing and refining molecular dynamics simulations of proteins with nuclear magnetic resonance data. Biophys Rev 2012; 4:189-203. [PMID: 28510078 DOI: 10.1007/s12551-012-0087-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2012] [Accepted: 06/12/2012] [Indexed: 11/28/2022] Open
Abstract
The sophistication of the force fields, algorithms and hardware used for molecular dynamics (MD) simulations of proteins is continuously increasing. No matter how advanced the methodology, however, it is essential to evaluate the appropriateness of the structures sampled in a simulation by comparison with quantitative experimental data. Solution nuclear magnetic resonance (NMR) data are particularly useful for checking the quality of protein simulations, as they provide both structural and dynamic information on a variety of temporal and spatial scales. Here, various features and implications of using NMR data to validate and bias MD simulations are outlined, including an overview of the different types of NMR data that report directly on structural properties and of relevant simulation techniques. The focus throughout is on how to properly account for conformational averaging, particularly within the context of the assumptions inherent in the relationships that link NMR data to structural properties.
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Affiliation(s)
- Jane R Allison
- Centre for Theoretical Chemistry and Physics, Institute of Natural Sciences, Massey University Albany, Albany Highway, Auckland, 0632, New Zealand.
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36
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Gath J, Habenstein B, Bousset L, Melki R, Meier BH, Böckmann A. Solid-state NMR sequential assignments of α-synuclein. BIOMOLECULAR NMR ASSIGNMENTS 2012; 6:51-55. [PMID: 21744165 DOI: 10.1007/s12104-011-9324-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Accepted: 06/27/2011] [Indexed: 05/31/2023]
Abstract
Parkinson's disease is amongst the most frequent and most devastating neurodegenerative diseases. It is tightly associated with the assembly of proteins into high-molecular weight protein species, which propagate between neurons in the central nervous system. The principal protein involved in this process is α-synuclein which is a structural component of the Lewy bodies observed in diseased brain. We here present the solid-state NMR sequential assignments of a new fibrillar form of this protein, the first one with a well-ordered and rigid N-terminal part.
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Affiliation(s)
- Julia Gath
- Physical Chemistry, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
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37
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Hou G, Yan S, Sun S, Han Y, Byeon IJL, Ahn J, Concel J, Samoson A, Gronenborn AM, Polenova T. Spin diffusion driven by R-symmetry sequences: applications to homonuclear correlation spectroscopy in MAS NMR of biological and organic solids. J Am Chem Soc 2011; 133:3943-53. [PMID: 21361320 PMCID: PMC3148607 DOI: 10.1021/ja108650x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a family of homonuclear (13)C-(13)C magic angle spinning spin diffusion experiments, based on R2(n)(v) (n = 1 and 2, v = 1 and 2) symmetry sequences. These experiments are well suited for (13)C-(13)C correlation spectroscopy in biological and organic systems and are especially advantageous at very fast MAS conditions, where conventional PDSD and DARR experiments fail. At very fast MAS frequencies the R2(1)(1), R2(2)(1), and R2(2)(2) sequences result in excellent quality correlation spectra both in model compounds and in proteins. Under these conditions, individual R2(n)(v) display different polarization transfer efficiency dependencies on isotropic chemical shift differences: R2(2)(1) recouples efficiently both small and large chemical shift differences (in proteins these correspond to aliphatic-to-aliphatic and carbonyl-to-aliphatic correlations, respectively), while R2(1)(1) and R2(2)(2) exhibit the maximum recoupling efficiency for the aliphatic-to-aliphatic or carbonyl-to-aliphatic correlations, respectively. At moderate MAS frequencies (10-20 kHz), all R2(n)(v) sequences introduced in this work display similar transfer efficiencies, and their performance is very similar to that of PDSD and DARR. Polarization transfer dynamics and chemical shift dependencies of these R2-driven spin diffusion (RDSD) schemes are experimentally evaluated and investigated by numerical simulations for [U-(13)C,(15)N]-alanine and the [U-(13)C,(15)N] N-formyl-Met-Leu-Phe (MLF) tripeptide. Further applications of this approach are illustrated for several proteins: spherical assemblies of HIV-1 U-(13)C,(15)N CA protein, U-(13)C,(15)N-enriched dynein light chain DLC8, and sparsely (13)C/uniformly (15)N enriched CAP-Gly domain of dynactin. Due to the excellent performance and ease of implementation, the presented R2(n)(v) symmetry sequences are expected to be of wide applicability in studies of proteins and protein assemblies as well as other organic solids by MAS NMR spectroscopy.
