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Senapati S, Tripathi K, Awad K, Rahimipour S. Multifunctional Liposomes Targeting Amyloid-β Oligomers for Early Diagnosis and Therapy of Alzheimer's Disease. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2311670. [PMID: 38461531 DOI: 10.1002/smll.202311670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/14/2024] [Indexed: 03/12/2024]
Abstract
Early detection and treatment are crucial for Alzheimer's disease (AD) management. Current diagnostic and therapeutic methods focus on late-stage amyloid fibrils and plaques, overlooking toxic soluble amyloid β oligomers (AβOs) accumulating early in AD. A multifunctional liposome-based platform is designed for early diagnosis and therapy of AD, leveraging a novel self-assembled cyclic d,l-α-peptide (CP-2) that selectively targets AβOs. Biocompatible CP-2 conjugated liposomes (CP-2-LPs) effectively disrupt Aβ aggregation and mitigate Aβ-mediated toxicity in human neuroblastoma cells. In transgenic Caenorhabditis elegans AD models, CP-2-LPs significantly outperformed free CP-2 by improving cognitive and behavioral functions, extending lifespan, and reducing toxic AβO levels. Intravenous injection of fluorescently labeled CP-2-LPs reveals effective blood-brain barrier penetration, with significantly higher brain fluorescence in transgenic mice than WT, enabling precise diagnosis. These findings underscore CP-2-LPs as a valuable tool for early detection and targeted therapy in AD.
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Affiliation(s)
- Sudipta Senapati
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Kuldeep Tripathi
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Khadeja Awad
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Shai Rahimipour
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, 5290002, Israel
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2
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The Association of Lipids with Amyloid Fibrils. J Biol Chem 2022; 298:102108. [PMID: 35688209 PMCID: PMC9293637 DOI: 10.1016/j.jbc.2022.102108] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 05/31/2022] [Accepted: 06/03/2022] [Indexed: 01/02/2023] Open
Abstract
Amyloid formation continues to be a widely studied area because of its association with numerous diseases, such as Alzheimer’s and Parkinson’s diseases. Despite a large body of work on protein aggregation and fibril formation, there are still significant gaps in our understanding of the factors that differentiate toxic amyloid formation in vivo from alternative misfolding pathways. In addition to proteins, amyloid fibrils are often associated in their cellular context with several types of molecule, including carbohydrates, polyanions, and lipids. This review focuses in particular on evidence for the presence of lipids in amyloid fibrils and the routes by which those lipids may become incorporated. Chemical analyses of fibril composition, combined with studies to probe the lipid distribution around fibrils, provide evidence that in some cases, lipids have a strong association with fibrils. In addition, amyloid fibrils formed in the presence of lipids have distinct morphologies and material properties. It is argued that lipids are an integral part of many amyloid deposits in vivo, where their presence has the potential to influence the nucleation, morphology, and mechanical properties of fibrils. The role of lipids in these structures is therefore worthy of further study.
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3
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Geng Y, Huang T, Zhou W, Shen L. Physical Mechanism of Amyloid-β Peptide Chain Aggregation on Fluidic Lipid Nanotubules. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:5752-5758. [PMID: 35476922 DOI: 10.1021/acs.langmuir.2c00357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The question of how peptide chain aggregation is influenced by lipid membranes with varying shapes and structures is crucial for a detailed understanding of the neurotoxicity effect of the peptide chains. Not like the more usual spherical liposomes and planar lipid membranes, herein, we use lipid nanotubules as a model of important neuron synapse nanowire structures and devote particular attention to the effect of nanotubule fluidity on amyloid-β peptide (Aβ) chain aggregation. We apply single-molecule tracking (SMT) to elucidate how Aβ chains diffuse and aggregate on lipid nanotubules with different fluidities. The physical mechanism implies that fluidic lipid nanotubules facilitate the super-diffusion of two-dimensional (2D)-mobile precursor Aβ chains and promote their aggregation. This aggregation mechanism is retarded on less fluidic lipid nanotubules where the super-diffusion of 2D-mobile precursor Aβ chains is restricted by "frozen" lipids with less mobility. This work provides a mechanistic explanation for Aβ chain aggregation on fluidic lipid nanotubules.
