1
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Bogin BA, Levine ZA. Drugging Disordered Proteins by Conformational Selection to Inform Therapeutic Intervention. J Chem Theory Comput 2025; 21:3204-3215. [PMID: 40029731 DOI: 10.1021/acs.jctc.4c01160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2025]
Abstract
Drugging intrinsically disordered proteins (IDPs) has historically been a major challenge due to their lack of stable binding sites, conformational heterogeneity, and rapid ability to self-associate or bind nonspecific neighbors. Furthermore, it is unclear whether binders of disordered proteins (i) induce entirely new conformations or (ii) target transient prestructured conformations via stabilizing existing states. To distinguish between these two mechanisms, we utilize molecular dynamics simulations to induce structured conformations in islet amyloid polypeptide (IAPP), a disordered endocrine peptide implicated in Type II Diabetes. Using umbrella sampling, we measure conformation-specific affinities of molecules previously shown to bind IAPP to determine if they can discriminate between two distinct IAPP conformations (fixed in either α-helix or β-sheet). We show that our two-state model of IAPP faithfully predicts the experimentally observed selectivity of two classes of IAPP binders while revealing differences in their molecular binding mechanisms. Specifically, the binding preferences of foldamers designed for human IAPP were not fully accounted for by conformational selection, unlike those of β-breaking peptides designed to mimic IAPP self-assembly sequences. Furthermore, the binding of these foldamers, but not β-breaking peptides, was disrupted by changes in the rat IAPP sequence. Taken together, our data quantify the sequence and conformational specificity for IAPP binders and reveal that conformational selection sometimes overrides sequence-level specificity. This work highlights the important role of conformational selection in stabilizing IDPs, and it reveals how fixed conformations can provide a tractable target for developing disordered protein binders.
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Affiliation(s)
- Bryan A Bogin
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut 06520, United States
- Altos Laboratories, San Diego Institute of Science, San Diego, California 92121, United States
| | - Zachary A Levine
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut 06520, United States
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut 06510, United States
- Altos Laboratories, San Diego Institute of Science, San Diego, California 92121, United States
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2
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Liu H, Zhao X, Chen J, Win YY, Cai J. Unnatural foldamers as inhibitors of Aβ aggregation via stabilizing the Aβ helix. Chem Commun (Camb) 2025; 61:4586-4594. [PMID: 40035705 PMCID: PMC11878269 DOI: 10.1039/d4cc05280c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2024] [Accepted: 02/24/2025] [Indexed: 03/06/2025]
Abstract
Protein aggregation is a critical factor in the development and progression of several human diseases, including Alzheimer's disease (AD), Huntington's disease, Parkinson's disease, and type 2 diabetes. Among these conditions, AD is recognized as the most prevalent progressive neurodegenerative disorder, characterized by the accumulation of amyloid-beta (Aβ) peptides. Neuronal toxicity is likely driven by soluble oligomeric intermediates of the Aβ peptide, which are thought to play a central role in the cascade leading to neuronal dysfunction and cognitive decline. In response, numerous therapeutic strategies have been developed to inhibit Aβ oligomerization, as this is believed to delay the formation of Aβ protofibrils. Traditional research has focused on discovering small molecules or peptides that antagonize Aβ oligomerization. However, recent studies have explored an alternative approach-developing ligands that stabilize the Aβ peptide in its α-helical conformation. This stabilization is thought to alter the peptide's natural aggregation kinetics, shifting it away from toxic oligomer formation and toward less harmful states. Crucially, by maintaining Aβ in this α-helical form, these ligands have been shown to rescue the peptide's associated cytotoxicity, offering a promising mechanism to mitigate the detrimental effects of Aβ in AD. While challenges remain, including treatment costs and side effects like ARIA (amyloid-related imaging abnormalities), anti-Aβ drug development represents a major advancement in Alzheimer's research and therapeutic options. This brief review aims to highlight the development and potential of these α-helix-stabilizing ligands as antagonists of Aβ aggregation, focusing on their interactions with Aβ and how these compounds induce and maintain secondary structural changes in the Aβ peptide. Notably, this innovative strategy holds promise beyond Aβ-related pathology, as the fundamental principles could be applied to other amyloidogenic proteins implicated in various amyloid-related diseases, potentially broadening the scope of therapeutic intervention for multiple neurodegenerative conditions.
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Affiliation(s)
- Heng Liu
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, FL, 33620, USA.
| | - Xue Zhao
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, FL, 33620, USA.
| | - Jianyu Chen
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, FL, 33620, USA.
| | - Yu Yu Win
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, FL, 33620, USA.
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, FL, 33620, USA.
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3
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Naik AR, Save SN, Sahoo SS, Yadav SS, Kumar A, Chugh J, Sharma S. Metabolic perturbations associated with hIAPP-induced insulin resistance in skeletal muscles: Implications to the development of type 2 diabetes. Int J Biochem Cell Biol 2024; 176:106665. [PMID: 39322038 DOI: 10.1016/j.biocel.2024.106665] [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: 04/23/2024] [Revised: 09/16/2024] [Accepted: 09/18/2024] [Indexed: 09/27/2024]
Abstract
The human islet amyloid polypeptide (hIAPP) tends to misfold and self-assemble to form amyloid fibrils, which has been associated with the loss of function and viability of pancreatic β-cells in type 2 diabetes mellitus (T2DM). The role of hIAPP in the development of insulin resistance (a hallmark of T2DM) in skeletal muscles - the major sites for glucose utilization - needs further investigation. Even though, insulin-resistant conditions have been known to stimulate hIAPP aggregation, the events that lead to the development of insulin resistance due to hIAPP aggregation in skeletal muscles remain unidentified. Here, we have attempted to identify metabolic perturbations in L6 myotubes that were exposed to increasing concentrations of recombinant hIAPP for different time durations. It was observed that hIAPP exposure was associated with increased mitochondrial and cellular ROS levels, loss in mitochondrial membrane potential and viability of the myotubes. Metabolomic investigations of hIAPP-treated myotubes revealed significant perturbations in o-phosphocholine, sn-glycero-3-phosphocholine and dimethylamine levels (p < 0.05). Therefore, we anticipate that defects in glycerophospholipid metabolism and the associated oxidative stress and membrane damage may play key roles in the development of insulin resistance due to protein misfolding in skeletal muscles. In summary, the perturbed metabolites and their pathways have not only the potential to be used as early biomarkers to predict the onset of insulin resistance and T2DM but also as therapeutic targets for the effective management of the same.
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Affiliation(s)
- Arya R Naik
- Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune 411007, India
| | - Shreyada N Save
- Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune 411007, India
| | - Soumya S Sahoo
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Saurabh S Yadav
- Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune 411007, India
| | - Ashutosh Kumar
- Department of Biosciences and Bioengineering, Indian institute of technology Bombay, Powai, Mumbai, Maharashtra 400076, India
| | - Jeetender Chugh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Shilpy Sharma
- Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune 411007, India.
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4
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Babych M, Garelja ML, Nguyen PT, Hay DL, Bourgault S. Converting the Amyloidogenic Islet Amyloid Polypeptide into a Potent Nonaggregating Peptide Ligand by Side Chain-to-Side Chain Macrocyclization. J Am Chem Soc 2024; 146:25513-25526. [PMID: 39225636 DOI: 10.1021/jacs.4c05297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
The islet amyloid polypeptide (IAPP), also known as amylin, is a hormone playing key physiological roles. However, its aggregation and deposition in the pancreatic islets are associated with type 2 diabetes. While this peptide adopts mainly a random coil structure in solution, its secondary conformational conversion into α-helix represents a critical step for receptor activation and contributes to amyloid formation and associated cytotoxicity. Considering the large conformational landscape and high amyloidogenicity of the peptide, as well as the complexity of the self-assembly process, it is challenging to delineate the delicate interplay between helical folding, peptide aggregation, and receptor activation. In the present study, we probed the roles of helical folding on the function-toxicity duality of IAPP by restricting its conformational ensemble through side chain-to-side chain stapling via azide-alkyne cycloaddition. Intramolecular macrocyclization (i; i + 4) constrained IAPP into α-helix and inhibited its aggregation into amyloid fibrils. These helical derivatives slowed down the self-assembly of unmodified IAPP. Site-specific macrocyclization modulated the capacity of IAPP to perturb lipid bilayers and cell plasma membrane and reduced, or even fully inhibited, the cytotoxicity associated with aggregation. Furthermore, the α-helical IAPP analogs showed moderate to high potency toward cognate G protein-coupled receptors. Overall, these results indicate that macrocyclization represents a promising strategy to protect an amyloidogenic peptide hormone from aggregation and associated toxicity, while maintaining high receptor activity.
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Affiliation(s)
- Margaryta Babych
- Department of Chemistry, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montréal H3C 3P8, Canada
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO, C.P. 8888, Succursale Centre-Ville, Montréal H3C 3P8, Canada
| | - Michael L Garelja
- Department of Pharmacology and Toxicology, University of Otago, 18 Frederick Street, Dunedin 9016, New Zealand
| | - Phuong Trang Nguyen
- Department of Chemistry, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montréal H3C 3P8, Canada
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO, C.P. 8888, Succursale Centre-Ville, Montréal H3C 3P8, Canada
| | - Debbie L Hay
- Department of Pharmacology and Toxicology, University of Otago, 18 Frederick Street, Dunedin 9016, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, 3A Symonds Street, Auckland 92019, New Zealand
| | - Steve Bourgault
- Department of Chemistry, Université du Québec à Montréal, C.P. 8888, Succursale Centre-Ville, Montréal H3C 3P8, Canada
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO, C.P. 8888, Succursale Centre-Ville, Montréal H3C 3P8, Canada
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5
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Chia S, Cataldi RL, Ruggeri FS, Limbocker R, Condado-Morales I, Pisani K, Possenti A, Linse S, Knowles TPJ, Habchi J, Mannini B, Vendruscolo M. A Relationship between the Structures and Neurotoxic Effects of Aβ Oligomers Stabilized by Different Metal Ions. ACS Chem Neurosci 2024; 15:1125-1134. [PMID: 38416693 PMCID: PMC10958495 DOI: 10.1021/acschemneuro.3c00718] [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: 11/05/2023] [Revised: 02/06/2024] [Accepted: 02/06/2024] [Indexed: 03/01/2024] Open
Abstract
Oligomeric assemblies of the amyloid β peptide (Aβ) have been investigated for over two decades as possible neurotoxic agents in Alzheimer's disease. However, due to their heterogeneous and transient nature, it is not yet fully established which of the structural features of these oligomers may generate cellular damage. Here, we study distinct oligomer species formed by Aβ40 (the 40-residue form of Aβ) in the presence of four different metal ions (Al3+, Cu2+, Fe2+, and Zn2+) and show that they differ in their structure and toxicity in human neuroblastoma cells. We then describe a correlation between the size of the oligomers and their neurotoxic activity, which provides a type of structure-toxicity relationship for these Aβ40 oligomer species. These results provide insight into the possible role of metal ions in Alzheimer's disease by the stabilization of Aβ oligomers.
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Affiliation(s)
- Sean Chia
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Rodrigo Lessa Cataldi
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Francesco Simone Ruggeri
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Ryan Limbocker
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Itzel Condado-Morales
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Katarina Pisani
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Andrea Possenti
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Sara Linse
- Department
of Biochemistry & Structural Biology, Center for Molecular Protein
Science, Lund University, PO box 124, 221 00 Lund, Sweden
| | - Tuomas P. J. Knowles
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
- Department
of Physics, Cavendish Laboratory, Cambridge CB3 0HE, U.K.
| | - Johnny Habchi
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Benedetta Mannini
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Michele Vendruscolo
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
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6
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Qiao Q, Wei G, Song Z. Structural diversity in the membrane-bound hIAPP dimer correlated with distinct membrane disruption mechanisms. Phys Chem Chem Phys 2024; 26:7090-7102. [PMID: 38345763 DOI: 10.1039/d3cp05887e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Amyloid deposits of the human islet amyloid polypeptide (hIAPP) have been identified in 90% of patients with type II diabetes. Cellular membranes accelerate the hIAPP fibrillation, and the integrity of membranes is also disrupted at the same time, leading to the apoptosis of β cells in pancreas. The molecular mechanism of hIAPP-induced membrane disruption, especially during the initial membrane disruption stage, has not been well understood yet. Herein, we carried out extensive all-atom molecular dynamics simulations investigating the hIAPP dimerization process in the anionic POPG membrane, to provide the detailed molecular mechanisms during the initial hIAPP aggregation stage in the membrane environment. Compared to the hIAPP monomer on the membrane, we observed not only an increase of α-helical structures, but also a substantial increase of β-sheet structures upon spontaneous dimerization. Moreover, the random coiled and α-helical dimer structures insert deep into the membrane interior with a few inter-chain contacts at the C-terminal region, while the β-sheet-rich structures reside on the membrane surface accompanied by strong inter-chain hydrophobic interactions. The coexistence of α and β structures constitutes a diverse structural ensemble of the membrane-bound hIAPP dimer. From α-helical to β-sheet structures, the degree of membrane disruption decreases gradually, and thus the membrane damage induced by random coiled and α-helical structures precedes that induced by β-sheet structures. We speculate that insertion of random coiled and α-helical structures contributes to the initial stage of membrane damage, while β-sheet structures on the membrane surface are more involved in the later stage of fibril-induced membrane disruption.