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Affiliation(s)
- Guangjin Hou
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Si Yan
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Shangjin Sun
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Yun Han
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - In-Ja L. Byeon
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Jinwoo Ahn
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Jason Concel
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Ago Samoson
- Tallinn University of Technology, Ehitajate tee 5, 19086, Tallinn, Estonia
- Physics Department, University of Warwick, Coventry, UK
| | - Angela M. Gronenborn
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Tatyana Polenova
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
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Saupe SJ. The [Het-s] prion of Podospora anserina and its role in heterokaryon incompatibility. Semin Cell Dev Biol 2011; 22:460-8. [PMID: 21334447 DOI: 10.1016/j.semcdb.2011.02.019] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Accepted: 02/10/2011] [Indexed: 11/29/2022]
Abstract
[Het-s] is a prion from the filamentous fungus Podospora anserina and corresponds to a self-perpetuating amyloid aggregate of the HET-s protein. This prion protein is involved in a fungal self/non-self discrimination process termed heterokaryon incompatibility corresponding to a cell death reaction occurring upon fusion of genetically unlike strains. Two antagonistic allelic variants of this protein exist: HET-s, the prion form of which corresponds to [Het-s] and HET-S, incapable of prion formation. Fusion of a [Het-s] and HET-S strain triggers the incompatibility reaction, so that interaction of HET-S with the [Het-s] prion leads to cell death. HET-s and HET-S are highly homologous two domain proteins with a N-terminal globular domain termed HeLo and a C-terminal unstructured prion forming domain (PFD). The structure of the prion form of the HET-s PFD has been solved by solid state NMR and corresponds to a very well ordered β-solenoid fold with a triangular hydrophobic core. The ability to form this β-solenoid fold is retained in a distant homolog of HET-s from another fungal species. A model for the mechanism of [Het-s]/HET-S incompatibility has been proposed. It is believe that when interacting with the [Het-s] prion seed, the HET-S C-terminal region adopts the β-solenoid fold. This would act as a conformational switch to induce refolding and activation of the HeLo domain which then would exert its toxicity by a yet unknown mechanism.
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Affiliation(s)
- Sven J Saupe
- Non-self recognition in fungi, Institut de Biochimie et de Génétique Cellulaire, UMR 5095, CNRS-Université de Bordeaux 2, 1 rue Camille St Saens, Bordeaux cedex, France.
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39
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Van Melckebeke H, Wasmer C, Lange A, Ab E, Loquet A, Böckmann A, Meier BH. Atomic-resolution three-dimensional structure of HET-s(218-289) amyloid fibrils by solid-state NMR spectroscopy. J Am Chem Soc 2011; 132:13765-75. [PMID: 20828131 DOI: 10.1021/ja104213j] [Citation(s) in RCA: 228] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
We present a strategy to solve the high-resolution structure of amyloid fibrils by solid-state NMR and use it to determine the atomic-resolution structure of the prion domain of the fungal prion HET-s in its amyloid form. On the basis of 134 unambiguous distance restraints, we recently showed that HET-s(218-289) in its fibrillar state forms a left-handed β-solenoid, and an atomic-resolution NMR structure of the triangular core was determined from unambiguous restraints only. In this paper, we go considerably further and present a comprehensive protocol using six differently labeled samples, a collection of optimized solid-state NMR experiments, and adapted structure calculation protocols. The high-resolution structure obtained includes the less ordered but biologically important C-terminal part and improves the overall accuracy by including a large number of ambiguous distance restraints.