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4
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Wong KM, Robang AS, Lint AH, Wang Y, Dong X, Xiao X, Seroski DT, Liu R, Shao Q, Hudalla GA, Hall CK, Paravastu AK. Engineering β-Sheet Peptide Coassemblies for Biomaterial Applications. J Phys Chem B 2021; 125:13599-13609. [PMID: 34905370 DOI: 10.1021/acs.jpcb.1c04873] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Peptide coassembly, wherein at least two different peptides interact to form multicomponent nanostructures, is an attractive approach for generating functional biomaterials. Current efforts seek to design pairs of peptides, A and B, that form nanostructures (e.g., β-sheets with ABABA-type β-strand patterning) while resisting self-assembly (e.g., AAAAA-type or BBBBB-type β-sheets). To confer coassembly behavior, most existing designs have been based on highly charged variants of known self-assembling peptides; like-charge repulsion limits self-assembly while opposite-charge attraction promotes coassembly. Recent analyses using solid-state NMR and coarse-grained simulations reveal that preconceived notions of structure and molecular organization are not always correct. This perspective highlights recent advances and key challenges to understanding and controlling peptide coassembly.
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Affiliation(s)
- Kong M Wong
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Alicia S Robang
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Annabelle H Lint
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Yiming Wang
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Xin Dong
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Xingqing Xiao
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Dillon T Seroski
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, 1275 Center Drive, Biomedical Sciences J293, P.O. BOX 116131, Gainesville, Florida 32611, United States
| | - Renjie Liu
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, 1275 Center Drive, Biomedical Sciences J293, P.O. BOX 116131, Gainesville, Florida 32611, United States
| | - Qing Shao
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Gregory A Hudalla
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, 1275 Center Drive, Biomedical Sciences J293, P.O. BOX 116131, Gainesville, Florida 32611, United States
| | - Carol K Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Anant K Paravastu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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5
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Wang J, Li Q, Hu L, Wang Y, Qi W, Su R, He Z. Self-Assembly of Ferrocenyl Phenylalanine into Nanohelical Arrays via Kinetic Control. ACS APPLIED BIO MATERIALS 2021; 4:4744-4752. [PMID: 35007024 DOI: 10.1021/acsabm.0c00607] [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] [Indexed: 11/30/2022]
Abstract
The spontaneous alignment of self-assembled chiral nanostructures at macroscopic scales is appealing because of their unique structural features and physicochemical properties. Here we present the construction of highly ordered bioorganometallic nanohelical arrays on the basis of the hierarchical chiral self-assembly of the simple ferrocenyl l-phenylalanine (Fc-l-F). The formation of nanohelical arrays is under kinetic control, which can be controlled by changing the growth time and the vapor temperature. The chiral nanoarrays can generate circularly polarized luminescence by the incorporation of fluorescent dyes. Moreover, due to the redox activity of the Fc moiety, the nanohelical arrays show enhanced electrical capacity compared with previously reported peptide nanomaterials. The results shed light on the highly ordered chiral self-assembled nanomaterials, which have potential applications in fields of optics, sensing, and energy storage.
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Affiliation(s)
- Jiahui Wang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China
| | - Qing Li
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China
| | - Liuping Hu
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China
| | - Yuefei Wang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China.,Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072, People's Republic of China
| | - Wei Qi
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China.,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, People's Republic of China.,Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072, People's Republic of China
| | - Rongxin Su
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China.,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, People's Republic of China.,Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072, People's Republic of China
| | - Zhimin He
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, People's Republic of China
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6
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Firdaus Z, Singh TD. An Insight in Pathophysiological Mechanism of Alzheimer's Disease and its Management Using Plant Natural Products. Mini Rev Med Chem 2021; 21:35-57. [PMID: 32744972 DOI: 10.2174/1389557520666200730155928] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 05/20/2020] [Accepted: 06/05/2020] [Indexed: 11/22/2022]
Abstract
Alzheimer's disease (AD) is an age-associated nervous system disorder and a leading cause of dementia worldwide. Clinically, it is described by cognitive impairment and pathophysiologically by deposition of amyloid plaques and neurofibrillary tangles in the brain and neurodegeneration. This article reviews the pathophysiology, course of neuronal degeneration, and the various possible hypothesis of AD progression. These hypotheses include amyloid cascade, tau hyperphosphorylation, cholinergic disruption, metal dysregulation, vascular dysfunction, oxidative stress, and neuroinflammation. There is an exponential increase in the occurrence of AD in the recent few years that indicate an urgent need to develop some effective treatment. Currently, only 2 classes of drugs are available for AD treatment, namely acetylcholinesterase inhibitor and NMDA receptor antagonist. Since AD is a complex neurological disorder and these drugs use a single target approach, alternatives are needed due to limited effectiveness and unpleasant side-effects of these drugs. Currently, plants have been used for drug development research especially because of their multiple sites of action and fewer side effects. Uses of some herbs and phytoconstituents for the management of neuronal disorders like AD have been documented in this article. Phytochemical screening of these plants shows the presence of many beneficial constituents like flavonoids, triterpenes, alkaloids, sterols, polyphenols, and tannins. These compounds show a wide array of pharmacological activities, such as anti-amyloidogenic, anticholinesterase, and antioxidants. This article summarizes the present understanding of AD progression and gathers biochemical evidence from various works on natural products that can be useful in the management of this disease.