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Affiliation(s)
- Qin Qiao
- Digital Medical Research Center, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.
- Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention, Shanghai 200032, China
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Science (Ministry of Education), Fudan University, Shanghai 200438, China
| | - Zhijian Song
- Digital Medical Research Center, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.
- Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention, Shanghai 200032, China
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7
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Mukherjee N, Contreras CJ, Lin L, Colglazier KA, Mather EG, Kalwat MA, Esser N, Kahn SE, Templin AT. RIPK3 promotes islet amyloid-induced β-cell loss and glucose intolerance in a humanized mouse model of type 2 diabetes. Mol Metab 2024; 80:101877. [PMID: 38218538 PMCID: PMC10830894 DOI: 10.1016/j.molmet.2024.101877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/29/2023] [Accepted: 01/09/2024] [Indexed: 01/15/2024] Open
Abstract
OBJECTIVE Aggregation of human islet amyloid polypeptide (hIAPP), a β-cell secretory product, leads to islet amyloid deposition, islet inflammation and β-cell loss in type 2 diabetes (T2D), but the mechanisms that underlie this process are incompletely understood. Receptor interacting protein kinase 3 (RIPK3) is a pro-death signaling molecule that has recently been implicated in amyloid-associated brain pathology and β-cell cytotoxicity. Here, we evaluated the role of RIPK3 in amyloid-induced β-cell loss using a humanized mouse model of T2D that expresses hIAPP and is prone to islet amyloid formation. METHODS We quantified amyloid deposition, cell death and caspase 3/7 activity in islets isolated from WT, Ripk3-/-, hIAPP and hIAPP; Ripk3-/- mice in real time, and evaluated hIAPP-stimulated inflammation in WT and Ripk3-/- bone marrow derived macrophages (BMDMs) in vitro. We also characterized the role of RIPK3 in glucose stimulated insulin secretion (GSIS) in vitro and in vivo. Finally, we examined the role of RIPK3 in high fat diet (HFD)-induced islet amyloid deposition, β-cell loss and glucose homeostasis in vivo. RESULTS We found that amyloid-prone hIAPP mouse islets exhibited increased cell death and caspase 3/7 activity compared to amyloid-free WT islets in vitro, and this was associated with increased RIPK3 expression. hIAPP; Ripk3-/- islets were protected from amyloid-induced cell death compared to hIAPP islets in vitro, although amyloid deposition and caspase 3/7 activity were not different between genotypes. We observed that macrophages are a source of Ripk3 expression in isolated islets, and that Ripk3-/- BMDMs were protected from hIAPP-stimulated inflammatory gene expression (Tnf, Il1b, Nos2). Following 52 weeks of HFD feeding, islet amyloid-prone hIAPP mice exhibited impaired glucose tolerance and decreased β-cell area compared to WT mice in vivo, whereas hIAPP; Ripk3-/- mice were protected from these impairments. CONCLUSIONS In conclusion, loss of RIPK3 protects from amyloid-induced inflammation and islet cell death in vitro and amyloid-induced β-cell loss and glucose intolerance in vivo. We propose that therapies targeting RIPK3 may reduce islet inflammation and β-cell loss and improve glucose homeostasis in the pathogenesis of T2D.
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Affiliation(s)
- Noyonika Mukherjee
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Christopher J Contreras
- Division of Endocrinology, Department of Medicine, Roudebush VA Medical Center and Indiana University School of Medicine, Indianapolis, IN, USA
| | - Li Lin
- Lilly Diabetes Center of Excellence, Indiana Biosciences Research Institute, Indianapolis, IN, USA
| | - Kaitlyn A Colglazier
- Lilly Diabetes Center of Excellence, Indiana Biosciences Research Institute, Indianapolis, IN, USA
| | - Egan G Mather
- Lilly Diabetes Center of Excellence, Indiana Biosciences Research Institute, Indianapolis, IN, USA
| | - Michael A Kalwat
- Lilly Diabetes Center of Excellence, Indiana Biosciences Research Institute, Indianapolis, IN, USA
| | - Nathalie Esser
- Division of Metabolism, Endocrinology and Nutrition, Department of Medicine, VA Puget Sound Health Care System and the University of Washington, Seattle, WA, USA
| | - Steven E Kahn
- Division of Metabolism, Endocrinology and Nutrition, Department of Medicine, VA Puget Sound Health Care System and the University of Washington, Seattle, WA, USA
| | - Andrew T Templin
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA; Division of Endocrinology, Department of Medicine, Roudebush VA Medical Center and Indiana University School of Medicine, Indianapolis, IN, USA; Lilly Diabetes Center of Excellence, Indiana Biosciences Research Institute, Indianapolis, IN, USA; Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN, USA.
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8
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Li XH, Yu CWH, Gomez-Navarro N, Stancheva V, Zhu H, Murthy A, Wozny M, Malhotra K, Johnson CM, Blackledge M, Santhanam B, Liu W, Huang J, Freund SMV, Miller EA, Babu MM. Dynamic conformational changes of a tardigrade group-3 late embryogenesis abundant protein modulate membrane biophysical properties. PNAS NEXUS 2024; 3:pgae006. [PMID: 38269070 PMCID: PMC10808001 DOI: 10.1093/pnasnexus/pgae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 12/26/2023] [Indexed: 01/26/2024]
Abstract
A number of intrinsically disordered proteins (IDPs) encoded in stress-tolerant organisms, such as tardigrade, can confer fitness advantage and abiotic stress tolerance when heterologously expressed. Tardigrade-specific disordered proteins including the cytosolic-abundant heat-soluble proteins are proposed to confer stress tolerance through vitrification or gelation, whereas evolutionarily conserved IDPs in tardigrades may contribute to stress tolerance through other biophysical mechanisms. In this study, we characterized the mechanism of action of an evolutionarily conserved, tardigrade IDP, HeLEA1, which belongs to the group-3 late embryogenesis abundant (LEA) protein family. HeLEA1 homologs are found across different kingdoms of life. HeLEA1 is intrinsically disordered in solution but shows a propensity for helical structure across its entire sequence. HeLEA1 interacts with negatively charged membranes via dynamic disorder-to-helical transition, mainly driven by electrostatic interactions. Membrane interaction of HeLEA1 is shown to ameliorate excess surface tension and lipid packing defects. HeLEA1 localizes to the mitochondrial matrix when expressed in yeast and interacts with model membranes mimicking inner mitochondrial membrane. Yeast expressing HeLEA1 shows enhanced tolerance to hyperosmotic stress under nonfermentative growth and increased mitochondrial membrane potential. Evolutionary analysis suggests that although HeLEA1 homologs have diverged their sequences to localize to different subcellular organelles, all homologs maintain a weak hydrophobic moment that is characteristic of weak and reversible membrane interaction. We suggest that such dynamic and weak protein-membrane interaction buffering alterations in lipid packing could be a conserved strategy for regulating membrane properties and represent a general biophysical solution for stress tolerance across the domains of life.
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Affiliation(s)
- Xiao-Han Li
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Conny W H Yu
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | | | - Hongni Zhu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Andal Murthy
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Michael Wozny
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Ketan Malhotra
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | - Martin Blackledge
- Université Grenoble Alpes, CNRS, Commissariat à l’Energie Atomique et aux Energies Alternatives, Institut de Biologie Structurale, 38000 Grenoble, France
| | - Balaji Santhanam
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
- Department of Structural Biology, Center of Excellence for Data-Driven Discovery, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Wei Liu
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Jinqing Huang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | | | | | - M Madan Babu
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
- Department of Structural Biology, Center of Excellence for Data-Driven Discovery, St Jude Children's Research Hospital, Memphis, TN 38105, USA
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9
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Louros N, Schymkowitz J, Rousseau F. Mechanisms and pathology of protein misfolding and aggregation. Nat Rev Mol Cell Biol 2023; 24:912-933. [PMID: 37684425 DOI: 10.1038/s41580-023-00647-2] [Citation(s) in RCA: 94] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2023] [Indexed: 09/10/2023]
Abstract
Despite advances in machine learning-based protein structure prediction, we are still far from fully understanding how proteins fold into their native conformation. The conventional notion that polypeptides fold spontaneously to their biologically active states has gradually been replaced by our understanding that cellular protein folding often requires context-dependent guidance from molecular chaperones in order to avoid misfolding. Misfolded proteins can aggregate into larger structures, such as amyloid fibrils, which perpetuate the misfolding process, creating a self-reinforcing cascade. A surge in amyloid fibril structures has deepened our comprehension of how a single polypeptide sequence can exhibit multiple amyloid conformations, known as polymorphism. The assembly of these polymorphs is not a random process but is influenced by the specific conditions and tissues in which they originate. This observation suggests that, similar to the folding of native proteins, the kinetics of pathological amyloid assembly are modulated by interactions specific to cells and tissues. Here, we review the current understanding of how intrinsic protein conformational propensities are modulated by physiological and pathological interactions in the cell to shape protein misfolding and aggregation pathology.
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Affiliation(s)
- Nikolaos Louros
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.
| | - Frederic Rousseau
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.
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10
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Sebastiao M, Quittot N, Marcotte I, Bourgault S. Fluorescence Resonance Energy Transfer to Detect Plasma Membrane Perturbations in Giant Plasma Membrane Vesicles. Bio Protoc 2023; 13:e4838. [PMID: 37817901 PMCID: PMC10560696 DOI: 10.21769/bioprotoc.4838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/30/2023] [Accepted: 08/03/2023] [Indexed: 10/12/2023] Open
Abstract
Disruptions and perturbations of the cellular plasma membrane by peptides have garnered significant interest in the elucidation of biological phenomena. Typically, these complex processes are studied using liposomes as model membranes-either by encapsulating a fluorescent dye or by other spectroscopic approaches, such as nuclear magnetic resonance. Despite incorporating physiologically relevant lipids, no synthetic model truly recapitulates the full complexity and molecular diversity of the plasma membrane. Here, biologically representative membrane models, giant plasma membrane vesicles (GPMVs), are prepared from eukaryotic cells by inducing a budding event with a chemical stressor. The GPMVs are then isolated, and bilayers are labelled with fluorescent lipophilic tracers and incubated in a microplate with a membrane-active peptide. As the membranes become damaged and/or aggregate, the resulting fluorescence resonance energy transfer (FRET) between the two tracers increases and is measured periodically in a microplate. This approach offers a particularly useful way to detect perturbations when the membrane complexity is an important variable to consider. Additionally, it provides a way to kinetically detect damage to the plasma membrane, which can be correlated with the kinetics of peptide self-assembly or structural rearrangements. Key features • Allows testing of various peptide-membrane interaction conditions (peptide:phospholipid ratio, ionic strength, buffer, etc.) at once. • Uses intact plasma membrane vesicles that can be prepared from a variety of cell lines. • Can offer comparable throughput as with traditional synthetic lipid models (e.g., dye-encapsulated liposomes).
