1
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Martial B, Raîche-Marcoux G, Lefèvre T, Audet P, Voyer N, Auger M. Structure of a Parkinson’s Disease-Involved α-Synuclein Peptide Is Modulated by Membrane Composition and Physical State. J Phys Chem B 2020; 124:3469-3481. [DOI: 10.1021/acs.jpcb.0c00945] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Benjamin Martial
- Department of Chemistry, Regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines (PROTEO), Centre de recherche sur les matériaux avancés (CERMA), Centre québécois sur les matériaux fonctionnels (CQMF), Université Laval, 1045 avenue de la médecine, Québec, Quebec G1V 0A6, Canada
| | - Gabrielle Raîche-Marcoux
- Department of Chemistry, Regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines (PROTEO), Centre de recherche sur les matériaux avancés (CERMA), Centre québécois sur les matériaux fonctionnels (CQMF), Université Laval, 1045 avenue de la médecine, Québec, Quebec G1V 0A6, Canada
| | - Thierry Lefèvre
- Department of Chemistry, Regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines (PROTEO), Centre de recherche sur les matériaux avancés (CERMA), Centre québécois sur les matériaux fonctionnels (CQMF), Université Laval, 1045 avenue de la médecine, Québec, Quebec G1V 0A6, Canada
| | - Pierre Audet
- Department of Chemistry, Université Laval, 1045 avenue de la médecine, Québec, Quebec G1V 0A6, Canada
| | - Normand Voyer
- Department of Chemistry, Regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines (PROTEO), Université Laval, 1045 avenue de la médecine, Québec, Quebec G1V 0A6, Canada
| | - Michèle Auger
- Department of Chemistry, Regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines (PROTEO), Centre de recherche sur les matériaux avancés (CERMA), Centre québécois sur les matériaux fonctionnels (CQMF), Université Laval, 1045 avenue de la médecine, Québec, Quebec G1V 0A6, Canada
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2
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Keeler EG, Michaelis VK, Wilson CB, Hung I, Wang X, Gan Z, Griffin RG. High-Resolution 17O NMR Spectroscopy of Structural Water. J Phys Chem B 2019; 123:3061-3067. [PMID: 30882222 PMCID: PMC6689193 DOI: 10.1021/acs.jpcb.9b02277] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The importance of studying site-specific interactions of structurally similar water molecules in complex systems is well known. We demonstrate the ability to resolve four distinct bound water environments within the crystal structure of lanthanum magnesium nitrate hydrate via 17O solid state nuclear magnetic resonance (NMR) spectroscopy. Using high-resolution multidimensional experiments at high magnetic fields (18.8-35.2 T), each individual water environment was resolved. The quadrupole coupling constants and asymmetry parameters of the 17O of each water were determined to be between 6.6 and 7.1 MHz, 0.83 and 0.90, respectively. The resolution of the four unique, yet similar, structural waters within a hydrated crystal via 17O NMR spectroscopy demonstrates the ability to decipher the unique electronic environment of structural water within a single hydrated crystal structure.
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Affiliation(s)
- Eric G. Keeler
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139 USA
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139 USA
| | - Vladimir K. Michaelis
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139 USA
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139 USA
| | - Christopher B. Wilson
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139 USA
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139 USA
| | - Ivan Hung
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Xiaoling Wang
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Zhehong Gan
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, United States
| | - Robert G. Griffin
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139 USA
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139 USA
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3
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Wang S, Yuan S, Chen W, Zhou Y, Hong YL, Miyoshi T. Structural Unit of Polymer Crystallization in Dilute Solution As Studied by Solid-State NMR and 13C Isotope Labeling. Macromolecules 2018. [DOI: 10.1021/acs.macromol.8b01950] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Shijun Wang
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325-3909, United States
| | - Shichen Yuan
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325-3909, United States
| | - Wei Chen
- State Key Lab of Pollution Control and Resource Reuse Study, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Yang Zhou
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325-3909, United States
| | - You-lee Hong
- RIKEN CLST-JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Toshikazu Miyoshi
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325-3909, United States
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4
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van der Wel PCA. Insights into protein misfolding and aggregation enabled by solid-state NMR spectroscopy. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2017; 88:1-14. [PMID: 29035839 PMCID: PMC5705391 DOI: 10.1016/j.ssnmr.2017.10.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/03/2017] [Accepted: 10/03/2017] [Indexed: 05/17/2023]
Abstract
The aggregation of proteins and peptides into a variety of insoluble, and often non-native, aggregated states plays a central role in many devastating diseases. Analogous processes undermine the efficacy of polypeptide-based biological pharmaceuticals, but are also being leveraged in the design of biologically inspired self-assembling materials. This Trends article surveys the essential contributions made by recent solid-state NMR (ssNMR) studies to our understanding of the structural features of polypeptide aggregates, and how such findings are informing our thinking about the molecular mechanisms of misfolding and aggregation. A central focus is on disease-related amyloid fibrils and oligomers involved in neurodegenerative diseases such as Alzheimer's, Parkinson's and Huntington's disease. SSNMR-enabled structural and dynamics-based findings are surveyed, along with a number of resulting emerging themes that appear common to different amyloidogenic proteins, such as their compact alternating short-β-strand/β-arc amyloid core architecture. Concepts, methods, future prospects and challenges are discussed.
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Affiliation(s)
- Patrick C A van der Wel
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.
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5
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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: 625] [Impact Index Per Article: 78.1] [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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6
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Michaelis VK, Keeler EG, Ong TC, Craigen KN, Penzel S, Wren JEC, Kroeker S, Griffin RG. Structural Insights into Bound Water in Crystalline Amino Acids: Experimental and Theoretical (17)O NMR. J Phys Chem B 2015; 119:8024-36. [PMID: 25996165 PMCID: PMC4894719 DOI: 10.1021/acs.jpcb.5b04647] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We demonstrate here that the (17)O NMR properties of bound water in a series of amino acids and dipeptides can be determined with a combination of nonspinning and magic-angle spinning experiments using a range of magnetic field strengths from 9.4 to 21.1 T. Furthermore, we propose a (17)O chemical shift fingerprint region for bound water molecules in biological solids that is well outside the previously determined ranges for carbonyl, carboxylic, and hydroxyl oxygens, thereby offering the ability to resolve multiple (17)O environments using rapid one-dimensional NMR techniques. Finally, we compare our experimental data against quantum chemical calculations using GIPAW and hybrid-DFT, finding intriguing discrepancies between the electric field gradients calculated from structures determined by X-ray and neutron diffraction.
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Affiliation(s)
- Vladimir K. Michaelis
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139 USA
| | - Eric G. Keeler
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139 USA
| | - Ta-Chung Ong
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139 USA
| | - Kimberley N. Craigen
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
| | - Susanne Penzel
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139 USA
| | - John E. C. Wren
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
| | - Scott Kroeker
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
| | - Robert G. Griffin
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139 USA
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7
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Su Y, Andreas L, Griffin RG. Magic angle spinning NMR of proteins: high-frequency dynamic nuclear polarization and (1)H detection. Annu Rev Biochem 2015; 84:465-97. [PMID: 25839340 DOI: 10.1146/annurev-biochem-060614-034206] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Magic angle spinning (MAS) NMR studies of amyloid and membrane proteins and large macromolecular complexes are an important new approach to structural biology. However, the applicability of these experiments, which are based on (13)C- and (15)N-detected spectra, would be enhanced if the sensitivity were improved. Here we discuss two advances that address this problem: high-frequency dynamic nuclear polarization (DNP) and (1)H-detected MAS techniques. DNP is a sensitivity enhancement technique that transfers the high polarization of exogenous unpaired electrons to nuclear spins via microwave irradiation of electron-nuclear transitions. DNP boosts NMR signal intensities by factors of 10(2) to 10(3), thereby overcoming NMR's inherent low sensitivity. Alternatively, it permits structural investigations at the nanomolar scale. In addition, (1)H detection is feasible primarily because of the development of MAS rotors that spin at frequencies of 40 to 60 kHz or higher and the preparation of extensively (2)H-labeled proteins.