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Affiliation(s)
- Zeba Firdaus
- Department of Medicinal Chemistry, Institute of Medical Sciences, Banaras Hindu University, Varanasi - 221005, India
| | - Tryambak Deo Singh
- Department of Medicinal Chemistry, Institute of Medical Sciences, Banaras Hindu University, Varanasi - 221005, India
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7
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Bridstrup J, Schreck JS, Jorgenson JL, Yuan JM. Stochastic Kinetic Treatment of Protein Aggregation and the Effects of Macromolecular Crowding. J Phys Chem B 2021; 125:6068-6079. [PMID: 34080429 DOI: 10.1021/acs.jpcb.1c00959] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Investigation of protein self-assembly processes is important for understanding the growth processes of functional proteins as well as disease-causing amyloids. Inside cells, intrinsic molecular fluctuations are so high that they cast doubt on the validity of the deterministic rate-equation approach. Furthermore, the protein environments inside cells are often crowded with other macromolecules, with volume fractions of the crowders as high as 40%. We have developed a stochastic kinetic framework using Gillespie's algorithm for general systems undergoing particle self-assembly, including particularly protein aggregation at the cellular level. The effects of macromolecular crowding are investigated using models built on scaled-particle and transition-state theories. The stochastic kinetic method can be formulated to provide information on the dominating aggregation mechanisms in a method called reaction frequency (or propensity) analysis. This method reveals that the change of scaling laws related to the lag time can be directly related to the change in the frequencies of reaction mechanisms. Further examination of the time evolution of the fibril mass and length quantities unveils that maximal fluctuations occur in the periods of rapid fibril growth and the fluctuations of both quantities can be sensitive functions of rate constants. The presence of crowders often amplifies the roles of primary and secondary nucleation and causes shifting in the relative importance of elongation, shrinking, fragmentation, and coagulation of linear aggregates. We also show a dual effect of changing volume on the halftime of aggregation for ApoC2 which is reduced in the presence of crowders. A comparison of the results of stochastic simulations with those of rate equations gives us information on the convergence relation between them and how the roles of reaction mechanisms change as the system volume is varied.
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Affiliation(s)
- John Bridstrup
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - John S Schreck
- National Center for Atmospheric Research, Boulder, Colorado 80305, United States
| | | | - Jian-Min Yuan
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, United States
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8
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Ghosh P, Pateras J, Rangachari V, Vaidya A. A Network Thermodynamic Analysis of Amyloid Aggregation along Competing Pathways. APPLIED MATHEMATICS AND COMPUTATION 2021; 393:125778. [PMID: 33551515 PMCID: PMC7861474 DOI: 10.1016/j.amc.2020.125778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Aggregation of proteins towards amyloid formation is a significant event in many neurodegenerative diseases. Low-molecular weight oligomers are considered to be the primary toxic agents in many of these maladies. Therefore, there is an increasing interest in understanding their formation and behavior. In this paper, we build on our previously established theoretical investigations on the interactions between Aβ and lipids (L) that adopt off-pathway fibril formation under the control of L concentrations. Our previously developed competing game theoretic framework between the on- and off-pathway dynamics has been expanded to understand the underlying network topological structures in the reaction kinetics of amyloid formation. The mass-action based dynamical systems are solved to identify dominant pathways in the system with fixed initial conditions, and variations in the occurrence of these dominant pathways are identified as a function of various seeding conditions. The mechanistic approach is supported by thermodynamic free energy computations which helps identify stable reactions. The resulting analysis provides possible intervention strategies that can draw the dynamics away from the off-pathways and potential toxic intermediates. We also draw upon the classic literature on network thermodynamics to suggest new approaches to better understand such complex systems.