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Affiliation(s)
- Mathew Sebastiao
- Department of Chemistry, Université du Québec à Montréal, Montréal, QC, Canada
- PROTEO, Quebec Network for Research on Protein Function, Engineering, and Applications, Montréal, QC, Canada
| | - Noé Quittot
- Harvard Medical School, Boston, MA, USA
- Alzheimer Research Unit, Department of Neurology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Isabelle Marcotte
- Department of Chemistry, Université du Québec à Montréal, Montréal, QC, Canada
- PROTEO, Quebec Network for Research on Protein Function, Engineering, and Applications, Montréal, QC, Canada
| | - Steve Bourgault
- Department of Chemistry, Université du Québec à Montréal, Montréal, QC, Canada
- PROTEO, Quebec Network for Research on Protein Function, Engineering, and Applications, Montréal, QC, Canada
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11
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Nandeshwar, Rout J, Panda SM, Tripathy U. Phytoconstituents of Ashwagandha as potential inhibitors of human islet amyloid polypeptide (hIAPP): an in silico investigation. J Biomol Struct Dyn 2023; 42:11020-11036. [PMID: 37753786 DOI: 10.1080/07391102.2023.2259491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 09/09/2023] [Indexed: 09/28/2023]
Abstract
Amylin or human islet amyloid polypeptide (hIAPP) is a small peptide co-secreted with insulin. Its peripheral aggregation on the lipid bilayer leads to fibril formation. The formation of hIAPP fibrils is hypothesized to rupture the membrane of β -cells, which culminates in β-cell death. Following additional studies, amylin fibril formation is a hallmark of T2DM and is also implicitly responsible for Alzheimer's disease. This study reports the virtual screening of 1000 phytoconstituents of traditional Indian medicinal plants to get potential inhibitors of amylin, which will likely restrict and block amyloid aggregation, preventing the progression of T2DM and Alzheimer's illness. The compounds having drug-likeness properties (acquired from ADMET calculations) and highest binding affinities (from molecular docking) are subjected to molecular dynamics (MD) simulation to investigate the temporal stability of the conformations of the complexes. This study discovers that Withaferin A and Withacoagulin have the highest binding affinity for amylin, and their stability with amylin was verified further by parameters such as RMSD, RMSF, number of H-bonds and MMPBSA. Individual principle component analysis (PCA) confirms the stable complex formation of amylin with Withaferin A and Withacoagulin. We strongly believe that wet-lab experiments and clinical trials will help to validate our computational findings.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nandeshwar
- Department of Physics, Indian Institute of Technology (Indian School of Mines), Dhanbad, Jharkhand, India
| | - Janmejaya Rout
- Department of Physics, Indian Institute of Technology (Indian School of Mines), Dhanbad, Jharkhand, India
| | - Smita Manjari Panda
- Department of Physics, Indian Institute of Technology (Indian School of Mines), Dhanbad, Jharkhand, India
| | - Umakanta Tripathy
- Department of Physics, Indian Institute of Technology (Indian School of Mines), Dhanbad, Jharkhand, India
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12
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McCalpin SD, Widanage MCD, Fu R, Ramamoorthy A. On-Pathway Oligomer of Human Islet Amyloid Polypeptide Induced and Stabilized by Mechanical Rotation during Magic Angle Spinning Nuclear Magnetic Resonance. J Phys Chem Lett 2023; 14:7644-7649. [PMID: 37602799 PMCID: PMC11559835 DOI: 10.1021/acs.jpclett.3c02009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
Intermediates along the fibrillation pathway are generally considered to be the toxic species responsible for the pathologies of amyloid diseases. However, structural studies of these species have been hampered by heterogeneity and poor stability under standard aqueous conditions. Here, we report a novel methodology for producing stable, on-pathway oligomers of the human type-2 diabetes-associated islet amyloid polypeptide (hIAPP or amylin) using the mechanical forces associated with magic angle spinning (MAS). The species were a heterogeneous mixture of globular and short rod-like species with significant β-sheet content and the capability of seeding hIAPP fibrillation. We used MAS nuclear magnetic resonance to demonstrate that the nature of the species was sensitive to sample conditions, including peptide concentration, ionic strength, and buffer. The methodology should be suitable for studies of other aggregating systems.
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Affiliation(s)
- Samuel D. McCalpin
- Biophysics Program, Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, Michigan Neuroscience Institute, University of Michigan, Arbor, MI 48109, USA
| | - Malitha C. Dickwella Widanage
- Biophysics Program, Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, Michigan Neuroscience Institute, University of Michigan, Arbor, MI 48109, USA
| | - Riqiang Fu
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, Michigan Neuroscience Institute, University of Michigan, Arbor, MI 48109, USA
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13
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Sang P, Cai J. Unnatural helical peptidic foldamers as protein segment mimics. Chem Soc Rev 2023; 52:4843-4877. [PMID: 37401344 PMCID: PMC10389297 DOI: 10.1039/d2cs00395c] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Indexed: 07/05/2023]
Abstract
Unnatural helical peptidic foldamers have attracted considerable attention owing to their unique folding behaviours, diverse artificial protein binding mechanisms, and promising applications in chemical, biological, medical, and material fields. Unlike the conventional α-helix consisting of molecular entities of native α-amino acids, unnatural helical peptidic foldamers are generally comprised of well-defined backbone conformers with unique and unnatural structural parameters. Their folded structures usually arise from unnatural amino acids such as N-substituted glycine, N-substituted-β-alanine, β-amino acid, urea, thiourea, α-aminoxy acid, α-aminoisobutyric acid, aza-amino acid, aromatic amide, γ-amino acid, as well as sulfono-γ-AA amino acid. They can exhibit intriguing and predictable three-dimensional helical structures, generally featuring superior resistance to proteolytic degradation, enhanced bioavailability, and improved chemodiversity, and are promising in mimicking helical segments of various proteins. Although it is impossible to include every piece of research work, we attempt to highlight the research progress in the past 10 years in exploring unnatural peptidic foldamers as protein helical segment mimics, by giving some representative examples and discussing the current challenges and future perspectives. We expect that this review will help elucidate the principles of structural design and applications of existing unnatural helical peptidic foldamers in protein segment mimicry, thereby attracting more researchers to explore and generate novel unnatural peptidic foldamers with unique structural and functional properties, leading to more unprecedented and practical applications.
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Affiliation(s)
- Peng Sang
- Tianjian Laboratory of Advanced Biomedical Sciences, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China.
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, Tampa, FL 33620, USA.
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14
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McCalpin SD, Widanage MCD, Fu R, Ramamoorthy A. On-Pathway Oligomer of Human Islet Amyloid Polypeptide Induced and Stabilized by Mechanical Rotation During MAS NMR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.06.547982. [PMID: 37461639 PMCID: PMC10350039 DOI: 10.1101/2023.07.06.547982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Intermediates along the fibrillation pathway are generally considered to be the toxic species responsible for the pathologies of amyloid diseases. However, structural studies of these species have been hampered by heterogeneity and poor stability in standard aqueous conditions. Here, we report a novel methodology for producing stable, on-pathway oligomers of the human Type-2 Diabetes-associated islet amyloid polypeptide (hIAPP, or amylin) using the mechanical forces associated with magic angle spinning (MAS). The species were a heterogeneous mixture of globular and short rod-like species with significant beta-sheet content and the capability of seeding hIAPP fibrillation. We used MAS NMR to demonstrate that the nature of the species was sensitive to sample conditions including peptide concentration, ionic strength, and buffer. The methodology should be suitable for studies of other aggregating systems.
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Affiliation(s)
- Samuel D. McCalpin
- Biophysics Program, Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, Michigan Neuroscience Institute, University of Michigan, Arbor, MI 48109, USA
| | - Malitha C. Dickwella Widanage
- Biophysics Program, Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, Michigan Neuroscience Institute, University of Michigan, Arbor, MI 48109, USA
| | - Riqiang Fu
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida 32310, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics Program, Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, Michigan Neuroscience Institute, University of Michigan, Arbor, MI 48109, USA
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15
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Sebastiao M, Babych M, Quittot N, Kumar K, Arnold AA, Marcotte I, Bourgault S. Development of a novel fluorescence assay for studying lipid bilayer perturbation induced by amyloidogenic peptides using cell plasma membrane vesicles. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184118. [PMID: 36621762 DOI: 10.1016/j.bbamem.2022.184118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 11/22/2022] [Accepted: 12/27/2022] [Indexed: 01/07/2023]
Abstract
Numerous pathophysiological conditions are associated with the misfolding and aggregation of proteins into insoluble amyloid fibrils. The mechanisms by which this process leads to cellular dysfunction remain elusive, though several hypotheses point toward the perturbation of the cell plasma membrane by pre-fibrillar intermediates and/or amyloid growth. However, current models to study membrane perturbations are largely limited to synthetic lipid vesicles and most of experimental approaches cannot be transposed to complex cell-derived plasma membrane systems. Herein, vesicles originating from the plasma membrane of erythrocytes and β-pancreatic cells were used to study the perturbations induced by an amyloidogenic peptide, the islet amyloid polypeptide (IAPP). These biologically relevant lipid vesicles displayed a characteristic clustering in the presence of the amyloidogenic peptide, which was able to rupture membranes. By exploiting Förster resonance energy transfer (FRET), a rapid, simple, and potentially high-throughput assay to detect membrane perturbations of intact mammalian cell plasma membrane vesicles was implemented. The FRET kinetics of membrane perturbations closely correlated with the kinetics of thioflavin-T fluorescence associated with amyloid formation. This novel kinetics assay expands the toolbox available to study amyloid-associated membrane damage, bridging the gap between synthetic lipid vesicles and living cells.
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Affiliation(s)
- Mathew Sebastiao
- Department of Chemistry, Université du Québec à Montréal, Montreal, QC, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications, PROTEO, Quebec, QC, Canada
| | - Margaryta Babych
- Department of Chemistry, Université du Québec à Montréal, Montreal, QC, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications, PROTEO, Quebec, QC, Canada
| | - Noé Quittot
- Department of Chemistry, Université du Québec à Montréal, Montreal, QC, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications, PROTEO, Quebec, QC, Canada
| | - Kiran Kumar
- Department of Chemistry, Université du Québec à Montréal, Montreal, QC, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications, PROTEO, Quebec, QC, Canada
| | - Alexandre A Arnold
- Department of Chemistry, Université du Québec à Montréal, Montreal, QC, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications, PROTEO, Quebec, QC, Canada
| | - Isabelle Marcotte
- Department of Chemistry, Université du Québec à Montréal, Montreal, QC, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications, PROTEO, Quebec, QC, Canada.
| | - Steve Bourgault
- Department of Chemistry, Université du Québec à Montréal, Montreal, QC, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications, PROTEO, Quebec, QC, Canada.
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16
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Sohrabi T, Mirzaei-Behbahani B, Zadali R, Pirhaghi M, Morozova-Roche LA, Meratan AA. Common Mechanisms Underlying α-Synuclein-Induced Mitochondrial Dysfunction in Parkinson's Disease. J Mol Biol 2023:167992. [PMID: 36736886 DOI: 10.1016/j.jmb.2023.167992] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/19/2023] [Accepted: 01/24/2023] [Indexed: 02/05/2023]
Abstract
Parkinson's disease (PD) is the most common neurological movement disorder characterized by the selective and irreversible loss of dopaminergic neurons in substantia nigra pars compacta resulting in dopamine deficiency in the striatum. While most cases are sporadic or environmental, about 10% of patients have a positive family history with a genetic cause. The misfolding and aggregation of α-synuclein (α-syn) as a casual factor in the pathogenesis of PD has been supported by a great deal of literature. Extensive studies of mechanisms underpinning degeneration of the dopaminergic neurons induced by α-syn dysfunction suggest a complex process that involves multiple pathways, including mitochondrial dysfunction and increased oxidative stress, impaired calcium homeostasis through membrane permeabilization, synaptic dysfunction, impairment of quality control systems, disruption of microtubule dynamics and axonal transport, endoplasmic reticulum/Golgi dysfunction, nucleus malfunction, and microglia activation leading to neuroinflammation. Among them mitochondrial dysfunction has been considered as the most primary target of α-syn-induced toxicity, leading to neuronal cell death in both sporadic and familial forms of PD. Despite reviewing many aspects of PD pathogenesis related to mitochondrial dysfunction, a systemic study on how α-syn malfunction/aggregation damages mitochondrial functionality and leads to neurodegeneration is missing in the literature. In this review, we give a detailed molecular overview of the proposed mechanisms by which α-syn, directly or indirectly, contributes to mitochondrial dysfunction. This may provide valuable insights for development of new therapeutic approaches in relation to PD. Antioxidant-based therapy as a potential strategy to protect mitochondria against oxidative damage, its challenges, and recent developments in the field are discussed.
