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Gautam I, Yarava JR, Xu Y, Li R, Scott FJ, Mentink-Vigier F, Momany M, Latgé JP, Wang T. Comparative Analysis of Polysaccharide and Cell Wall Structure in Aspergillus nidulans and Aspergillus fumigatus by Solid-State NMR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.13.607833. [PMID: 39185159 PMCID: PMC11343165 DOI: 10.1101/2024.08.13.607833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Invasive aspergillosis poses a significant threat to immunocompromised patients, leading to high mortality rates associated with these infections. Targeting the biosynthesis of cell wall carbohydrates is a promising strategy for antifungal drug development and will be advanced by a molecular-level understanding of the native structures of polysaccharides within their cellular context. Solid-state NMR spectroscopy has recently provided detailed insights into the cell wall organization of Aspergillus fumigatus, but genetic and biochemical evidence highlights species-specific differences among Aspergillus species. In this study, we employed a combination of 13C, 15N, and 1H-detection solid-state NMR, supplemented by Dynamic Nuclear Polarization (DNP), to compare the structural organization of cell wall polymers and their assembly in the cell walls of A. fumigatus and A. nidulans, both of which are key model organisms and human pathogens. The two species exhibited a similar rigid core architecture, consisting of chitin, α-glucan, and β-glucan, which contributed to comparable cell wall properties, including polymer dynamics, water retention, and supramolecular organization. However, differences were observed in the chitin, galactosaminogalactan, protein, and lipid content, as well as in the dynamics of galactomannan and the structure of the glucan matrix.
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Affiliation(s)
- Isha Gautam
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
| | | | - Yifan Xu
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
| | - Reina Li
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
| | - Faith J. Scott
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL, USA
| | | | - Michelle Momany
- Department of Plant Biology, University of Georgia, Athens, GA, USA
| | - Jean-Paul Latgé
- Institute of Molecular Biology and Biotechnology, University of Crete, Heraklion, Greece
- Fungal Respiratory Infections Research Unit and SFR ICAT, University of Angers, France
| | - Tuo Wang
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
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2
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Juković M, Ratkaj I, Kalafatovic D, Bradshaw NJ. Amyloids, amorphous aggregates and assemblies of peptides - Assessing aggregation. Biophys Chem 2024; 308:107202. [PMID: 38382283 DOI: 10.1016/j.bpc.2024.107202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/31/2024] [Accepted: 02/14/2024] [Indexed: 02/23/2024]
Abstract
Amyloid and amorphous aggregates represent the two major categories of aggregates associated with diseases, and although exhibiting distinct features, researchers often treat them as equivalent, which demonstrates the need for more thorough characterization. Here, we compare amyloid and amorphous aggregates based on their biochemical properties, kinetics, and morphological features. To further decipher this issue, we propose the use of peptide self-assemblies as minimalistic models for understanding the aggregation process. Peptide building blocks are significantly smaller than proteins that participate in aggregation, however, they make a plausible means to bridge the gap in discerning the aggregation process at the more complex, protein level. Additionally, we explore the potential use of peptide-inspired models to research the liquid-liquid phase separation as a feasible mechanism preceding amyloid formation. Connecting these concepts can help clarify our understanding of aggregation-related disorders and potentially provide novel drug targets to impede and reverse these serious illnesses.
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Affiliation(s)
- Maja Juković
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia
| | - Ivana Ratkaj
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia
| | - Daniela Kalafatovic
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia.
| | - Nicholas J Bradshaw
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia.
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3
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Agha MM, Uversky VN. Morphological features and types of aggregated structures. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 206:85-109. [PMID: 38811090 DOI: 10.1016/bs.pmbts.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
In vivo, protein aggregation arises due to incorrect folding or misfolding. The aggregation of proteins into amyloid fibrils is the characteristic feature of various misfolding diseases known as amyloidosis, such as Alzheimer's and Parkinson's disease. The heterogeneous nature of these fibrils restricts the extent to which their structure may be characterized. Advancements in techniques, such as X-ray diffraction, cryo-electron microscopy, and solid-state NMR have yielded intricate insights into structures of different amyloid fibrils. These studies have unveiled a diverse range of polymorphic structures that typically conform to the cross-β amyloid pattern. This chapter provides a concise overview of the information acquired in the field of protein aggregation, with particular focus on amyloids.
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Affiliation(s)
- Mansoureh Mirza Agha
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Vladimir N Uversky
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institute for Biological Instrumentation, Pushchino, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States.
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4
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Li T, Kambanis J, Sorenson TL, Sunde M, Shen Y. From Fundamental Amyloid Protein Self-Assembly to Development of Bioplastics. Biomacromolecules 2024; 25:5-23. [PMID: 38147506 PMCID: PMC10777412 DOI: 10.1021/acs.biomac.3c01129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/03/2023] [Accepted: 12/04/2023] [Indexed: 12/28/2023]
Abstract
Proteins can self-assemble into a range of nanostructures as a result of molecular interactions. Amyloid nanofibrils, as one of them, were first discovered with regard to the relevance of neurodegenerative diseases but now have been exploited as building blocks to generate multiscale materials with designed functions for versatile applications. This review interconnects the mechanism of amyloid fibrillation, the current approaches to synthesizing amyloid protein-based materials, and the application in bioplastic development. We focus on the fundamental structures of self-assembled amyloid fibrils and how external factors can affect protein aggregation to optimize the process. Protein self-assembly is essentially the autonomous congregation of smaller protein units into larger, organized structures. Since the properties of the self-assembly can be manipulated by changing intrinsic factors and external conditions, protein self-assembly serves as an excellent building block for bioplastic development. Building on these principles, general processing methods and pathways from raw protein sources to mature state materials are proposed, providing a guide for the development of large-scale production. Additionally, this review discusses the diverse properties of protein-based amyloid nanofibrils and how they can be utilized as bioplastics. The economic feasibility of the protein bioplastics is also compared to conventional plastics in large-scale production scenarios, supporting their potential as sustainable bioplastics for future applications.
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Affiliation(s)
- Tianchen Li
- School
of Chemical and Biomolecular Engineering and Sydney Nano, The University of Sydney, PNR Building, Darlington NSW 2008, Australia
| | - Jordan Kambanis
- School
of Chemical and Biomolecular Engineering and Sydney Nano, The University of Sydney, PNR Building, Darlington NSW 2008, Australia
| | - Timothy L. Sorenson
- School
of Chemical and Biomolecular Engineering and Sydney Nano, The University of Sydney, PNR Building, Darlington NSW 2008, Australia
| | - Margaret Sunde
- School
of Medical Sciences and Sydney Nano, The
University of Sydney, Sydney NSW 2006, Australia
| | - Yi Shen
- School
of Chemical and Biomolecular Engineering and Sydney Nano, The University of Sydney, PNR Building, Darlington NSW 2008, Australia
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5
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Understanding the mechanism of amylin aggregation: From identifying crucial segments to tracing dominant sequential events to modeling potential aggregation suppressors. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140866. [PMID: 36272537 DOI: 10.1016/j.bbapap.2022.140866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/07/2022] [Accepted: 10/13/2022] [Indexed: 11/13/2022]
Abstract
One of the most abundant, prevailing, and life-threatening human diseases that are currently baffling the scientific community is type 2 diabetes (T2D). The self-association of human amylin has been implicated in the pathogenesis of T2D, though with an inconclusive understanding of the mechanism. Hence, we focused on the characterization of the conformational ensembles of all the species that are believed to define the structural polymorphism of the aggregation process - the functional monomeric, the initially self-associated oligomeric, and the structured protofibril - by employing near-equilibrium, non-equilibrium, and equilibrium atomistic simulations on the sporadic, two familial variants (S20G and G33R), and their proline-substituted forms (S20P and G33P). The dynamic near-equilibrium assays hint toward - the abundance of helical conformation in the monomeric state, the retainment of the helicity in the initial self-associated oligomeric phase pointing toward the existence of the helix-helix association mechanism, the difference in preference of specific segments to have definite secondary structural features, the phase-dependent variability in the dominance of specific segments and mutation sites, and the simultaneous presence of generic and unique features among various sequences. Furthermore, the non-equilibrium pulling assays exemplify a generic sequential unzipping mechanism of the protofibrils, however, the sequence-dependent uniqueness comes from the difference in location and magnitude of the control of a specific terminus. Importantly, the equilibrium thermodynamic assays efficiently rank order the potential of aggregability among sequences and consequently suggests the probability of designing effective aggregation suppressors against sporadic and familial amylin variants incorporating proline as the mutation.
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van der Wel PCA. Dihedral Angle Measurements for Structure Determination by Biomolecular Solid-State NMR Spectroscopy. Front Mol Biosci 2021; 8:791090. [PMID: 34938776 PMCID: PMC8685456 DOI: 10.3389/fmolb.2021.791090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 11/22/2021] [Indexed: 11/13/2022] Open
Abstract
In structural studies of immobilized, aggregated and self-assembled biomolecules, solid-state NMR (ssNMR) spectroscopy can provide valuable high-resolution structural information. Among the structural restraints provided by magic angle spinning (MAS) ssNMR the canonical focus is on inter-atomic distance measurements. In the current review, we examine the utility of ssNMR measurements of angular constraints, as a complement to distance-based structure determination. The focus is on direct measurements of angular restraints via the judicious recoupling of multiple anisotropic ssNMR parameters, such as dipolar couplings and chemical shift anisotropies. Recent applications are highlighted, with a focus on studies of nanocrystalline polypeptides, aggregated peptides and proteins, receptor-substrate interactions, and small molecule interactions with amyloid protein fibrils. The review also examines considerations of when and where ssNMR torsion angle experiments are (most) effective, and discusses challenges and opportunities for future applications.
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Affiliation(s)
- Patrick C. A. van der Wel
- Solid-state NMR Group, Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
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Shcherbakov AA, Medeiros-Silva J, Tran N, Gelenter MD, Hong M. From Angstroms to Nanometers: Measuring Interatomic Distances by Solid-State NMR. Chem Rev 2021; 122:9848-9879. [PMID: 34694769 DOI: 10.1021/acs.chemrev.1c00662] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Internuclear distances represent one of the main structural constraints in molecular structure determination using solid-state NMR spectroscopy, complementing chemical shifts and orientational restraints. Although a large number of magic-angle-spinning (MAS) NMR techniques have been available for distance measurements, traditional 13C and 15N NMR experiments are inherently limited to distances of a few angstroms due to the low gyromagnetic ratios of these nuclei. Recent development of fast MAS triple-resonance 19F and 1H NMR probes has stimulated the design of MAS NMR experiments that measure distances in the 1-2 nm range with high sensitivity. This review describes the principles and applications of these multiplexed multidimensional correlation distance NMR experiments, with an emphasis on 19F- and 1H-based distance experiments. Representative applications of these long-distance NMR methods to biological macromolecules as well as small molecules are reviewed.
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Affiliation(s)
- Alexander A Shcherbakov
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - João Medeiros-Silva
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Nhi Tran
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Martin D Gelenter
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
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8
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Current Understanding of the Structure, Stability and Dynamic Properties of Amyloid Fibrils. Int J Mol Sci 2021; 22:ijms22094349. [PMID: 33919421 PMCID: PMC8122407 DOI: 10.3390/ijms22094349] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 04/17/2021] [Accepted: 04/18/2021] [Indexed: 02/07/2023] Open
Abstract
Amyloid fibrils are supramolecular protein assemblies represented by a cross-β structure and fibrous morphology, whose structural architecture has been previously investigated. While amyloid fibrils are basically a main-chain-dominated structure consisting of a backbone of hydrogen bonds, side-chain interactions also play an important role in determining their detailed structures and physicochemical properties. In amyloid fibrils comprising short peptide segments, a steric zipper where a pair of β-sheets with side chains interdigitate tightly is found as a fundamental motif. In amyloid fibrils comprising longer polypeptides, each polypeptide chain folds into a planar structure composed of several β-strands linked by turns or loops, and the steric zippers are formed locally to stabilize the structure. Multiple segments capable of forming steric zippers are contained within a single protein molecule in many cases, and polymorphism appears as a result of the diverse regions and counterparts of the steric zippers. Furthermore, the β-solenoid structure, where the polypeptide chain folds in a solenoid shape with side chains packed inside, is recognized as another important amyloid motif. While side-chain interactions are primarily achieved by non-polar residues in disease-related amyloid fibrils, the participation of hydrophilic and charged residues is prominent in functional amyloids, which often leads to spatiotemporally controlled fibrillation, high reversibility, and the formation of labile amyloids with kinked backbone topology. Achieving precise control of the side-chain interactions within amyloid structures will open up a new horizon for designing useful amyloid-based nanomaterials.
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Zhou J, Venturelli L, Keiser L, Sekatskii SK, Gallaire F, Kasas S, Longo G, Knowles TPJ, Ruggeri FS, Dietler G. Environmental Control of Amyloid Polymorphism by Modulation of Hydrodynamic Stress. ACS NANO 2021; 15:944-953. [PMID: 33348981 DOI: 10.1021/acsnano.0c07570] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The phenomenon of amyloid polymorphism is a key feature of protein aggregation. Unravelling this phenomenon is of great significance for understanding the underlying molecular mechanisms associated with neurodegenerative diseases and for the development of amyloid-based functional biomaterials. However, the understanding of the molecular origins and the physicochemical factors modulating amyloid polymorphs remains challenging. Herein, we demonstrate an association between amyloid polymorphism and environmental stress in solution, induced by an air/water interface in motion. Our results reveal that low-stress environments produce heterogeneous amyloid polymorphs, including twisted, helical, and rod-like fibrils, whereas high-stress conditions generate only homogeneous rod-like fibrils. Moreover, high environmental stress converts twisted fibrils into rod-like fibrils both in-pathway and after the completion of mature amyloid formation. These results enrich our understanding of the environmental origin of polymorphism of pathological amyloids and shed light on the potential of environmentally controlled fabrication of homogeneous amyloid biomaterials for biotechnological applications.
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Affiliation(s)
- Jiangtao Zhou
- Laboratory of Physics of Living Matter, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Leonardo Venturelli
- Laboratory of Physics of Living Matter, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ludovic Keiser
- Laboratory of Fluid Mechanics and Instabilities, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Sergey K Sekatskii
- Laboratory of Physics of Living Matter, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - François Gallaire
- Laboratory of Fluid Mechanics and Instabilities, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Sandor Kasas
- Laboratory of Physics of Living Matter, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Giovanni Longo
- Istituto di Struttura della Materia, CNR, Via del Fosso del Cavaliere 100, 00133, Roma, Italy
| | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
- Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, U.K
| | - Francesco S Ruggeri
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
- Laboratory of Organic Chemistry, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
- Laboratory of Physical Chemistry, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Giovanni Dietler
- Laboratory of Physics of Living Matter, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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Kawasaki T, Yamaguchi Y, Ueda T, Ishikawa Y, Yaji T, Ohta T, Tsukiyama K, Idehara T, Saiki M, Tani M. Irradiation effect of a submillimeter wave from 420 GHz gyrotron on amyloid peptides in vitro. BIOMEDICAL OPTICS EXPRESS 2020; 11:5341-5351. [PMID: 33014618 PMCID: PMC7510884 DOI: 10.1364/boe.395218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 08/07/2020] [Accepted: 08/07/2020] [Indexed: 06/11/2023]
Abstract
On using the far-infrared radiation system, whether the irradiation effect is thermal or non-thermal is controversial. We irradiated amyloid peptides that are causal factors for amyloidosis by using a submillimeter wave from 420 GHz gyrotron. Fluorescence reagent assay, optical and electron microscopies, and synchrotron-radiation infrared microscopy showed that the irradiation increased the fibrous conformation of peptides at room temperature for 30 min. The temperature increase on the sample was only below 5 K, and a simple heating up to 318 K hardly induced the fibril formation. Therefore, the amyloid aggregation was driven by the far-infrared radiation with little thermal effect.
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Affiliation(s)
- Takayasu Kawasaki
- IR-FEL Research Center, Research Institute for Science and Technology, Organization for Research Advancement, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Yuusuke Yamaguchi
- Research Center for Development of Far-Infrared Region, University of Fukui, 3-9-1 Bunkyo, Fukui, Fukui 910-8507, Japan
| | - Tomomi Ueda
- Department of Applied Chemistry, Faculty of Engineering, Sanyo-Onoda City University, 1-1-1 Daigakudori, Sanyo-Onoda, Yamaguchi 756-0884, Japan
| | - Yuya Ishikawa
- Research Center for Development of Far-Infrared Region, University of Fukui, 3-9-1 Bunkyo, Fukui, Fukui 910-8507, Japan
| | - Toyonari Yaji
- SR Center, Research Organization of Science and Technology, Ritsumeikan University, 1-1-1 Noji-Higasi, Kusatsu, Shiga 525-8577, Japan
| | - Toshiaki Ohta
- SR Center, Research Organization of Science and Technology, Ritsumeikan University, 1-1-1 Noji-Higasi, Kusatsu, Shiga 525-8577, Japan
| | - Koichi Tsukiyama
- IR-FEL Research Center, Research Institute for Science and Technology, Organization for Research Advancement, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Toshitaka Idehara
- Research Center for Development of Far-Infrared Region, University of Fukui, 3-9-1 Bunkyo, Fukui, Fukui 910-8507, Japan
| | - Masatoshi Saiki
- Department of Applied Chemistry, Faculty of Engineering, Sanyo-Onoda City University, 1-1-1 Daigakudori, Sanyo-Onoda, Yamaguchi 756-0884, Japan
| | - Masahiko Tani
- Research Center for Development of Far-Infrared Region, University of Fukui, 3-9-1 Bunkyo, Fukui, Fukui 910-8507, Japan
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Bousset L, Luckgei N, Kabani M, Gardiennet C, Schütz AK, Melki R, Meier BH, Böckmann A. Prion Amyloid Polymorphs - The Tag Might Change It All. Front Mol Biosci 2020; 7:190. [PMID: 32850974 PMCID: PMC7423878 DOI: 10.3389/fmolb.2020.00190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/20/2020] [Indexed: 11/13/2022] Open
Abstract
Sup35p is a protein from Saccharomyces cerevisiae. It can propagate using a prion-like mechanism, which means that it can recruit non-prion soluble Sup35p into insoluble fibrils. Sup35p is a large protein showing three distinct domains, N, M and an extended globular domain. We have previously studied the conformations of the full-length and truncated NM versions carrying poly-histidine tags on the N-terminus. Comparison with structural data from C-terminally poly-histidine tagged NM from the literature surprisingly revealed discrepancies. Here we investigated fibrils from the untagged, as well as a C-terminally poly-histidine tagged NM construct, using solid-state NMR. We find that the conformation of untagged NM is very close to the N-terminally tagged NM and confirms our previous findings. The C-terminal poly-histidine tag, in contrast, drastically changes the NM fibril structure, and yields data consistent with results obtained previously on this construct. We conclude that the C-terminally located Sup35p globular domain influences the structure of the fibrillar core at the N domain, as previously shown. We further conclude, based on the present data, that small tags on NM C-terminus have a substantial, despite different, impact. Modifications at this remote localization thus shows an unexpected influence on the fibril structure, and importantly also its propensity to induce [PSI+].
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Affiliation(s)
- Luc Bousset
- Institut Francois Jacob (MIRCen), CEA and Laboratory of Neurodegenerative Diseases, CNRS, Fontenay-aux-Roses, France
| | - Nina Luckgei
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS, Universite de Lyon, Lyon, France
| | - Mehdi Kabani
- Institut Francois Jacob (MIRCen), CEA and Laboratory of Neurodegenerative Diseases, CNRS, Fontenay-aux-Roses, France
| | - Carole Gardiennet
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS, Universite de Lyon, Lyon, France
| | - Anne K Schütz
- ETH Zürich, Laboratory of Physical Chemistry, Zurich, Switzerland
| | - Ronald Melki
- Institut Francois Jacob (MIRCen), CEA and Laboratory of Neurodegenerative Diseases, CNRS, Fontenay-aux-Roses, France
| | - Beat H Meier
- ETH Zürich, Laboratory of Physical Chemistry, Zurich, Switzerland
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS, Universite de Lyon, Lyon, France
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12
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Boatz JC, Piretra T, Lasorsa A, Matlahov I, Conway JF, van der Wel PCA. Protofilament Structure and Supramolecular Polymorphism of Aggregated Mutant Huntingtin Exon 1. J Mol Biol 2020; 432:4722-4744. [PMID: 32598938 DOI: 10.1016/j.jmb.2020.06.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 06/01/2020] [Accepted: 06/18/2020] [Indexed: 12/11/2022]
Abstract
Huntington's disease is a progressive neurodegenerative disease caused by expansion of the polyglutamine domain in the first exon of huntingtin (HttEx1). The extent of expansion correlates with disease progression and formation of amyloid-like protein deposits within the brain. The latter display polymorphism at the microscopic level, both in cerebral tissue and in vitro. Such polymorphism can dramatically influence cytotoxicity, leading to much interest in the conditions and mechanisms that dictate the formation of polymorphs. We examine conditions that govern HttEx1 polymorphism in vitro, including concentration and the role of the non-polyglutamine flanking domains. Using electron microscopy, we observe polymorphs that differ in width and tendency for higher-order bundling. Strikingly, aggregation yields different polymorphs at low and high concentrations. Narrow filaments dominate at low concentrations that may be more relevant in vivo. We dissect the role of N- and C-terminal flanking domains using protein with the former (httNT or N17) largely removed. The truncated protein is generated by trypsin cleavage of soluble HttEx1 fusion protein, which we analyze in some detail. Dye binding and solid-state NMR studies reveal changes in fibril surface characteristics and flanking domain mobility. Higher-order interactions appear facilitated by the C-terminal tail, while the polyglutamine forms an amyloid core resembling those of other polyglutamine deposits. Fibril-surface-mediated branching, previously attributed to secondary nucleation, is reduced in absence of httNT. A new model for the architecture of the HttEx1 filaments is presented and discussed in context of the assembly mechanism and biological activity.
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Affiliation(s)
- Jennifer C Boatz
- Department of Structural Biology, School of Medicine, University of Pittsburgh, 3501 5th Ave, Biomedical Science Tower 3, Pittsburgh, PA 15213, USA.
| | - Talia Piretra
- Department of Structural Biology, School of Medicine, University of Pittsburgh, 3501 5th Ave, Biomedical Science Tower 3, Pittsburgh, PA 15213, USA.
| | - Alessia Lasorsa
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, the Netherlands.
| | - Irina Matlahov
- Department of Structural Biology, School of Medicine, University of Pittsburgh, 3501 5th Ave, Biomedical Science Tower 3, Pittsburgh, PA 15213, USA; Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, the Netherlands.
| | - James F Conway
- Department of Structural Biology, School of Medicine, University of Pittsburgh, 3501 5th Ave, Biomedical Science Tower 3, Pittsburgh, PA 15213, USA.
| | - Patrick C A van der Wel
- Department of Structural Biology, School of Medicine, University of Pittsburgh, 3501 5th Ave, Biomedical Science Tower 3, Pittsburgh, PA 15213, USA; Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, the Netherlands.
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13
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Wong KM, Wang Y, Seroski DT, Larkin GE, Mehta AK, Hudalla GA, Hall CK, Paravastu AK. Molecular complementarity and structural heterogeneity within co-assembled peptide β-sheet nanofibers. NANOSCALE 2020; 12:4506-4518. [PMID: 32039428 DOI: 10.1039/c9nr08725g] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Self-assembling peptides have garnered an increasing amount of interest as a functional biomaterial for medical and biotechnological applications. Recently, β-sheet peptide designs utilizing complementary pairs of peptides composed of charged amino acids positioned to impart co-assembly behavior have expanded the portfolio of peptide aggregate structures. Structural characterization of these charge-complementary peptide co-assemblies has been limited. Thus, it is not known how the complementary peptides organize on the molecular level. Through a combination of solid-state NMR measurements and discontinuous molecular dynamics simulations, we investigate the molecular organization of King-Webb peptide nanofibers. KW+ and KW- peptides co-assemble into near stoichiometric two-component β-sheet structures as observed by computational simulations and 13C-13C dipolar couplings. A majority of β-strands are aligned with antiparallel nearest neighbors within the β-sheet as previously suggested by Fourier transform infrared spectroscopy measurements. Surprisingly, however, a significant proportion of β-strand neighbors are parallel. While charge-complementary peptides were previously assumed to organize in an ideal (AB)n pattern, dipolar recoupling measurements on isotopically diluted nanofiber samples reveal a non-negligible amount of self-associated (AA and BB) pairs. Furthermore, computational simulations predict these different structures can coexist within the same nanofiber. Our results highlight structural disorder at the molecular level in a charge-complementary peptide system with implications on co-assembling peptide designs.
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Affiliation(s)
- Kong M Wong
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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14
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Wu H, Saltzberg DJ, Kratochvil HT, Jo H, Sali A, DeGrado WF. Glutamine Side Chain 13C═ 18O as a Nonperturbative IR Probe of Amyloid Fibril Hydration and Assembly. J Am Chem Soc 2019; 141:7320-7326. [PMID: 30998340 DOI: 10.1021/jacs.9b00577] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Infrared (IR) spectroscopy has provided considerable insight into the structures, dynamics, and formation mechanisms of amyloid fibrils. IR probes, such as main chain 13C═18O, have been widely employed to obtain site-specific structural information, yet only secondary structures and strand-to-strand arrangements can be probed. Very few nonperturbative IR probes are available to report on the side-chain conformation and environments, which are critical to determining sheet-to-sheet arrangements in steric zippers within amyloids. Polar residues, such as glutamine, contribute significantly to the stability of amyloids and thus are frequently found in core regions of amyloid peptides/proteins. Furthermore, polyglutamine (polyQ) repeats form toxic aggregates in several neurodegenerative diseases. Here we report the synthesis and application of a new nonperturbative IR probe-glutamine side chain 13C═18O. We use side chain 13C═18O labeling and isotope dilution to detect the presence of intermolecularly hydrogen-bonded arrays of glutamine side chains (Gln ladders) in amyloid-forming peptides. Moreover, the line width of the 13C═18O peak is highly sensitive to its local hydration environment. The IR data from side chain labeling allows us to unambiguously determine the sheet-to-sheet arrangement in a short amyloid-forming peptide, GNNQQNY, providing insight that was otherwise inaccessible through main chain labeling. With several different fibril samples, we also show the versatility of this IR probe in studying the structures and aggregation kinetics of amyloids. Finally, we demonstrate the capability of modeling amyloid structures with IR data using the integrative modeling platform (IMP) and the potential of integrating IR with other biophysical methods for more accurate structural modeling. Together, we believe that side chain 13C═18O will complement main chain isotope labeling in future IR studies of amyloids and integrative modeling using IR data will significantly expand the power of IR spectroscopy to elucidate amyloid assemblies.
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15
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Amino acid conformations control the morphological and chiral features of the self-assembled peptide nanostructures: Young investigators perspective. J Colloid Interface Sci 2019; 548:244-254. [PMID: 31004957 DOI: 10.1016/j.jcis.2019.04.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 04/03/2019] [Accepted: 04/05/2019] [Indexed: 01/11/2023]
Abstract
HYPOTHESIS A variety of nanostructures with different chiral features can be self-assembled from short peptides with highly similar sequences. We hypothesize that these supramolecular nanostructures are ruled by the constituent amino acid residues which adopt their conformations under the influence of intra-/inter-molecular interactions during peptide self-assembly. APPROACH Through reviewing recent advances in the self-assembly of short peptides and focusing on the relationship between amino acid conformations, peptide secondary structures and intra-/inter-molecular interactions within the supramolecular architectures, we aim to rationalize the complex interactive processes involved in the self-assembly of short, designed peptides. RESULTS Given the highly complexing interactive processes, the adoption of amino acid conformations and their control over peptide self-assembly consist of 4 main steps: (1) Each amino acid residue adopts its unique conformation in a specific sequence; (2) The sequence exhibits its own main chain geometry and determines the propensity of the intermolecular alignment within the building block; (3) The structural propensity of the building block and the packing mode between them determine the self-assembled structural features such as twisting, growth and chirality; (4) In addition to intra-/inter-molecular interactions, inter-sheet and inter-building block interactions could also affect the residue conformations and nanostructures, causing structural readjustment.
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16
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Nassar R, Wong E, Bui JM, Yip CK, Li H, Gsponer J, Lamour G. Mechanical Anisotropy in GNNQQNY Amyloid Crystals. J Phys Chem Lett 2018; 9:4901-4909. [PMID: 30102541 DOI: 10.1021/acs.jpclett.8b02027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Mapping the nanomechanical properties of amyloids can provide valuable insights into structure and assembly mechanisms of protein aggregates that underlie the development of various human diseases. Although it is well-known that amyloids exhibit an intrinsic stiffness comparable to that of silk (1-10 GPa), a detailed understanding of the directional dependence (anisotropy) of the stiffness of amyloids and how it relates to structural features in these protein aggregates is missing. Here we used steered molecular dynamics (SMD) simulations and amplitude modulation-frequency modulation (AM-FM) atomic force microscopy to measure the directional variation in stiffness of GNNQQNY amyloid crystals. We reveal that individual crystals display significant mechanical anisotropy and relate this anisotropy to subtle but mechanically important differences in interactions between interfaces that define the crystal architecture. Our results provide detailed insights into the structure-mechanics relationship of amyloid that may help in designing amyloid-based nanomaterials with tailored mechanical properties.
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Affiliation(s)
- Roy Nassar
- Michael Smith Laboratories , The University of British Colombia , Vancouver , BC Canada V6T 1Z4
- Department of Biochemistry & Molecular Biology , The University of British Colombia , Vancouver , BC Canada V6T 1Z3
| | - Eric Wong
- Michael Smith Laboratories , The University of British Colombia , Vancouver , BC Canada V6T 1Z4
- Department of Biochemistry & Molecular Biology , The University of British Colombia , Vancouver , BC Canada V6T 1Z3
| | - Jennifer M Bui
- Michael Smith Laboratories , The University of British Colombia , Vancouver , BC Canada V6T 1Z4
- Department of Biochemistry & Molecular Biology , The University of British Colombia , Vancouver , BC Canada V6T 1Z3
| | - Calvin K Yip
- Department of Biochemistry & Molecular Biology , The University of British Colombia , Vancouver , BC Canada V6T 1Z3
| | - Hongbin Li
- Department of Chemistry , The University of British Columbia , Vancouver , BC Canada V6T 1Z1
| | - Jörg Gsponer
- Michael Smith Laboratories , The University of British Colombia , Vancouver , BC Canada V6T 1Z4
- Department of Biochemistry & Molecular Biology , The University of British Colombia , Vancouver , BC Canada V6T 1Z3
| | - Guillaume Lamour
- Michael Smith Laboratories , The University of British Colombia , Vancouver , BC Canada V6T 1Z4
- Department of Biochemistry & Molecular Biology , The University of British Colombia , Vancouver , BC Canada V6T 1Z3
- Department of Chemistry , The University of British Columbia , Vancouver , BC Canada V6T 1Z1
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17
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Adamcik J, Mezzenga R. Amyloid Polymorphism in the Protein Folding and Aggregation Energy Landscape. Angew Chem Int Ed Engl 2018; 57:8370-8382. [DOI: 10.1002/anie.201713416] [Citation(s) in RCA: 150] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Indexed: 12/30/2022]
Affiliation(s)
- Jozef Adamcik
- Department of Health Sciences & Technology ETH Zurich Schmelzbergstrasse 9 8092 Zurich Switzerland
| | - Raffaele Mezzenga
- Department of Health Sciences & Technology ETH Zurich Schmelzbergstrasse 9 8092 Zurich Switzerland
- Department of Materials ETH Zurich Wolfgang-Pauli-Strasse 10 8093 Zurich Switzerland
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18
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Adamcik J, Mezzenga R. Amyloid‐Polymorphie in der Energielandschaft der Faltung und Aggregation von Proteinen. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201713416] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Jozef Adamcik
- Departement Gesundheitswissenschaften und Technologie ETH Zürich Schmelzbergstrasse 9 8092 Zürich Schweiz
| | - Raffaele Mezzenga
- Departement Gesundheitswissenschaften und Technologie ETH Zürich Schmelzbergstrasse 9 8092 Zürich Schweiz
- Departement Materialwissenschaft ETH Zürich Wolfgang-Pauli-Strasse 10 8093 Zürich Schweiz
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19
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Matlahov I, van der Wel PCA. Hidden motions and motion-induced invisibility: Dynamics-based spectral editing in solid-state NMR. Methods 2018; 148:123-135. [PMID: 29702226 DOI: 10.1016/j.ymeth.2018.04.015] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/05/2018] [Accepted: 04/16/2018] [Indexed: 10/17/2022] Open
Abstract
Solid-state nuclear magnetic resonance (ssNMR) spectroscopy enables the structural characterization of a diverse array of biological assemblies that include amyloid fibrils, non-amyloid aggregates, membrane-associated proteins and viral capsids. Such biological samples feature functionally relevant molecular dynamics, which often affect different parts of the sample in different ways. Solid-state NMR experiments' sensitivity to dynamics represents a double-edged sword. On the one hand, it offers a chance to measure dynamics in great detail. On the other hand, certain types of motion lead to signal loss and experimental inefficiencies that at first glance interfere with the application of ssNMR to overly dynamic proteins. Dynamics-based spectral editing (DYSE) ssNMR methods leverage motion-dependent signal losses to simplify spectra and enable the study of sub-structures with particular motional properties.
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Affiliation(s)
- Irina Matlahov
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15213, USA
| | - Patrick C A van der Wel
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA 15213, USA; Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
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20
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Periole X, Huber T, Bonito-Oliva A, Aberg KC, van der Wel PCA, Sakmar TP, Marrink SJ. Energetics Underlying Twist Polymorphisms in Amyloid Fibrils. J Phys Chem B 2018; 122:1081-1091. [PMID: 29254334 PMCID: PMC5857390 DOI: 10.1021/acs.jpcb.7b10233] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Amyloid fibrils are highly ordered protein aggregates associated with more than 40 human diseases. The exact conditions under which the fibrils are grown determine many types of reported fibril polymorphism, including different twist patterns. Twist-based polymorphs display unique mechanical properties in vitro, and the relevance of twist polymorphism in amyloid diseases has been suggested. We present transmission electron microscopy images of Aβ42-derived (amyloid β) fibrils, which are associated with Alzheimer's disease, demonstrating the presence of twist variability even within a single long fibril. To better understand the molecular underpinnings of twist polymorphism, we present a structural and thermodynamics analysis of molecular dynamics simulations of the twisting of β-sheet protofilaments of a well-characterized cross-β model: the GNNQQNY peptide from the yeast prion Sup35. The results show that a protofilament model of GNNQQNY is able to adopt twist angles from -11° on the left-hand side to +8° on the right-hand side in response to various external conditions, keeping an unchanged peptide structure. The potential of mean force (PMF) of this cross-β structure upon twisting revealed that only ∼2kBT per peptide are needed to stabilize a straight conformation with respect to the left-handed free-energy minimum. The PMF also shows that the canonical structural core of β-sheets, i.e., the hydrogen-bonded backbone β-strands, favors the straight conformation. However, the concerted effects of the side chains contribute to twisting, which provides a rationale to correlate polypeptide sequence, environmental growth conditions and number of protofilaments in a fibril with twist polymorphisms.
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Affiliation(s)
- Xavier Periole
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Groningen 9747 AG, The Netherlands
| | - Thomas Huber
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University , 1230 York Avenue, New York, New York 10065, United States
| | - Alessandra Bonito-Oliva
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University , 1230 York Avenue, New York, New York 10065, United States
| | - Karina C Aberg
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University , 1230 York Avenue, New York, New York 10065, United States
| | - Patrick C A van der Wel
- Department of Structural Biology and Center for Protein Conformational Diseases, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania 15260, United States
| | - Thomas P Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University , 1230 York Avenue, New York, New York 10065, United States
- Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Karolinska Institutet , 141 57 Huddinge, Sweden
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Groningen 9747 AG, The Netherlands
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21
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Huang D, Hudson BC, Gao Y, Roberts EK, Paravastu AK. Solid-State NMR Structural Characterization of Self-Assembled Peptides with Selective 13C and 15N Isotopic Labels. Methods Mol Biol 2018; 1777:23-68. [PMID: 29744827 PMCID: PMC7490753 DOI: 10.1007/978-1-4939-7811-3_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
For the structural characterization methods discussed here, information on molecular conformation and intermolecular organization within nanostructured peptide assemblies is discerned through analysis of solid-state NMR spectral features. This chapter reviews general NMR methodologies, requirements for sample preparation, and specific descriptions of key experiments. An attempt is made to explain choices of solid-state NMR experiments and interpretation of results in a way that is approachable to a nonspecialist. Measurements are designed to determine precise NMR peak positions and line widths, which are correlated with secondary structures, and probe nuclear spin-spin interactions that report on three-dimensional organization of atoms. The formulation of molecular structural models requires rationalization of data sets obtained from multiple NMR experiments on samples with carefully chosen 13C and 15N isotopic labels. The information content of solid-state NMR data has been illustrated mostly through the use of simulated data sets and references to recent structural work on amyloid fibril-forming peptides and designer self-assembling peptides.
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Affiliation(s)
- Danting Huang
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Benjamin C Hudson
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Yuan Gao
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Evan K Roberts
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Anant K Paravastu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
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22
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Reynolds NP, Adamcik J, Berryman JT, Handschin S, Zanjani AAH, Li W, Liu K, Zhang A, Mezzenga R. Competition between crystal and fibril formation in molecular mutations of amyloidogenic peptides. Nat Commun 2017; 8:1338. [PMID: 29109399 PMCID: PMC5673901 DOI: 10.1038/s41467-017-01424-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 09/12/2017] [Indexed: 12/18/2022] Open
Abstract
Amyloidogenic model peptides are invaluable for investigating assembly mechanisms in disease related amyloids and in protein folding. During aggregation, such peptides can undergo bifurcation leading to fibrils or crystals, however the mechanisms of fibril-to-crystal conversion are unclear. We navigate herein the energy landscape of amyloidogenic peptides by studying a homologous series of hexapeptides found in animal, human and disease related proteins. We observe fibril-to-crystal conversion occurring within single aggregates via untwisting of twisted ribbon fibrils possessing saddle-like curvature and cross-sectional aspect ratios approaching unity. Changing sequence, pH or concentration shifts the growth towards larger aspect ratio species assembling into stable helical ribbons possessing mean-curvature. By comparing atomistic calculations of desolvation energies for association of peptides we parameterise a kinetic model, providing a physical explanation of fibril-to-crystal interconversion. These results shed light on the self-assembly of amyloidogenic peptides, suggesting amyloid crystals, not fibrils, represent the ground state of the protein folding energy landscape. Aggregation of amyloidogenic peptides into fibrils and crystals has incidence in several amyloid-related diseases. Here, the authors investigate the origins of the fibril-to-crystal conversion in amyloidogenic hexapeptides pointing to the amyloid crystals as the ground state in the protein folding energy landscape.
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Affiliation(s)
- Nicholas P Reynolds
- Swinburne University of Technology, ARC Training Centre for Biodevices, Faculty of Science, Engineering and Technology, John Street, Melbourne, VIC, 3122, Australia
| | - Jozef Adamcik
- ETH Zurich, Department of Health Sciences & Technology, Schmelzbergstrasse 9, LFO, E23, 8092, Zürich, Switzerland
| | - Joshua T Berryman
- University of Luxembourg, Department of Physics and Materials Science, 162a Avenue de la Faïencerie, Luxembourg City, L-1511, Luxembourg
| | - Stephan Handschin
- ETH Zurich, Department of Health Sciences & Technology, Schmelzbergstrasse 9, LFO, E23, 8092, Zürich, Switzerland
| | - Ali Asghar Hakami Zanjani
- University of Luxembourg, Department of Physics and Materials Science, 162a Avenue de la Faïencerie, Luxembourg City, L-1511, Luxembourg
| | - Wen Li
- Shanghai University, Department of Polymer Materials, Nanchen Street 333, Shanghai, 200444, China
| | - Kun Liu
- Shanghai University, Department of Polymer Materials, Nanchen Street 333, Shanghai, 200444, China
| | - Afang Zhang
- Shanghai University, Department of Polymer Materials, Nanchen Street 333, Shanghai, 200444, China
| | - Raffaele Mezzenga
- ETH Zurich, Department of Health Sciences & Technology, Schmelzbergstrasse 9, LFO, E23, 8092, Zürich, Switzerland. .,ETH Zurich, Department of Materials, Wolfgang-Pauli-Strasse 10, 8093, Zurich, Switzerland.
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23
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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: 44] [Impact Index Per Article: 6.3] [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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24
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Cremades N, Dobson CM. The contribution of biophysical and structural studies of protein self-assembly to the design of therapeutic strategies for amyloid diseases. Neurobiol Dis 2017; 109:178-190. [PMID: 28709995 DOI: 10.1016/j.nbd.2017.07.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 06/26/2017] [Accepted: 07/10/2017] [Indexed: 01/26/2023] Open
Abstract
Many neurodegenerative disorders, including Alzheimer's, Parkinson's and the prion diseases, are characterized by a conformational conversion of normally soluble proteins or peptides into pathological species, by a process of misfolding and self-assembly that leads ultimately to the formation of amyloid fibrils. Recent studies support the idea that multiple intermediate species with a wide variety of degrees of neuronal toxicity are generated during such processes. The development of a high level of knowledge of the nature and structure of the pathogenic amyloid species would significantly enhance efforts to underline the molecular origins of these disorders and also to develop both accurate diagnoses and effective therapeutic interventions for these types of conditions. In this review, we discuss recent biophysical and structural information concerning different types of amyloid aggregates and the way in which such information can guide rational therapeutic approaches designed to target specific pathogenic events that occur during the development of these highly debilitating and increasingly common diseases.
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Affiliation(s)
- Nunilo Cremades
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Unit BIFI-IQFR(CSIC), Universidad de Zaragoza, Zaragoza 50018, Spain.
| | - Christopher M Dobson
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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25
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Cieślik-Boczula K. Alpha-helix to beta-sheet transition in long-chain poly-l-lysine: Formation of alpha-helical fibrils by poly-l-lysine. Biochimie 2017; 137:106-114. [PMID: 28315381 DOI: 10.1016/j.biochi.2017.03.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 03/12/2017] [Indexed: 01/06/2023]
Abstract
The temperature-induced α-helix to β-sheet transition in long-chain poly-l-lysine (PLL), accompanied by the gauche-to-trans isomerization of CH2 groups in the hydrocarbon side chains of Lys amino acid residues, and formation of β-sheet as well as α-helix fibrillar aggregates of PLL have been studied using Fourier-transform infrared (FT-IR) and vibrational circular dichroism (VCD) spectroscopy, and transmission electron microscopy (TEM). In a low-temperature alkaline water solution or in a methanol-rich water mixture, the secondary structure of PLL is represented by α-helical conformations with unordered and gauche-rich hydrocarbon side chains. Under these conditions, PLL molecules aggregate into α-helical fibrils. PLLs dominated by extended antiparallel β-sheet structures with highly ordered trans-rich hydrocarbon side chains are formed in a high-temperature range at alkaline pD and aggregate into fibrillar, protofibrillar, and spherical forms. Presented data support the idea that fibrillar aggregation is a varied phenomenon possible in repetitive structural elements with not only a β-sheet-rich conformation, but also an α-helical-rich conformation.
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26
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Disaggregation of Amylin Aggregate by Novel Conformationally Restricted Aminobenzoic Acid containing α/β and α/γ Hybrid Peptidomimetics. Sci Rep 2017; 7:40095. [PMID: 28054630 PMCID: PMC5214534 DOI: 10.1038/srep40095] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 12/01/2016] [Indexed: 11/24/2022] Open
Abstract
Diabetes has emerged as a threat to the current world. More than ninety five per cent of all the diabetic population has type 2 diabetes mellitus (T2DM). Aggregates of Amylin hormone, which is co-secreted with insulin from the pancreatic β-cells, inhibit the activities of insulin and glucagon and cause T2DM. Importance of the conformationally restricted peptides for drug design against T2DM has been invigorated by recent FDA approval of Symlin, which is a large conformationally restricted peptide. However, Symlin still has some issues including solubility, oral bioavailability and cost of preparation. Herein, we introduced a novel strategy for conformationally restricted peptide design adopting a minimalistic approach for cost reduction. We have demonstrated efficient inhibition of amyloid formation of Amylin and its disruption by a novel class of conformationally restricted β-sheet breaker hybrid peptidomimetics (BSBHps). We have inserted β, γ and δ -aminobenzoic acid separately into an amyloidogenic peptide sequence, synthesized α/β, α/γ and α/δ hybrid peptidomimetics, respectively. Interestingly, we observed the aggregation inhibitory efficacy of α/β and α/γ BSBHps, but not of α/δ analogues. They also disrupt existing amyloids into non-toxic forms. Results may be useful for newer drug design against T2DM as well as other amyloidoses and understanding amyloidogenesis.
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27
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Lei J, Qi R, Xie L, Xi W, Wei G. Inhibitory effect of hydrophobic fullerenes on the β-sheet-rich oligomers of a hydrophilic GNNQQNY peptide revealed by atomistic simulations. RSC Adv 2017. [DOI: 10.1039/c6ra27608c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Fullerenes suppress fibril-like β-sheet oligomers by interacting strongly with the nonpolar aliphatic groups of polar residues of GNNQQNY peptide, thus inhibit peptide aggregation.
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Affiliation(s)
- Jiangtao Lei
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education)
- Department of Physics
- Fudan University
- Shanghai
| | - Ruxi Qi
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education)
- Department of Physics
- Fudan University
- Shanghai
| | - Luogang Xie
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education)
- Department of Physics
- Fudan University
- Shanghai
| | - Wenhui Xi
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education)
- Department of Physics
- Fudan University
- Shanghai
| | - Guanghong Wei
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education)
- Department of Physics
- Fudan University
- Shanghai
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28
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Quinn CM, Polenova T. Structural biology of supramolecular assemblies by magic-angle spinning NMR spectroscopy. Q Rev Biophys 2017; 50:e1. [PMID: 28093096 PMCID: PMC5483179 DOI: 10.1017/s0033583516000159] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In recent years, exciting developments in instrument technology and experimental methodology have advanced the field of magic-angle spinning (MAS) nuclear magnetic resonance (NMR) to new heights. Contemporary MAS NMR yields atomic-level insights into structure and dynamics of an astounding range of biological systems, many of which cannot be studied by other methods. With the advent of fast MAS, proton detection, and novel pulse sequences, large supramolecular assemblies, such as cytoskeletal proteins and intact viruses, are now accessible for detailed analysis. In this review, we will discuss the current MAS NMR methodologies that enable characterization of complex biomolecular systems and will present examples of applications to several classes of assemblies comprising bacterial and mammalian cytoskeleton as well as human immunodeficiency virus 1 and bacteriophage viruses. The body of work reviewed herein is representative of the recent advancements in the field, with respect to the complexity of the systems studied, the quality of the data, and the significance to the biology.
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Affiliation(s)
- Caitlin M. Quinn
- University of Delaware, Department of Chemistry and Biochemistry, Newark, DE 19711; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15306
| | - Tatyana Polenova
- University of Delaware, Department of Chemistry and Biochemistry, Newark, DE 19711; Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15306
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29
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Vugmeyster L, Ostrovsky D, Clark MA, Falconer IB, Hoatson GL, Qiang W. Fast Motions of Key Methyl Groups in Amyloid-β Fibrils. Biophys J 2016; 111:2135-2148. [PMID: 27851938 PMCID: PMC5113154 DOI: 10.1016/j.bpj.2016.10.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/18/2016] [Accepted: 10/05/2016] [Indexed: 11/28/2022] Open
Abstract
Amyloid-β (Aβ) peptide is the major component of plaques found in Alzheimer's disease patients. Using solid-state 2H NMR relaxation performed on selectively deuterated methyl groups, we probed the dynamics in the threefold symmetric and twofold symmetric polymorphs of native Aβ as well as the protofibrils of the D23N mutant. Specifically, we investigated the methyl groups of two leucine residues that belong to the hydrophobic core (L17 and L34) as well as M35 residues belonging to the hydrophobic interface between the cross-β subunits, which has been previously found to be water-accessible. Relaxation measurements performed over 310-140 K and two magnetic field strengths provide insights into conformational variability within and between polymorphs. Core packing variations within a single polymorph are similar to what is observed for globular proteins for the core residues, whereas M35 exhibits a larger degree of variability. M35 site is also shown to undergo a solvent-dependent dynamical transition in which slower amplitude motions of methyl axes are activated at high temperature. The motions, modeled as a diffusion of methyl axis, have activation energy by a factor of 2.7 larger in the twofold compared with the threefold polymorph, whereas D23N protofibrils display a value similar to the threefold polymorph. This suggests enhanced flexibility of the hydrophobic interface in the threefold polymorph. This difference is only observed in the hydrated state and is absent in the dry fibrils, highlighting the role of solvent at the cavity. In contrast, the dynamic behavior of the core is hydration-independent.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado at Denver, Denver, Colorado.
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado at Denver, Denver, Colorado
| | - Matthew A Clark
- Department of Chemistry, University of Alaska Anchorage, Anchorage, Alaska
| | - Isaac B Falconer
- Department of Chemistry, University of Colorado at Denver, Denver, Colorado
| | - Gina L Hoatson
- Department of Physics, College of William and Mary, Williamsburg, Virginia
| | - Wei Qiang
- Department of Chemistry, Binghamton University, Binghamton, New York
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30
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Matthes D, Gapsys V, Brennecke JT, de Groot BL. An Atomistic View of Amyloidogenic Self-assembly: Structure and Dynamics of Heterogeneous Conformational States in the Pre-nucleation Phase. Sci Rep 2016; 6:33156. [PMID: 27616019 PMCID: PMC5018807 DOI: 10.1038/srep33156] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/22/2016] [Indexed: 01/01/2023] Open
Abstract
The formation of well-defined filamentous amyloid structures involves a polydisperse collection of oligomeric states for which relatively little is known in terms of structural organization. Here we use extensive, unbiased explicit solvent molecular dynamics (MD) simulations to investigate the structural and dynamical features of oligomeric aggregates formed by a number of highly amyloidogenic peptides at atomistic resolution on the μs time scale. A consensus approach has been adopted to analyse the simulations in multiple force fields, yielding an in-depth characterization of pre-fibrillar oligomers and their global and local structure properties. A collision cross section analysis revealed structurally heterogeneous aggregate ensembles for the individual oligomeric states that lack a single defined quaternary structure during the pre-nucleation phase. To gain insight into the conformational space sampled in early aggregates, we probed their substructure and found emerging β-sheet subunit layers and a multitude of ordered intermolecular β-structure motifs with growing aggregate size. Among those, anti-parallel out-of-register β-strands compatible with toxic β-barrel oligomers were particularly prevalent already in smaller aggregates and formed prior to ordered fibrillar structure elements. Notably, also distinct fibril-like conformations emerged in the oligomeric state and underscore the notion that pre-nucleated oligomers serve as a critical intermediate step on-pathway to fibrils.
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Affiliation(s)
- Dirk Matthes
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Vytautas Gapsys
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Julian T Brennecke
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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31
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Structural Characterization of Fibrils from Recombinant Human Islet Amyloid Polypeptide by Solid-State NMR: The Central FGAILS Segment Is Part of the β-Sheet Core. PLoS One 2016; 11:e0161243. [PMID: 27607147 PMCID: PMC5015977 DOI: 10.1371/journal.pone.0161243] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 08/02/2016] [Indexed: 11/19/2022] Open
Abstract
Amyloid deposits formed from islet amyloid polypeptide (IAPP) are a hallmark of type 2 diabetes mellitus and are known to be cytotoxic to pancreatic β-cells. The molecular structure of the fibrillar form of IAPP is subject of intense research, and to date, different models exist. We present results of solid-state NMR experiments on fibrils of recombinantly expressed and uniformly 13C, 15N-labeled human IAPP in the non-amidated, free acid form. Complete sequential resonance assignments and resulting constraints on secondary structure are shown. A single set of chemical shifts is found for most residues, which is indicative of a high degree of homogeneity. The core region comprises three to four β-sheets. We find that the central 23-FGAILS-28 segment, which is of critical importance for amyloid formation, is part of the core region and forms a β-strand in our sample preparation. The eight N-terminal amino acid residues of IAPP, forming a ring-like structure due to a disulfide bridge between residues C2 and C7, appear to be well defined but with an increased degree of flexibility. This study supports the elucidation of the structural basis of IAPP amyloid formation and highlights the extent of amyloid fibril polymorphism.
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32
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Vugmeyster L, Clark MA, Falconer IB, Ostrovsky D, Gantz D, Qiang W, Hoatson GL. Flexibility and Solvation of Amyloid-β Hydrophobic Core. J Biol Chem 2016; 291:18484-95. [PMID: 27402826 DOI: 10.1074/jbc.m116.740530] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Indexed: 11/06/2022] Open
Abstract
Amyloid fibril deposits found in Alzheimer disease patients are composed of amyloid-β (Aβ) protein forming a number of hydrophobic interfaces that are believed to be mostly rigid. We have investigated the μs-ms time-scale dynamics of the intra-strand hydrophobic core and interfaces of the fibrils composed of Aβ1-40 protein. Using solid-state (2)H NMR line shape experiments performed on selectively deuterated methyl groups, we probed the 3-fold symmetric and 2-fold symmetric polymorphs of native Aβ as well as the protofibrils of D23N Iowa mutant, associated with an early onset of Alzheimer disease. The dynamics of the hydrophobic regions probed at Leu-17, Leu-34, Val-36, and Met-35 side chains were found to be very pronounced at all sites and in all polymorphs of Aβ, with methyl axis motions persisting down to 230-200 K for most of the sites. The dominant mode of motions is the rotameric side chain jumps, with the Met-35 displaying the most complex multi-modal behavior. There are distinct differences in the dynamics among the three protein variants, with the Val-36 site displaying the most variability. Solvation of the fibrils does not affect methyl group motions within the hydrophobic core of individual cross-β subunits but has a clear effect on the motions at the hydrophobic interface between the cross-β subunits, which is defined by Met-35 contacts. In particular, hydration activates transitions between additional rotameric states that are not sampled in the dry protein. Thus, these results support the existence of water-accessible cavity recently predicted by molecular dynamics simulations and suggested by cryo-EM studies.
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Affiliation(s)
| | | | | | | | - Donald Gantz
- Boston University School of Medicine, Boston, Massachusetts 02118
| | - Wei Qiang
- Binghamton University, Binghamton, New York 13902, and
| | - Gina L Hoatson
- College of William and Mary, Williamsburg, Virginia 23187
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33
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Wang S, Matsuda I, Long F, Ishii Y. Spectral editing at ultra-fast magic-angle-spinning in solid-state NMR: facilitating protein sequential signal assignment by HIGHLIGHT approach. JOURNAL OF BIOMOLECULAR NMR 2016; 64:131-141. [PMID: 26781951 DOI: 10.1007/s10858-016-0014-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 01/12/2016] [Indexed: 06/05/2023]
Abstract
This study demonstrates a novel spectral editing technique for protein solid-state NMR (SSNMR) to simplify the spectrum drastically and to reduce the ambiguity for protein main-chain signal assignments in fast magic-angle-spinning (MAS) conditions at a wide frequency range of 40-80 kHz. The approach termed HIGHLIGHT (Wang et al., in Chem Comm 51:15055-15058, 2015) combines the reverse (13)C, (15)N-isotope labeling strategy and selective signal quenching using the frequency-selective REDOR pulse sequence under fast MAS. The scheme allows one to selectively observe the signals of "highlighted" labeled amino-acid residues that precede or follow unlabeled residues through selectively quenching (13)CO or (15)N signals for a pair of consecutively labeled residues by recoupling (13)CO-(15)N dipolar couplings. Our numerical simulation results showed that the scheme yielded only ~15% loss of signals for the highlighted residues while quenching as much as ~90% of signals for non-highlighted residues. For lysine-reverse-labeled micro-crystalline GB1 protein, the 2D (15)N/(13)Cα correlation and 2D (13)Cα/(13)CO correlation SSNMR spectra by the HIGHLIGHT approach yielded signals only for six residues following and preceding the unlabeled lysine residues, respectively. The experimental dephasing curves agreed reasonably well with the corresponding simulation results for highlighted and quenched residues at spinning speeds of 40 and 60 kHz. The compatibility of the HIGHLIGHT approach with fast MAS allows for sensitivity enhancement by paramagnetic assisted data collection (PACC) and (1)H detection. We also discuss how the HIGHLIGHT approach facilitates signal assignments using (13)C-detected 3D SSNMR by demonstrating full sequential assignments of lysine-reverse-labeled micro-crystalline GB1 protein (~300 nmol), for which data collection required only 11 h. The HIGHLIGHT approach offers valuable means of signal assignments especially for larger proteins through reducing the number of resonance and clarifying multiple starting points in sequential assignment with enhanced sensitivity.
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Affiliation(s)
- Songlin Wang
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Isamu Matsuda
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Fei Long
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Yoshitaka Ishii
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA.
- Center for Structural Biology, University of Illinois at Chicago, Chicago, IL, 60607, USA.
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34
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Huntingtin exon 1 fibrils feature an interdigitated β-hairpin-based polyglutamine core. Proc Natl Acad Sci U S A 2016; 113:1546-51. [PMID: 26831073 DOI: 10.1073/pnas.1521933113] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Polyglutamine expansion within the exon1 of huntingtin leads to protein misfolding, aggregation, and cytotoxicity in Huntington's disease. This incurable neurodegenerative disease is the most prevalent member of a family of CAG repeat expansion disorders. Although mature exon1 fibrils are viable candidates for the toxic species, their molecular structure and how they form have remained poorly understood. Using advanced magic angle spinning solid-state NMR, we directly probe the structure of the rigid core that is at the heart of huntingtin exon1 fibrils and other polyglutamine aggregates, via measurements of long-range intramolecular and intermolecular contacts, backbone and side-chain torsion angles, relaxation measurements, and calculations of chemical shifts. These experiments reveal the presence of β-hairpin-containing β-sheets that are connected through interdigitating extended side chains. Despite dramatic differences in aggregation behavior, huntingtin exon1 fibrils and other polyglutamine-based aggregates contain identical β-strand-based cores. Prior structural models, derived from X-ray fiber diffraction and computational analyses, are shown to be inconsistent with the solid-state NMR results. Internally, the polyglutamine amyloid fibrils are coassembled from differently structured monomers, which we describe as a type of "intrinsic" polymorphism. A stochastic polyglutamine-specific aggregation mechanism is introduced to explain this phenomenon. We show that the aggregation of mutant huntingtin exon1 proceeds via an intramolecular collapse of the expanded polyglutamine domain and discuss the implications of this observation for our understanding of its misfolding and aggregation mechanisms.
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35
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Yoon G, Lee M, Kim K, In Kim J, Joon Chang H, Baek I, Eom K, Na S. Morphology and mechanical properties of multi-stranded amyloid fibrils probed by atomistic and coarse-grained simulations. Phys Biol 2015; 12:066021. [DOI: 10.1088/1478-3975/12/6/066021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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36
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Poloni C, Stuart MCA, van der Meulen P, Szymanski W, Feringa BL. Light and heat control over secondary structure and amyloid-like fiber formation in an overcrowded-alkene-modified Trp zipper. Chem Sci 2015; 6:7311-7318. [PMID: 28757990 PMCID: PMC5512536 DOI: 10.1039/c5sc02735g] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 09/18/2015] [Indexed: 12/14/2022] Open
Abstract
The external photocontrol over peptide folding, by the incorporation of molecular photoswitches into their structure, provides a powerful tool to study biological processes. However, it is limited so far to switches that exhibit only a rather limited geometrical change upon photoisomerization and that show thermal instability of the photoisomer. Here we describe the use of an overcrowded alkene photoswitch to control a model β-hairpin peptide. This photoresponsive unit undergoes a large conformational change and has two thermally stable isomers which has major influence on the secondary structure and the aggregation of the peptide, permitting the phototriggered formation of amyloid-like fibrils.
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Affiliation(s)
- Claudia Poloni
- Centre for Systems Chemistry , Stratingh Institute for Chemistry , Faculty of Mathematics and Natural Sciences , University of Groningen , Nijenborgh 4 , 9747AG Groningen , The Netherlands . ;
| | - Marc C A Stuart
- Centre for Systems Chemistry , Stratingh Institute for Chemistry , Faculty of Mathematics and Natural Sciences , University of Groningen , Nijenborgh 4 , 9747AG Groningen , The Netherlands . ;
| | - Pieter van der Meulen
- Centre for Systems Chemistry , Stratingh Institute for Chemistry , Faculty of Mathematics and Natural Sciences , University of Groningen , Nijenborgh 4 , 9747AG Groningen , The Netherlands . ;
| | - Wiktor Szymanski
- Centre for Systems Chemistry , Stratingh Institute for Chemistry , Faculty of Mathematics and Natural Sciences , University of Groningen , Nijenborgh 4 , 9747AG Groningen , The Netherlands . ;
- Department of Radiology , University of Groningen , University Medical Center Groningen , Hanzeplein 1 , 9713 GZ , Groningen , The Netherlands
| | - Ben L Feringa
- Centre for Systems Chemistry , Stratingh Institute for Chemistry , Faculty of Mathematics and Natural Sciences , University of Groningen , Nijenborgh 4 , 9747AG Groningen , The Netherlands . ;
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37
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Srivastava A, Balaji PV. Molecular events during the early stages of aggregation of GNNQQNY: An all atom MD simulation study of randomly dispersed peptides. J Struct Biol 2015; 192:376-391. [DOI: 10.1016/j.jsb.2015.09.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 09/26/2015] [Accepted: 09/30/2015] [Indexed: 12/11/2022]
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38
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Nochebuena J, Ireta J. On cooperative effects and aggregation of GNNQQNY and NNQQNY peptides. J Chem Phys 2015; 143:135103. [DOI: 10.1063/1.4932083] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Jorge Nochebuena
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, A.P. 55-534, México D.F. 09340, Mexico
| | - Joel Ireta
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, A.P. 55-534, México D.F. 09340, Mexico
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39
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Lamley JM, Lougher MJ, Sass HJ, Rogowski M, Grzesiek S, Lewandowski JR. Unraveling the complexity of protein backbone dynamics with combined (13)C and (15)N solid-state NMR relaxation measurements. Phys Chem Chem Phys 2015; 17:21997-2008. [PMID: 26234369 DOI: 10.1039/c5cp03484a] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Typically, protein dynamics involve a complex hierarchy of motions occurring on different time scales between conformations separated by a range of different energy barriers. NMR relaxation can in principle provide a site-specific picture of both the time scales and amplitudes of these motions, but independent relaxation rates sensitive to fluctuations in different time scale ranges are required to obtain a faithful representation of the underlying dynamic complexity. This is especially pertinent for relaxation measurements in the solid state, which report on dynamics in a broader window of time scales by more than 3 orders of magnitudes compared to solution NMR relaxation. To aid in unraveling the intricacies of biomolecular dynamics we introduce (13)C spin-lattice relaxation in the rotating frame (R1ρ) as a probe of backbone nanosecond-microsecond motions in proteins in the solid state. We present measurements of (13)C'R1ρ rates in fully protonated crystalline protein GB1 at 600 and 850 MHz (1)H Larmor frequencies and compare them to (13)C'R1, (15)N R1 and R1ρ measured under the same conditions. The addition of carbon relaxation data to the model free analysis of nitrogen relaxation data leads to greatly improved characterization of time scales of protein backbone motions, minimizing the occurrence of fitting artifacts that may be present when (15)N data is used alone. We also discuss how internal motions characterized by different time scales contribute to (15)N and (13)C relaxation rates in the solid state and solution state, leading to fundamental differences between them, as well as phenomena such as underestimation of picosecond-range motions in the solid state and nanosecond-range motions in solution.
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Affiliation(s)
- Jonathan M Lamley
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK.
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40
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Chatterjee S, Prados-Rosales R, Tan S, Itin B, Casadevall A, Stark RE. Demonstration of a common indole-based aromatic core in natural and synthetic eumelanins by solid-state NMR. Org Biomol Chem 2015; 12:6730-6. [PMID: 25047903 DOI: 10.1039/c4ob01066c] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Despite the essential functions of melanin pigments in diverse organisms and their roles in inspiring designed nanomaterials for electron transport and drug delivery, the structural frameworks of the natural materials and their biomimetic analogs remain poorly understood. To overcome the investigative challenges posed by these insoluble heterogeneous pigments, we have used l-tyrosine or dopamine enriched with stable (13)C and (15)N isotopes to label eumelanins metabolically in cell-free and Cryptococcus neoformans cell systems and to define their molecular structures and supramolecular architectures. Using high-field two-dimensional solid-state nuclear magnetic resonance (NMR), our study directly evaluates the assumption of structural commonality between synthetic melanin models and the corresponding natural pigments, demonstrating a common indole-based aromatic core in the products from contrasting synthetic protocols for the first time.
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Affiliation(s)
- Subhasish Chatterjee
- Department of Chemistry, City College of New York, Graduate Center and Institute for Macromolecular Assemblies, City University of New York, MR-1208B, 160 Convent Avenue, New York, NY 10031-9101, USA.
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41
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Langkilde AE, Morris KL, Serpell LC, Svergun DI, Vestergaard B. The architecture of amyloid-like peptide fibrils revealed by X-ray scattering, diffraction and electron microscopy. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:882-95. [PMID: 25849399 PMCID: PMC4388266 DOI: 10.1107/s1399004715001674] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 01/25/2015] [Indexed: 11/12/2022]
Abstract
Structural analysis of protein fibrillation is inherently challenging. Given the crucial role of fibrils in amyloid diseases, method advancement is urgently needed. A hybrid modelling approach is presented enabling detailed analysis of a highly ordered and hierarchically organized fibril of the GNNQQNY peptide fragment of a yeast prion protein. Data from small-angle X-ray solution scattering, fibre diffraction and electron microscopy are combined with existing high-resolution X-ray crystallographic structures to investigate the fibrillation process and the hierarchical fibril structure of the peptide fragment. The elongation of these fibrils proceeds without the accumulation of any detectable amount of intermediate oligomeric species, as is otherwise reported for, for example, glucagon, insulin and α-synuclein. Ribbons constituted of linearly arranged protofilaments are formed. An additional hierarchical layer is generated via the pairing of ribbons during fibril maturation. Based on the complementary data, a quasi-atomic resolution model of the protofilament peptide arrangement is suggested. The peptide structure appears in a β-sheet arrangement reminiscent of the β-zipper structures evident from high-resolution crystal structures, with specific differences in the relative peptide orientation. The complexity of protein fibrillation and structure emphasizes the need to use multiple complementary methods.
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Affiliation(s)
- Annette E. Langkilde
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Kyle L. Morris
- School of Life Sciences, University of Sussex, Falmer, Brighton, England
| | - Louise C. Serpell
- School of Life Sciences, University of Sussex, Falmer, Brighton, England
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, 22607 Hamburg, Germany
| | - Bente Vestergaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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42
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Lamley JM, Iuga D, Öster C, Sass HJ, Rogowski M, Oss A, Past J, Reinhold A, Grzesiek S, Samoson A, Lewandowski JR. Solid-State NMR of a Protein in a Precipitated Complex with a Full-Length Antibody. J Am Chem Soc 2014; 136:16800-6. [DOI: 10.1021/ja5069992] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Jonathan M. Lamley
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Dinu Iuga
- Department
of Physics, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
| | - Carl Öster
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
| | | | - Marco Rogowski
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Andres Oss
- NMR
Institute and Tehnomeedikum, Tallinn University of Technology, Akadeemia
tee 15a, 19086 Tallinn, Estonia
| | - Jaan Past
- NMR
Institute and Tehnomeedikum, Tallinn University of Technology, Akadeemia
tee 15a, 19086 Tallinn, Estonia
| | - Andres Reinhold
- NMR
Institute and Tehnomeedikum, Tallinn University of Technology, Akadeemia
tee 15a, 19086 Tallinn, Estonia
| | | | - Ago Samoson
- NMR
Institute and Tehnomeedikum, Tallinn University of Technology, Akadeemia
tee 15a, 19086 Tallinn, Estonia
| | - Józef R. Lewandowski
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
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43
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Hoop CL, Lin HK, Kar K, Hou Z, Poirier MA, Wetzel R, van der Wel PCA. Polyglutamine amyloid core boundaries and flanking domain dynamics in huntingtin fragment fibrils determined by solid-state nuclear magnetic resonance. Biochemistry 2014; 53:6653-66. [PMID: 25280367 PMCID: PMC4211650 DOI: 10.1021/bi501010q] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
In Huntington’s disease, expansion
of a polyglutamine (polyQ)
domain in the huntingtin (htt) protein leads to misfolding and aggregation.
There is much interest in the molecular features that distinguish
monomeric, oligomeric, and fibrillar species that populate the aggregation
pathway and likely differ in cytotoxicity. The mechanism and rate
of aggregation are greatly affected by the domains flanking the polyQ
segment within exon 1 of htt. A “protective” C-terminal
proline-rich flanking domain inhibits aggregation by inducing polyproline
II structure (PPII) within an extended portion of polyQ. The N-terminal
flanking segment (httNT) adopts an α-helical structure
as it drives aggregation, helps stabilize oligomers and fibrils, and
is seemingly integral to their supramolecular assembly. Via solid-state
nuclear magnetic resonance (ssNMR), we probe how, in the mature fibrils,
the htt flanking domains impact the polyQ domain and in particular
the localization of the β-structured amyloid core. Using residue-specific
and uniformly labeled samples, we find that the amyloid core occupies
most of the polyQ domain but ends just prior to the prolines. We probe
the structural and dynamical features of the remarkably abrupt β-sheet
to PPII transition and discuss the potential connections to certain
htt-binding proteins. We also examine the httNT α-helix
outside the polyQ amyloid core. Despite its presumed structural and
demonstrated stabilizing roles in the fibrils, quantitative ssNMR
measurements of residue-specific dynamics show that it undergoes distinct
solvent-coupled motion. This dynamical feature seems reminiscent of
molten-globule-like α-helix-rich features attributed to the
nonfibrillar oligomeric species of various amyloidogenic proteins.
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Affiliation(s)
- Cody L Hoop
- Department of Structural Biology, University of Pittsburgh School of Medicine , Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15260, United States
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Schütz AK, Habenstein B, Luckgei N, Bousset L, Sourigues Y, Nielsen AB, Melki R, Böckmann A, Meier BH. Solid-state NMR sequential assignments of the amyloid core of full-length Sup35p. BIOMOLECULAR NMR ASSIGNMENTS 2014; 8:349-356. [PMID: 23943018 DOI: 10.1007/s12104-013-9515-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 08/01/2013] [Indexed: 06/02/2023]
Abstract
Sup35p is a yeast prion and is responsible for the [PSI(+)] trait in Saccharomyces cerevisiae. With 685 amino acids, full-length soluble and fibrillar Sup35p are challenging targets for structural biology as they cannot be investigated by X-ray crystallography or NMR in solution. We present solid-state NMR studies of fibrils formed by the full-length Sup35 protein. We detect an ordered and rigid core of the protein that gives rise to narrow and strong peaks, while large parts of the protein show either static disorder or dynamics on time scales which interfere with dipolar polarization transfer or shorten the coherence lifetime. Thus, only a small subset of resonances is observed in 3D spectra. Here we describe in detail the sequential assignments of the 22 residues for which resonances are observed in 3D spectra: their chemical shifts mostly corresponding to β-sheet secondary structure. We suspect that these residues form the amyloid core of the fibril.
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Affiliation(s)
- Anne K Schütz
- Physical Chemistry, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093, Zurich, Switzerland
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Tycko R. Physical and structural basis for polymorphism in amyloid fibrils. Protein Sci 2014; 23:1528-39. [PMID: 25179159 DOI: 10.1002/pro.2544] [Citation(s) in RCA: 176] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 08/28/2014] [Accepted: 08/29/2014] [Indexed: 12/24/2022]
Abstract
As our understanding of the molecular structures of amyloid fibrils has matured over the past 15 years, it has become clear that, while amyloid fibrils do have well-defined molecular structures, their molecular structures are not uniquely determined by the amino acid sequences of their constituent peptides and proteins. Self-propagating molecular-level polymorphism is a common phenomenon. This article reviews current information about amyloid fibril structures, variations in molecular structures that underlie amyloid polymorphism, and physical considerations that explain the development and persistence of amyloid polymorphism. Much of this information has been obtained through solid state nuclear magnetic resonance measurements. The biological significance of amyloid polymorphism is also discussed briefly. Although this article focuses primarily on studies of fibrils formed by amyloid-β peptides, the same principles apply to many amyloid-forming peptides and proteins.
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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
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C-terminal domain swapping of SSB changes the size of the ssDNA binding site. BIOMED RESEARCH INTERNATIONAL 2014; 2014:573936. [PMID: 25162017 PMCID: PMC4137731 DOI: 10.1155/2014/573936] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 07/09/2014] [Indexed: 01/29/2023]
Abstract
Single-stranded DNA-binding protein (SSB) plays an important role in DNA metabolism, including DNA replication, repair, and recombination, and is therefore essential for cell survival. Bacterial SSB consists of an N-terminal ssDNA-binding/oligomerization domain and a flexible C-terminal protein-protein interaction domain. We characterized the ssDNA-binding properties of Klebsiella pneumoniae SSB (KpSSB), Salmonella enterica Serovar Typhimurium LT2 SSB (StSSB), Pseudomonas aeruginosa PAO1 SSB (PaSSB), and two chimeric KpSSB proteins, namely, KpSSBnStSSBc and KpSSBnPaSSBc. The C-terminal domain of StSSB or PaSSB was exchanged with that of KpSSB through protein chimeragenesis. By using the electrophoretic mobility shift assay, we characterized the stoichiometry of KpSSB, StSSB, PaSSB, KpSSBnStSSBc, and KpSSBnPaSSBc, complexed with a series of ssDNA homopolymers. The binding site sizes were determined to be 26 ± 2, 21 ± 2, 29 ± 2, 21 ± 2, and 29 ± 2 nucleotides (nt), respectively. Comparison of the binding site sizes of KpSSB, KpSSBnStSSBc, and KpSSBnPaSSBc showed that the C-terminal domain swapping of SSB changes the size of the binding site. Our observations suggest that not only the conserved N-terminal domain but also the C-terminal domain of SSB is an important determinant for ssDNA binding.
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Srivastava A, Balaji PV. Interplay of sequence, topology and termini charge in determining the stability of the aggregates of GNNQQNY mutants: a molecular dynamics study. PLoS One 2014; 9:e96660. [PMID: 24817093 PMCID: PMC4015988 DOI: 10.1371/journal.pone.0096660] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 04/11/2014] [Indexed: 01/16/2023] Open
Abstract
This study explores the stabilities of single sheet parallel systems of three sequence variants of 1GNNQQNY7, N2D, N2S and N6D, with variations in aggregate size (5–8) and termini charge (charged or neutral). The aggregates were simulated at 300 and 330 K. These mutations decrease amyloid formation in the yeast prion protein Sup35. The present study finds that these mutations cause instability even in the peptide context. The protonation status of termini is found to be a key determinant of stabilities; other determinants are sequence, position of mutation and aggregate size. All systems with charged termini are unstable, whereas both stable and unstable systems are found when the termini are neutral. When termini are charged, the largest stable aggregate for the N2S and N6D systems has 3 to 4 peptides whereas N2D mutation supports oligomers of larger size (5-and 6-mers) as well. Mutation at 2nd position (N2S and N2D) results in fewer H-bonds at the mutated as well as neighboring (Gly1/Gln4) positions. However, no such effect is found if mutation is at 6th position (N6D). The effect of Asn→Asp mutation depends on the position and termini charge: it is more destabilizing at the 2nd position than at the 6th in case of neutral termini, however, the opposite is true in case of charged termini. Appearance of twist in stable systems and in smaller aggregates formed in unstable systems suggests that twist is integral to amyloid arrangement. Disorder, dissociation or rearrangement of peptides, disintegration or collapse of aggregates and formation of amorphous aggregates observed in these simulations are likely to occur during the early stages of aggregation also. The smaller aggregates formed due to such events have a variety of arrangements of peptides. This suggests polymorphic nature of oligomers and presence of a heterogeneous mixture of oligomers during early stages of aggregation.
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Affiliation(s)
- Alka Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Petety V. Balaji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
- * E-mail:
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Niu Z, Zhao W, Zhang Z, Xiao F, Tang X, Yang J. The Molecular Structure of Alzheimer β-Amyloid Fibrils Formed in the Presence of Phospholipid Vesicles. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201311106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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49
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Niu Z, Zhao W, Zhang Z, Xiao F, Tang X, Yang J. The molecular structure of Alzheimer β-amyloid fibrils formed in the presence of phospholipid vesicles. Angew Chem Int Ed Engl 2014; 53:9294-7. [PMID: 24810551 DOI: 10.1002/anie.201311106] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Indexed: 11/06/2022]
Abstract
β-amyloid (Aβ) fibrils are the major species involved in Alzheimer's disease (AD). An atomic-resolution molecular structure of Aβ40 fibrils formed in the presence of lipid vesicles was obtained by using magic angle spinning (MAS) solid-state NMR spectroscopy. The fibril structures formed in the presence of the lipid vesicles are remarkably different from those formed in solution. These results provide insights into the molecular mechanism of Aβ aggregation in the presence of lipid vesicles.
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Affiliation(s)
- Zheng Niu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071 (P.R. China)
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Hauser CAE, Maurer-Stroh S, Martins IC. Amyloid-based nanosensors and nanodevices. Chem Soc Rev 2014; 43:5326-45. [DOI: 10.1039/c4cs00082j] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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