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Affiliation(s)
- P Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23220
| | - J Pateras
- Department of Mathematics, Montclair State University, Montclair, NJ 07043
| | - V Rangachari
- Department of Chemistry & Biochemistry, 118 College Dr, # 5043 University of Southern Mississippi, Hattiesburg, MS 39406
- Center for Cellular and Molecular Biosciences, University of Southern Mississippi, Hattiesburg MS 39406
| | - A Vaidya
- Department of Mathematics, Montclair State University, Montclair, NJ 07043
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9
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Curcumin as Scaffold for Drug Discovery against Neurodegenerative Diseases. Biomedicines 2021; 9:biomedicines9020173. [PMID: 33572457 PMCID: PMC7916200 DOI: 10.3390/biomedicines9020173] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/02/2021] [Accepted: 02/08/2021] [Indexed: 02/06/2023] Open
Abstract
Neurodegenerative diseases (NDs) are one of major public health problems and their impact is continuously growing. Curcumin has been proposed for the treatment of several of these pathologies, such as Alzheimer's disease (AD) and Parkinson's disease (PD) due to the ability of this molecule to reduce inflammation and aggregation of involved proteins. Nevertheless, the poor metabolic stability and bioavailability of curcumin reduce the possibilities of its practical use. For these reasons, many curcumin derivatives were synthetized in order to overcome some limitations. In this review will be highlighted recent results on modification of curcumin scaffold in the search of new effective therapeutic agents against NDs, with particular emphasis on AD.
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10
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Abdelrahman S, Alghrably M, Lachowicz JI, Emwas AH, Hauser CAE, Jaremko M. "What Doesn't Kill You Makes You Stronger": Future Applications of Amyloid Aggregates in Biomedicine. Molecules 2020; 25:E5245. [PMID: 33187056 PMCID: PMC7696280 DOI: 10.3390/molecules25225245] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/24/2020] [Accepted: 10/27/2020] [Indexed: 02/06/2023] Open
Abstract
Amyloid proteins are linked to the pathogenesis of several diseases including Alzheimer's disease, but at the same time a range of functional amyloids are physiologically important in humans. Although the disease pathogenies have been associated with protein aggregation, the mechanisms and factors that lead to protein aggregation are not completely understood. Paradoxically, unique characteristics of amyloids provide new opportunities for engineering innovative materials with biomedical applications. In this review, we discuss not only outstanding advances in biomedical applications of amyloid peptides, but also the mechanism of amyloid aggregation, factors affecting the process, and core sequences driving the aggregation. We aim with this review to provide a useful manual for those who engineer amyloids for innovative medicine solutions.
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Affiliation(s)
- Sherin Abdelrahman
- Laboratory for Nanomedicine, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia;
| | - Mawadda Alghrably
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia;
| | - Joanna Izabela Lachowicz
- Department of Medical Sciences and Public Health, University of Cagliari, Policlinico Universitario, I-09042 Monserrato, Italy
| | - Abdul-Hamid Emwas
- Core Labs, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia;
| | - Charlotte A. E. Hauser
- Laboratory for Nanomedicine, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia;
| | - Mariusz Jaremko
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia;
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11
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Siposova K, Kozar T, Stupakova M, Musatov A. Complementary experimental and computational analysis of the effects of non-ionic detergents and phospholipids on insulin amyloid aggregation. Colloids Surf B Biointerfaces 2020; 197:111428. [PMID: 33129101 DOI: 10.1016/j.colsurfb.2020.111428] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/05/2020] [Accepted: 10/17/2020] [Indexed: 10/23/2022]
Abstract
Amphiphilic compounds, both detergents and lipids, are important tools for in vitro analysis of water-soluble and integral membrane proteins. A key question is whether these two groups of amphiphilic molecules use the same pathway to affect structural and functional integrity of proteins. In the present study, we tested the effect of non-ionic detergent dodecyl maltoside (DDM), two phospholipids, 1,2-dimyristoyl-sn-glycero-3- phosphocholine (DMPC), 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC), and the detergent-phospholipid mixtures on insulin amyloidogenesis in vitro. Amyloidogenesis of insulin is significantly affected by DDM in a time-and dose-dependent manner, but only slightly affected by either of phospholipids. Addition of DHPC or DMPC to detergent does not alter the inhibiting pattern, suggesting that DDM preferably binds to insulin. The molecular modeling revealed that DDM and the phospholipids occupy equivalent binding sites. DDM, due to the presence of maltose with several oxygen atoms (hydroxylic, glycosidic and ring) is involved in more hydrogen bonds than DHPC or DMPC. Hydrophobic interactions are important factors to stabilize both, DDM and phospholipids in their binding sites. Our results indicate that certain detergents (applying DDM as an example) and selected phospholipids are not always interchangeable in their use to investigate the effect of amphiphilic compounds on the behavior of amyloid-prone proteins.