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Affiliation(s)
- Hélène Van Melckebeke
- Physical Chemistry, ETH Zürich, Wolfgang-Pauli-Strasse 10, CH-8093 Zurich, Switzerland
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40
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Van Melckebeke H, Schanda P, Gath J, Wasmer C, Verel R, Lange A, Meier BH, Böckmann A. Probing Water Accessibility in HET-s(218–289) Amyloid Fibrils by Solid-State NMR. J Mol Biol 2011; 405:765-72. [DOI: 10.1016/j.jmb.2010.11.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Revised: 09/28/2010] [Accepted: 11/01/2010] [Indexed: 11/29/2022]
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41
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Abstract
Current interest in amyloid fibrils stems from their involvement in neurodegenerative and other diseases and from their role as an alternative structural state for many peptides and proteins. Solid-state nuclear magnetic resonance (NMR) methods have the unique capability of providing detailed structural constraints for amyloid fibrils, sufficient for the development of full molecular models. In this article, recent progress in the application of solid-state NMR to fibrils associated with Alzheimer's disease, prion fibrils, and related systems is reviewed, along with relevant developments in solid-state NMR techniques and technology.
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Affiliation(s)
- Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA.
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42
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Franks WT, Atreya HS, Szyperski T, Rienstra CM. GFT projection NMR spectroscopy for proteins in the solid state. JOURNAL OF BIOMOLECULAR NMR 2010; 48:213-23. [PMID: 21052779 PMCID: PMC3058792 DOI: 10.1007/s10858-010-9451-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2010] [Accepted: 09/26/2010] [Indexed: 05/12/2023]
Abstract
Recording of four-dimensional (4D) spectra for proteins in the solid state has opened new avenues to obtain virtually complete resonance assignments and three-dimensional (3D) structures of proteins. As in solution state NMR, the sampling of three indirect dimensions leads per se to long minimal measurement time. Furthermore, artifact suppression in solid state NMR relies primarily on radio-frequency pulse phase cycling. For an n-step phase cycle, the minimal measurement times of both 3D and 4D spectra are increased n times. To tackle the associated 'sampling problem' and to avoid sampling limited data acquisition, solid state G-Matrix Fourier Transform (SS GFT) projection NMR is introduced to rapidly acquire 3D and 4D spectral information. Specifically, (4,3)D (HA)CANCOCX and (3,2)D (HACA)NCOCX were implemented and recorded for the 6 kDa protein GB1 within about 10% of the time required for acquiring the conventional congeners with the same maximal evolution times and spectral widths in the indirect dimensions. Spectral analysis was complemented by comparative analysis of expected spectral congestion in conventional and GFT NMR experiments, demonstrating that high spectral resolution of the GFT NMR experiments enables one to efficiently obtain nearly complete resonance assignments even for large proteins.
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Affiliation(s)
- W. Trent Franks
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Hanudatta S. Atreya
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260, USA
| | - Thomas Szyperski
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260, USA
| | - Chad M. Rienstra
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA. Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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43
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Bayro MJ, Maly T, Birkett NR, MacPhee CE, Dobson CM, Griffin RG. High-resolution MAS NMR analysis of PI3-SH3 amyloid fibrils: backbone conformation and implications for protofilament assembly and structure . Biochemistry 2010; 49:7474-84. [PMID: 20707313 PMCID: PMC2932965 DOI: 10.1021/bi100864t] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The SH3 domain of the PI3 kinase (PI3-SH3 or PI3K-SH3) readily aggregates into fibrils in vitro and has served as an important model system in the investigation of the molecular properties and mechanism of formation of amyloid fibrils. We describe the molecular conformation of PI3-SH3 in amyloid fibril form as revealed by magic-angle spinning (MAS) solid-state nuclear magnetic resonance (NMR) spectroscopy. The MAS NMR spectra of these fibrils display excellent resolution, with narrow (13)C and (15)N line widths, representing a high degree of structural order and the absence of extensive molecular motion for the majority of the polypeptide chain. We have identified the spin systems of 82 of the 86 residues in the protein and obtained sequential resonance assignments for 75 of them. Chemical shift analysis indicates that the protein subunits making up the fibril adopt a compact conformation consisting of four well-defined beta-sheet regions and four random-coil elements with varying degrees of local dynamics or disorder. The backbone conformation of PI3-SH3 in fibril form differs significantly from that of the native state of the protein, both in secondary structure and in the location of dynamic or disordered segments. The site-specific MAS NMR analysis of PI3-SH3 fibrils we report here is compared with previously published mechanistic and structural data, resulting in a detailed interpretation of the factors that mediate fibril formation by PI3-SH3 and allowing us to propose a possible model of the core structure of the fibrils. Our results confirm the structural similarities between PI3-SH3 fibrils and amyloid assemblies directly related to degenerative and infectious diseases.