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Affiliation(s)
- Tahereh Sohrabi
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran
| | - Behnaz Mirzaei-Behbahani
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran
| | - Ramin Zadali
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Mitra Pirhaghi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | | | - Ali Akbar Meratan
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran.
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17
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Elenbaas BO, Kremsreiter SM, Khemtemourian L, Killian JA, Sinnige T. Fibril elongation by human islet amyloid polypeptide is the main event linking aggregation to membrane damage. BBA ADVANCES 2023; 3:100083. [PMID: 37082256 PMCID: PMC10074975 DOI: 10.1016/j.bbadva.2023.100083] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
Abstract
The aggregation of human islet amyloid polypeptide (hIAPP) is linked to the death of pancreatic β-cells in type II diabetes. The process of fibril formation by hIAPP is thought to cause membrane damage, but the precise mechanisms are still unclear. Previously, we showed that the aggregation of hIAPP in the presence of membranes containing anionic lipids is dominated by secondary nucleation events, which occur at the interface between existing fibrils and the membrane surface. Here, we used vesicles with different lipid composition to explore the connection between hIAPP aggregation and vesicle leakage. We found that different anionic lipids promote hIAPP aggregation to the same extent, whereas remarkably stochastic behaviour is observed on purely zwitterionic membranes. Vesicle leakage induced by hIAPP consists of two distinct phases for any of the used membrane compositions: (i) an initial phase in which hIAPP binding causes a certain level of leakage that is strongly dependent on osmotic conditions, membrane composition and the used dye, and (ii) a main leakage event that we attribute to elongation of hIAPP fibrils, based on seeded experiments. Altogether, our results shed more light on the relationship between hIAPP fibril formation and membrane damage, and strongly suggest that oligomeric intermediates do not considerably contribute to vesicle leakage.
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Affiliation(s)
- Barend O.W. Elenbaas
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Stefanie M. Kremsreiter
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Lucie Khemtemourian
- Institute of Chemistry & Biology of Membranes & Nanoobjects (CBMN), CNRS UMR5248, University of Bordeaux, Bordeaux INP, allée Geoffroy St-Hilaire, 33600, Pessac, France
| | - J. Antoinette Killian
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Tessa Sinnige
- Membrane Biochemistry and Biophysics, Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
- Corresponding author.
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18
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Maity D. Inhibition of Amyloid Protein Aggregation Using Selected Peptidomimetics. ChemMedChem 2023; 18:e202200499. [PMID: 36317359 DOI: 10.1002/cmdc.202200499] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/28/2022] [Indexed: 11/24/2022]
Abstract
Aberrant protein aggregation leads to the formation of amyloid fibrils. This phenomenon is linked to the development of more than 40 irremediable diseases such as Alzheimer's disease, Parkinson's disease, type 2 diabetes, and cancer. Plenty of research efforts have been given to understanding the underlying mechanism of protein aggregation, associated toxicity, and the development of amyloid inhibitors. Recently, the peptidomimetic approach has emerged as a potential tool to modulate several protein-protein interactions (PPIs). In this review, we discussed selected peptidomimetic-based approaches for the modulation of important amyloid proteins (Islet Amyloid Polypeptide, Amyloid Beta, α-synuclein, mutant p53, and insulin) aggregation. This approach holds a powerful platform for creating an essential stepping stone for the vital development of anti-amyloid therapeutic agents.
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Affiliation(s)
- Debabrata Maity
- Department of Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad, 500007, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
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19
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Understanding the mechanism of amylin aggregation: From identifying crucial segments to tracing dominant sequential events to modeling potential aggregation suppressors. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140866. [PMID: 36272537 DOI: 10.1016/j.bbapap.2022.140866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/07/2022] [Accepted: 10/13/2022] [Indexed: 11/13/2022]
Abstract
One of the most abundant, prevailing, and life-threatening human diseases that are currently baffling the scientific community is type 2 diabetes (T2D). The self-association of human amylin has been implicated in the pathogenesis of T2D, though with an inconclusive understanding of the mechanism. Hence, we focused on the characterization of the conformational ensembles of all the species that are believed to define the structural polymorphism of the aggregation process - the functional monomeric, the initially self-associated oligomeric, and the structured protofibril - by employing near-equilibrium, non-equilibrium, and equilibrium atomistic simulations on the sporadic, two familial variants (S20G and G33R), and their proline-substituted forms (S20P and G33P). The dynamic near-equilibrium assays hint toward - the abundance of helical conformation in the monomeric state, the retainment of the helicity in the initial self-associated oligomeric phase pointing toward the existence of the helix-helix association mechanism, the difference in preference of specific segments to have definite secondary structural features, the phase-dependent variability in the dominance of specific segments and mutation sites, and the simultaneous presence of generic and unique features among various sequences. Furthermore, the non-equilibrium pulling assays exemplify a generic sequential unzipping mechanism of the protofibrils, however, the sequence-dependent uniqueness comes from the difference in location and magnitude of the control of a specific terminus. Importantly, the equilibrium thermodynamic assays efficiently rank order the potential of aggregability among sequences and consequently suggests the probability of designing effective aggregation suppressors against sporadic and familial amylin variants incorporating proline as the mutation.
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20
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Maity D, Oh Y, Gremer L, Hoyer W, Magzoub M, Hamilton AD. Cucurbit[7]uril Inhibits Islet Amyloid Polypeptide Aggregation by Targeting N Terminus Hot Segments and Attenuates Cytotoxicity. Chemistry 2022; 28:e202200456. [DOI: 10.1002/chem.202200456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Debabrata Maity
- Department of Chemistry New York University New York NY 10003 USA
- Present Address: Department of Organic Synthesis and Process Chemistry CSIR-Indian Institute of Chemical Technology (CSIR-IICT) Hyderabad 500007 India
| | - Yujeong Oh
- Biology Program New York University Abu Dhabi P.O. Box 129188, Saadiyat Island Campus Abu Dhabi United Arab Emirates
| | - Lothar Gremer
- Institut für Physikalische Biologie Heinrich-Heine-Universität Düsseldorf 40225 Düsseldorf Germany
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct: Jülich Center for Structural Biology Forschungszentrum Jülich 52425 Jülich Germany
| | - Wolfgang Hoyer
- Institut für Physikalische Biologie Heinrich-Heine-Universität Düsseldorf 40225 Düsseldorf Germany
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct: Jülich Center for Structural Biology Forschungszentrum Jülich 52425 Jülich Germany
| | - Mazin Magzoub
- Biology Program New York University Abu Dhabi P.O. Box 129188, Saadiyat Island Campus Abu Dhabi United Arab Emirates
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21
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Hnath B, Dokholyan NV. Toxic SOD1 trimers are off-pathway in the formation of amyloid-like fibrils in ALS. Biophys J 2022; 121:2084-2095. [PMID: 35505609 DOI: 10.1016/j.bpj.2022.04.037] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 04/01/2022] [Accepted: 04/28/2022] [Indexed: 11/26/2022] Open
Abstract
Accumulation of insoluble amyloid fibrils is widely studied as a critical factor in the pathology of multiple neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), a fatal neurodegenerative disease. Misfolded Cu, Zn superoxide dismutase (SOD1) was the first protein linked to ALS, and non-native SOD1 trimeric oligomers were recently linked to cytotoxicity, while larger oligomers were protective to cells. The balance between trimers and larger aggregates in the process of SOD1 aggregation is, thus, a critical determinant of potential therapeutic approaches to treat ALS. Yet, it is unknown whether these trimeric oligomers are a necessary intermediate for larger aggregate formation or a distinct off-pathway species competing with fibril formation. Depending on the on- or off-pathway scenario of trimer formation, we expect drastically different therapeutic approaches. Here, we show that the toxic SOD1 trimer is an off-pathway intermediate competing with protective fibril formation. We design mutant SOD1 constructs that remain in a trimeric state (super stable trimers) and show that stabilizing the trimeric SOD1 prevents formation of fibrils in vitro and in a motor neuron like cell model (NSC-34). Using size exclusion chromatography, we track the aggregation kinetics of purified SOD1 and show direct competition of trimeric SOD1 with larger oligomer and fibril formation. Finally, we show the trimer is structurally independent of both larger soluble oligomers and insoluble fibrils using circular dichroism spectroscopy and limited proteolysis.
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Affiliation(s)
- Brianna Hnath
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA; Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
| | - Nikolay V Dokholyan
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA; Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA; Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA, USA
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22
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Ahmed J, Fitch TC, Donnelly CM, Joseph JA, Ball TD, Bassil MM, Son A, Zhang C, Ledreux A, Horowitz S, Qin Y, Paredes D, Kumar S. Foldamers reveal and validate therapeutic targets associated with toxic α-synuclein self-assembly. Nat Commun 2022; 13:2273. [PMID: 35477706 PMCID: PMC9046208 DOI: 10.1038/s41467-022-29724-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 03/22/2022] [Indexed: 12/23/2022] Open
Abstract
Parkinson's disease (PD) is a progressive neurodegenerative disorder for which there is no successful prevention or intervention. The pathological hallmark for PD involves the self-assembly of functional Alpha-Synuclein (αS) into non-functional amyloid structures. One of the potential therapeutic interventions against PD is the effective inhibition of αS aggregation. However, the bottleneck towards achieving this goal is the identification of αS domains/sequences that are essential for aggregation. Using a protein mimetic approach, we have identified αS sequences-based targets that are essential for aggregation and will have significant therapeutic implications. An extensive array of in vitro, ex vivo, and in vivo assays is utilized to validate αS sequences and their structural characteristics that are essential for aggregation and propagation of PD phenotypes. The study aids in developing significant mechanistic and therapeutic insights into various facets of αS aggregation, which will pave the way for effective treatments for PD.
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Affiliation(s)
- Jemil Ahmed
- Molecular and Cellular Biophysics Program, University of Denver, Denver, CO, 80210, USA.,The Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, 80210, USA
| | - Tessa C Fitch
- The Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, 80210, USA.,Department of Chemistry and Biochemistry, University of Denver, Denver, CO, 80210, USA
| | - Courtney M Donnelly
- The Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, 80210, USA.,Department of Chemistry and Biochemistry, University of Denver, Denver, CO, 80210, USA
| | - Johnson A Joseph
- The Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, 80210, USA.,Department of Chemistry and Biochemistry, University of Denver, Denver, CO, 80210, USA
| | - Tyler D Ball
- The Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, 80210, USA.,Department of Chemistry and Biochemistry, University of Denver, Denver, CO, 80210, USA
| | - Mikaela M Bassil
- The Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, 80210, USA.,Department of Chemistry and Biochemistry, University of Denver, Denver, CO, 80210, USA
| | - Ahyun Son
- The Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, 80210, USA.,Department of Chemistry and Biochemistry, University of Denver, Denver, CO, 80210, USA
| | - Chen Zhang
- Department of Biological Sciences, University of Denver, Denver, CO, 80210, USA
| | - Aurélie Ledreux
- The Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, 80210, USA
| | - Scott Horowitz
- Molecular and Cellular Biophysics Program, University of Denver, Denver, CO, 80210, USA.,The Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, 80210, USA.,Department of Chemistry and Biochemistry, University of Denver, Denver, CO, 80210, USA
| | - Yan Qin
- Department of Biological Sciences, University of Denver, Denver, CO, 80210, USA
| | - Daniel Paredes
- The Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, 80210, USA
| | - Sunil Kumar
- Molecular and Cellular Biophysics Program, University of Denver, Denver, CO, 80210, USA. .,The Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, 80210, USA. .,Department of Chemistry and Biochemistry, University of Denver, Denver, CO, 80210, USA.
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23
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Mukherjee N, Lin L, Contreras CJ, Templin AT. β-Cell Death in Diabetes: Past Discoveries, Present Understanding, and Potential Future Advances. Metabolites 2021; 11:796. [PMID: 34822454 PMCID: PMC8620854 DOI: 10.3390/metabo11110796] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/15/2021] [Accepted: 11/18/2021] [Indexed: 12/19/2022] Open
Abstract
β-cell death is regarded as a major event driving loss of insulin secretion and hyperglycemia in both type 1 and type 2 diabetes mellitus. In this review, we explore past, present, and potential future advances in our understanding of the mechanisms that promote β-cell death in diabetes, with a focus on the primary literature. We first review discoveries of insulin insufficiency, β-cell loss, and β-cell death in human diabetes. We discuss findings in humans and mouse models of diabetes related to autoimmune-associated β-cell loss and the roles of autoreactive T cells, B cells, and the β cell itself in this process. We review discoveries of the molecular mechanisms that underlie β-cell death-inducing stimuli, including proinflammatory cytokines, islet amyloid formation, ER stress, oxidative stress, glucotoxicity, and lipotoxicity. Finally, we explore recent perspectives on β-cell death in diabetes, including: (1) the role of the β cell in its own demise, (2) methods and terminology for identifying diverse mechanisms of β-cell death, and (3) whether non-canonical forms of β-cell death, such as regulated necrosis, contribute to islet inflammation and β-cell loss in diabetes. We believe new perspectives on the mechanisms of β-cell death in diabetes will provide a better understanding of this pathological process and may lead to new therapeutic strategies to protect β cells in the setting of diabetes.
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Affiliation(s)
- Noyonika Mukherjee
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
- Lilly Diabetes Center of Excellence, Indiana Biosciences Research Institute, Indianapolis, IN 46202, USA; (L.L.); (C.J.C.)
| | - Li Lin
- Lilly Diabetes Center of Excellence, Indiana Biosciences Research Institute, Indianapolis, IN 46202, USA; (L.L.); (C.J.C.)
| | - Christopher J. Contreras
- Lilly Diabetes Center of Excellence, Indiana Biosciences Research Institute, Indianapolis, IN 46202, USA; (L.L.); (C.J.C.)
- Department of Medicine, Roudebush Veterans Affairs Medical Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Andrew T. Templin
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
- Lilly Diabetes Center of Excellence, Indiana Biosciences Research Institute, Indianapolis, IN 46202, USA; (L.L.); (C.J.C.)
- Department of Medicine, Roudebush Veterans Affairs Medical Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Center for Diabetes and Metabolic Diseases, School of Medicine, Indiana University, Indianapolis, IN 46202, USA
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24
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Pathak BK, Dey S, Mozumder S, Sengupta J. The role of membranes in function and dysfunction of intrinsically disordered amyloidogenic proteins. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 128:397-434. [PMID: 35034725 DOI: 10.1016/bs.apcsb.2021.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Membrane-protein interactions play a major role in human physiology as well as in diseases pathology. Interaction of a protein with the membrane was previously thought to be dependent on well-defined three-dimensional structure of the protein. In recent decades, however, it has become evident that a large fraction of the proteome, particularly in eukaryotes, stays disordered in solution and these proteins are termed as intrinsically disordered proteins (IDPs). Also, a vast majority of human proteomes have been reported to contain substantially long disordered regions, called intrinsically disordered regions (IDRs), in addition to the structurally ordered regions. IDPs exist in an ensemble of conformations and the conformational flexibility enables IDPs to achieve functional diversity. IDPs (and IDRs) are found to be important players in cell signaling, where biological membranes act as anchors for signaling cascades. Therefore, IDPs modulate the membrane architectures, at the same time membrane composition also affects the binding of IDPs. Because of intrinsic disorders, misfolding of IDPs often leads to formation of oligomers, protofibrils and mature fibrils through progressive self-association. Accumulation of amyloid-like aggregates of some of the IDPs is a known causative agent for numerous diseases. In this chapter we highlight recent advances in understanding membrane interactions of some of the intrinsically disordered proteins involved in the pathogenesis of human diseases.
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Affiliation(s)
- Bani Kumar Pathak
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata, India
| | - Sandip Dey
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata, India
| | - Sukanya Mozumder
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Jayati Sengupta
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
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25
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Sepehri A, Nepal B, Lazaridis T. Distinct Modes of Action of IAPP Oligomers on Membranes. J Chem Inf Model 2021; 61:4645-4655. [PMID: 34499498 DOI: 10.1021/acs.jcim.1c00767] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Islet amyloid polypeptide (IAPP, also known as amylin) is a peptide hormone that is co-secreted with insulin by pancreatic β-cells and forms amyloid aggregates in type II diabetes. Various lines of evidence indicate that oligomers of this peptide may induce toxicity by disrupting or forming pores in cell membranes, but the structure of these pores is unknown. Here, we create models of pores for both helical and β-structured peptides using implicit membrane modeling and test their stability using multimicrosecond all-atom simulations. We find that the helical peptides behave similarly to antimicrobial peptides; they remain stably inserted in a highly tilted or partially unfolded configuration creating a narrow water channel. Parallel helix orientation creates a somewhat larger pore. An octameric β barrel of parallel β-hairpins is highly stable in the membrane, whereas the corresponding barrel made of antiparallel hairpins is not. We propose that certain experiments probe the helical pore state while others probe the β-structured pore state; this provides a possible explanation for lack of correlation that is sometimes observed between in vivo toxicity and in vitro liposome permeabilization experiments.
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Affiliation(s)
- Aliasghar Sepehri
- Department of Chemistry, City College of New York, New York, New York 10031, United States
| | - Binod Nepal
- Department of Chemistry, City College of New York, New York, New York 10031, United States
| | - Themis Lazaridis
- Department of Chemistry, City College of New York, New York, New York 10031, United States.,Graduate Programs in Chemistry, Biochemistry, and Physics, The Graduate Center, City University of New York, New York, New York, New York 10016, United States
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26
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Li D, Ma C, Xiang J, Zhang K, Yang L, Gan Q. A Disulfide Switch Providing Absolute Handedness Control in Double Helices via Conversion from the Antiparallel to Parallel Helical Pattern. Chemistry 2021; 27:11663-11669. [PMID: 34014575 DOI: 10.1002/chem.202101221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Indexed: 11/09/2022]
Abstract
A strategy to reversibly switch the parallel/antiparallel helical conformation of aromatic double helices through the formation/breakage of a disulfide bond is presented. Single-crystal X-ray structures, NMR, and circular dichroism spectroscopy demonstrate that the double helices with terminal thiol groups favor an antiparallel helical arrangement both in the solid state and in solution, while the P/M bias of helicity induced by chiral segments from another extremity of the sequence is weak in this structural motif. The antiparallel helices can be rearranged to parallel helices through the disulfide connection of the sequences. This change enhances the bias of helical handedness and results in absolute chirality control of the double helices. The handedness-mediated process can be governed by the oxidation-reduction cycle, thereby switching the structural arrangement and the enhancement of chiral bias. In addition, we find that the sequences can dimerize into an intermolecular double helix with the disulfide connection. And the helical handedness is also fully controlled due to the head-to-head structural motif.
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Affiliation(s)
- Dongyao Li
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Chunmiao Ma
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Junfeng Xiang
- Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Kai Zhang
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Ling Yang
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Quan Gan
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
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27
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Identification of transmissible proteotoxic oligomer-like fibrils that expand conformational diversity of amyloid assemblies. Commun Biol 2021; 4:939. [PMID: 34354242 PMCID: PMC8342456 DOI: 10.1038/s42003-021-02466-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 07/19/2021] [Indexed: 11/08/2022] Open
Abstract
Protein misfolding and amyloid deposition are associated with numerous diseases. The detailed characterization of the proteospecies mediating cell death remains elusive owing to the (supra)structural polymorphism and transient nature of the assemblies populating the amyloid pathway. Here we describe the identification of toxic amyloid fibrils with oligomer-like characteristics, which were assembled from an islet amyloid polypeptide (IAPP) derivative containing an Asn-to-Gln substitution (N21Q). While N21Q filaments share structural properties with cytocompatible fibrils, including the 4.7 Å inter-strand distance and β-sheet-rich conformation, they concurrently display characteristics of oligomers, such as low thioflavin-T binding, high surface hydrophobicity and recognition by the A11 antibody, leading to high potency to disrupt membranes and cause cellular dysfunction. The toxic oligomer-like conformation of N21Q fibrils, which is preserved upon elongation, is transmissible to naïve IAPP. These stable fibrils expanding the conformational diversity of amyloid assemblies represent an opportunity to elucidate the structural basis of amyloid disorders. Nguyen et al identified cytotoxic amyloid fibrils with oligomer-like characteristics, which were assembled from an islet amyloid polypeptide (IAPP) derivative containing an Asn-to-Gln substitution (N21Q). They presented evidence to show that these stable fibrils expand the conformational diversity of amyloid assemblies, which represents an opportunity to elucidate the structural basis of amyloid disorders.
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28
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Tan Q, Liu H, Duan M, Huo S. Interplay between human islet amyloid polypeptide aggregates and micro-heterogeneous membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183691. [PMID: 34224702 DOI: 10.1016/j.bbamem.2021.183691] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 06/29/2021] [Accepted: 06/30/2021] [Indexed: 10/20/2022]
Abstract
Human islet amyloid polypeptides (hIAPP) aggregate into amyloid deposits in the pancreatic islets of Langerhans, contributing to the loss of β-cells of patients with type 2 diabetes. Despite extensive studies of membrane disruption associated with hIAPP aggregates, the molecular details regarding the complex interplay between hIAPP aggregates and raft-containing membranes are still very limited. Using all-atom molecular dynamics simulations, we investigate the impact of hIAPP aggregate insertion on lipid segregation. We have found that the domain separation of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) is enhanced upon hIAPP membrane permeabilization in the absence of cholesterol, while within our simulation timescale, we cannot provide definitive evidence regarding the impact of hIAPP insertion on domain segregation in the ternary mixture (DOPC/DPPC/cholesterol). When the lipid domains are perturbed, their restoration occurs rapidly and spontaneously in the presence of hIAPP aggregates. hIAPP insertion affects membrane thickness in its immediate surroundings. On average, hIAPP causes the fluidity of lipids to increase and even cholesterol shows enhanced diffusivity. The acyl chain packing of the lipids near hIAPP is disrupted as compared to that further away from it. Cholesterol not only modulates membrane mobility and ordering but also hIAPP aggregates' structure and relative orientation to the membrane. Our investigations on the interaction between hIAPP aggregates and raft-containing membranes could lead to a better understanding of the mechanisms of amyloid cytotoxicity.
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Affiliation(s)
- Qingzhe Tan
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, MA 01610, USA
| | - Hanzhong Liu
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, MA 01610, USA
| | - Mojie Duan
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, MA 01610, USA; Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Shuanghong Huo
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, MA 01610, USA.
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29
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FoxA2 and RNA Pol II mediate human islet amyloid polypeptide turnover in ER-stressed pancreatic β-cells. Biochem J 2021; 478:1261-1282. [PMID: 33650632 DOI: 10.1042/bcj20200984] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/26/2021] [Accepted: 03/02/2021] [Indexed: 12/25/2022]
Abstract
Here, we investigated transcriptional and trafficking mechanisms of human islet amyloid polypeptide (hIAPP) in normal and stressed β-cells. In high glucose-challenged human islets and rat insulinoma cells overexpressing hIAPP, cell fractionation studies revealed increased accumulation of hIAPP. Unexpectedly, a significant fraction (up to 22%) of hIAPP was found in the nuclear soluble and chromatin-enriched fractions of cultured human islet and rat insulinoma cells. The nucleolar accumulation of monomeric forms of hIAPP did not have any adverse effect on the proliferation of β-cells nor did it affect nucleolar organization or function. However, intact nucleolar organization and function were essential for hIAPP expression under normal and ER-stress conditions as RNA polymerase II inhibitor, α-amanitin, reduced hIAPP protein expression evoked by high glucose and thapsigargin. Promoter activity studies revealed the essential role of transcription factor FoxA2 in hIAPP promoter activation in ER-stressed β-cells. Transcriptome and secretory studies demonstrate that the biosynthetic and secretory capacity of islet β-cells was preserved during ER stress. Thus, the main reason for increased intracellular hIAPP accumulation is its enhanced biosynthesis under these adverse conditions.
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30
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Gonzalez-Garcia M, Fusco G, De Simone A. Membrane Interactions and Toxicity by Misfolded Protein Oligomers. Front Cell Dev Biol 2021; 9:642623. [PMID: 33791300 PMCID: PMC8006268 DOI: 10.3389/fcell.2021.642623] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/08/2021] [Indexed: 01/13/2023] Open
Abstract
The conversion of otherwise soluble proteins into insoluble amyloid aggregates is associated with a range of neurodegenerative disorders, including Alzheimer’s and Parkinson’s diseases, as well as non-neuropathic conditions such as type II diabetes and systemic amyloidoses. It is increasingly evident that the most pernicious species among those forming during protein aggregation are small prefibrillar oligomers. In this review, we describe the recent progress in the characterization of the cellular and molecular interactions by toxic misfolded protein oligomers. A fundamental interaction by these aggregates involves biological membranes, resulting in two major model mechanisms at the onset of the cellular toxicity. These include the membrane disruption model, resulting in calcium imbalance, mitochondrial dysfunction and intracellular reactive oxygen species, and the direct interaction with membrane proteins, leading to the alteration of their native function. A key challenge remains in the characterization of transient interactions involving heterogeneous protein aggregates. Solving this task is crucial in the quest of identifying suitable therapeutic approaches to suppress the cellular toxicity in protein misfolding diseases.
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Affiliation(s)
- Mario Gonzalez-Garcia
- Department of Life Sciences, Imperial College London, South Kensington, United Kingdom
| | - Giuliana Fusco
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, South Kensington, United Kingdom.,Department of Pharmacy, University of Naples Federico II, Naples, Italy
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31
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Gomes GN, Levine ZA. Defining the Neuropathological Aggresome across in Silico, in Vitro, and ex Vivo Experiments. J Phys Chem B 2021; 125:1974-1996. [PMID: 33464098 PMCID: PMC8362740 DOI: 10.1021/acs.jpcb.0c09193] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The loss of proteostasis over the life course is associated with a wide range of debilitating degenerative diseases and is a central hallmark of human aging. When left unchecked, proteins that are intrinsically disordered can pathologically aggregate into highly ordered fibrils, plaques, and tangles (termed amyloids), which are associated with countless disorders such as Alzheimer's disease, Parkinson's disease, type II diabetes, cancer, and even certain viral infections. However, despite significant advances in protein folding and solution biophysics techniques, determining the molecular cause of these conditions in humans has remained elusive. This has been due, in part, to recent discoveries showing that soluble protein oligomers, not insoluble fibrils or plaques, drive the majority of pathological processes. This has subsequently led researchers to focus instead on heterogeneous and often promiscuous protein oligomers. Unfortunately, significant gaps remain in how to prepare, model, experimentally corroborate, and extract amyloid oligomers relevant to human disease in a systematic manner. This Review will report on each of these techniques and their successes and shortcomings in an attempt to standardize comparisons between protein oligomers across disciplines, especially in the context of neurodegeneration. By standardizing multiple techniques and identifying their common overlap, a clearer picture of the soluble neuropathological aggresome can be constructed and used as a baseline for studying human disease and aging.
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Affiliation(s)
- Gregory-Neal Gomes
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Zachary A. Levine
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06511, USA
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32
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Milardi D, Gazit E, Radford SE, Xu Y, Gallardo RU, Caflisch A, Westermark GT, Westermark P, Rosa CL, Ramamoorthy A. Proteostasis of Islet Amyloid Polypeptide: A Molecular Perspective of Risk Factors and Protective Strategies for Type II Diabetes. Chem Rev 2021; 121:1845-1893. [PMID: 33427465 PMCID: PMC10317076 DOI: 10.1021/acs.chemrev.0c00981] [Citation(s) in RCA: 138] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The possible link between hIAPP accumulation and β-cell death in diabetic patients has inspired numerous studies focusing on amyloid structures and aggregation pathways of this hormone. Recent studies have reported on the importance of early oligomeric intermediates, the many roles of their interactions with lipid membrane, pH, insulin, and zinc on the mechanism of aggregation of hIAPP. The challenges posed by the transient nature of amyloid oligomers, their structural heterogeneity, and the complex nature of their interaction with lipid membranes have resulted in the development of a wide range of biophysical and chemical approaches to characterize the aggregation process. While the cellular processes and factors activating hIAPP-mediated cytotoxicity are still not clear, it has recently been suggested that its impaired turnover and cellular processing by proteasome and autophagy may contribute significantly toward toxic hIAPP accumulation and, eventually, β-cell death. Therefore, studies focusing on the restoration of hIAPP proteostasis may represent a promising arena for the design of effective therapies. In this review we discuss the current knowledge of the structures and pathology associated with hIAPP self-assembly and point out the opportunities for therapy that a detailed biochemical, biophysical, and cellular understanding of its aggregation may unveil.
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Affiliation(s)
- Danilo Milardi
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Via P. Gaifami 18, 95126 Catania, Italy
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Yong Xu
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Rodrigo U Gallardo
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zürich, Zürich CH-8057, Switzerland
| | - Gunilla T Westermark
- Department of Medical Cell Biology, Uppsala University, SE-751 23 Uppsala, Sweden
| | - Per Westermark
- Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Carmelo La Rosa
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Ayyalusamy Ramamoorthy
- Biophysics, Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, Michigan 41809-1055, United States
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33
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Quittot N, Fortier M, Babych M, Nguyen PT, Sebastiao M, Bourgault S. Cell surface glycosaminoglycans exacerbate plasma membrane perturbation induced by the islet amyloid polypeptide. FASEB J 2021; 35:e21306. [DOI: 10.1096/fj.202001845r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 11/14/2020] [Accepted: 12/09/2020] [Indexed: 11/11/2022]
Affiliation(s)
- Noé Quittot
- Department of Chemistry Université du Québec à Montréal Montreal QC Canada
- Center of Excellence in Research on Orphan Diseases ‐ Courtois Foundation Montreal Canada
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO Quebec City Canada
| | - Mathilde Fortier
- Department of Chemistry Université du Québec à Montréal Montreal QC Canada
- Center of Excellence in Research on Orphan Diseases ‐ Courtois Foundation Montreal Canada
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO Quebec City Canada
| | - Margaryta Babych
- Department of Chemistry Université du Québec à Montréal Montreal QC Canada
- Center of Excellence in Research on Orphan Diseases ‐ Courtois Foundation Montreal Canada
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO Quebec City Canada
| | - Phuong Trang Nguyen
- Department of Chemistry Université du Québec à Montréal Montreal QC Canada
- Center of Excellence in Research on Orphan Diseases ‐ Courtois Foundation Montreal Canada
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO Quebec City Canada
| | - Mathew Sebastiao
- Department of Chemistry Université du Québec à Montréal Montreal QC Canada
- Center of Excellence in Research on Orphan Diseases ‐ Courtois Foundation Montreal Canada
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO Quebec City Canada
| | - Steve Bourgault
- Department of Chemistry Université du Québec à Montréal Montreal QC Canada
- Center of Excellence in Research on Orphan Diseases ‐ Courtois Foundation Montreal Canada
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO Quebec City Canada
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34
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Cawood EE, Karamanos TK, Wilson AJ, Radford SE. Visualizing and trapping transient oligomers in amyloid assembly pathways. Biophys Chem 2021; 268:106505. [PMID: 33220582 PMCID: PMC8188297 DOI: 10.1016/j.bpc.2020.106505] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 10/29/2020] [Accepted: 11/01/2020] [Indexed: 12/31/2022]
Abstract
Oligomers which form during amyloid fibril assembly are considered to be key contributors towards amyloid disease. However, understanding how such intermediates form, their structure, and mechanisms of toxicity presents significant challenges due to their transient and heterogeneous nature. Here, we discuss two different strategies for addressing these challenges: use of (1) methods capable of detecting lowly-populated species within complex mixtures, such as NMR, single particle methods (including fluorescence and force spectroscopy), and mass spectrometry; and (2) chemical and biological tools to bias the amyloid energy landscape towards specific oligomeric states. While the former methods are well suited to following the kinetics of amyloid assembly and obtaining low-resolution structural information, the latter are capable of producing oligomer samples for high-resolution structural studies and inferring structure-toxicity relationships. Together, these different approaches should enable a clearer picture to be gained of the nature and role of oligomeric intermediates in amyloid formation and disease.
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Affiliation(s)
- Emma E Cawood
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK
| | - Theodoros K Karamanos
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK; Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew J Wilson
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, LS2 9JT, UK.
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK.
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35
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Gallardo R, Iadanza MG, Xu Y, Heath GR, Foster R, Radford SE, Ranson NA. Fibril structures of diabetes-related amylin variants reveal a basis for surface-templated assembly. Nat Struct Mol Biol 2020; 27:1048-1056. [PMID: 32929282 PMCID: PMC7617688 DOI: 10.1038/s41594-020-0496-3] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 08/04/2020] [Indexed: 12/19/2022]
Abstract
Aggregation of the peptide hormone amylin into amyloid deposits is a pathological hallmark of type-2 diabetes (T2D). While no causal link between T2D and amyloid has been established, the S20G mutation in amylin is associated with early-onset T2D. Here we report cryo-EM structures of amyloid fibrils of wild-type human amylin and its S20G variant. The wild-type fibril structure, solved to 3.6-Å resolution, contains two protofilaments, each built from S-shaped subunits. S20G fibrils, by contrast, contain two major polymorphs. Their structures, solved at 3.9-Å and 4.0-Å resolution, respectively, share a common two-protofilament core that is distinct from the wild-type structure. Remarkably, one polymorph contains a third subunit with another, distinct, cross-β conformation. The presence of two different backbone conformations within the same fibril may explain the increased aggregation propensity of S20G, and illustrates a potential structural basis for surface-templated fibril assembly.
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Affiliation(s)
- Rodrigo Gallardo
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, University of Leeds, Leeds, UK
| | - Matthew G Iadanza
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, University of Leeds, Leeds, UK
| | - Yong Xu
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, University of Leeds, Leeds, UK
| | - George R Heath
- Astbury Centre for Structural Molecular Biology, School of Physics & Astronomy, University of Leeds, Leeds, UK
| | - Richard Foster
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, Leeds, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, University of Leeds, Leeds, UK.
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, University of Leeds, Leeds, UK.
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Zheng Q, Carty SN, Lazo ND. Helix Dipole and Membrane Electrostatics Delineate Conformational Transitions in the Self-Assembly of Amyloidogenic Peptides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:8389-8397. [PMID: 32628488 PMCID: PMC8095063 DOI: 10.1021/acs.langmuir.0c00723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The self-assembly of amyloidogenic peptides on membrane surfaces is associated with the death of neurons and β-cells in Alzheimer's disease and type 2 diabetes, respectively. The early events of self-assembly in vivo are not known, but there is increasing evidence for the importance of the α-helix. To test the hypothesis that electrostatic interactions involving the helix dipole play a key role in membrane-mediated peptide self-assembly, we studied IAPP[11-25(S20G)-NH2] (R11LANFLVHSGNNFGA25-NH2), which under certain conditions self-assembles in hydro to form β-sheet assemblies through an α-helix-containing intermediate. In the presence of small unilamellar vesicles composed solely of zwitterionic lipids, the peptide does not self-assemble presumably because of the absence of stabilizing electrostatic interactions between the membrane surface and the helix dipole. In the presence of vesicles composed solely of anionic lipids, the peptide forms a long-lived α-helix presumably stabilized by dipole-dipole interactions between adjacent helix dipoles. This helix represents a kinetic trap that inhibits β-sheet formation. Intriguingly, when the amount of anionic lipids was decreased to mimic the ratio of zwitterionic and anionic lipids in cells, the α-helix was short-lived and underwent an α-helix to β-sheet conformational transition. Our work suggests that the helix dipole and membrane electrostatics delineate the conformational transitions occurring along the self-assembly pathway to the amyloid.
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Affiliation(s)
- Qiuchen Zheng
- Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, Massachusetts 01610, United States
| | - Senegal N Carty
- Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, Massachusetts 01610, United States
| | - Noel D Lazo
- Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, Massachusetts 01610, United States
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Roeters SJ, Sawall M, Eskildsen CE, Panman MR, Tordai G, Koeman M, Neymeyr K, Jansen J, Smilde AK, Woutersen S. Unraveling VEALYL Amyloid Formation Using Advanced Vibrational Spectroscopy and Microscopy. Biophys J 2020; 119:87-98. [PMID: 32562617 DOI: 10.1016/j.bpj.2020.05.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 04/23/2020] [Accepted: 05/11/2020] [Indexed: 12/19/2022] Open
Abstract
Intermediate species are hypothesized to play an important role in the toxicity of amyloid formation, a process associated with many diseases. This process can be monitored with conventional and two-dimensional infrared spectroscopy, vibrational circular dichroism, and optical and electron microscopy. Here, we present how combining these techniques provides insight into the aggregation of the hexapeptide VEALYL (Val-Glu-Ala-Leu-Tyr-Leu), the B-chain residue 12-17 segment of insulin that forms amyloid fibrils (intermolecularly hydrogen-bonded β-sheets) when the pH is lowered below 4. Under such circumstances, the aggregation commences after approximately an hour and continues to develop over a period of weeks. Singular value decompositions of one-dimensional and two-dimensional infrared spectroscopy spectra indicate that intermediate species are formed during the aggregation process. Multivariate curve resolution analyses of the one and two-dimensional infrared spectroscopy data show that the intermediates are more fibrillar and deprotonated than the monomers, whereas they are less ordered than the final fibrillar structure that is slowly formed from the intermediates. A comparison between the vibrational circular dichroism spectra and the scanning transmission electron microscopy and optical microscope images shows that the formation of mature fibrils of VEALYL correlates with the appearance of spherulites that are on the order of several micrometers, which give rise to a "giant" vibrational circular dichroism effect.
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Affiliation(s)
- Steven J Roeters
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, the Netherlands.
| | - Mathias Sawall
- Institut für Mathematik, Universität Rostock, Rostock, Germany
| | - Carl E Eskildsen
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands
| | - Matthijs R Panman
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Gergely Tordai
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Mike Koeman
- Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands
| | - Klaus Neymeyr
- Institut für Mathematik, Universität Rostock, Rostock, Germany; Leibniz-Institut für Katalyse, Rostock, Germany
| | - Jeroen Jansen
- Institute for Molecules and Materials, Radboud University, Nijmegen, the Netherlands
| | - Age K Smilde
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Sander Woutersen
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, the Netherlands
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38
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Asiri MMH, Engelsman S, Eijkelkamp N, Höppener JWM. Amyloid Proteins and Peripheral Neuropathy. Cells 2020; 9:E1553. [PMID: 32604774 PMCID: PMC7349787 DOI: 10.3390/cells9061553] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/20/2020] [Accepted: 06/22/2020] [Indexed: 12/14/2022] Open
Abstract
Painful peripheral neuropathy affects millions of people worldwide. Peripheral neuropathy develops in patients with various diseases, including rare familial or acquired amyloid polyneuropathies, as well as some common diseases, including type 2 diabetes mellitus and several chronic inflammatory diseases. Intriguingly, these diseases share a histopathological feature-deposits of amyloid-forming proteins in tissues. Amyloid-forming proteins may cause tissue dysregulation and damage, including damage to nerves, and may be a common cause of neuropathy in these, and potentially other, diseases. Here, we will discuss how amyloid proteins contribute to peripheral neuropathy by reviewing the current understanding of pathogenic mechanisms in known inherited and acquired (usually rare) amyloid neuropathies. In addition, we will discuss the potential role of amyloid proteins in peripheral neuropathy in some common diseases, which are not (yet) considered as amyloid neuropathies. We conclude that there are many similarities in the molecular and cell biological defects caused by aggregation of the various amyloid proteins in these different diseases and propose a common pathogenic pathway for "peripheral amyloid neuropathies".
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Affiliation(s)
- Mohammed M. H. Asiri
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, The Netherlands; (M.M.H.A.); (S.E.); (J.W.M.H.)
- The National Centre for Genomic Technology, Life Science and Environment Research Institute, King Abdulaziz City for Science and Technology, P.O. Box 6086, 11461 Riyadh, Saudi Arabia
| | - Sjoukje Engelsman
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, The Netherlands; (M.M.H.A.); (S.E.); (J.W.M.H.)
| | - Niels Eijkelkamp
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, The Netherlands; (M.M.H.A.); (S.E.); (J.W.M.H.)
| | - Jo W. M. Höppener
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, The Netherlands; (M.M.H.A.); (S.E.); (J.W.M.H.)
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, The Netherlands
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Gallardo R, Ranson NA, Radford SE. Amyloid structures: much more than just a cross-β fold. Curr Opin Struct Biol 2020; 60:7-16. [PMID: 31683043 PMCID: PMC7617690 DOI: 10.1016/j.sbi.2019.09.001] [Citation(s) in RCA: 149] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 09/04/2019] [Indexed: 01/10/2023]
Abstract
In recent years our understanding of amyloid structure has been revolutionised by innovations in cryo-electron microscopy, electron diffraction and solid-state NMR. These techniques have yielded high-resolution structures of fibrils isolated from patients with neurodegenerative disease, as well as those formed from amyloidogenic proteins in vitro. The results not only show the expected cross-β amyloid structure, but also reveal that the amyloid fold is unexpectedly diverse and complex. Here, we discuss this diversity, highlighting dynamic regions, ligand binding motifs, cavities, non-protein components, and structural polymorphism. Collectively, these variations combine to allow the generic amyloid fold to be realised in three dimensions in different ways, and this diversity may be related to the roles of fibrils in disease.
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Affiliation(s)
- Rodrigo Gallardo
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.
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40
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Levine ZA, Teranishi K, Okada AK, Langen R, Shea JE. The Mitochondrial Peptide Humanin Targets but Does Not Denature Amyloid Oligomers in Type II Diabetes. J Am Chem Soc 2019; 141:14168-14179. [DOI: 10.1021/jacs.9b04995] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Zachary A. Levine
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut 06520, United States
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut 06520, United States
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Godin E, Nguyen PT, Zottig X, Bourgault S. Identification of a hinge residue controlling islet amyloid polypeptide self-assembly and cytotoxicity. J Biol Chem 2019; 294:8452-8463. [PMID: 30975901 DOI: 10.1074/jbc.ra118.006454] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 04/04/2019] [Indexed: 11/06/2022] Open
Abstract
The islet amyloid polypeptide (IAPP) is a 37-residue peptide hormone whose deposition as amyloid fibrils in the pancreatic islets is associated with type 2 diabetes. Previous studies have suggested that residue Asn-21 plays a critical role in the in vitro self-assembly of IAPP. Herein, we studied structure-self-assembly relationships focusing on position 21 to gain detailed insights into the molecular mechanisms of IAPP self-assembly and to probe the conformational nature of the toxic assemblies associated with β-cell death. Thioflavin T (ThT) fluorescence, CD spectroscopy, and transmission EM analysis revealed that the Asn-21 amide side chain is not required for IAPP nucleation and amyloid elongation, as N21A and N21G variants assembled into prototypical fibrils. In contrast, Asn-21 substitution with the conformationally constrained and turn-inducing residue Pro accelerated IAPP self-assembly. Successive substitutions with hydrophobic residues led to the formation of ThT-negative β-sheet-rich aggregates having high surface hydrophobicity. Cell-based assays revealed no direct correlation between the in vitro amyloidogenicity of these variants and their toxicity. In contrast, leakage of anionic lipid vesicles disclosed that membrane disruption is closely associated with cytotoxicity. We observed that the N21F variant self-assembles into worm-like aggregates, causing loss of lipid membrane structural integrity and inducing β-cell apoptosis. These results indicate that specific intra- and intermolecular interactions involving Asn-21 promote IAPP primary nucleation events by modulating the conformational conversion of the oligomeric intermediates into amyloid fibrils. Our study identifies position 21 as a hinge residue that modulates IAPP amyloidogenicity and cytotoxicity.
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Affiliation(s)
- Elizabeth Godin
- Department of Chemistry, Pharmaqam, Université du Québec à Montréal, Montreal, Quebec H3C 3P8, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications, PROTEO, Quebec G1V 0A6, Canada
| | - Phuong Trang Nguyen
- Department of Chemistry, Pharmaqam, Université du Québec à Montréal, Montreal, Quebec H3C 3P8, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications, PROTEO, Quebec G1V 0A6, Canada
| | - Ximena Zottig
- Department of Chemistry, Pharmaqam, Université du Québec à Montréal, Montreal, Quebec H3C 3P8, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications, PROTEO, Quebec G1V 0A6, Canada
| | - Steve Bourgault
- Department of Chemistry, Pharmaqam, Université du Québec à Montréal, Montreal, Quebec H3C 3P8, Canada; Quebec Network for Research on Protein Function, Engineering, and Applications, PROTEO, Quebec G1V 0A6, Canada.
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42
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Wang Z, An HW, Hou D, Wang M, Zeng X, Zheng R, Wang L, Wang K, Wang H, Xu W. Addressable Peptide Self-Assembly on the Cancer Cell Membrane for Sensitizing Chemotherapy of Renal Cell Carcinoma. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1807175. [PMID: 30663139 DOI: 10.1002/adma.201807175] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/02/2019] [Indexed: 05/06/2023]
Abstract
Chemotherapy has been validated unavailable for treatment of renal cell carcinoma (RCC) in clinic due to its intrinsic drug resistance. Sensitization of chemo-drug response plays a crucial role in RCC treatment and increase of patient survival. Herein, a recognition-reaction-aggregation (RRA) cascaded strategy is utilized to in situ construct peptide-based superstructures on the renal cancer cell membrane, enabling specifically perturbing the permeability of cell membranes and enhancing chemo-drug sensitivity in vitro and in vivo. First, P1-DBCO can specifically recognize renal cancer cells by targeting carbonic anhydrase IX. Subsequently, P2-N3 is introduced and efficiently reacts with P1-DBCO to form a peptide P3, which exhibits enhanced hydrophobicity and simultaneously aggregates into a superstructure. Interestingly, the superstructure retains on the cell membrane and perturbs its integrity/permeability, allowing more doxorubicin (DOX) uptaken by renal cancer cells. Owing to this increased influx, the IC50 is significantly reduced by nearly 3.5-fold compared with that treated with free DOX. Finally, RRA strategy significantly inhibits the tumor growth of xenografted mice with a 3.2-fold enhanced inhibition rate compared with that treated with free DOX. In summary, this newly developed RRA strategy will open a new avenue for chemically engineering cell membranes with diverse biomedical applications.
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Affiliation(s)
- Ziqi Wang
- Department of Urology, The Fourth Hospital of Harbin Medical University, Heilongjiang Key Laboratory of Scientific Research in Urology, Harbin, 150001, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China
| | - Hong-Wei An
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Yuquan Road, Beijing, 100049, China
| | - Dayong Hou
- Department of Urology, The Fourth Hospital of Harbin Medical University, Heilongjiang Key Laboratory of Scientific Research in Urology, Harbin, 150001, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China
| | - Mandi Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China
| | - Xiangzhong Zeng
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China
| | - Rui Zheng
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China
| | - Lu Wang
- Department of Urology, The Fourth Hospital of Harbin Medical University, Heilongjiang Key Laboratory of Scientific Research in Urology, Harbin, 150001, China
| | - Keliang Wang
- Department of Urology, The Fourth Hospital of Harbin Medical University, Heilongjiang Key Laboratory of Scientific Research in Urology, Harbin, 150001, China
| | - Hao Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing, 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wanhai Xu
- Department of Urology, The Fourth Hospital of Harbin Medical University, Heilongjiang Key Laboratory of Scientific Research in Urology, Harbin, 150001, China
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43
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Imaging individual protein aggregates to follow aggregation and determine the role of aggregates in neurodegenerative disease. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:870-878. [PMID: 30611780 PMCID: PMC6676340 DOI: 10.1016/j.bbapap.2018.12.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 12/06/2018] [Accepted: 12/29/2018] [Indexed: 01/07/2023]
Abstract
Protein aggregates play a key role in the initiation and spreading of neurodegenerative disease but have been difficult to study due to their low abundance and heterogeneity, in both size and structure. Fluorescence based methods capable of detecting and characterising single aggregates have recently been developed and can be used to measure many important aggregate properties, and can be combined with sensitive assays to measure aggregate toxicity. Here we review these methods and discuss recent examples of their application to determine the molecular mechanism of aggregation and the detection of aggregates in cells and cerebrospinal fluid. The further development of these methods and their application to the aggregates present in humans has the potential to solve a major problem in the field and allow the identification of the key toxic species that should be targeted in therapies. Individual protein aggregates can be imaged using fluorescence imaging. Ultra-sensitive assays have been developed to measure aggregate toxicity. The aggregation mechanism of proteins can be determined. Experiments can be performed in cells or human cerebrospinal fluid. These methods can potentially identify the toxic aggregates that cause neurodegenerative disease.
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44
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Qiao Q, Wei G, Yao D, Song Z. Formation of α-helical and β-sheet structures in membrane-bound human IAPP monomer and the resulting membrane deformation. Phys Chem Chem Phys 2019; 21:20239-20251. [DOI: 10.1039/c9cp03151k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Upon adsorption on membrane, human IAPP monomer takes conformational changes from coils to α-helices and β-sheets. The helices inserted and β on surface cause different types of membrane deformation, implying two distinct aggregation mechanisms.
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Affiliation(s)
- Qin Qiao
- Digital Medical Research Center
- School of Basic Medical Sciences
- Fudan University
- Shanghai 200032
- China
| | - Guanghong Wei
- Department of Physics
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Science (Ministry of Education)
- Fudan University
- Shanghai 200438
| | - Demin Yao
- Digital Medical Research Center
- School of Basic Medical Sciences
- Fudan University
- Shanghai 200032
- China
| | - Zhijian Song
- Digital Medical Research Center
- School of Basic Medical Sciences
- Fudan University
- Shanghai 200032
- China
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45
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46
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Divakara MB, Martinez D, Ravi A, Bhavana V, Ramana V, Habenstein B, Loquet A, Santosh MS. Molecular mechanisms for the destabilization of model membranes by islet amyloid polypeptide. Biophys Chem 2018; 245:34-40. [PMID: 30576976 DOI: 10.1016/j.bpc.2018.12.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 11/29/2018] [Accepted: 12/10/2018] [Indexed: 12/30/2022]
Abstract
Misfolding of human islet amyloid polypeptide (hIAPP) into insoluble aggregates is associated with Type 2 diabetes. It has been suggested that hIAPP toxicity may be due to its accumulation in pancreatic islets, causing membrane disruption and cell permeabilization, however the molecular basis underlying its lipid association are still unclear. Here, we combine solid-state NMR, fluorescence and bright field microscopy to investigate hIAPP - lipid membrane interactions. Real-time microscopy highlights a time-dependent penetration of hIAPP oligomers toward the most buried layers of the lipid vesicles until the membrane disrupts. Deuterium NMR was conducted on liposomes at different hIAPP concentration to probe lipid internal order and thermotropism. The gel-to-fluid phase transition of the lipids is decreased by the presence of hIAPP, and site-specific analysis of the order parameter showed a significant increase of lipid order for the first eight positions of the acyl chain, suggesting a partial insertion of the peptide inside the bilayer. These results offer experimental insight into the membrane destabilization of hIAPP on model membrane vesicles.
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Affiliation(s)
- Madhihalli Basavaraju Divakara
- Center for Incubation, Innovation, Research and Consultancy (CIIRC), Jyothy Institute of Technology, Thataguni, Off Kanakapura Road, Bangalore 560082, Karnataka, India; Visvesvaraya Technological University, Regional Research Centre, Jnana Sangama, Belagavi 590018, Karnataka, India
| | - Denis Martinez
- Institute of Chemistry and Biology of Membranes and Nanoobjects, Institut Européen de Chimie et Biologie (CNRS UMR 5248), Université de Bordeaux, 2 Rue Robert Escarpit, 33600 Pessac, France
| | - Ashwini Ravi
- Center for Incubation, Innovation, Research and Consultancy (CIIRC), Jyothy Institute of Technology, Thataguni, Off Kanakapura Road, Bangalore 560082, Karnataka, India; Visvesvaraya Technological University, Regional Research Centre, Jnana Sangama, Belagavi 590018, Karnataka, India
| | - Veer Bhavana
- Center for Incubation, Innovation, Research and Consultancy (CIIRC), Jyothy Institute of Technology, Thataguni, Off Kanakapura Road, Bangalore 560082, Karnataka, India; Visvesvaraya Technological University, Regional Research Centre, Jnana Sangama, Belagavi 590018, Karnataka, India
| | - Venkata Ramana
- DRDO BU CLS, Bharathiar University Campus, Coimbatore 641046, Tamil Nadu, India
| | - Birgit Habenstein
- Institute of Chemistry and Biology of Membranes and Nanoobjects, Institut Européen de Chimie et Biologie (CNRS UMR 5248), Université de Bordeaux, 2 Rue Robert Escarpit, 33600 Pessac, France.
| | - Antoine Loquet
- Institute of Chemistry and Biology of Membranes and Nanoobjects, Institut Européen de Chimie et Biologie (CNRS UMR 5248), Université de Bordeaux, 2 Rue Robert Escarpit, 33600 Pessac, France.
| | - Mysore Sridhar Santosh
- Center for Incubation, Innovation, Research and Consultancy (CIIRC), Jyothy Institute of Technology, Thataguni, Off Kanakapura Road, Bangalore 560082, Karnataka, India.
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47
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Lee YH, Lin Y, Cox SJ, Kinoshita M, Sahoo BR, Ivanova M, Ramamoorthy A. Zinc boosts EGCG's hIAPP amyloid Inhibition both in solution and membrane. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1867:529-536. [PMID: 30468883 DOI: 10.1016/j.bbapap.2018.11.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/14/2018] [Accepted: 11/17/2018] [Indexed: 12/22/2022]
Abstract
Amyloid aggregation of human islet amyloid polypeptide (hIAPP) is linked to insulin-producing islet cell death in type II diabetes. Previous studies have shown that zinc (Zn(II)) and insulin, co-secreted with hIAPP, have an inhibition effect on hIAPP aggregation. Lipid membranes have also been shown to significantly influence the aggregation kinetics of hIAPP. An increasing number of studies report the importance of developing small molecule inhibitors to suppress the hIAPP's aggregation and subsequent toxicity. The ability of epigallocatechin-gallate (EGCG) to inhibit aggregation of a variety of amyloid peptide/proteins initiated numerous studies as well as the development of derivative compounds to potentially treat amyloid diseases. In this study, a combination of Thioflavin-T fluorescence kinetics, transmission electron microscopy, isothermal titration calorimetery, circular dicrosim and nucelar magnetic resonance experiments were used to demonstrate a significant enhancement in EGCG's efficiency when complexed with Zn(II). We demonstrate that the Zn-EGCG complex is able to significantly suppress hIAPP's amyloid aggregation both in presence and absence of lipid membrane. Circular dichroism experiments indicate the formation and stabilization of a helical structure of hIAPP in presence of the EGCG:Zn(II) complex. Our results also reveal the ability of EGCG or EGCG:Zn(II) to efficiently suppress hIAPP's cellular toxicity. We believe that the reported results could be useful to develop strategies to trap hIAPP intermediates for further biophysical and structural studies, and also to devise approaches to abolish amyloid aggregation and cellular toxicity.
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Affiliation(s)
- Young-Ho Lee
- Institute for Protein research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan; Protein Structure Research Group, Division of Bioconvergence Analysis, Korea Basic Science Institute, Chungcheongbuk-do 28119, South Korea
| | - Yuxi Lin
- Department of Chemistry, Sookmyung Women's University, Cheongpa-ro 47-gil 100, Yongsan-gu, Seoul 04310, South Korea
| | - Sarah J Cox
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Misaki Kinoshita
- Institute for Protein research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - Bikash R Sahoo
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Magdalena Ivanova
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
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48
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Silva A, Sárkány Z, Fraga JS, Taboada P, Macedo-Ribeiro S, Martins PM. Probing the Occurrence of Soluble Oligomers through Amyloid Aggregation Scaling Laws. Biomolecules 2018; 8:biom8040108. [PMID: 30287796 PMCID: PMC6316134 DOI: 10.3390/biom8040108] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 09/29/2018] [Accepted: 10/01/2018] [Indexed: 12/24/2022] Open
Abstract
Drug discovery frequently relies on the kinetic analysis of physicochemical reactions that are at the origin of the disease state. Amyloid fibril formation has been extensively investigated in relation to prevalent and rare neurodegenerative diseases, but thus far no therapeutic solution has directly arisen from this knowledge. Other aggregation pathways producing smaller, hard-to-detect soluble oligomers are increasingly appointed as the main reason for cell toxicity and cell-to-cell transmissibility. Here we show that amyloid fibrillation kinetics can be used to unveil the protein oligomerization state. This is illustrated for human insulin and ataxin-3, two model proteins for which the amyloidogenic and oligomeric pathways are well characterized. Aggregation curves measured by the standard thioflavin-T (ThT) fluorescence assay are shown to reflect the relative composition of protein monomers and soluble oligomers measured by nuclear magnetic resonance (NMR) for human insulin, and by dynamic light scattering (DLS) for ataxin-3. Unconventional scaling laws of kinetic measurables were explained using a single set of model parameters consisting of two rate constants, and in the case of ataxin-3, an additional order-of-reaction. The same fitted parameters were used in a discretized population balance that adequately describes time-course measurements of fibril size distributions. Our results provide the opportunity to study oligomeric targets using simple, high-throughput compatible, biophysical assays.
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Affiliation(s)
- Alexandra Silva
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal.
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.
| | - Zsuzsa Sárkány
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal.
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.
| | - Joana S Fraga
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal.
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.
- ICBAS-Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal.
| | - Pablo Taboada
- Área de Física de la Materia Condensada, Facultad de Física, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
- Instituto de Investigación Sanitaria (IDIS), 15706 de Santiago de Compostela, Spain.
| | - Sandra Macedo-Ribeiro
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal.
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.
| | - Pedro M Martins
- IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal.
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.
- ICBAS-Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal.
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Kiriyama Y, Nochi H. Role and Cytotoxicity of Amylin and Protection of Pancreatic Islet β-Cells from Amylin Cytotoxicity. Cells 2018; 7:cells7080095. [PMID: 30082607 PMCID: PMC6115925 DOI: 10.3390/cells7080095] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 07/28/2018] [Accepted: 08/01/2018] [Indexed: 12/26/2022] Open
Abstract
Amylin, (or islet amyloid polypeptide; IAPP), a 37-amino acid peptide hormone, is released in response to nutrients, including glucose, lipids or amino acids. Amylin is co-stored and co-secreted with insulin by pancreatic islet β-cells. Amylin inhibits food intake, delays gastric emptying, and decreases blood glucose levels, leading to the reduction of body weight. Therefore, amylin as well as insulin play important roles in controlling the level of blood glucose. However, human amylin aggregates and human amylin oligomers cause membrane disruption, endoplasmic reticulum (ER) stress and mitochondrial damage. Since cytotoxicity of human amylin oligomers to pancreatic islet β-cells can lead to diabetes, the protection of pancreatic islet β cells from cytotoxic amylin is crucial. Human amylin oligomers also inhibit autophagy, although autophagy can function to remove amylin aggregates and damaged organelles. Small molecules, including β-sheet breaker peptides, chemical chaperones, and foldamers, inhibit and disaggregate amyloid formed by human amylin, suggesting the possible use of these small molecules in the treatment of diabetes. In this review, we summarize recent findings regarding the role and cytotoxicity of amylin and the protection of pancreatic islet β-cells from cytotoxicity of amylin.
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Affiliation(s)
- Yoshimitsu Kiriyama
- Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, Shido 1314-1, Kagawa, Sanuki 769-2193, Japan.
| | - Hiromi Nochi
- Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, Shido 1314-1, Kagawa, Sanuki 769-2193, Japan.
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50
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Endoplasmic Reticulum Stress in Metabolic Disorders. Cells 2018; 7:cells7060063. [PMID: 29921793 PMCID: PMC6025008 DOI: 10.3390/cells7060063] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 06/12/2018] [Accepted: 06/14/2018] [Indexed: 02/06/2023] Open
Abstract
Metabolic disorders have become among the most serious threats to human health, leading to severe chronic diseases such as obesity, type 2 diabetes, and non-alcoholic fatty liver disease, as well as cardiovascular diseases. Interestingly, despite the fact that each of these diseases has different physiological and clinical symptoms, they appear to share certain pathological traits such as intracellular stress and inflammation induced by metabolic disturbance stemmed from over nutrition frequently aggravated by a modern, sedentary life style. These modern ways of living inundate cells and organs with saturating levels of sugar and fat, leading to glycotoxicity and lipotoxicity that induce intracellular stress signaling ranging from oxidative to ER stress response to cope with the metabolic insults (Mukherjee, et al., 2015). In this review, we discuss the roles played by cellular stress and its responses in shaping metabolic disorders. We have summarized here current mechanistic insights explaining the pathogenesis of these disorders. These are followed by a discussion of the latest therapies targeting the stress response pathways.
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