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Affiliation(s)
- Katarina Siposova
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Kosice, Slovakia.
| | - Tibor Kozar
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, P. J. Safarik University, Jesenna 5, 040 01 Kosice, Slovakia.
| | - Michaela Stupakova
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Kosice, Slovakia
| | - Andrey Musatov
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Kosice, Slovakia
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12
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Schreck JS, Bridstrup J, Yuan JM. Investigating the Effects of Molecular Crowding on the Kinetics of Protein Aggregation. J Phys Chem B 2020; 124:9829-9839. [PMID: 33104345 DOI: 10.1021/acs.jpcb.0c07175] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The thermodynamics and kinetics of protein folding and protein aggregation in vivo are of great importance in numerous scientific areas including fundamental biophysics research, nanotechnology, and medicine. However, these processes remain poorly understood in both in vivo and in vitro systems. Here we extend an established model for protein aggregation that is based on the kinetic equations for the moments of the polymer size distribution by introducing macromolecular crowding particles into the model using scaled-particle and transition-state theories. The model predicts that the presence of crowders can either speed up, cause no change to, or slow down the progress of the aggregation compared to crowder-free solutions, in striking agreement with experimental results from nine different amyloid-forming proteins that utilized dextran as the crowder. These different dynamic effects of macromolecular crowding can be understood in terms of the change of excluded volume associated with each reaction step.
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Affiliation(s)
- John S Schreck
- National Center for Atmospheric Research, Boulder, Colorado 80305, United States.,Department of Chemistry, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - John Bridstrup
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Jian-Min Yuan
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, United States
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13
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Sheng J, Olrichs NK, Gadella BM, Kaloyanova DV, Helms JB. Regulation of Functional Protein Aggregation by Multiple Factors: Implications for the Amyloidogenic Behavior of the CAP Superfamily Proteins. Int J Mol Sci 2020; 21:E6530. [PMID: 32906672 PMCID: PMC7554809 DOI: 10.3390/ijms21186530] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/01/2020] [Accepted: 09/03/2020] [Indexed: 12/13/2022] Open
Abstract
The idea that amyloid fibrils and other types of protein aggregates are toxic for cells has been challenged by the discovery of a variety of functional aggregates. However, an identification of crucial differences between pathological and functional aggregation remains to be explored. Functional protein aggregation is often reversible by nature in order to respond properly to changing physiological conditions of the cell. In addition, increasing evidence indicates that fast fibril growth is a feature of functional amyloids, providing protection against the long-term existence of potentially toxic oligomeric intermediates. It is becoming clear that functional protein aggregation is a complexly organized process that can be mediated by a multitude of biomolecular factors. In this overview, we discuss the roles of diverse biomolecules, such as lipids/membranes, glycosaminoglycans, nucleic acids and metal ions, in regulating functional protein aggregation. Our studies on the protein GAPR-1 revealed that several of these factors influence the amyloidogenic properties of this protein. These observations suggest that GAPR-1, as well as the cysteine-rich secretory proteins, antigen 5 and pathogenesis-related proteins group 1 (CAP) superfamily of proteins that it belongs to, require the assembly into an amyloid state to exert several of their functions. A better understanding of functional aggregate formation may also help in the prevention and treatment of amyloid-related diseases.
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Affiliation(s)
| | | | | | | | - J. Bernd Helms
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CM Utrecht, The Netherlands; (J.S.); (N.K.O.); (B.M.G.); (D.V.K.)
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14
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Sosa AFC, de Olivera da Silva SM, Morgan GP, Schwartz DK, Kaar JL. Mixed Phospholipid Vesicles Catalytically Inhibit and Reverse Amyloid Fibril Formation. J Phys Chem Lett 2020; 11:7417-7422. [PMID: 32803986 PMCID: PMC10164471 DOI: 10.1021/acs.jpclett.0c02074] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
While many approaches to reduce fibrillation of amyloid-β (Aβ) have been aimed at slowing fibril formation, the degradation of fibrils remains challenging. We provide insight into fibril degradation as well as the inhibition of fiber formation by lipid vesicles composed of 1,2-dioleoyl-sn-glycero-3-phosphocholine and 1,2-dioleoyl-sn-glycero-3-phospho-(1'-rac-glycerol). In the presence of vesicles with the optimal lipid composition, fibril formation was inhibited up to 76%. Additionally, by tuning the lipid composition, mature fibril content decreased up to 74% and the β-sheet content of Aβ was significantly reduced. The reduction in fibril and β-sheet content was consistent with a decrease in fibril diameter and could be attributed to the chaperone-like activity of the mixed vesicles. While demonstrating this remarkable activity, our findings present new evidence that lipid composition has a significant effect on the strength of the interaction between lipid bilayers and Aβ peptides/fibrils. This understanding has intriguing therapeutic implications in treating protein misfolding diseases.
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Affiliation(s)
- Andres F. Chaparro Sosa
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80309
| | | | - Garry P. Morgan
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, 80309
| | - Daniel K. Schwartz
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80309
- Corresponding Authors: Daniel K. Schwartz, University of Colorado Boulder, Department of Chemical and Biological Engineering, Campus Box 596, Boulder, CO 80309, Tel: (303) 735-0240, Fax: (303) 492-4341, ; Joel L. Kaar, University of Colorado Boulder, Department of Chemical and Biological Engineering, Campus Box 596, Boulder, CO 80309, Tel: (303) 492-6031, Fax: (303) 492-4341,
| | - Joel L. Kaar
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO 80309
- Corresponding Authors: Daniel K. Schwartz, University of Colorado Boulder, Department of Chemical and Biological Engineering, Campus Box 596, Boulder, CO 80309, Tel: (303) 735-0240, Fax: (303) 492-4341, ; Joel L. Kaar, University of Colorado Boulder, Department of Chemical and Biological Engineering, Campus Box 596, Boulder, CO 80309, Tel: (303) 492-6031, Fax: (303) 492-4341,
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15
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Tian M, Shen L. Self-Coiling of Single-Stranded Protofibrils into Rings: A Pathway of Alzheimer's β-Peptide Amyloidosis on Lipid Membranes. ACS Macro Lett 2020; 9:813-818. [PMID: 35648531 DOI: 10.1021/acsmacrolett.0c00262] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
An amyloidosis pathway of Alzheimer's β-peptide Aβ40 on lipid membranes, the self-coiling of single-stranded protofibrils into thermodynamically stable ring structures, is uncovered. Distinct from Aβ amyloid structures reported previously, the coiled rings observed here exhibit a narrow distribution of diameters centered at ∼170 nm and their circumference thicknesses increase as a longer single-stranded protofibril wraps around the ring, indicating the coaxial loop-by-loop winding of individual protofibrils. Such self-coiling is dominated by elastic properties of the flexible protofibrils subject to thermal fluctuations and surface interactions, as supported by an entropic elasticity model from polymer physics concepts. This work not only provides insights into the fundamental physics of Alzheimer's β-peptide amyloidosis but also is useful for designing amyloid filament materials.
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Affiliation(s)
- Mengting Tian
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan 430070, China
| | - Lei Shen
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan 430070, China
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16
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Fibrillization of 40-Residue β-Amyloid Peptides in Membrane-Like Environments Leads to Different Fibril Structures and Reduced Molecular Polymorphisms. Biomolecules 2020; 10:biom10060881. [PMID: 32521743 PMCID: PMC7356566 DOI: 10.3390/biom10060881] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 05/28/2020] [Accepted: 06/04/2020] [Indexed: 12/31/2022] Open
Abstract
The molecular-level polymorphism in β-Amyloid (Aβ) fibrils have recently been considered as a pathologically relevant factor in Alzheimer’s disease (AD). Studies showed that the structural deviations in human-brain-seeded Aβ fibrils potentially correlated with the clinical histories of AD patients. For the 40-residue Aβ (Aβ40) fibrils derived from human brain tissues, a predominant molecular structure was proposed based on solid-state nuclear magnetic resonance (ssNMR) spectroscopy. However, previous studies have shown that the molecular structures of Aβ40 fibrils were sensitive to their growth conditions in aqueous environments. We show in this work that biological membranes and their phospholipid bilayer mimics serve as environmental factors to reduce the structural heterogeneity in Aβ40 fibrils. Fibrillization in the presence of membranes leads to fibril structures that are significantly different to the Aβ40 fibrils grown in aqueous solutions. Fibrils grown from multiple types of membranes, including the biological membranes extracted from the rats’ synaptosomes, shared similar ssNMR spectral features. Our studies emphasize the biological relevance of membranes in Aβ40 fibril structures and fibrillization processes.
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17
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M A, M K, H H. Study of Nanofibrils Formation of Fibroin Protein in Specific Thermal and Acidity Conditions. J Biomed Phys Eng 2020; 10:39-50. [PMID: 32158710 PMCID: PMC7036415 DOI: 10.31661/jbpe.v0i0.1092] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 01/28/2019] [Indexed: 01/21/2023]
Abstract
Background: Amyloid fibrils are insoluble arranged aggregates of proteins that are fibrillar in structure and related to many diseases (at least 20 types of illnesses) and also create many pathologic conditions. Therefore understanding the circumstance of fibril formation is very important Objectives: This study aims to work on fibrillar structure formation of fibroin (as a model protein) Material and Methods: In this experimental study, fibroin was extracted from bombyx mori silk cocoon, and the concentration was obtained by Bradford method. The protein was incubated in a wide range of times (0 min to 7 days) in specific acidity and thermal conditions (pH=1.6, T=70 °C). The assays of UV-vis spectroscopy with congo red, field emission scanning electron microscopy, transmission electron microscopy, atomic force microscopy and circular dichroism spectroscopy were employed to monitor the fibrillation process. Results: Fibroin assemblies were formed upon the process of aggregation and fibril formation with a variety of morphology ranging from nanoparticles to elongated fibrils. Conclusion: The results showed progressive pathway of fibril formation
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Affiliation(s)
- Ahrami M
- MSc, Department of Nanomedicine, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
- MSc, Nanomedicine and Nanobiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Khatami M
- MSc, NanoBioeletrochemistry Research Center, Bam University of Medical Sciences, Bam, Iran
| | - Heli H
- PhD, Nanomedicine and Nanobiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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18
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Baumer KM, Koone JC, Shaw BF. Kinetic Variability in Seeded Formation of ALS-Linked SOD1 Fibrils Across Multiple Generations. ACS Chem Neurosci 2020; 11:304-313. [PMID: 31895541 DOI: 10.1021/acschemneuro.9b00464] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The unseeded aggregation of superoxide dismutase-1 (SOD1) into amyloid-like fibrils occurs stochastically in vitro and in vivo, that is, isolated populations of SOD1 proteins (within microplate wells or living cells) self-assemble into amyloid at rates that span a probability distribution. This stochasticity has been attributed to variable degrees of monomer depletion by competing pathways of amorphous and fibrillar aggregation (inter alia). Here, microplate-based thioflavin-T (ThT) fluorescence assays were performed at high iteration (∼300) to establish whether this observed stochasticity persists when progenitor ("parent") SOD1 fibrils are used to seed the formation of multiple generations of progeny fibrils (daughter, granddaughter, and great-granddaughter fibrils). Populations of progenitor fibrils formed stochastically at different rates and fluorescence intensity, however, progeny fibrils formed at more similar rates regardless of the formation rate of the progenitor fibril. For example, populations of progenitor fibrils that formed with a lag time of ∼30 h or ∼15 h both produced progeny fibrils with lag times of ∼8 h. Likewise, populations of progenitor fibrils with high or low maximum fluorescence (e.g., ∼450 or ∼75 A.U.) both produced progeny fibrils with more similar maximum fluorescence (∼125 A.U.). The rate of propagation was found to be more dependent on monomer concentration than seed concentration. These results can be rationalized by classical rate laws for primary nucleation and monomer-dependent secondary nucleation. We also find that the seeding propensity of some "families" of in vitro grown fibrils exhibit a finite lifetime (similar to that observed in the seeding of small molecule crystals and colloids). The single biological takeaway of this study is that the concentration of native SOD1 in a cell can have a stronger effect on rates of seeded aggregation than the concentration of prion-like seed that infected the cell.
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Affiliation(s)
- Katelyn M Baumer
- Department of Chemistry and Biochemistry , Baylor University , Waco , Texas 76706 , United States
| | - Jordan C Koone
- Department of Chemistry and Biochemistry , Baylor University , Waco , Texas 76706 , United States
| | - Bryan F Shaw
- Department of Chemistry and Biochemistry , Baylor University , Waco , Texas 76706 , United States
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19
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Sanderson JM. Far from Inert: Membrane Lipids Possess Intrinsic Reactivity That Has Consequences for Cell Biology. Bioessays 2020; 42:e1900147. [PMID: 31995246 DOI: 10.1002/bies.201900147] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 12/06/2019] [Indexed: 12/19/2022]
Abstract
In this article, it is hypothesized that a fundamental chemical reactivity exists between some non-lipid constituents of cellular membranes and ester-based lipids, the significance of which is not generally recognized. Many peptides and smaller organic molecules have now been shown to undergo lipidation reactions in model membranes in circumstances where direct reaction with the lipid is the only viable route for acyl transfer. Crucially, drugs like propranolol are lipidated in vivo with product profiles that are comparable to those produced in vitro. Some compounds have also been found to promote lipid hydrolysis. Drugs with high lytic activity in vivo tend to have higher toxicity in vitro. Deacylases and lipases are proposed as key enzymes that protect cells against the effects of intrinsic lipidation. The toxic effects of intrinsic lipidation are hypothesized to include a route by which nucleation can occur during the formation of amyloid fibrils.
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20
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Hosseinpour S, Roeters SJ, Bonn M, Peukert W, Woutersen S, Weidner T. Structure and Dynamics of Interfacial Peptides and Proteins from Vibrational Sum-Frequency Generation Spectroscopy. Chem Rev 2020; 120:3420-3465. [DOI: 10.1021/acs.chemrev.9b00410] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Saman Hosseinpour
- Institute of Particle Technology (LFG), Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
| | | | - Mischa Bonn
- Molecular Spectroscopy Department, Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Wolfgang Peukert
- Institute of Particle Technology (LFG), Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
| | - Sander Woutersen
- Van’t Hoff Institute for Molecular Sciences, University of Amsterdam, 1098 EP Amsterdam, The Netherlands
| | - Tobias Weidner
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
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21
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Qu L, Fudo S, Matsuzaki K, Hoshino T. Computational Study on the Assembly of Amyloid β-Peptides in the Hydrophobic Environment. Chem Pharm Bull (Tokyo) 2019; 67:959-965. [DOI: 10.1248/cpb.c19-00171] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Liang Qu
- Graduate School of Pharmaceutical Sciences, Chiba University
| | - Satoshi Fudo
- Graduate School of Pharmaceutical Sciences, Chiba University
| | | | - Tyuji Hoshino
- Graduate School of Pharmaceutical Sciences, Chiba University
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22
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Ilie IM, Caflisch A. Simulation Studies of Amyloidogenic Polypeptides and Their Aggregates. Chem Rev 2019; 119:6956-6993. [DOI: 10.1021/acs.chemrev.8b00731] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Ioana M. Ilie
- Department of Biochemistry, University of Zürich, Zürich CH-8057, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zürich, Zürich CH-8057, Switzerland
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23
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Influence of crowding and surfaces on protein amyloidogenesis: A thermo-kinetic perspective. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:941-953. [PMID: 30928692 DOI: 10.1016/j.bbapap.2019.03.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/22/2019] [Accepted: 03/23/2019] [Indexed: 01/24/2023]
Abstract
The last few decades have irreversibly implicated protein self-assembly and aggregation leading to amyloid fibril formation in proteopathies that include several neurodegenerative diseases. Emerging studies recognize the importance of eliciting the pathways leading to protein aggregation in the context of the crowded intracellular environment rather than in conventional in vitro conditions. It is found that crowded environments can have acceleratory as well as inhibitory effects on protein aggregation, depending on the interplay of underlying factors on the crucial rate limiting steps. The aggregation mechanism and transient species formed along the pathway are further altered when they interface with natural and artificial surfaces in the cellular milieu. An increasing number of studies probe the autocatalytic nature of amyloid surfaces as well as membrane bilayer effects on amyloidogenesis. