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Mendes LFS, Gimenes CO, da Silva MDO, Rout SK, Riek R, Costa‐Filho AJ. The potential role of liquid-liquid phase separation in the cellular fate of the compartments for unconventional protein secretion. Protein Sci 2024; 33:e5085. [PMID: 38923199 PMCID: PMC11201811 DOI: 10.1002/pro.5085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/30/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024]
Abstract
Eukaryotic cells have developed intricate mechanisms for biomolecule transport, particularly in stressful conditions. This interdisciplinary study delves into unconventional protein secretion (UPS) pathways activated during starvation, facilitating the export of proteins bypassing most of the components of the classical secretory machinery. Specifically, we focus on the underexplored mechanisms of the GRASP's role in UPS, particularly in biogenesis and cargo recruitment for the vesicular-like compartment for UPS. Our results show that liquid-liquid phase separation (LLPS) plays a key role in the coacervation of Grh1, the GRASP yeast homologue, under starvation-like conditions. This association seems a precursor to the Compartment for Unconventional Protein Secretion (CUPS) biogenesis. Grh1's self-association is regulated by electrostatic, hydrophobic, and hydrogen-bonding interactions. Importantly, our study demonstrates that phase-separated states of Grh1 can recruit UPS cargo under starvation-like situations. Additionally, we explore how the coacervate liquid-to-solid transition could impact cells' ability to return to normal post-stress states. Our findings offer insights into intracellular protein dynamics and cell adaptive responses to stress.
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Affiliation(s)
- Luis Felipe S. Mendes
- Group of Biophysics and Structural Biology "Sergio Mascarenhas". São Carlos Institute of PhysicsUniversity of São PauloSão CarlosSão PauloBrazil
- Department of Physics, Ribeirão Preto School of Philosophy, Science, and LiteratureUniversity of São PauloRibeirão PretoSão PauloBrazil
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH HönggerbergZürichSwitzerland
| | - Carolina O. Gimenes
- Department of Physics, Ribeirão Preto School of Philosophy, Science, and LiteratureUniversity of São PauloRibeirão PretoSão PauloBrazil
| | - Marília D. O. da Silva
- Group of Biophysics and Structural Biology "Sergio Mascarenhas". São Carlos Institute of PhysicsUniversity of São PauloSão CarlosSão PauloBrazil
| | - Saroj K. Rout
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH HönggerbergZürichSwitzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH HönggerbergZürichSwitzerland
| | - Antonio J. Costa‐Filho
- Department of Physics, Ribeirão Preto School of Philosophy, Science, and LiteratureUniversity of São PauloRibeirão PretoSão PauloBrazil
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2
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Jayawardena BM, Azzi A, Jones CE. Investigating the role of phenylalanine residues for amyloid formation of the neuropeptide neurokinin B. Biochem Biophys Res Commun 2024; 705:149732. [PMID: 38447390 DOI: 10.1016/j.bbrc.2024.149732] [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: 02/14/2024] [Accepted: 02/26/2024] [Indexed: 03/08/2024]
Abstract
Neurokinin B (NKB) is a tachykinin peptide that has diverse roles in biology, including in human reproductive development. Cellular processing of this peptide is thought to involve formation of a dense core vesicle during transit through the regulated secretory pathway. The ability of NKB to rapidly form an amyloid can contribute to formation of the secretory granule but features that support amyloid formation of NKB are not well understood. NKB contains a diphenylalanine sequence well recognised as an important motif for self-assembly of other peptides including amyloid β. Using mutations of the diphenylalanine motif we show that this motif in NKB is necessary for amyloid formation, and it is the unique combination of aromaticity and hydrophobicity of phenylalanine that is crucial for aggregation. Using disulfide cross-linking we propose that phenylalanine at sequence position 6 is important for stabilising inter-sheet interactions in the NKB amyloid fibril. Although having a highly conserved sequence, the NKB peptide from zebrafish only contains a single phenylalanine and does not fibrillise as extensively as mammalian NKB. Analysis of self-assembly of NKB-like peptides from different species may help in elucidating their biological roles. Taken together, this work shows that mammalian NKB has evolved, within only 10 residues, a sequence optimised for rapid self-assembly, whilst also containing residues for metal-binding, receptor binding and receptor discrimination.
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Affiliation(s)
- Bhawantha M Jayawardena
- School of Science, Western Sydney University, Locked Bag 1797, Penrith, 2751, New South Wales, Australia
| | - Annabelle Azzi
- School of Science, Western Sydney University, Locked Bag 1797, Penrith, 2751, New South Wales, Australia
| | - Christopher E Jones
- School of Science, Western Sydney University, Locked Bag 1797, Penrith, 2751, New South Wales, Australia.
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3
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Ribes JM, Patel MP, Halim HA, Berretta A, Tooze SA, Klöhn PC. Prion protein conversion at two distinct cellular sites precedes fibrillisation. Nat Commun 2023; 14:8354. [PMID: 38102121 PMCID: PMC10724300 DOI: 10.1038/s41467-023-43961-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 11/24/2023] [Indexed: 12/17/2023] Open
Abstract
The self-templating nature of prions plays a central role in prion pathogenesis and is associated with infectivity and transmissibility. Since propagation of proteopathic seeds has now been acknowledged a principal pathogenic process in many types of dementia, more insight into the molecular mechanism of prion replication is vital to delineate specific and common disease pathways. By employing highly discriminatory anti-PrP antibodies and conversion-tolerant PrP chimera, we here report that de novo PrP conversion and formation of fibril-like PrP aggregates are distinct in mechanistic and kinetic terms. De novo PrP conversion occurs within minutes after infection at two subcellular locations, while fibril-like PrP aggregates are formed exclusively at the plasma membrane, hours after infection. Phenotypically distinct pools of abnormal PrP at perinuclear sites and the plasma membrane show differences in N-terminal processing, aggregation state and fibril formation and are linked by exocytic transport via synaptic and large-dense core vesicles.
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Affiliation(s)
- Juan Manuel Ribes
- Medical Research Council Prion Unit at UCL, Institute of Prion Diseases, University College London, London, W1W 7FF, UK
| | - Mitali P Patel
- Medical Research Council Prion Unit at UCL, Institute of Prion Diseases, University College London, London, W1W 7FF, UK
| | - Hazim A Halim
- Medical Research Council Prion Unit at UCL, Institute of Prion Diseases, University College London, London, W1W 7FF, UK
| | - Antonio Berretta
- Medical Research Council Prion Unit at UCL, Institute of Prion Diseases, University College London, London, W1W 7FF, UK
| | - Sharon A Tooze
- Molecular Cell Biology of Autophagy Laboratory, the Francis Crick Institute, London, NW1 1BF, UK
| | - Peter-Christian Klöhn
- Medical Research Council Prion Unit at UCL, Institute of Prion Diseases, University College London, London, W1W 7FF, UK.
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4
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Marichal L, Bagnard L, Sire O, Vendrely C, Bruckert F, Weidenhaupt M. Phenol-soluble modulins form amyloids in contact with multiple surface chemistries. Biochim Biophys Acta Gen Subj 2023; 1867:130450. [PMID: 37640168 DOI: 10.1016/j.bbagen.2023.130450] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 08/31/2023]
Abstract
Functional amyloids are commonly produced by many microorganisms and their biological functions are numerous. Staphylococcus aureus can secrete a group of peptides named phenol-soluble modulins (PSMs) in their biofilm extracellular matrix. PSMs have been found inside biofilms both in their soluble form and assembled into amyloid structures. Yet, the actual biological function of these amyloids has been highly debated. Here, we assessed the ability of PSMs to form amyloids in contact with different abiotic surfaces to unravel a potential unknown bioadhesive and/or biofilm stabilization function. We combined surface plasmon resonance imaging, fluorescence aggregation kinetics, and FTIR spectroscopy in order to evaluate the PSM adsorption as well as amyloid formation properties in the presence of various surface chemistries. Overall, PSMs adsorb even on low-binding surfaces, making them highly adaptable adsorbants in the context of bioadhesion. Moreover, the PSM aggregation potential to form amyloid aggregates is not impacted by the presence of the surface chemistries tested. This versatility regarding adsorption and amyloid formation may imply a possible role of PSMs in biofilm adhesion and/or structure integrity.
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Affiliation(s)
- Laurent Marichal
- Université Grenoble Alpes, CNRS, Grenoble-INP LMGP, Grenoble F-38000, France
| | - Lucie Bagnard
- Université Grenoble Alpes, CNRS, Grenoble-INP LMGP, Grenoble F-38000, France
| | - Olivier Sire
- IRDL, UMR CNRS 6027, Université Bretagne Sud, Vannes, France
| | - Charlotte Vendrely
- Université Grenoble Alpes, CNRS, Grenoble-INP LMGP, Grenoble F-38000, France
| | - Franz Bruckert
- Université Grenoble Alpes, CNRS, Grenoble-INP LMGP, Grenoble F-38000, France
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5
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Li Q, Min J, Zhang J, Reches M, Shen Y, Su R, Wang Y, Qi W. Enzyme-Driven, Switchable Catalysis Based on Dynamic Self-Assembly of Peptides. Angew Chem Int Ed Engl 2023; 62:e202309830. [PMID: 37602955 DOI: 10.1002/anie.202309830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/16/2023] [Accepted: 08/21/2023] [Indexed: 08/22/2023]
Abstract
Covalent regulatory systems of enzymes are widely used to modulate biological enzyme activities. Inspired by the regulation of reactive-site phosphorylation in organisms, we developed peptide-based catecholase mimetics with switchable catalytic activity and high selectivity through the co-assembly of nanofibers comprising peptides and copper ions (Cu2+ ). Through careful design and modification of the peptide backbone structure based on the change in the free energy of the system, we identified the peptide with the most effective reversible catalytic activity. Kinase/phosphatase switches were used to control the reversible transition of nanofiber formation and depolymerization, as well as to modulate the active-site microenvironment. Notably, the self-assembly and disassembly processes of nanofibers were simulated using coarse-grained molecular dynamics. Furthermore, theoretical calculations confirmed the coordination of the peptide and Cu2+ , forming a zipper-like four-ligand structure at the catalytically active center of the nanofibers. Additionally, we conducted a comprehensive analysis of the catalytic mechanism. This study opens novel avenues for designing biomimetic enzymes with ordered structures and dynamic catalytic activities.