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Affiliation(s)
- Marvin J. Bayro
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Thorsten Maly
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Neil R. Birkett
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Cait E. MacPhee
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh, EH9 3JZ, UK
| | - Christopher M. Dobson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Robert G. Griffin
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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44
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Tycko R, Hu KN. A Monte Carlo/simulated annealing algorithm for sequential resonance assignment in solid state NMR of uniformly labeled proteins with magic-angle spinning. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2010; 205:304-14. [PMID: 20547467 PMCID: PMC2902575 DOI: 10.1016/j.jmr.2010.05.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Revised: 05/19/2010] [Accepted: 05/21/2010] [Indexed: 05/05/2023]
Abstract
We describe a computational approach to sequential resonance assignment in solid state NMR studies of uniformly (15)N,(13)C-labeled proteins with magic-angle spinning. As input, the algorithm uses only the protein sequence and lists of (15)N/(13)C(alpha) crosspeaks from 2D NCACX and NCOCX spectra that include possible residue-type assignments of each crosspeak. Assignment of crosspeaks to specific residues is carried out by a Monte Carlo/simulated annealing algorithm, implemented in the program MC_ASSIGN1. The algorithm tolerates substantial ambiguity in residue-type assignments and coexistence of visible and invisible segments in the protein sequence. We use MC_ASSIGN1 and our own 2D spectra to replicate and extend the sequential assignments for uniformly-labeled HET-s(218-289) fibrils previously determined manually by Siemer et al. (J. Biomol. NMR, 34 (2006) 75-87) from a more extensive set of 2D and 3D spectra. Accurate assignments by MC_ASSIGN1 do not require data that are of exceptionally high quality. Use of MC_ASSIGN1 (and its extensions to other types of 2D and 3D data) is likely to alleviate many of the difficulties and uncertainties associated with manual resonance assignments in solid state NMR studies of uniformly labeled proteins, where spectral resolution and signal-to-noise are often sub-optimal.
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Affiliation(s)
- Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA.
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45
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Abstract
The prion hypothesis states that the prion and non-prion form of a protein differ only in their 3D conformation and that different strains of a prion differ by their 3D structure. Recent technical developments have enabled solid-state NMR to address the atomic-resolution structures of full-length prions, and a first comparative study of two of them, HET-s and Ure2p, in fibrillar form, has recently appeared as a pair of companion papers. Interestingly, the two structures are rather different: HET-s features an exceedingly well-ordered prion domain and a partially disordered globular domain. Ure2p in contrast features a very well ordered globular domain with a conserved fold, and-most probably-a partially ordered prion domain. For HET-s, the structure of the prion domain is characterized at atomic-resolution. For Ure2p, structure determination is under way, but the highly resolved spectra clearly show that information at atomic resolution should be achievable.
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Affiliation(s)
- Anja Böckmann
- IBCP UMR 5086 CNRS/Université de Lyon, Lyon, France.
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46
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Hamley IW, Nutt DR, Brown GD, Miravet JF, Escuder B, Rodríguez-Llansola F. Influence of the solvent on the self-assembly of a modified amyloid beta peptide fragment. II. NMR and computer simulation investigation. J Phys Chem B 2010; 114:940-51. [PMID: 20039666 DOI: 10.1021/jp906107p] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The conformation of a model peptide AAKLVFF based on a fragment of the amyloid beta peptide Abeta16-20, KLVFF, is investigated in methanol and water via solution NMR experiments and molecular dynamics computer simulations. In previous work, we have shown that AAKLVFF forms peptide nanotubes in methanol and twisted fibrils in water. Chemical shift measurements were used to investigate the solubility of the peptide as a function of concentration in methanol and water. This enabled the determination of critical aggregation concentrations. The solubility was lower in water. In dilute solution, diffusion coefficients revealed the presence of intermediate aggregates in concentrated solution, coexisting with NMR-silent larger aggregates, presumed to be beta-sheets. In water, diffusion coefficients did not change appreciably with concentration, indicating the presence mainly of monomers, coexisting with larger aggregates in more concentrated solution. Concentration-dependent chemical shift measurements indicated a folded conformation for the monomers/intermediate aggregates in dilute methanol, with unfolding at higher concentration. In water, an antiparallel arrangement of strands was indicated by certain ROESY peak correlations. The temperature-dependent solubility of AAKLVFF in methanol was well described by a van't Hoff analysis, providing a solubilization enthalpy and entropy. This pointed to the importance of solvophobic interactions in the self-assembly process. Molecular dynamics simulations constrained by NOE values from NMR suggested disordered reverse turn structures for the monomer, with an antiparallel twisted conformation for dimers. To model the beta-sheet structures formed at higher concentration, possible model arrangements of strands into beta-sheets with parallel and antiparallel configurations and different stacking sequences were used as the basis for MD simulations; two particular arrangements of antiparallel beta-sheets were found to be stable, one being linear and twisted and the other twisted in two directions. These structures were used to simulate circular dichroism spectra. The roles of aromatic stacking interactions and charge transfer effects were also examined. Simulated spectra were found to be similar to those observed experimentally (in water or methanol) which show a maximum at 215 or 218 nm due to pi-pi* interactions, when allowance is made for a 15-18 nm red-shift that may be due to light scattering effects.
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Affiliation(s)
- I W Hamley
- Department of Chemistry, University of Reading, Reading RG6 6AD, UK
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47
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Han Y, Ahn J, Concel J, Byeon IJL, Gronenborn AM, Yang J, Polenova T. Solid-state NMR studies of HIV-1 capsid protein assemblies. J Am Chem Soc 2010; 132:1976-87. [PMID: 20092249 PMCID: PMC2829833 DOI: 10.1021/ja908687k] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In mature HIV-1 virions, the 26.6 kDa CA protein is assembled into a characteristic cone-shaped core (capsid) that encloses the RNA viral genome. The assembled capsid structure is best described by a fullerene cone model that is made up from a hexameric lattice containing a variable number of CA pentamers, thus allowing for closure of tubular or conical structures. In this paper, we present a solid-state NMR analysis of the wild-type HIV-1 CA protein, prepared as conical and spherical assemblies that are stable and are not affected by magic angle spinning of the samples at frequencies between 10 and 25 kHz. Multidimensional homo- and heteronuclear correlation spectra of CA assemblies of uniformly (13)C,(15)N-labeled CA exhibit narrow lines, indicative of the conformational homogeneity of the protein in these assemblies. For the conical assemblies, partial residue-specific resonance assignments were obtained. Analysis of the NMR spectra recorded for the conical and spherical assemblies indicates that the CA protein structure is not significantly different in the different morphologies. The present results demonstrate that the assemblies of CA protein are amenable to detailed structural analysis by solid-state NMR spectroscopy.
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Affiliation(s)
- Yun Han
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Jinwoo Ahn
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Jason Concel
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - In-Ja L. Byeon
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Angela M. Gronenborn
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Structural Biology, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
| | - Jun Yang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
| | - Tatyana Polenova
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA 15261, United States
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, United States
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48
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Yang J, Tasayco ML, Polenova T. Dynamics of reassembled thioredoxin studied by magic angle spinning NMR: snapshots from different time scales. J Am Chem Soc 2009; 131:13690-702. [PMID: 19736935 DOI: 10.1021/ja9037802] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Solid-state NMR spectroscopy can be used to probe internal protein dynamics in the absence of the overall molecular tumbling. In this study, we report (15)N backbone dynamics in differentially enriched 1-73(U-(13)C,(15)N)/74-108(U-(15)N) reassembled thioredoxin on multiple time scales using a series of 2D and 3D MAS NMR experiments probing the backbone amide (15)N longitudinal relaxation, (1)H-(15)N dipolar order parameters, (15)N chemical shift anisotropy (CSA), and signal intensities in the temperature-dependent and (1)H T(2)'-filtered NCA experiments. The spin-lattice relaxation rates R(1) (R(1) = 1/T(1)) were observed in the range from 0.012 to 0.64 s(-1), indicating large site-to-site variations in dynamics on pico- to nanosecond time scales. The (1)H-(15)N dipolar order parameters, <S>, and (15)N CSA anisotropies, delta(sigma), reveal the backbone mobilities in reassembled thioredoxin, as reflected in the average <S> = 0.89 +/- 0.06 and delta(sigma) = 92.3 +/- 5.2 ppm, respectively. From the aggregate of experimental data from different dynamics methods, some degree of correlation between the motions on the different time scales has been suggested. Analysis of the dynamics parameters derived from these solid-state NMR experiments indicates higher mobilities for the residues constituting irregular secondary structure elements than for those located in the alpha-helices and beta-sheets, with no apparent systematic differences in dynamics between the alpha-helical and beta-sheet residues. Remarkably, the dipolar order parameters derived from the solid-state NMR measurements and the corresponding solution NMR generalized order parameters display similar qualitative trends as a function of the residue number. The comparison of the solid-state dynamics parameters to the crystallographic B-factors has identified the contribution of static disorder to the B-factors. The combination of longitudinal relaxation, dipolar order parameter, and CSA line shape analyses employed in this study provides snapshots of dynamics and a new insight on the correlation of these motions on multiple time scales.
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Affiliation(s)
- Jun Yang
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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Wasmer C, Schütz A, Loquet A, Buhtz C, Greenwald J, Riek R, Böckmann A, Meier BH. The Molecular Organization of the Fungal Prion HET-s in Its Amyloid Form. J Mol Biol 2009; 394:119-27. [DOI: 10.1016/j.jmb.2009.09.015] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Revised: 09/07/2009] [Accepted: 09/08/2009] [Indexed: 10/20/2022]
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Lange A, Gattin Z, Van Melckebeke H, Wasmer C, Soragni A, van Gunsteren WF, Meier BH. A combined solid-state NMR and MD characterization of the stability and dynamics of the HET-s(218-289) prion in its amyloid conformation. Chembiochem 2009; 10:1657-65. [PMID: 19504509 DOI: 10.1002/cbic.200900019] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The three-dimensional structure of amyloid fibrils of the prion-forming part of the HET-s protein [HET-s(218-289)], as determined by solid-state NMR, contains rigid and remarkably well-ordered parts, as witnessed by the narrow solid-state NMR line widths for this system. On the other hand, high-resolution magic-angle-spinning (HRMAS) NMR results have shown that HET-s(218-289) amyloid fibrils contain highly flexible parts as well. Here, we further explore this unexpected behaviour using solid-state NMR and molecular dynamics (MD). The NMR data provide new information on order and dynamics in the rigid and flexible parts of HET-s(218-289), respectively. The MD study addresses whether or not small multimers, in an amyloid conformation, are stable on the 10 ns timescale of the MD run and provides insight into the dynamic parameters on the nanosecond timescale. The atom-positional, root-mean-squared fluctuations (RMSFs) and order parameters S(2) obtained are in agreement with the NMR data. A flexible loop and the N terminus exhibit dynamics on the ps-ns timescale, whereas the hydrophobic core of HET-s(218-289) is rigid. The high degree of order in the core region of HET-s(218-289) amyloids, as observed in the MD simulations, is in agreement with the narrow, solid-state, NMR lines. Finally, we employed MD to predict the behaviour of the salt-bridge network in HET-s(218-289), which cannot be obtained easily by experiment. Simulations at different temperatures indicated that the network is highly dynamic and that it contributes to the thermostability of the HET-s(218-289) amyloids.
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Affiliation(s)
- Adam Lange
- Physical Chemistry, ETH Zürich, Wolfgang-Pauli-Strasse 10, Zürich, Switzerland.
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