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Affiliation(s)
- Yongchao Su
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139;
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8
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Udomprasert A, Bongiovanni MN, Sha R, Sherman WB, Wang T, Arora PS, Canary JW, Gras SL, Seeman NC. Amyloid fibrils nucleated and organized by DNA origami constructions. NATURE NANOTECHNOLOGY 2014; 9:537-41. [PMID: 24880222 PMCID: PMC4082467 DOI: 10.1038/nnano.2014.102] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 04/23/2014] [Indexed: 05/24/2023]
Abstract
Amyloid fibrils are ordered, insoluble protein aggregates that are associated with neurodegenerative conditions such as Alzheimer's disease. The fibrils have a common rod-like core structure, formed from an elongated stack of β-strands, and have a rigidity similar to that of silk (Young's modulus of 0.2-14 GPa). They also exhibit high thermal and chemical stability and can be assembled in vitro from short synthetic non-disease-related peptides. As a result, they are of significant interest in the development of self-assembled materials for bionanotechnology applications. Synthetic DNA molecules have previously been used to form intricate structures and organize other materials such as metal nanoparticles and could in principle be used to nucleate and organize amyloid fibrils. Here, we show that DNA origami nanotubes can sheathe amyloid fibrils formed within them. The fibrils are built by modifying the synthetic peptide fragment corresponding to residues 105-115 of the amyloidogenic protein transthyretin and a DNA origami construct is used to form 20-helix DNA nanotubes with sufficient space for the fibrils inside. Once formed, the fibril-filled nanotubes can be organized onto predefined two-dimensional platforms via DNA-DNA hybridization interactions.
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Affiliation(s)
| | - Marie N. Bongiovanni
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - William B. Sherman
- Bard High School Early College - Queens, 30-20 Thomson Ave., Queens, NY 11101, USA
| | - Tong Wang
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Paramjit S. Arora
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - James W. Canary
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Sally L. Gras
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Nadrian C. Seeman
- Department of Chemistry, New York University, New York, NY 10003, USA
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9
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Su Y, Sarell CJ, Eddy MT, Debelouchina GT, Andreas LB, Pashley CL, Radford SE, Griffin RG. Secondary structure in the core of amyloid fibrils formed from human β₂m and its truncated variant ΔN6. J Am Chem Soc 2014; 136:6313-25. [PMID: 24679070 PMCID: PMC4017606 DOI: 10.1021/ja4126092] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
![]()
Amyloid
fibrils formed from initially soluble proteins with diverse
sequences are associated with an array of human diseases. In the human
disorder, dialysis-related amyloidosis (DRA), fibrils contain two
major constituents, full-length human β2-microglobulin
(hβ2m) and a truncation variant, ΔN6 which
lacks the N-terminal six amino acids. These fibrils are assembled
from initially natively folded proteins with an all antiparallel β-stranded
structure. Here, backbone conformations of wild-type hβ2m and ΔN6 in their amyloid forms have been determined
using a combination of dilute isotopic labeling strategies and multidimensional
magic angle spinning (MAS) NMR techniques at high magnetic fields,
providing valuable structural information at the atomic-level about
the fibril architecture. The secondary structures of both fibril types,
determined by the assignment of ∼80% of the backbone resonances
of these 100- and 94-residue proteins, respectively, reveal substantial
backbone rearrangement compared with the location of β-strands
in their native immunoglobulin folds. The identification of seven
β-strands in hβ2m fibrils indicates that approximately
70 residues are in a β-strand conformation in the fibril core.
By contrast, nine β-strands comprise the fibrils formed from
ΔN6, indicating a more extensive core. The precise location
and length of β-strands in the two fibril forms also differ.
The results indicate fibrils of ΔN6 and hβ2m have an extensive core architecture involving the majority of residues
in the polypeptide sequence. The common elements of the backbone structure
of the two proteins likely facilitates their ability to copolymerize
during amyloid fibril assembly.
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Affiliation(s)
- Yongchao Su
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology Cambridge, Massachusetts 02139, United States
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10
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Debelouchina GT, Bayro MJ, Fitzpatrick AW, Ladizhansky V, Colvin MT, Caporini MA, Jaroniec CP, Bajaj VS, Rosay M, Macphee CE, Vendruscolo M, Maas WE, Dobson CM, Griffin RG. Higher order amyloid fibril structure by MAS NMR and DNP spectroscopy. J Am Chem Soc 2013; 135:19237-47. [PMID: 24304221 DOI: 10.1021/ja409050a] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Protein magic angle spinning (MAS) NMR spectroscopy has generated structural models of several amyloid fibril systems, thus providing valuable information regarding the forces and interactions that confer the extraordinary stability of the amyloid architecture. Despite these advances, however, obtaining atomic resolution information describing the higher levels of structural organization within the fibrils remains a significant challenge. Here, we detail MAS NMR experiments and sample labeling schemes designed specifically to probe such higher order amyloid structure, and we have applied them to the fibrils formed by an eleven-residue segment of the amyloidogenic protein transthyretin (TTR(105-115)). These experiments have allowed us to define unambiguously not only the arrangement of the peptide β-strands into β-sheets but also the β-sheet interfaces within each protofilament, and in addition to identify the nature of the protofilament-to-protofilament contacts that lead to the formation of the complete fibril. Our efforts have resulted in 111 quantitative distance and torsion angle restraints (10 per residue) that describe the various levels of structure organization. The experiments benefited extensively from the use of dynamic nuclear polarization (DNP), which in some cases allowed us to shorten the data acquisition time from days to hours and to improve significantly the signal-to-noise ratios of the spectra. The β-sheet interface and protofilament interactions identified here revealed local variations in the structure that result in multiple peaks for the exposed N- and C-termini of the peptide and in inhomogeneous line-broadening for the residues buried within the interior of the fibrils.
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Affiliation(s)
- Galia T Debelouchina
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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11
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Weingarth M, Baldus M. Solid-state NMR-based approaches for supramolecular structure elucidation. Acc Chem Res 2013; 46:2037-46. [PMID: 23586937 DOI: 10.1021/ar300316e] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Supramolecular chemistry provides structural and conformational information about complexes formed from multiple molecules. While the molecule is held together by strong intramolecular contacts like covalent bonds, supramolecular structures can be further stabilized by weaker or transient intermolecular interactions. These interactions can confer a great diversity and sensitivity to exogenous factors like temperature, pressure, or ionic strength to multimolecular arrangements. Solid-state nuclear magnetic resonance (ssNMR) can provide atomic-scale structural and dynamical information in highly disordered or heterogeneous biological systems, even in complex environments such as cellular membranes or whole cells. In these systems, the molecule of interest no longer exists as a separate unit, but it entangles with its surroundings in a dynamic interplay. Researchers have long accounted for the complexity of these intermolecular arrangements through a rather phenomenological description. But now the focus is shifting toward a detailed understanding of supramolecular structure at atomic resolution, constantly expanding our understanding of the stunning influence of the environment. In this Account, we discuss how ssNMR can help to dissect the remarkable interplay between intra- and intermolecular interactions. We describe biochemical and spectroscopic strategies that tailor ssNMR spectroscopic methods to the challenge of supramolecular structure investigation. In particular, we consider protein-protein interactions or the protein-membrane topology, and we review recent applications of these techniques. Furthermore, we summarize methods for integrating ssNMR information with other experimental techniques or computational methods, and we offer perspectives on how this overall information allows us to target increasingly large and intricate supramolecular structures of biomolecules. Advancements in ssNMR methodology and instrumentation, including the incorporation of signal enhancement methods such as dynamic nuclear polarization will further increase the potential of ssNMR spectroscopy, and together with additional developments in the field of NMR-hybrid strategies, ssNMR may become an ideal tool to study the heterogeneous, dynamic, and often transient nature of molecular interactions in complex biological systems.
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Affiliation(s)
- Markus Weingarth
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Marc Baldus
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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12
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Rodríguez-Pérez JC, Hamley IW, Squires AM. Determination of orientations of aromatic groups in self-assembled peptide fibrils by polarised Raman spectroscopy. Phys Chem Chem Phys 2013; 15:13940-50. [PMID: 23852406 DOI: 10.1039/c3cp52595c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
In this paper we describe a novel combination of Raman spectroscopy, isotope editing and X-ray scattering as a powerful approach to give detailed structural information on aromatic side chains in peptide fibrils. The orientation of the tyrosine residues in fibrils of the peptide YTIAALLSPYS with respect to the fibril axis has been determined from a combination of polarised Raman spectroscopy and X-ray diffraction measurements. The Raman intensity of selected tyrosine bands collected at different polarisation geometries is related to the values and orientation of the Raman tensor for those specific vibrations. Using published Raman tensor values we solved the relevant expressions for both of the two tyrosine residues present in this peptide. Ring deuteration in one of the two tyrosine side chains allowed for the calculation to be performed individually for both, by virtue of the isotopic shift that eliminates band overlapping. Sample disorder was taken into account by obtaining the distribution of orientations of the samples from X-ray diffraction experiments. The results provide previously unavailable details about the molecular conformation of this peptide, and demonstrate the value of this approach for the study of amyloid fibrils.
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13
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Hong YL, Miyoshi T. Chain-Folding Structure of a Semicrystalline Polymer in Bulk Crystals Determined by 13C- 13C Double Quantum NMR. ACS Macro Lett 2013; 2:501-505. [PMID: 35581806 DOI: 10.1021/mz300630j] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A unique approach using 13C-13C double quantum (DQ) NMR combined with selective 13C isotope labeling is proposed to investigate the chain trajectory of the synthetic polymer in bulk crystals. Since the DQ buildup curve highly depends upon coupled spin number, topology, and internuclear distance, which originated from the chain trajectory of selectively 13C-labeled polymers, the adjacent re-entry site and fraction under finite chain-folding number can be determined.
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Affiliation(s)
- You-lee Hong
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325, United States
| | - Toshikazu Miyoshi
- Department of Polymer Science, The University of Akron, Akron, Ohio 44325, United States
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14
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Porrini M, Zachariae U, Barran PE, MacPhee CE. Effect of Protonation State on the Stability of Amyloid Oligomers Assembled from TTR(105-115). J Phys Chem Lett 2013; 4:1233-1238. [PMID: 26282135 DOI: 10.1021/jz400372u] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Amyloid fibrils are self-assembled aggregates of polypeptides that are implicated in the development of several human diseases. A peptide derived from amino acids 105-115 of the human plasma protein transthyretin forms homogeneous and well-defined fibrils and, as a model system, has been the focus of a number of studies investigating the formation and structure of this class of aggregates. Self-assembly of TTR(105-115) occurs at low pH, and this work explores the effect of protonation on the growth and stability of small cross-β aggregates. Using molecular dynamics simulations of structures up to the decamer in both protonated and deprotonated states, we find that, whereas hexamers are more stable for protonated peptides, higher order oligomers are more stable when the peptides are deprotonated. Our findings imply a change in the acid pK of the protonated C-terminal group during the formation of fibrils, which leads to stabilization of higher-order oligomers through electrostatic interactions.
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Affiliation(s)
- Massimiliano Porrini
- †School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, The King's Buildings, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom
| | - Ulrich Zachariae
- †School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, The King's Buildings, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom
| | - Perdita E Barran
- ‡EastChem School of Chemistry, University of Edinburgh, Joseph Black Building, The King's Buildings, West Mains Road, Edinburgh EH9 3JJ, United Kingdom
| | - Cait E MacPhee
- †School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, The King's Buildings, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom
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Fitzpatrick AWP, Debelouchina GT, Bayro MJ, Clare DK, Caporini MA, Bajaj VS, Jaroniec CP, Wang L, Ladizhansky V, Müller SA, MacPhee CE, Waudby CA, Mott HR, De Simone A, Knowles TPJ, Saibil HR, Vendruscolo M, Orlova EV, Griffin RG, Dobson CM. Atomic structure and hierarchical assembly of a cross-β amyloid fibril. Proc Natl Acad Sci U S A 2013; 110:5468-73. [PMID: 23513222 PMCID: PMC3619355 DOI: 10.1073/pnas.1219476110] [Citation(s) in RCA: 412] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The cross-β amyloid form of peptides and proteins represents an archetypal and widely accessible structure consisting of ordered arrays of β-sheet filaments. These complex aggregates have remarkable chemical and physical properties, and the conversion of normally soluble functional forms of proteins into amyloid structures is linked to many debilitating human diseases, including several common forms of age-related dementia. Despite their importance, however, cross-β amyloid fibrils have proved to be recalcitrant to detailed structural analysis. By combining structural constraints from a series of experimental techniques spanning five orders of magnitude in length scale--including magic angle spinning nuclear magnetic resonance spectroscopy, X-ray fiber diffraction, cryoelectron microscopy, scanning transmission electron microscopy, and atomic force microscopy--we report the atomic-resolution (0.5 Å) structures of three amyloid polymorphs formed by an 11-residue peptide. These structures reveal the details of the packing interactions by which the constituent β-strands are assembled hierarchically into protofilaments, filaments, and mature fibrils.
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Affiliation(s)
- Anthony W. P. Fitzpatrick
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Galia T. Debelouchina
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Marvin J. Bayro
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Daniel K. Clare
- Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, United Kingdom
| | - Marc A. Caporini
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Vikram S. Bajaj
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Christopher P. Jaroniec
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Luchun Wang
- Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, United Kingdom
| | - Vladimir Ladizhansky
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | - Cait E. MacPhee
- School of Physics, University of Edinburgh, Edinburgh EH9 3JZ, United Kingdom
| | - Christopher A. Waudby
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, United Kingdom
| | - Helen R. Mott
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom; and
| | - Alfonso De Simone
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Tuomas P. J. Knowles
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Helen R. Saibil
- Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, United Kingdom
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Elena V. Orlova
- Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, United Kingdom
| | - Robert G. Griffin
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
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Bongiovanni MN, Puri D, Goldie KN, Gras SL. Noncore Residues Influence the Kinetics of Functional TTR105–115-Based Amyloid Fibril Assembly. J Mol Biol 2012; 421:256-69. [DOI: 10.1016/j.jmb.2011.12.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2011] [Revised: 12/07/2011] [Accepted: 12/08/2011] [Indexed: 11/25/2022]
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Rodríguez-Pérez JC, Hamley IW, Gras SL, Squires AM. Local orientational disorder in peptide fibrils probed by a combination of residue-specific 13C–18O labelling, polarised infrared spectroscopy and molecular combing. Chem Commun (Camb) 2012; 48:11835-7. [DOI: 10.1039/c2cc35586h] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Helmus JJ, Surewicz K, Apostol MI, Surewicz WK, Jaroniec CP. Intermolecular alignment in Y145Stop human prion protein amyloid fibrils probed by solid-state NMR spectroscopy. J Am Chem Soc 2011; 133:13934-7. [PMID: 21827207 DOI: 10.1021/ja206469q] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The Y145Stop mutant of human prion protein, huPrP23-144, has been linked to PrP cerebral amyloid angiopathy, an inherited amyloid disease, and also serves as a valuable in vitro model for investigating the molecular basis of amyloid strains. Prior studies of huPrP23-144 amyloid by magic-angle-spinning (MAS) solid-state NMR spectroscopy revealed a compact β-rich amyloid core region near the C-terminus and an unstructured N-terminal domain. Here, with the focus on understanding the higher-order architecture of huPrP23-144 fibrils, we probed the intermolecular alignment of β-strands within the amyloid core using MAS NMR techniques and fibrils formed from equimolar mixtures of (15)N-labeled protein and (13)C-huPrP23-144 prepared with [1,3-(13)C(2)] or [2-(13)C]glycerol. Numerous intermolecular correlations involving backbone atoms observed in 2D (15)N-(13)C spectra unequivocally suggest an overall parallel in-register alignment of the β-sheet core. Additional experiments that report on intermolecular (15)N-(13)CO and (15)N-(13)Cα dipolar couplings yielded an estimated strand spacing that is within ∼10% of the distances of 4.7-4.8 Å typical for parallel β-sheets.
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Affiliation(s)
- Jonathan J Helmus
- Department of Chemistry, The Ohio State University, Columbus, 43210, United States
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Bayro MJ, Debelouchina GT, Eddy MT, Birkett NR, MacPhee CE, Rosay M, Maas WE, Dobson CM, Griffin RG. Intermolecular structure determination of amyloid fibrils with magic-angle spinning and dynamic nuclear polarization NMR. J Am Chem Soc 2011; 133:13967-74. [PMID: 21774549 DOI: 10.1021/ja203756x] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We describe magic-angle spinning NMR experiments designed to elucidate the interstrand architecture of amyloid fibrils. Three methods are introduced for this purpose, two being based on the analysis of long-range (13)C-(13)C correlation spectra and the third based on the identification of intermolecular interactions in (13)C-(15)N spectra. We show, in studies of fibrils formed by the 86-residue SH3 domain of PI3 kinase (PI3-SH3 or PI3K-SH3), that efficient (13)C-(13)C correlation spectra display a resonance degeneracy that establishes a parallel, in-register alignment of the proteins in the amyloid fibrils. In addition, this degeneracy can be circumvented to yield direct intermolecular constraints. The (13)C-(13)C experiments are corroborated by (15)N-(13)C correlation spectra obtained from a mixed [(15)N,(12)C]/[(14)N,(13)C] sample which directly quantify interstrand distances. Furthermore, when the spectra are recorded with signal enhancement provided by dynamic nuclear polarization (DNP) at 100 K, we demonstrate a dramatic increase (from 23 to 52) in the number of intermolecular (15)N-(13)C constraints detectable in the spectra. The increase in the information content is due to the enhanced signal intensities and to the fact that dynamic processes, leading to spectral intensity losses, are quenched at low temperatures. Thus, acquisition of low temperature spectra addresses a problem that is frequently encountered in MAS spectra of proteins. In total, the experiments provide 111 intermolecular (13)C-(13)C and (15)N-(13)C constraints that establish that the PI3-SH3 protein strands are aligned in a parallel, in-register arrangement within the amyloid fibril.
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Affiliation(s)
- Marvin J Bayro
- Francis Bitter Magnet Laboratory, Department of Chemistry, Massachusetts Institute of Technology, Cambridge, 02139, United States
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Chan JCC. Solid-state NMR techniques for the structural determination of amyloid fibrils. Top Curr Chem (Cham) 2011; 306:47-88. [PMID: 21630137 DOI: 10.1007/128_2011_154] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
This review discusses the solid-state NMR techniques developed for the study of amyloid fibrils. Literature up to the end of 2010 has been surveyed and the materials are organized according to five categories, viz. homonuclear dipolar recoupling and polarization transfer via J-coupling, heteronuclear dipolar recoupling, correlation spectroscopy, recoupling of chemical shift anisotropy, and tensor correlation. Our emphasis is on the NMR techniques and their practical aspects. The biological implications of the results obtained for amyloid fibrils are only briefly discussed. Our main objective is to showcase the power of NMR in the study of biological unoriented solids.
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Affiliation(s)
- Jerry C C Chan
- Department of Chemistry, National Taiwan University, Taipei, Taiwan.
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van der Wel PC, Lewandowski JR, Griffin RG. Structural characterization of GNNQQNY amyloid fibrils by magic angle spinning NMR. Biochemistry 2010; 49:9457-69. [PMID: 20695483 PMCID: PMC3026921 DOI: 10.1021/bi100077x] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Several human diseases are associated with the formation of amyloid aggregates, but experimental characterization of these amyloid fibrils and their oligomeric precursors has remained challenging. Experimental and computational analysis of simpler model systems has therefore been necessary, for instance, on the peptide fragment GNNQQNY7−13 of yeast prion protein Sup35p. Expanding on a previous publication, we report here a detailed structural characterization of GNNQQNY fibrils using magic angle spinning (MAS) NMR. On the basis of additional chemical shift assignments we confirm the coexistence of three distinct peptide conformations within the fibrillar samples, as reflected in substantial chemical shift differences. Backbone torsion angle measurements indicate that the basic structure of these coexisting conformers is an extended β-sheet. We structurally characterize a previously identified localized distortion of the β-strand backbone specific to one of the conformers. Intermolecular contacts are consistent with each of the conformers being present in its own parallel and in-register sheet. Overall the MAS NMR data indicate a substantial difference between the structure of the fibrillar and crystalline forms of these peptides, with a clearly increased complexity in the GNNQQNY fibril structure. These experimental data can provide guidance for future work, both experimental and theoretical, and provide insights into the distinction between fibril growth and crystal formation.
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Affiliation(s)
| | | | - Robert G. Griffin
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
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