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Affiliation(s)
- Qing Li
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Jiwei Min
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Jiaxing Zhang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Meital Reches
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Yuhe Shen
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Rongxin Su
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Yuefei Wang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin, 300072, P. R. China
| | - Wei Qi
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin, 300072, P. R. China
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6
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Yang J, Ding W, Zhu B, Zhen S, Kuang S, Yang J, Zhang C, Wang P, Yang F, Yang L, Yin W, Tanzi RE, Shen S, Ran C. Bioluminescence Imaging with Functional Amyloid Reservoirs in Alzheimer's Disease Models. Anal Chem 2023; 95:14261-14270. [PMID: 37712902 DOI: 10.1021/acs.analchem.3c02358] [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] [Indexed: 09/16/2023]
Abstract
Bioluminescence imaging has changed the daily practice of preclinical research on cancer and other diseases over the last few decades; however, it has rarely been applied in preclinical research on Alzheimer's disease (AD). In this Article, we demonstrated that bioluminescence imaging could be used to report the levels of amyloid beta (Aβ) species in vivo. We hypothesized that AkaLumine, a newly discovered substrate for luciferase, could bind to Aβ aggregates and plaques. We further speculated that the Aβ aggregates/fibrils/plaques could be considered as "functional amyloids", which have a reservoir function to sequester and release AkaLumine to control the bioluminescence intensity, which could be used to report the levels of Aβs. Our hypotheses have been validated via in vitro solution tests, mimic studies with brain tissues and mice, two-photon imaging with AD mice, and in vivo bioluminescence imaging using transgenic AD mice that were virally transduced with AkaLuciferase (AkaLuc), a new luciferase that generates bioluminescence in the near-infrared window. As expected, compared to the control group, we observed that the Aβ group showed lower bioluminescence intensity due to AkaLumine sequestering at early time points, while higher intensity was due to AkaLumine releasing at later time points. Lastly, we demonstrated that this method could be used to monitor AD progression and the therapeutic effectiveness of avagacestat, a well-studied gamma-secretase inhibitor. Importantly, a good correlation (R2 = 0.81) was established between in vivo bioluminescence signals and Aβ burdens of the tested AD mice. We believe that our approach can be easily implemented into daily imaging experiments and has tremendous potential to change the daily practice of preclinical AD research.
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Affiliation(s)
- Jing Yang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Room 2301, Building 149, Charlestown, Boston, Massachusetts 02129,United States
- School of Engineering, China Pharmaceutical University, Nanjing 210009, China
| | - Weihua Ding
- MGH Center for Translational Pain Research, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Biyue Zhu
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Room 2301, Building 149, Charlestown, Boston, Massachusetts 02129,United States
| | - Sherri Zhen
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts 02129, United States
| | - Shi Kuang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Room 2301, Building 149, Charlestown, Boston, Massachusetts 02129,United States
| | - Jun Yang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Room 2301, Building 149, Charlestown, Boston, Massachusetts 02129,United States
| | - Can Zhang
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts 02129, United States
| | - Peng Wang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Room 2301, Building 149, Charlestown, Boston, Massachusetts 02129,United States
- School of Engineering, China Pharmaceutical University, Nanjing 210009, China
| | - Fan Yang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Room 2301, Building 149, Charlestown, Boston, Massachusetts 02129,United States
| | - Liuyue Yang
- MGH Center for Translational Pain Research, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Wei Yin
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Room 2301, Building 149, Charlestown, Boston, Massachusetts 02129,United States
| | - Rudolph E Tanzi
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts 02129, United States
| | - Shiqian Shen
- MGH Center for Translational Pain Research, Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Chongzhao Ran
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Room 2301, Building 149, Charlestown, Boston, Massachusetts 02129,United States
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7
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Milton NGN. SARS-CoV-2 amyloid, is COVID-19-exacerbated dementia an amyloid disorder in the making? FRONTIERS IN DEMENTIA 2023; 2:1233340. [PMID: 39081980 PMCID: PMC11285677 DOI: 10.3389/frdem.2023.1233340] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 06/26/2023] [Indexed: 08/02/2024]
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8
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Buchanan JA, Varghese NR, Johnston CL, Sunde M. Functional Amyloids: Where Supramolecular Amyloid Assembly Controls Biological Activity or Generates New Functionality. J Mol Biol 2023; 435:167919. [PMID: 37330295 DOI: 10.1016/j.jmb.2022.167919] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/05/2022] [Accepted: 12/05/2022] [Indexed: 06/19/2023]
Abstract
Functional amyloids are a rapidly expanding class of fibrillar protein structures, with a core cross-β scaffold, where novel and advantageous biological function is generated by the assembly of the amyloid. The growing number of amyloid structures determined at high resolution reveal how this supramolecular template both accommodates a wide variety of amino acid sequences and also imposes selectivity on the assembly process. The amyloid fibril can no longer be considered a generic aggregate, even when associated with disease and loss of function. In functional amyloids the polymeric β-sheet rich structure provides multiple different examples of unique control mechanisms and structures that are finely tuned to deliver assembly or disassembly in response to physiological or environmental cues. Here we review the range of mechanisms at play in natural, functional amyloids, where tight control of amyloidogenicity is achieved by environmental triggers of conformational change, proteolytic generation of amyloidogenic fragments, or heteromeric seeding and amyloid fibril stability. In the amyloid fibril form, activity can be regulated by pH, ligand binding and higher order protofilament or fibril architectures that impact the arrangement of associated domains and amyloid stability. The growing understanding of the molecular basis for the control of structure and functionality delivered by natural amyloids in nearly all life forms should inform the development of therapies for amyloid-associated diseases and guide the design of innovative biomaterials.
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Affiliation(s)
- Jessica A Buchanan
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia.
| | - Nikhil R Varghese
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia.
| | - Caitlin L Johnston
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia.
| | - Margaret Sunde
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia.
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9
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Jayawardena BM, Menon R, Jones MR, Jones CE. Spectral Phasor Analysis of Nile Red Identifies Membrane Microenvironment Changes in the Presence of Amyloid Peptides. Cell Biochem Biophys 2023; 81:19-27. [PMID: 36203076 DOI: 10.1007/s12013-022-01105-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 09/24/2022] [Indexed: 11/29/2022]
Abstract
The interaction of protein and peptide amyloid oligomers with membranes is thought to be one of the mechanisms contributing to cellular toxicity. However, techniques to study these interactions in the complex membrane environment of live cells are lacking. Spectral phasor analysis is a recently developed biophysical technique that can enable visualisation and analysis of membrane-associated fluorescent dyes. When the spectral profile of these dyes changes as a result of changes to the membrane microenvironment, spectral phasor analysis can localise those changes to discrete membrane regions. In this study, we investigated whether spectral phasor analysis could detect changes in the membrane microenvironment of live cells in the presence of fibrillar aggregates of the disease-related Aβ42 peptide or the functional amyloid neurokinin B. Our results show that the fibrils cause distinct changes to the microenvironment of nile red associated with both the plasma and the nuclear membrane. We attribute these shifts in nile red spectral properties to changes in membrane fluidity. Results from this work suggest that cells have mechanisms to avoid or control membrane interactions arising from functional amyloids which have implications for how these peptides are stored in dense core vesicles. Furthermore, the work highlights the utility of spectral phasor analysis to monitor microenvironment changes to fluorescent probes in live cells.
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Affiliation(s)
- Bhawantha M Jayawardena
- School of Science, Western Sydney University, Locked Bag 1797, Penrith, 2751, NSW, Australia
| | - Resmi Menon
- School of Science, Western Sydney University, Locked Bag 1797, Penrith, 2751, NSW, Australia.,PYC Therapeutics, QEII Medical Centre, 6 Verdun St, Nedlands, 6009, WA, Australia
| | - Mark R Jones
- School of Science, Western Sydney University, Locked Bag 1797, Penrith, 2751, NSW, Australia
| | - Christopher E Jones
- School of Science, Western Sydney University, Locked Bag 1797, Penrith, 2751, NSW, Australia.
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10
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Liu Y, Liu J, He X. Different p Ka Shifts of Internal GLU8 in Human β-Endorphin Amyloid Revealing a Coupling of Internal Ionization and Stepwise Fibril Disassembly. J Phys Chem B 2023; 127:1089-1096. [PMID: 36696655 DOI: 10.1021/acs.jpcb.2c06706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
As a functional amyloid, human β-endorphin amyloid fibril features a β-solenoid conformation and store peptide hormones within acidic secretory granules, which would be released into the blood through fibril disassembly when the cellular milieu pH increases from acidic to neutral level on exocytosis. To gain detailed atomic mechanism of β-endorphin amyloid fibrils' pH-responsive disassembly, we conduct constant pH molecular dynamics simulations to investigate the structural and dynamical properties of β-endorphin amyloid fibrils in experiencing the environmental pH changes. Our results demonstrate a clear pKa shift of the internal ionizable residue of GLU8, and this shift becomes even more pronounced when it is buried more deeply in the amyloid fibrils. The unusual pKa of GLU8 reveals that its protonation state changes from the protonated state in the acidic secretory granule to the deprotonated state in the neutral pH conditions in the blood, where the deprotonation of GLU8 leads to unfavorable interactions within the hydrophobic core of the amyloid and subsequent fibril disassembly. The different pKa shifts of GLU8 relative to its positions in the amyloid fibril indicate that the β-endorphin amyloid fibril disassembly is a stepwise process, accounting for the experimental observation that the disassembly always initiates from the outermost layer. This study reveals the critical role of the protonation state of GLU8 in amyloid fibrils' pH-responsive disassembly, and provides clear insights for understanding the structural transitions of amyloids in hormone secretion. This study also provides theoretical basis for designing pH-sensitive biological tools for specific use with precise positioning of ionizable residues into the hydrophobic interior of proteins.
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Affiliation(s)
- Yiwei Liu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
| | - Jinfeng Liu
- Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China.,New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai, 200062, China
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11
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Kaygisiz K, Ender AM, Gačanin J, Kaczmarek LA, Koutsouras DA, Nalakath AN, Winterwerber P, Mayer FJ, Räder HJ, Marszalek T, Blom PWM, Synatschke CV, Weil T. Photoinduced Amyloid Fibril Degradation for Controlled Cell Patterning. Macromol Biosci 2023; 23:e2200294. [PMID: 36281903 DOI: 10.1002/mabi.202200294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/14/2022] [Indexed: 11/12/2022]
Abstract
Amyloid-like fibrils are a special class of self-assembling peptides that emerge as a promising nanomaterial with rich bioactivity for applications such as cell adhesion and growth. Unlike the extracellular matrix, the intrinsically stable amyloid-like fibrils do not respond nor adapt to stimuli of their natural environment. Here, a self-assembling motif (CKFKFQF), in which a photosensitive o-nitrobenzyl linker (PCL) is inserted, is designed. This peptide (CKFK-PCL-FQF) assembles into amyloid-like fibrils comparable to the unsubstituted CKFKFQF and reveals a strong response to UV-light. After UV irradiation, the secondary structure of the fibrils, fibril morphology, and bioactivity are lost. Thus, coating surfaces with the pre-formed fibrils and exposing them to UV-light through a photomask generate well-defined areas with patterns of intact and destroyed fibrillar morphology. The unexposed, fibril-coated surface areas retain their ability to support cell adhesion in culture, in contrast to the light-exposed regions, where the cell-supportive fibril morphology is destroyed. Consequently, the photoresponsive peptide nanofibrils provide a facile and efficient way of cell patterning, exemplarily demonstrated for A549, Chinese Hamster Ovary, and Raw Dual type cells. This study introduces photoresponsive amyloid-like fibrils as adaptive functional materials to precisely arrange cells on surfaces.
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Affiliation(s)
- Kübra Kaygisiz
- Department Synthesis of Macromolecules, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Adriana M Ender
- Department Synthesis of Macromolecules, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Jasmina Gačanin
- Department Synthesis of Macromolecules, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - L Alix Kaczmarek
- Department Synthesis of Macromolecules, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Dimitrios A Koutsouras
- Department of Molecular Electronics, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Abin N Nalakath
- Department of Molecular Electronics, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Pia Winterwerber
- Department Synthesis of Macromolecules, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Franz J Mayer
- Department Synthesis of Macromolecules, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Hans-Joachim Räder
- Department Synthesis of Macromolecules, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Tomasz Marszalek
- Department of Molecular Electronics, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany.,Department of Molecular Physics, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, Lodz, 90-924, Poland
| | - Paul W M Blom
- Department of Molecular Electronics, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Christopher V Synatschke
- Department Synthesis of Macromolecules, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Tanja Weil
- Department Synthesis of Macromolecules, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
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12
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Becker N, Frieg B, Gremer L, Kupreichyk T, Gardon L, Freiburg P, Neudecker P, Willbold D, Gohlke H, Heise H. Atomic Resolution Insights into pH Shift Induced Deprotonation Events in LS-Shaped Aβ(1-42) Amyloid Fibrils. J Am Chem Soc 2023; 145:2161-2169. [PMID: 36653015 PMCID: PMC9896559 DOI: 10.1021/jacs.2c09231] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Alzheimer's disease is a neurodegenerative disorder associated with the deposition of misfolded aggregates of the amyloid-β protein (Aβ). Aβ(1-42) is one of the most aggregation-prone components in senile plaques of AD patients. We demonstrated that relatively homogeneous Aβ(1-42) fibrils with one predominant fold visible in solid-state NMR spectra can be obtained at acidic pH. The structure of these fibrils differs remarkably from some other polymorphs obtained at neutral pH. In particular, the entire N-terminal region is part of the rigid fibril core. Here, we investigate the effects of a pH shift on the stability and the fold of these fibrils at higher pH values. Fibril bundling at neutral pH values renders cryo-EM studies impractical, but solid-state NMR spectroscopy, molecular dynamics simulations, and biophysical methods provide residue-specific structural information under these conditions. The LS-fold of the Aβ(1-42) fibrils does not change over the complete pH range from pH 2 to pH 7; in particular, the N-terminus remains part of the fibril core. We observe changes in the protonation state of charged residues starting from pH 5 on a residue-specific level. The deprotonation of the C-terminal carboxyl group of A42 in the intermolecular salt bridge with D1 and K28 is slow on the NMR time scale, with a local pKa of 5.4, and local conformations of the involved residues are affected by deprotonation of A42. Thus, we demonstrate that this fibril form is stable at physiological pH values.
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Affiliation(s)
- Nina Becker
- Institute
of Biological Information Processing (IBI-7: Structural Biochemistry)
and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany,Physikalische
Biologie, Heinrich-Heine-Universität
Düsseldorf, 40225 Düsseldorf, Germany
| | - Benedikt Frieg
- Institute
of Biological Information Processing (IBI-7: Structural Biochemistry)
and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany,John
von Neumann Institute for Computing (NIC), Jülich Supercomputing
Centre (JSC), Forschungszentrum Jülich
GmbH, 52425 Jülich, Germany
| | - Lothar Gremer
- Institute
of Biological Information Processing (IBI-7: Structural Biochemistry)
and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany,Physikalische
Biologie, Heinrich-Heine-Universität
Düsseldorf, 40225 Düsseldorf, Germany
| | - Tatsiana Kupreichyk
- Institute
of Biological Information Processing (IBI-7: Structural Biochemistry)
and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany,Physikalische
Biologie, Heinrich-Heine-Universität
Düsseldorf, 40225 Düsseldorf, Germany
| | - Luis Gardon
- Institute
of Biological Information Processing (IBI-7: Structural Biochemistry)
and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany,Physikalische
Biologie, Heinrich-Heine-Universität
Düsseldorf, 40225 Düsseldorf, Germany
| | - Patrick Freiburg
- Physikalische
Biologie, Heinrich-Heine-Universität
Düsseldorf, 40225 Düsseldorf, Germany
| | - Philipp Neudecker
- Institute
of Biological Information Processing (IBI-7: Structural Biochemistry)
and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany,Physikalische
Biologie, Heinrich-Heine-Universität
Düsseldorf, 40225 Düsseldorf, Germany
| | - Dieter Willbold
- Institute
of Biological Information Processing (IBI-7: Structural Biochemistry)
and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany,Physikalische
Biologie, Heinrich-Heine-Universität
Düsseldorf, 40225 Düsseldorf, Germany
| | - Holger Gohlke
- Institute
of Biological Information Processing (IBI-7: Structural Biochemistry)
and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany,John
von Neumann Institute for Computing (NIC), Jülich Supercomputing
Centre (JSC), Forschungszentrum Jülich
GmbH, 52425 Jülich, Germany,Institute
for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany,
| | - Henrike Heise
- Institute
of Biological Information Processing (IBI-7: Structural Biochemistry)
and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany,Physikalische
Biologie, Heinrich-Heine-Universität
Düsseldorf, 40225 Düsseldorf, Germany,
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13
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Jayawardena BM, Peacey L, Gamsjaeger R, Jones CE. Essential Role of Histidine for Rapid Copper(II)-Mediated Disassembly of Neurokinin B Amyloid. Biomolecules 2022; 12:biom12111585. [PMID: 36358935 PMCID: PMC9687585 DOI: 10.3390/biom12111585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/21/2022] [Accepted: 10/25/2022] [Indexed: 12/02/2022] Open
Abstract
Neurokinin B is a tachykinin peptide involved in a diverse range of neuronal functions. It rapidly forms an amyloid, which is considered physiologically important for efficient packing into dense core secretory vesicles within hypothalamic neurons. Disassembly of the amyloid is thought to require the presence of copper ions, which interact with histidine at the third position in the peptide sequence. However, it is unclear how the histidine is involved in the amyloid structure and why copper coordination can trigger disassembly. In this work, we demonstrate that histidine contributes to the amyloid structure via π-stacking interactions with nearby phenylalanine residues. The ability of neurokinin B to form an amyloid is dependent on any aromatic residue at the third position in the sequence; however, only the presence of histidine leads to both amyloid formation and rapid copper-induced disassembly.
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14
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Siemer AB. What makes functional amyloids work? Crit Rev Biochem Mol Biol 2022; 57:399-411. [PMID: 35997712 PMCID: PMC9588633 DOI: 10.1080/10409238.2022.2113030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 06/29/2022] [Accepted: 08/10/2022] [Indexed: 01/27/2023]
Abstract
Although first described in the context of disease, cross-β (amyloid) fibrils have also been found as functional entities in all kingdoms of life. However, what are the specific properties of the cross-β fibril motif that convey biological function, make them especially suited for their particular purpose, and distinguish them from other fibrils found in biology? This review approaches these questions by arguing that cross-β fibrils are highly periodic, stable, and self-templating structures whose formation is accompanied by substantial conformational change that leads to a multimerization of their core and framing sequences. A discussion of each of these properties is followed by selected examples of functional cross-β fibrils that show how function is usually achieved by leveraging many of these properties.
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Affiliation(s)
- Ansgar B Siemer
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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15
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Liu Y, Wang Y, Tong C, Wei G, Ding F, Sun Y. Molecular Insights into the Self-Assembly of Block Copolymer Suckerin Polypeptides into Nanoconfined β-Sheets. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2202642. [PMID: 35901284 PMCID: PMC9420834 DOI: 10.1002/smll.202202642] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Suckerin in squid sucker ring teeth is a block-copolymer peptide comprised of two repeating modules-the alanine and histidine-rich M1 and the glycine-rich M2. Suckerin self-assemblies display excellent thermo-plasticity and pH-responsive properties, along with the high biocompatibility, biodegradability, and sustainability. However, the self-assembly mechanism and the detailed role of each module are still elusive, limiting the capability of applying and manipulating such biomaterials. Here, the self-assembly dynamics of the two modules and two minimalist suckerin-mimetic block-copolymers, M1-M2-M1 and M2-M1-M2, in silico is investigated. The simulation results demonstrate that M2 has a stronger self-association but weaker β-sheet propensities than M1. The high self-assembly propensity of M2 allows the minimalist block-copolymer peptides to coalesce with microphase separation, enabling the formation of nanoconfined β-sheets in the matrix formed by M1-M2 contacts. Since these glycine-rich fragments with scatted hydrophobic and aromatic residues are building blocks of many other block-copolymer peptides, the study suggests that these modules function as the "molecular glue" in addition to the flexible linker or spacer to drive the self-assembly and microphase separation. The uncovered molecular insights may help understand the structure and function of suckerin and also aid in the design of functional block-copolymer peptides for nanotechnology and biomedicine applications.
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Affiliation(s)
- Yuying Liu
- Department of Physics, Ningbo University, Ningbo 315211, China
| | - Ying Wang
- Department of Physics, Ningbo University, Ningbo 315211, China
| | - Chaohui Tong
- Department of Physics, Ningbo University, Ningbo 315211, China
| | - Guanghong Wei
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai 200433, China
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Yunxiang Sun
- Department of Physics, Ningbo University, Ningbo 315211, China
- State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai 200433, China
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
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16
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Lauth LM, Voigt B, Bhatia T, Machner L, Balbach J, Ott M. Heparin promotes rapid fibrillation of the basic Parathyroid Hormone at physiological pH. FEBS Lett 2022; 596:2928-2939. [PMID: 35903816 DOI: 10.1002/1873-3468.14455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 06/14/2022] [Accepted: 07/09/2022] [Indexed: 11/06/2022]
Abstract
In acidic secretory granules of mammalian cells, peptide hormones including the parathyroid hormone (PTH) are presumably stored in the form of functional amyloid fibrils. Mature PTH, however, is considerably positively charged in acidic environments, a condition known to impede unassisted self-aggregation into fibrils. Here, we studied the role of the polyanion heparin on promoting fibril formation of PTH. Employing ITC, CD spectroscopy, NMR, SAXS and fluorescence-based assays we could demonstrate that heparin binds PTH with submicromolar affinity and facilitates its conversion into fibrillar seeds, enabling rapid formation of amyloid fibrils under acidic conditions. In absence of heparin, PTH remained in a soluble monomeric state. We suspect that heparin-like surfaces are required in vivo to convert PTH efficiently into fibrillar deposits.
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Affiliation(s)
- Luca M Lauth
- Department of Biochemistry and Biotechnology, Martin-Luther-University, Halle-Wittenberg, Halle, Germany
| | - Bruno Voigt
- Department of Biophysics, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Twinkle Bhatia
- Department of Biochemistry and Biotechnology, Martin-Luther-University, Halle-Wittenberg, Halle, Germany
| | - Lisa Machner
- Department of Molecular Medicine, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Jochen Balbach
- Department of Biophysics, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Maria Ott
- Department of Biochemistry and Biotechnology, Martin-Luther-University, Halle-Wittenberg, Halle, Germany
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17
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Lipid membrane-mediated assembly of the functional amyloid-forming peptide Somatostatin-14. Biophys Chem 2022; 287:106830. [DOI: 10.1016/j.bpc.2022.106830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/03/2022] [Accepted: 05/17/2022] [Indexed: 11/20/2022]
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18
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Abstract
In the last two decades, solid-state nuclear magnetic resonance (ssNMR) spectroscopy has transformed from a spectroscopic technique investigating small molecules and industrial polymers to a potent tool decrypting structure and underlying dynamics of complex biological systems, such as membrane proteins, fibrils, and assemblies, in near-physiological environments and temperatures. This transformation can be ascribed to improvements in hardware design, sample preparation, pulsed methods, isotope labeling strategies, resolution, and sensitivity. The fundamental engagement between nuclear spins and radio-frequency pulses in the presence of a strong static magnetic field is identical between solution and ssNMR, but the experimental procedures vastly differ because of the absence of molecular tumbling in solids. This review discusses routinely employed state-of-the-art static and MAS pulsed NMR methods relevant for biological samples with rotational correlation times exceeding 100's of nanoseconds. Recent developments in signal filtering approaches, proton methodologies, and multiple acquisition techniques to boost sensitivity and speed up data acquisition at fast MAS are also discussed. Several examples of protein structures (globular, membrane, fibrils, and assemblies) solved with ssNMR spectroscopy have been considered. We also discuss integrated approaches to structurally characterize challenging biological systems and some newly emanating subdisciplines in ssNMR spectroscopy.
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Affiliation(s)
- Sahil Ahlawat
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Kaustubh R Mote
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Nils-Alexander Lakomek
- University of Düsseldorf, Institute for Physical Biology, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Vipin Agarwal
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
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19
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Hassan MN, Nabi F, Khan AN, Hussain M, Siddiqui WA, Uversky VN, Khan RH. The amyloid state of proteins: A boon or bane? Int J Biol Macromol 2022; 200:593-617. [PMID: 35074333 DOI: 10.1016/j.ijbiomac.2022.01.115] [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: 12/13/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 11/05/2022]
Abstract
Proteins and their aggregation is significant field of research due to their association with various conformational maladies including well-known neurodegenerative diseases like Alzheimer's (AD), Parkinson's (PD), and Huntington's (HD) diseases. Amyloids despite being given negative role for decades are also believed to play a functional role in bacteria to humans. In this review, we discuss both facets of amyloid. We have shed light on AD, which is one of the most common age-related neurodegenerative disease caused by accumulation of Aβ fibrils as extracellular senile plagues. We also discuss PD caused by the aggregation and deposition of α-synuclein in form of Lewy bodies and neurites. Other amyloid-associated diseases such as HD and amyotrophic lateral sclerosis (ALS) are also discussed. We have also reviewed functional amyloids that have various biological roles in both prokaryotes and eukaryotes that includes formation of biofilm and cell attachment in bacteria to hormone storage in humans, We discuss in detail the role of Curli fibrils' in biofilm formation, chaplins in cell attachment to peptide hormones, and Pre-Melansomal Protein (PMEL) roles. The disease-related and functional amyloids are compared with regard to their structural integrity, variation in regulation, and speed of forming aggregates and elucidate how amyloids have turned from foe to friend.
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Affiliation(s)
- Md Nadir Hassan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Faisal Nabi
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Asra Nasir Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Murtaza Hussain
- Department of Biochemistry, Aligarh Muslim University, Aligarh 202002, India
| | - Waseem A Siddiqui
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Vladimir N Uversky
- Protein Research Group, Institute for Biological Instrumentation of the Russian Academy of Sciences, 10 Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy 11 of Sciences", Pushchino, Moscow Region 142290, Russia; Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College 13 of Medicine, University of South Florida, Tampa, FL 33612, United States
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India.
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20
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Liu Y, Zhang Y, Sun Y, Ding F. A buried glutamate in the cross-β core renders β-endorphin fibrils reversible. NANOSCALE 2021; 13:19593-19603. [PMID: 34812835 PMCID: PMC8674924 DOI: 10.1039/d1nr05679d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Functional amyloids are abundant in living organisms from prokaryotes to eukaryotes playing diverse biological roles. In contrast to the irreversible aggregation of most known pathological amyloids, we postulate that naturally-occurring functional amyloids are reversible under evolutionary pressure to be able to modulate the fibrillization process, reuse the composite peptides, or perform their biological functions. β-Endorphin, an endogenous opioid peptide hormone, forms such kinds of reversible amyloid fibrils in secretory granules for efficient storage and returns to the functional state of monomers upon release into the blood. The environmental change between low pH in secretory granules and neutral pH in extracellular spaces is believed to drive the reversible fibrillization of β-endorphin. Here, we investigate the critical role of a buried glutamate, Glu8, in the pH-responsive disassembly of β-endorphin fibrils using all-atom molecular dynamics simulations along with structure-based pKa prediction. The fibril was stable at pH 5.5 or lower with all the buried Glu8 residues protonated and neutrally charged. After switching to neutral pH, the Glu8 residues of peptides at the outer layers of the ordered fibrils became deprotonated due to partial solvent exposure, causing sheet-to-coil conformational changes and subsequent exposure of adjacent Glu8 residues in the inner chains. Via iterative deprotonation of Glu8 and induced structural disruption, all Glu8 residues would be progressively deprotonated. Electrostatic repulsion between deprotonated Glu8 residues along with their high solvation tendency disrupted the hydrogen bonding between the β1 strands and increased the solvent exposure of those otherwise buried residues in the cross-β core. Overall, our computational study reveals that the strategic positioning of ionizable residues into the cross-β core is a potential approach for designing reversible amyloid fibrils as pH-responsive smart bio-nanomaterials.
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Affiliation(s)
- Yuying Liu
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Yu Zhang
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Yunxiang Sun
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, USA.
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, USA.
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21
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Root-Bernstein R, Churchill B. Co-Evolution of Opioid and Adrenergic Ligands and Receptors: Shared, Complementary Modules Explain Evolution of Functional Interactions and Suggest Novel Engineering Possibilities. Life (Basel) 2021; 11:life11111217. [PMID: 34833093 PMCID: PMC8623292 DOI: 10.3390/life11111217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/29/2021] [Accepted: 11/03/2021] [Indexed: 12/14/2022] Open
Abstract
Cross-talk between opioid and adrenergic receptors is well-characterized and involves second messenger systems, the formation of receptor heterodimers, and the presence of extracellular allosteric binding regions for the complementary ligand; however, the evolutionary origins of these interactions have not been investigated. We propose that opioid and adrenergic ligands and receptors co-evolved from a common set of modular precursors so that they share binding functions. We demonstrate the plausibility of this hypothesis through a review of experimental evidence for molecularly complementary modules and report unexpected homologies between the two receptor types. Briefly, opioids form homodimers also bind adrenergic compounds; opioids bind to conserved extracellular regions of adrenergic receptors while adrenergic compounds bind to conserved extracellular regions of opioid receptors; opioid-like modules appear in both sets of receptors within key ligand-binding regions. Transmembrane regions associated with homodimerization of each class of receptors are also highly conserved across receptor types and implicated in heterodimerization. This conservation of multiple functional modules suggests opioid–adrenergic ligand and receptor co-evolution and provides mechanisms for explaining the evolution of their crosstalk. These modules also suggest the structure of a primordial receptor, providing clues for engineering receptor functions.
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22
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Sawaya MR, Hughes MP, Rodriguez JA, Riek R, Eisenberg DS. The expanding amyloid family: Structure, stability, function, and pathogenesis. Cell 2021; 184:4857-4873. [PMID: 34534463 PMCID: PMC8772536 DOI: 10.1016/j.cell.2021.08.013] [Citation(s) in RCA: 158] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/26/2021] [Accepted: 08/11/2021] [Indexed: 02/05/2023]
Abstract
The hidden world of amyloid biology has suddenly snapped into atomic-level focus, revealing over 80 amyloid protein fibrils, both pathogenic and functional. Unlike globular proteins, amyloid proteins flatten and stack into unbranched fibrils. Stranger still, a single protein sequence can adopt wildly different two-dimensional conformations, yielding distinct fibril polymorphs. Thus, an amyloid protein may define distinct diseases depending on its conformation. At the heart of this conformational variability lies structural frustrations. In functional amyloids, evolution tunes frustration levels to achieve either stability or sensitivity according to the fibril's biological function, accounting for the vast versatility of the amyloid fibril scaffold.
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Affiliation(s)
- Michael R Sawaya
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, UCLA, Los Angeles, CA 90095, USA; UCLA-DOE Institute, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Michael P Hughes
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, UCLA, Los Angeles, CA 90095, USA; UCLA-DOE Institute, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Jose A Rodriguez
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, UCLA, Los Angeles, CA 90095, USA; UCLA-DOE Institute, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Roland Riek
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland
| | - David S Eisenberg
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, UCLA, Los Angeles, CA 90095, USA; UCLA-DOE Institute, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA.
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23
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Weismiller HA, Holub TJ, Krzesinski BJ, Margittai M. A thiol-based intramolecular redox switch in four-repeat tau controls fibril assembly and disassembly. J Biol Chem 2021; 297:101021. [PMID: 34339733 PMCID: PMC8387771 DOI: 10.1016/j.jbc.2021.101021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/17/2021] [Accepted: 07/28/2021] [Indexed: 02/06/2023] Open
Abstract
Oxidative stress has been implicated in the pathogenesis and progression of several tauopathies, including Alzheimer's disease. The deposition of fibrillar inclusions made of tau protein is one of the pathological hallmarks of these disorders. Although it is becoming increasingly evident that the specific fibril structure may vary from one tauopathy to another and it is recognized that different types of isoforms (three-repeat and four-repeat tau) can be selectively deposited, little is known about the role oxidation may play in aggregation. Four-repeat tau contains two cysteines that can form an intramolecular disulfide bond, resulting in a structurally restrained compact monomer. There is discrepancy as to whether this monomer can aggregate or not. Using isolated four-repeat tau monomers (htau40) with intramolecular disulfide bonds, we demonstrate that these proteins form fibrils. The fibrils are less stable than fibrils formed under reducing conditions but are highly effective in seeding oxidized tau monomers. Conversely, a strong seeding barrier prevents incorporation of reduced tau monomers, tau mimics in which the cysteines have been replaced by alanines or serines, and three-repeat tau (htau23), a single-cysteine isoform. The barrier also holds true when seed and monomer types are reversed, indicating that oxidized and reduced tau are incompatible with each other. Surprisingly, fibrils composed of compact tau disaggregate upon reduction, highlighting the importance of the intramolecular disulfide bond for fibril stability. The findings uncover a novel binary redox switch that controls the aggregation and disaggregation of these fibrils and extend the conformational spectrum of tau aggregates.
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Affiliation(s)
- Hilary A Weismiller
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado, USA
| | - Tyler J Holub
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado, USA
| | - Brad J Krzesinski
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado, USA
| | - Martin Margittai
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado, USA.
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24
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Abstract
AbstractChaperones protect other proteins against misfolding and aggregation, a key requirement for maintaining biological function. Experimental observations of changes in solubility of amyloid proteins in the presence of certain chaperones are discussed here in terms of thermodynamic driving forces. We outline how chaperones can enhance amyloid solubility through the formation of heteromolecular aggregates (co-aggregates) based on the second law of thermodynamics and the flux towards equal chemical potential of each compound in all phases of the system. Higher effective solubility of an amyloid peptide in the presence of chaperone implies that the chemical potential of the peptide is higher in the aggregates formed under these conditions compared to peptide-only aggregates. This must be compensated by a larger reduction in chemical potential of the chaperone in the presence of peptide compared to chaperone alone. The driving force thus relies on the chaperone being very unhappy on its own (high chemical potential), thus gaining more free energy than the amyloid peptide loses upon forming the co-aggregate. The formation of heteromolecular aggregates also involves the kinetic suppression of the formation of homomolecular aggregates. The unhappiness of the chaperone can explain the ability of chaperones to favour an increased population of monomeric client protein even in the absence of external energy input, and with broad client specificity. This perspective opens for a new direction of chaperone research and outlines a set of outstanding questions that aim to provide additional cues for therapeutic development in this area.
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25
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Daskalov A, El Mammeri N, Lends A, Shenoy J, Lamon G, Fichou Y, Saad A, Martinez D, Morvan E, Berbon M, Grélard A, Kauffmann B, Ferber M, Bardiaux B, Habenstein B, Saupe SJ, Loquet A. Structures of Pathological and Functional Amyloids and Prions, a Solid-State NMR Perspective. Front Mol Neurosci 2021; 14:670513. [PMID: 34276304 PMCID: PMC8280340 DOI: 10.3389/fnmol.2021.670513] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 05/26/2021] [Indexed: 12/20/2022] Open
Abstract
Infectious proteins or prions are a remarkable class of pathogens, where pathogenicity and infectious state correspond to conformational transition of a protein fold. The conformational change translates into the formation by the protein of insoluble amyloid aggregates, associated in humans with various neurodegenerative disorders and systemic protein-deposition diseases. The prion principle, however, is not limited to pathogenicity. While pathological amyloids (and prions) emerge from protein misfolding, a class of functional amyloids has been defined, consisting of amyloid-forming domains under natural selection and with diverse biological roles. Although of great importance, prion amyloid structures remain challenging for conventional structural biology techniques. Solid-state nuclear magnetic resonance (SSNMR) has been preferentially used to investigate these insoluble, morphologically heterogeneous aggregates with poor crystallinity. SSNMR methods have yielded a wealth of knowledge regarding the fundamentals of prion biology and have helped to solve the structures of several prion and prion-like fibrils. Here, we will review pathological and functional amyloid structures and will discuss some of the obtained structural models. We will finish the review with a perspective on integrative approaches combining solid-state NMR, electron paramagnetic resonance and cryo-electron microscopy, which can complement and extend our toolkit to structurally explore various facets of prion biology.
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Affiliation(s)
- Asen Daskalov
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Nadia El Mammeri
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Alons Lends
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | | | - Gaelle Lamon
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Yann Fichou
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Ahmad Saad
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Denis Martinez
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Estelle Morvan
- CNRS, INSERM, IECB, UMS 3033, University of Bordeaux, Pessac, France
| | - Melanie Berbon
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Axelle Grélard
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Brice Kauffmann
- CNRS, INSERM, IECB, UMS 3033, University of Bordeaux, Pessac, France
| | | | | | | | - Sven J. Saupe
- CNRS, IBGC UMR 5095, University of Bordeaux, Bordeaux, France
| | - Antoine Loquet
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
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26
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Toward the equilibrium and kinetics of amyloid peptide self-assembly. Curr Opin Struct Biol 2021; 70:87-98. [PMID: 34153659 DOI: 10.1016/j.sbi.2021.05.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/09/2021] [Accepted: 05/09/2021] [Indexed: 01/28/2023]
Abstract
Several devastating human diseases are linked to peptide self-assembly, but our understanding their onset and progression is not settled. This is a sign of the complexity of the aggregation process, which is prevented, catalyzed, or retarded by numerous factors in body fluids and cells, varying in time and space. Biophysical studies of pure peptide solutions contribute insights into the underlying steps in the process and quantitative parameters relating to rate constants (energy barriers) and equilibrium constants (population distributions). This requires methods to quantify the concentration of at least one species in the process. Translation to an in vivo situation poses an enormous challenge, and the effects of selected components (bottom up) or entire body fluids (top down) need to be quantified.
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27
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Brown A, Török M. Functional amyloids in the human body. Bioorg Med Chem Lett 2021; 40:127914. [PMID: 33691165 DOI: 10.1016/j.bmcl.2021.127914] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/20/2021] [Accepted: 02/23/2021] [Indexed: 11/18/2022]
Abstract
Amyloids have long been associated with a variety of human degenerative diseases. Discoveries indicate, however, that there are several amyloids that serve functional roles in the human body. These amyloids are involved in a variety of biological processes ranging from storage of peptide hormones to necroptosis of cells. Additionally, there are distinct differences between toxic amyloids and their functional counterparts including kinetics of assembly/disassembly and structural features. This digest article surveys the biological roles of functional amyloids found in the human body, key differences between functional and toxic amyloids, and potential therapeutic applications.
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Affiliation(s)
- Amy Brown
- Department of Chemistry, University of Massachusetts Boston, 100 Morrissey Blvd., Boston, MA 02125, USA
| | - Marianna Török
- Department of Chemistry, University of Massachusetts Boston, 100 Morrissey Blvd., Boston, MA 02125, USA.
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28
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Zhang S, Guaglianone G, Morris MA, Yoo S, Howitz WJ, Xing L, Zheng JG, Jusuf H, Huizar G, Lin J, Kreutzer AG, Nowick JS. Expression of N-Terminal Cysteine Aβ 42 and Conjugation to Generate Fluorescent and Biotinylated Aβ 42. Biochemistry 2021; 60:1191-1200. [PMID: 33793198 PMCID: PMC9059633 DOI: 10.1021/acs.biochem.1c00105] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Fluorescent derivatives of the β-amyloid peptides (Aβ) are valuable tools for studying the interactions of Aβ with cells. Facile access to labeled expressed Aβ offers the promise of Aβ with greater sequence and stereochemical integrity, without impurities from amino acid deletion and epimerization. Here, we report methods for the expression of Aβ42 with an N-terminal cysteine residue, Aβ(C1-42), and its conjugation to generate Aβ42 bearing fluorophores or biotin. The methods rely on the hitherto unrecognized observation that expression of the Aβ(MC1-42) gene yields the Aβ(C1-42) peptide, because the N-terminal methionine is endogenously excised by Escherichia coli. Conjugation of Aβ(C1-42) with maleimide-functionalized fluorophores or biotin affords the N-terminally labeled Aβ42. The expression affords ∼14 mg of N-terminal cysteine Aβ from 1 L of bacterial culture. Subsequent conjugation affords ∼3 mg of labeled Aβ from 1 L of bacterial culture with minimal cost for labeling reagents. High-performance liquid chromatography analysis indicates the N-terminal cysteine Aβ to be >97% pure and labeled Aβ peptides to be 94-97% pure. Biophysical studies show that the labeled Aβ peptides behave like unlabeled Aβ and suggest that labeling of the N-terminus does not substantially alter the properties of the Aβ. We further demonstrate applications of the fluorophore-labeled Aβ peptides by using fluorescence microscopy to visualize their interactions with mammalian cells and bacteria. We anticipate that these methods will provide researchers convenient access to useful N-terminally labeled Aβ, as well as Aβ with an N-terminal cysteine that enables further functionalization.
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Affiliation(s)
- Sheng Zhang
- Department of Chemistry, University of California-Irvine, Irvine, California 92697-2025, United States
| | - Gretchen Guaglianone
- Department of Chemistry, University of California-Irvine, Irvine, California 92697-2025, United States
| | - Michael A. Morris
- Department of Chemistry, University of California-Irvine, Irvine, California 92697-2025, United States
| | - Stan Yoo
- Department of Chemistry, University of California-Irvine, Irvine, California 92697-2025, United States
| | - William J. Howitz
- Department of Chemistry, University of California-Irvine, Irvine, California 92697-2025, United States
| | - Li Xing
- Irvine Materials Research Institute (IMRI), University of California-Irvine, Irvine, California 92697-2575, United States
| | - Jian-Guo Zheng
- Irvine Materials Research Institute (IMRI), University of California-Irvine, Irvine, California 92697-2575, United States
| | - Hannah Jusuf
- Department of Chemistry, University of California-Irvine, Irvine, California 92697-2025, United States
| | - Grace Huizar
- Department of Chemistry, University of California-Irvine, Irvine, California 92697-2025, United States
| | - Jonathan Lin
- Department of Chemistry, University of California-Irvine, Irvine, California 92697-2025, United States
| | - Adam G. Kreutzer
- Department of Chemistry, University of California-Irvine, Irvine, California 92697-2025, United States
| | - James S. Nowick
- Department of Chemistry, University of California-Irvine, Irvine, California 92697-2025, United States
- Department of Pharmaceutical Sciences, University of California-Irvine, Irvine, California 92697-2025, United States
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29
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Reif B, Ashbrook SE, Emsley L, Hong M. Solid-state NMR spectroscopy. NATURE REVIEWS. METHODS PRIMERS 2021; 1:2. [PMID: 34368784 PMCID: PMC8341432 DOI: 10.1038/s43586-020-00002-1] [Citation(s) in RCA: 172] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/29/2020] [Indexed: 12/18/2022]
Abstract
Solid-state nuclear magnetic resonance (NMR) spectroscopy is an atomic-level method used to determine the chemical structure, three-dimensional structure, and dynamics of solids and semi-solids. This Primer summarizes the basic principles of NMR as applied to the wide range of solid systems. The fundamental nuclear spin interactions and the effects of magnetic fields and radiofrequency pulses on nuclear spins are the same as in liquid-state NMR. However, because of the anisotropy of the interactions in the solid state, the majority of high-resolution solid-state NMR spectra is measured under magic-angle spinning (MAS), which has profound effects on the types of radiofrequency pulse sequences required to extract structural and dynamical information. We describe the most common MAS NMR experiments and data analysis approaches for investigating biological macromolecules, organic materials, and inorganic solids. Continuing development of sensitivity-enhancement approaches, including 1H-detected fast MAS experiments, dynamic nuclear polarization, and experiments tailored to ultrahigh magnetic fields, is described. We highlight recent applications of solid-state NMR to biological and materials chemistry. The Primer ends with a discussion of current limitations of NMR to study solids, and points to future avenues of development to further enhance the capabilities of this sophisticated spectroscopy for new applications.
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Affiliation(s)
- Bernd Reif
- Technische Universität München, Department Chemie, Lichtenbergstr. 4, D-85747 Garching, Germany
| | - Sharon E. Ashbrook
- School of Chemistry, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Lyndon Emsley
- École Polytechnique Fédérale de Lausanne (EPFL), Institut des sciences et ingénierie chimiques, CH-1015 Lausanne, Switzerland
| | - Mei Hong
- Department of Chemistry and Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA 02139
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30
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Dharmadana D, Adamcik J, Ryan TM, Appiah Danso S, Chong CJH, Conn CE, Reynolds NP, Mezzenga R, Valéry C. Human neuropeptide substance P self-assembles into semi-flexible nanotubes that can be manipulated for nanotechnology. NANOSCALE 2020; 12:22680-22687. [PMID: 33165459 DOI: 10.1039/d0nr05622g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Substance P neuropeptide is here reported to self-assemble into well-defined semi-flexible nanotubes. Using a blend of synchrotron small angle X-ray scattering, atomic force microscopy and other biophysical techniques, the natural peptide is shown to self-assemble into monodisperse 6 nm wide nanotubes, which can closely associate into nano-arrays with nematic properties. Using simple protocols, the nanotubes could be precipitated or mineralised while conserving their dimensions and core-shell morphology. Our discovery expands the small number of available monodisperse peptide nanotube systems for nanotechnology, beyond direct relevance to biologically functional peptide nanostructures since the substance P nanotubes are fundamentally different from typical amyloid fibrils.
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Affiliation(s)
- Durga Dharmadana
- School of Health and Biomedical Sciences, Translational Immunology and Nanotechnology (TIN) Program, RMIT University, Bundoora VIC3083, Australia.
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31
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Baldry M, Bojer MS, Najarzadeh Z, Vestergaard M, Meyer RL, Otzen DE, Ingmer H. Phenol-Soluble Modulins Modulate Persister Cell Formation in Staphylococcus aureus. Front Microbiol 2020; 11:573253. [PMID: 33240231 PMCID: PMC7680730 DOI: 10.3389/fmicb.2020.573253] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/16/2020] [Indexed: 12/03/2022] Open
Abstract
Staphylococcus aureus is a human pathogen that can cause chronic and recurrent infections and is recalcitrant to antibiotic chemotherapy. This trait is partly attributed to its ability to form persister cells, which are subpopulations of cells that are tolerant to lethal concentrations of antibiotics. Recently, we showed that the phenol-soluble modulins (PSMs) expressed by S. aureus reduce persister cell formation. PSMs are a versatile group of toxins that, in addition to toxicity, form amyloid-like fibrils thought to support biofilm structures. Here, we examined individual or combined synthetic PSMα peptides and their equivalent amyloid-like fibrils on ciprofloxacin-selected S. aureus persister cells. We found that PSMα2 and the mixture of all four alpha peptides consistently were able to reduce persister frequency in all growth phases, and this activity was specifically linked to the presence of the soluble peptide as no effect was seen with fibrillated peptides. Persister reduction was particularly striking in a mutant that, due to mutations in the Krebs cycle, has enhanced ability to form persisters with PSMα4 and the combination of peptides being most effective. In biofilms, only the combination of peptides displayed persister reducing activity. Collectively, we report the individual contributions of PSMα peptides to persister cell reduction and that the combination of peptides generally was most effective. Strikingly, the fibrillated peptides lost activity and thus, if formed in bacterial cultures, they will be inactive against persister cells. Further studies will be needed to address the biological role of phenol-soluble modulins in reducing persister cells.
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Affiliation(s)
- Mara Baldry
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Martin S. Bojer
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Zahra Najarzadeh
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Martin Vestergaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Rikke Louise Meyer
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Daniel Erik Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
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32
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Seuring C, Verasdonck J, Gath J, Ghosh D, Nespovitaya N, Wälti MA, Maji SK, Cadalbert R, Güntert P, Meier BH, Riek R. The three-dimensional structure of human β-endorphin amyloid fibrils. Nat Struct Mol Biol 2020; 27:1178-1184. [PMID: 33046908 DOI: 10.1038/s41594-020-00515-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 09/08/2020] [Indexed: 11/09/2022]
Abstract
In the pituitary gland, hormones are stored in a functional amyloid state within acidic secretory granules before they are released into the blood. To gain a detailed understanding of the structure-function relationship of amyloids in hormone secretion, the three-dimensional (3D) structure of the amyloid fibril of the human hormone β-endorphin was determined by solid-state NMR. We find that β-endorphin fibrils are in a β-solenoid conformation with a protonated glutamate residue in their fibrillar core. During exocytosis of the hormone amyloid the pH increases from acidic in the secretory granule to neutral level in the blood, thus it is suggested-and supported with mutagenesis data-that the pH change in the cellular milieu acts through the deprotonation of glutamate 8 to release the hormone from the amyloid. For amyloid disassembly in the blood, it is proposed that the pH change acts together with a buffer composition change and hormone dilution. In the pituitary gland, peptide hormones can be stored as amyloid fibrils within acidic secretory granules before release into the blood stream. Here, we use solid-state NMR to determine the 3D structure of the amyloid fiber formed by the human hormone β-endorphin. We find that β-endorphin fibrils are in a β-solenoid conformation that is generally reminiscent of other functional amyloids. In the β-endorphin amyloid, every layer of the β-solenoid is composed of a single peptide and protonated Glu8 is located in the fibrillar core. The secretory granule has an acidic pH but, on exocytosis, the β-endorphin fibril would encounter neutral pH conditions (pH 7.4) in the blood; this pH change would result in deprotonation of Glu8 to release the hormone peptide from the amyloid. Analyses of β-endorphin variants carrying mutations in Glu8 support the role of the protonation state of this residue in fibril disassembly, among other environmental changes.
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Affiliation(s)
- Carolin Seuring
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland.,Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - Joeri Verasdonck
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland
| | - Julia Gath
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland
| | - Dhimam Ghosh
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland.,Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, India
| | | | | | - Samir K Maji
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, India
| | | | - Peter Güntert
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland.,Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Frankfurt am Main, Germany.,Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Beat H Meier
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland.
| | - Roland Riek
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland. .,Structural Biology Laboratory, The Salk Institute, La Jolla, CA, USA.
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33
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Sang Y, Han J, Zhao T, Duan P, Liu M. Circularly Polarized Luminescence in Nanoassemblies: Generation, Amplification, and Application. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1900110. [PMID: 31394014 DOI: 10.1002/adma.201900110] [Citation(s) in RCA: 423] [Impact Index Per Article: 105.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 05/13/2019] [Indexed: 05/22/2023]
Abstract
Currently, the development of circularly polarized luminescent (CPL) materials has drawn extensive attention due to the numerous potential applications in optical data storage, displays, backlights in 3D displays, and so on. While the fabrication of CPL-active materials generally requires chiral luminescent molecules, the introduction of the "self-assembly" concept offers a new perspective in obtaining the CPL-active materials. Following this approach, various self-assembled materials, including organic-, inorganic-, and hybrid systems can be endowed with CPL properties. Benefiting from the advantages of self-assembly, not only chiral molecules, but also achiral species, as well as inorganic nanoparticles have potential to be self-assembled into chiral nanoassemblies showing CPL activity. In addition, the dissymmetry factor, an important parameter of CPL materials, can be enhanced through various pathways of self-assembly. Here, the present status and progress of self-assembled nanomaterials with CPL activity are reviewed. An overview of the key factors in regulating chiral emission materials at the supramolecular level will largely boost their application in multidisciplinary fields.
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Affiliation(s)
- Yutao Sang
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Colloid Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, No. 2 ZhongGuanCun BeiYiJie, Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Jianlei Han
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, Division of Nanophotonics, National Center for Nanoscience and Technology (NCNST), No. 11 ZhongGuanCun BeiYiTiao, Beijing, 100190, P. R. China
| | - Tonghan Zhao
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, Division of Nanophotonics, National Center for Nanoscience and Technology (NCNST), No. 11 ZhongGuanCun BeiYiTiao, Beijing, 100190, P. R. China
| | - Pengfei Duan
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, Division of Nanophotonics, National Center for Nanoscience and Technology (NCNST), No. 11 ZhongGuanCun BeiYiTiao, Beijing, 100190, P. R. China
| | - Minghua Liu
- Beijing National Laboratory for Molecular Science, CAS Key Laboratory of Colloid Interface and Chemical Thermodynamics, Institute of Chemistry, Chinese Academy of Sciences, No. 2 ZhongGuanCun BeiYiJie, Beijing, 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, Division of Nanophotonics, National Center for Nanoscience and Technology (NCNST), No. 11 ZhongGuanCun BeiYiTiao, Beijing, 100190, P. R. China
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Smith JW, Jiang X, An H, Barclay AM, Licari G, Tajkhorshid E, Moore EG, Rienstra CM, Moore JS, Chen Q. Polymer-Peptide Conjugates Convert Amyloid into Protein Nanobundles through Fragmentation and Lateral Association. ACS APPLIED NANO MATERIALS 2020; 3:937-945. [PMID: 32149271 PMCID: PMC7059651 DOI: 10.1021/acsanm.9b01331] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The assembly of proteins into amyloid fibrils has become linked not only with the progression of myriad human diseases, but also important biological functions. Understanding and controlling the formation, structure, and stability of amyloid fibrils is therefore a major scientific goal. Here we utilize electron microscopy-based approaches combined with quantitative statistical analysis to show how recently developed kind of amyloid modulators-multivalent polymer-peptide conjugates (mPPCs)-can be applied to control the structure and stability of amyloid fibrils. In doing so, we demonstrate that mPPCs are able to convert 40-residue amyloid beta fibrils into ordered nanostructures through a combination of fragmentation and bundling. Fragmentation is shown to be consistent with a model where the rate constant of fibril breakage is independent of the fibril length, suggesting a local and specific interaction between fibrils and mPPCs. Subsequent bundling, which was previously not observed, leads to the formation of sheet-like nanostructures which are surprisingly much more uniform than the starting fibrils. These nanostructures have dimensions independent of the molecular weight of the mPPC and retain the molecular-level ordering of the starting amyloid fibrils. Collectively, we reveal quantitative and nanoscopic understanding of how mPPCs can be applied to control amyloid structure and stability, and demonstrate approaches to elucidate nanoscale amyloid phase behavior in the presence of functional macromolecules and other modulators.
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Affiliation(s)
- John W. Smith
- Department of Materials Science and Engineering, University of Illinois, Urbana, Illinois 61801, United States
| | - Xing Jiang
- Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, Illinois 61801, United States
| | - Hyosung An
- Department of Materials Science and Engineering, University of Illinois, Urbana, Illinois 61801, United States
- Materials Research Laboratory, University of Illinois, Urbana, Illinois 61801, United States
| | - Alexander M. Barclay
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Giuseppe Licari
- Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, Illinois 61801, United States
| | - Emad Tajkhorshid
- Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Edwin G. Moore
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Chad M. Rienstra
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
- Corresponding Authors: , ,
| | - Jeffrey S. Moore
- Department of Materials Science and Engineering, University of Illinois, Urbana, Illinois 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
- Corresponding Authors: , ,
| | - Qian Chen
- Department of Materials Science and Engineering, University of Illinois, Urbana, Illinois 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, Illinois 61801, United States
- Materials Research Laboratory, University of Illinois, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
- Corresponding Authors: , ,
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35
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Abstract
When protein/peptides aggregate, they usually form the amyloid state consisting of cross β-sheet structure built by repetitively stacked β-strands forming long fibrils. Amyloids are usually associated with disease including Alzheimer's. However, amyloid has many useful features. It efficiently transforms protein from the soluble to the insoluble state in an essentially two-state process, while its repetitive structure provides high stability and a robust prion-like replication mechanism. Accordingly, amyloid is used by nature in multifaceted and ingenious ways of life, ranging from bacteria and fungi to mammals. These include (1) Structure: Templating for small chemical molecules (Pmel17), biofilm formation in bacteria (curli), assisting aerial hyphae formation in streptomycetes (chaplins) or monolayer formation at a surface (hydrophobins). (2) Reservoirs: A storage state for peptide/proteins to protect them from their surroundings or vice versa (storage of peptide hormones in mammalian secretory granules or major basic protein in eosinophils). (3) Information carriers: The fungal immune system (HET-s prion in Podospora anserina, yeast prions) or long-term memory (e.g., mnemons in yeast, cytoplasmic polyadenylation element-binding protein in aplysia). Aggregation is also used to (4) "suppress" the function of the soluble protein (e.g., Cdc19 in yeast stress granules), or (5) "signaling" through formation of oligomers (e.g., HET-s prion, necroptosis-related proteins RIP1/RIP3). This review summarizes current knowledge on functional amyloids with a focus on the amyloid systems curli in bacteria, HET-s prion in P. anserina, and peptide hormone storage in mammals together with an attempt to highlight differences between functional and disease-associated amyloids.
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Affiliation(s)
- Daniel Otzen
- iNANO, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Roland Riek
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, CH-8093 Zürich, Switzerland
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36
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Jayawardena BM, Jones MR, Hong Y, Jones CE. Copper ions trigger disassembly of neurokinin B functional amyloid and inhibit de novo assembly. J Struct Biol 2019; 208:107394. [DOI: 10.1016/j.jsb.2019.09.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/23/2019] [Accepted: 09/23/2019] [Indexed: 01/24/2023]
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Sebastiao M, Quittot N, Marcotte I, Bourgault S. Glycosaminoglycans Induce Amyloid Self-Assembly of a Peptide Hormone by Concerted Secondary and Quaternary Conformational Transitions. Biochemistry 2019; 58:1214-1225. [PMID: 30720275 DOI: 10.1021/acs.biochem.8b01206] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Amyloids are polypeptide supramolecular assemblies that have been historically associated with numerous pathologies. Nonetheless, recent studies have identified many amyloid structures that accomplish vital physiological functions. Interestingly, amyloid fibrils, either pathological or functional, have been reported to be consistently associated with other biomolecules such as RNA and glycosaminoglycans (GAGs). These linear polyanions, RNA and GAGs, have also demonstrated an inherent ability to accelerate and/or promote amyloid formation. GAGs, including heparan sulfate, are highly charged polysaccharides that may have essential roles in the storage of peptide hormones in the form of amyloids. In this study, we evaluated the ability of sulfated GAGs to promote the self-assembly of the peptide (neuro)hormone PACAP27 and investigated the secondary and quaternary conformational transitions associated with the amyloidogenic process. PACAP27 readily self-assembled into insoluble, α-helix-rich globular particulates in the presence of sulfated GAGs, which gradually condensed and disappeared as nontoxic β-sheet-rich amyloid fibrils were formed. By designing a PACAP27 derivative for which helical folding was hindered, we observed that the α-helix-to-β-sheet conformational transition within the amorphous particulates constitutes the rate-limiting step of primary nucleation events. The proposed mechanism of GAG-induced self-assembly within insoluble particulates appears to be fundamentally different from usual amyloidogenic systems, which commonly implicates the formation of soluble prefibrillar proteospecies. Overall, this study provides new insights into the mechanistic details involved in the formation of functional amyloids catalyzed by polyanions, such as the assembly of nuclear amyloid bodies and the storage of peptide hormones.
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Affiliation(s)
- Mathew Sebastiao
- Department of Chemistry , Université du Québec à Montréal , C.P. 8888, Succursale Centre-Ville , Montreal H3C 3P8 , Canada.,Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO , Université Laval , Québec G1V 0A6 , Canada
| | - Noe Quittot
- Department of Chemistry , Université du Québec à Montréal , C.P. 8888, Succursale Centre-Ville , Montreal H3C 3P8 , Canada.,Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO , Université Laval , Québec G1V 0A6 , Canada
| | - Isabelle Marcotte
- Department of Chemistry , Université du Québec à Montréal , C.P. 8888, Succursale Centre-Ville , Montreal H3C 3P8 , Canada.,Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO , Université Laval , Québec G1V 0A6 , Canada
| | - Steve Bourgault
- Department of Chemistry , Université du Québec à Montréal , C.P. 8888, Succursale Centre-Ville , Montreal H3C 3P8 , Canada.,Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO , Université Laval , Québec G1V 0A6 , Canada
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38
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Protein Nanofibrils as Storage Forms of Peptide Drugs and Hormones. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1174:265-290. [PMID: 31713202 DOI: 10.1007/978-981-13-9791-2_8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Amyloids are highly organized cross β-sheet protein nanofibrils that are associated with both diseases and functions. Thermodynamically amyloids are stable structures as they represent the lowest free energy state that proteins can attain. However, recent studies suggest that amyloid fibrils can be dissociated by a change in environmental parameters such as pH and ionic strength. This reversibility of amyloids can not only be associated with disease, but function as well. In disease-associated amyloids, fibrils can act as reservoirs of cytotoxic oligomers. Recently, in higher organisms such as mammals, hormones were found to be stored in amyloid-like state, where these were reported to act as a reservoir of functional monomers. These hormone amyloids can dissociate to monomers upon release from the secretory granules, and subsequently bind to their respective receptors and perform their functions. In this book chapter, we describe in detail how these protein nanofibrils represent the densest possible peptide packing and are suitable for long-term storage. Thus, mimicking the feature of amyloids to release functional monomers, it is possible to formulate amyloid-based peptide/protein drugs, which can be used for sustained release.
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Gobeaux F, Wien F. Reversible Assembly of a Drug Peptide into Amyloid Fibrils: A Dynamic Circular Dichroism Study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:7180-7191. [PMID: 29772895 DOI: 10.1021/acs.langmuir.8b00094] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The common view on the amyloid fibril formation is that it is a multistep process that involves many oligomeric intermediate species, which leads to a high degree of polymorphism. This view derives from numerous kinetic studies whose vast majority was carried out with amyloid β fragments or other pathological amyloidogenic sequences. Yet, it is not clear whether the mechanisms inferred from these studies are universal and also apply to functional amyloids, in particular to peptide hormones which form reversible amyloid structures. In the present work, we study the self-assembly properties of atosiban, a nonapeptide drug, whose sequence is very close to those of the oxytocin and vasopressin hormones. We show that this very soluble peptide consistently self-assembles into 7 nm wide amyloid fibrils above a critical aggregation concentration (2-10 w/w % depending on the buffer conditions). The peptide system is characterized in details, from the monomeric to the assembled form, with osmotic concentration measurements, transmission electron microscopy, small-angle X-ray scattering, infrared and fluorescence spectroscopy, and circular dichroism (CD). We have followed in situ the fibril assembly with fluorescence and synchrotron radiation CD and noticed that the peptide undergoes conformational changes during the process. However, several lines of evidence point toward the association of monomers and dimers into fibrils without passing through oligomeric intermediate species contrary to what is usually reported for pathogenic amyloids. The native β-hairpin conformation of the monomer could explain the straightforward assembly. The tyrosine stacking is also shown to play an important role.
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Affiliation(s)
- Frédéric Gobeaux
- LIONS-NIMBE CEA, CNRS, Université Paris-Saclay, CEA Saclay , 91191 Gif-sur-Yvette Cedex , France
| | - Frank Wien
- SOLEIL Synchrotron , Saint Aubin 91190 , France
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40
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Greenwald J, Kwiatkowski W, Riek R. Peptide Amyloids in the Origin of Life. J Mol Biol 2018; 430:3735-3750. [PMID: 29890117 DOI: 10.1016/j.jmb.2018.05.046] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 05/29/2018] [Accepted: 05/31/2018] [Indexed: 10/14/2022]
Abstract
How life can emerge from non-living matter is one of the fundamental mysteries of the universe. A bottom-up approach to this problem focuses on the potential chemical precursors of life, in particular the nature of the first replicative molecules. Such thinking has led to the currently most popular idea: that an RNA-like molecule played a central role as the first replicative and catalytic molecule. Here, we review an alternative hypothesis that has recently gained experimental support, focusing on the role of amyloidogenic peptides rather than nucleic acids, in what has been by some termed "the amyloid-world" hypothesis. Amyloids are well-ordered peptide aggregates that have a fibrillar morphology due to their underlying structure of a one-dimensional crystal-like array of peptides in a β-strand conformation. While they are notorious for their implication in several neurodegenerative diseases including Alzheimer's disease, amyloids also have many biological functions. In this review, we will elaborate on the following properties of amyloids in relation to their fitness as a prebiotic entity: they can be formed by very short peptides with simple amino acids sequences; as aggregates they are more chemically stable than their isolated component peptides; they can possess diverse catalytic activities; they can form spontaneously during the prebiotic condensation of amino acids; they can act as templates in their own chemical replication; they have a structurally repetitive nature that enables them to interact with other structurally repetitive biopolymers like RNA/DNA and polysaccharides, as well as with structurally repetitive surfaces like amphiphilic membranes and minerals.
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Affiliation(s)
- Jason Greenwald
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Witek Kwiatkowski
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland.
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41
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Abstract
Amyloid fibrils are protein homopolymers that adopt diverse cross-β conformations. Some amyloid fibrils are associated with the pathogenesis of devastating neurodegenerative disorders, including Alzheimer's disease and Parkinson's disease. Conversely, functional amyloids play beneficial roles in melanosome biogenesis, long-term memory formation and release of peptide hormones. Here, we showcase advances in our understanding of amyloid assembly and structure, and how distinct amyloid strains formed by the same protein can cause distinct neurodegenerative diseases. We discuss how mutant steric zippers promote deleterious amyloidogenesis and aberrant liquid-to-gel phase transitions. We also highlight effective strategies to combat amyloidogenesis and related toxicity, including: (1) small-molecule drugs (e.g. tafamidis) to inhibit amyloid formation or (2) stimulate amyloid degradation by the proteasome and autophagy, and (3) protein disaggregases that disassemble toxic amyloid and soluble oligomers. We anticipate that these advances will inspire therapeutics for several fatal neurodegenerative diseases. Summary: This Review showcases important advances in our understanding of amyloid structure, assembly and disassembly, which are inspiring novel therapeutic strategies for amyloid disorders.
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Affiliation(s)
- Edward Chuang
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.,Pharmacology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Acacia M Hori
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christina D Hesketh
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA .,Pharmacology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
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42
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Abstract
This paper is the thirty-ninth consecutive installment of the annual review of research concerning the endogenous opioid system. It summarizes papers published during 2016 that studied the behavioral effects of molecular, pharmacological and genetic manipulation of opioid peptides, opioid receptors, opioid agonists and opioid antagonists. The particular topics that continue to be covered include the molecular-biochemical effects and neurochemical localization studies of endogenous opioids and their receptors related to behavior, and the roles of these opioid peptides and receptors in pain and analgesia, stress and social status, tolerance and dependence, learning and memory, eating and drinking, drug abuse and alcohol, sexual activity and hormones, pregnancy, development and endocrinology, mental illness and mood, seizures and neurologic disorders, electrical-related activity and neurophysiology, general activity and locomotion, gastrointestinal, renal and hepatic functions, cardiovascular responses, respiration and thermoregulation, and immunological responses.
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Affiliation(s)
- Richard J Bodnar
- Department of Psychology and CUNY Neuroscience Collaborative, Queens College, City University of New York, Flushing, NY 11367, United States.
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43
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Quittot N, Sebastiao M, Al-Halifa S, Bourgault S. Kinetic and Conformational Insights into Islet Amyloid Polypeptide Self-Assembly Using a Biarsenical Fluorogenic Probe. Bioconjug Chem 2018; 29:517-527. [DOI: 10.1021/acs.bioconjchem.7b00827] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Noé Quittot
- Department of Chemistry, Quebec Network
for Research on Protein Function, Engineering and Applications, PROTEO, University of Québec in Montreal, C.P. 8888, Succursale Centre-Ville, Montreal, Québec H3C 3P8, Canada
| | - Mathew Sebastiao
- Department of Chemistry, Quebec Network
for Research on Protein Function, Engineering and Applications, PROTEO, University of Québec in Montreal, C.P. 8888, Succursale Centre-Ville, Montreal, Québec H3C 3P8, Canada
| | - Soultan Al-Halifa
- Department of Chemistry, Quebec Network
for Research on Protein Function, Engineering and Applications, PROTEO, University of Québec in Montreal, C.P. 8888, Succursale Centre-Ville, Montreal, Québec H3C 3P8, Canada
| | - Steve Bourgault
- Department of Chemistry, Quebec Network
for Research on Protein Function, Engineering and Applications, PROTEO, University of Québec in Montreal, C.P. 8888, Succursale Centre-Ville, Montreal, Québec H3C 3P8, Canada
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44
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Davis CM, Gruebele M, Sukenik S. How does solvation in the cell affect protein folding and binding? Curr Opin Struct Biol 2018; 48:23-29. [PMID: 29035742 DOI: 10.1016/j.sbi.2017.09.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/19/2017] [Accepted: 09/22/2017] [Indexed: 12/21/2022]
Abstract
The cellular environment is highly diverse and capable of rapid changes in solute composition and concentrations. Decades of protein studies have highlighted their sensitivity to solute environment, yet these studies were rarely performed in situ. Recently, new techniques capable of monitoring proteins in their natural context within a live cell have emerged. A recurring theme of these investigations is the importance of the often-neglected cellular solvation environment to protein function. An emerging consensus is that protein processes in the cell are affected by a combination of steric and non-steric interactions with this solution. Here we explain how protein surface area and volume changes control these two interaction types, and give recent examples that highlight how even mild environmental changes can alter cellular processes.
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Affiliation(s)
- Caitlin M Davis
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Martin Gruebele
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Shahar Sukenik
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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45
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Vermeer LS, Hamon L, Schirer A, Schoup M, Cosette J, Majdoul S, Pastré D, Stockholm D, Holic N, Hellwig P, Galy A, Fenard D, Bechinger B. Vectofusin-1, a potent peptidic enhancer of viral gene transfer forms pH-dependent α-helical nanofibrils, concentrating viral particles. Acta Biomater 2017; 64:259-268. [PMID: 29017974 DOI: 10.1016/j.actbio.2017.10.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 10/02/2017] [Accepted: 10/06/2017] [Indexed: 01/13/2023]
Abstract
Gene transfer using lentiviral vectors has therapeutic applications spanning from monogenic and infectious diseases to cancer. Such gene therapy has to be improved by enhancing the levels of viral infection of target cells and/or reducing the amount of lentivirus for greater safety and reduced costs. Vectofusin-1, a recently developed cationic amphipathic peptide with a pronounced capacity to enhance such viral transduction, strongly promotes the entry of several retroviral pseudotypes into target cells when added to the culture medium. To clarify the molecular basis of its action the peptide was investigated on a molecular and a supramolecular level by a variety of biophysical approaches. We show that in culture medium vectofusin-1 rapidly forms complexes in the 10 nm range that further assemble into annular and extended nanofibrils. These associate with viral particles allowing them to be easily pelleted for optimal virus-cell interaction. Thioflavin T fluorescence, circular dichroism and infrared spectroscopies indicate that these fibrils have a unique α-helical structure whereas most other viral transduction enhancers form β-amyloid fibrils. A vectofusin-1 derivative (LAH2-A4) is inefficient in biological assays and does not form nanofibrils, suggesting that supramolecular assembly is essential for transduction enhancement. Our observations define vectofusin-1 as a member of a new class of α-helical enhancers of lentiviral infection. Its fibril formation is reversible which bears considerable advantages in handling the peptide in conditions well-adapted to Good Manufacturing Practices and scalable gene therapy protocols.
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Affiliation(s)
- Louic S Vermeer
- CNRS, Univ. of Strasbourg, Institut de Chimie UMR_7177, Strasbourg, France
| | - Loic Hamon
- INSERM, Univ. of Evry, UMR_S1204, Evry, France
| | | | - Michel Schoup
- CNRS, Univ. of Strasbourg, Institut de Chimie UMR_7177, Strasbourg, France
| | | | - Saliha Majdoul
- Genethon, INSERM, Univ. of Evry, EPHE-PSL Research University, Research Unit Integrare UMR_S951, Evry, France
| | | | - Daniel Stockholm
- Genethon, INSERM, Univ. of Evry, EPHE-PSL Research University, Research Unit Integrare UMR_S951, Evry, France
| | - Nathalie Holic
- Genethon, INSERM, Univ. of Evry, EPHE-PSL Research University, Research Unit Integrare UMR_S951, Evry, France
| | - Petra Hellwig
- CNRS, Univ. of Strasbourg, UMR 7140, Strasbourg, France
| | - Anne Galy
- Genethon, INSERM, Univ. of Evry, EPHE-PSL Research University, Research Unit Integrare UMR_S951, Evry, France
| | | | - Burkhard Bechinger
- CNRS, Univ. of Strasbourg, Institut de Chimie UMR_7177, Strasbourg, France.
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46
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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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47
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Controlling the bioactivity of a peptide hormone in vivo by reversible self-assembly. Nat Commun 2017; 8:1026. [PMID: 29044101 PMCID: PMC5647335 DOI: 10.1038/s41467-017-01114-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 08/18/2017] [Indexed: 01/17/2023] Open
Abstract
The use of peptides as therapeutic agents is undergoing a renaissance with the expectation of new drugs with enhanced levels of efficacy and safety. Their clinical potential will be only fully realised once their physicochemical and pharmacokinetic properties have been precisely controlled. Here we demonstrate a reversible peptide self-assembly strategy to control and prolong the bioactivity of a native peptide hormone in vivo. We show that oxyntomodulin, a peptide with potential to treat obesity and diabetes, self-assembles into a stable nanofibril formulation which subsequently dissociates to release active peptide and produces a pharmacological effect in vivo. The subcutaneous administration of the nanofibrils in rats results in greatly prolonged exposure, with a constant oxyntomodulin bioactivity detectable in serum for at least 5 days as compared to free oxyntomodulin which is undetectable after only 4 h. Such an approach is simple, cost-efficient and generic in addressing the limitations of peptide therapeutics. The clinical potential of peptide therapeutic agents can only be fully realised once their physicochemical and pharmacokinetic properties are precisely controlled. Here the authors show a reversible peptide self-assembly strategy to control and prolong the bioactivity of a native peptide hormone in vivo.
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48
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McGlinchey RP, Lee JC. Reversing the amyloid trend: Mechanism of fibril assembly and dissolution of the repeat domain from a human functional amyloid. Isr J Chem 2017; 57:613-621. [PMID: 28993712 PMCID: PMC5630176 DOI: 10.1002/ijch.201600080] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Amyloids are traditionally observed in the context of disease. However, there is growing momentum that these structures can serve a beneficial role where the amyloid carries out a specific function. These so called 'functional amyloids' have all the structural hallmarks of disease-associated amyloids, raising the question as to what differentiates a well-behaved benign amyloid from a lethally destructive one. Here, we review our work on the repeat domain (RPT) from Pmel17, an important functional amyloid involved in melanin biosynthesis. Particularly, we focused our attention on the unique reversible aggregation-disaggregation process of RPT that is controlled strictly by solution pH. This pH dependence of RPT amyloid formation functions as a switch to control fibril assembly and maintains the benign nature that is associated with functional amyloids.
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Affiliation(s)
- Ryan P. McGlinchey
- Laboratory of Protein Conformation and Dynamics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, U.S.A
| | - Jennifer C. Lee
- Laboratory of Protein Conformation and Dynamics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, U.S.A
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49
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Kubánková M, López-Duarte I, Bull JA, Vadukul DM, Serpell LC, de Saint Victor M, Stride E, Kuimova MK. Probing supramolecular protein assembly using covalently attached fluorescent molecular rotors. Biomaterials 2017. [PMID: 28622603 DOI: 10.1016/j.biomaterials.2017.06.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Changes in microscopic viscosity and macromolecular crowding accompany the transition of proteins from their monomeric forms into highly organised fibrillar states. Previously, we have demonstrated that viscosity sensitive fluorophores termed 'molecular rotors', when freely mixed with monomers of interest, are able to report on changes in microrheology accompanying amyloid formation, and measured an increase in rigidity of approximately three orders of magnitude during aggregation of lysozyme and insulin. Here we extend this strategy by covalently attaching molecular rotors to several proteins capable of assembly into fibrils, namely lysozyme, fibrinogen and amyloid-β peptide (Aβ(1-42)). We demonstrate that upon covalent attachment the molecular rotors can successfully probe supramolecular assembly in vitro. Importantly, our new strategy has wider applications in cellulo and in vivo, since covalently attached molecular rotors can be successfully delivered in situ and will colocalise with the aggregating protein, for example inside live cells. This important advantage allowed us to follow the microscopic viscosity changes accompanying blood clotting and during Aβ(1-42) aggregation in live SH-SY5Y cells. Our results demonstrate that covalently attached molecular rotors are a widely applicable tool to study supramolecular protein assembly and can reveal microrheological features of aggregating protein systems both in vitro and in cellulo not observable through classical fluorescent probes operating in light switch mode.
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Affiliation(s)
- Markéta Kubánková
- Chemistry Department, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
| | - Ismael López-Duarte
- Chemistry Department, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
| | - James A Bull
- Chemistry Department, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
| | - Devkee M Vadukul
- School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK
| | - Louise C Serpell
- School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK
| | | | - Eleanor Stride
- Institute of Biomedical Engineering, University of Oxford, Oxford, OX3 7DQ, UK
| | - Marina K Kuimova
- Chemistry Department, Imperial College London, Exhibition Road, London, SW7 2AZ, UK.
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50
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Quittot N, Sebastiao M, Bourgault S. Modulation of amyloid assembly by glycosaminoglycans: from mechanism to biological significance. Biochem Cell Biol 2017; 95:329-337. [DOI: 10.1139/bcb-2016-0236] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Glycosaminoglycans (GAGs) are long and unbranched polysaccharides that are abundant in the extracellular matrix and basement membrane of multicellular organisms. These linear polyanionic macromolecules are involved in many physiological functions from cell adhesion to cellular signaling. Interestingly, amyloid fibrils extracted from patients afflicted with protein misfolding diseases are virtually always associated with GAGs. Amyloid fibrils are highly organized nanostructures that have been historically associated with pathological states, such as Alzheimer’s disease and systemic amyloidoses. However, recent studies have identified functional amyloids that accomplish crucial physiological roles in almost all living organisms, from bacteria to insects and mammals. Over the last 2 decades, numerous reports have revealed that sulfated GAGs accelerate and (or) promote the self-assembly of a large diversity of proteins, both inherently amyloidogenic and non-aggregation prone. Despite the fact that many studies have investigated the molecular mechanism(s) by which GAGs induce amyloid assembly, the mechanistic elucidation of GAG-mediated amyloidogenesis still remains the subject of active research. In this review, we expose the contribution of GAGs in amyloid assembly, and we discuss the pathophysiological and functional significance of GAG-mediated fibrillization. Finally, we propose mechanistic models of the unique and potent ability of sulfated GAGs to hasten amyloid fibril formation.
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Affiliation(s)
- Noé Quittot
- Department of Chemistry, Pharmaqam, C.P. 8888, Succursale Centre-Ville, Université du Québec à Montréal (UQAM), Montreal, QC H3C 3P8, Canada
- Department of Chemistry, Pharmaqam, C.P. 8888, Succursale Centre-Ville, Université du Québec à Montréal (UQAM), Montreal, QC H3C 3P8, Canada
| | - Mathew Sebastiao
- Department of Chemistry, Pharmaqam, C.P. 8888, Succursale Centre-Ville, Université du Québec à Montréal (UQAM), Montreal, QC H3C 3P8, Canada
- Department of Chemistry, Pharmaqam, C.P. 8888, Succursale Centre-Ville, Université du Québec à Montréal (UQAM), Montreal, QC H3C 3P8, Canada
| | - Steve Bourgault
- Department of Chemistry, Pharmaqam, C.P. 8888, Succursale Centre-Ville, Université du Québec à Montréal (UQAM), Montreal, QC H3C 3P8, Canada
- Department of Chemistry, Pharmaqam, C.P. 8888, Succursale Centre-Ville, Université du Québec à Montréal (UQAM), Montreal, QC H3C 3P8, Canada
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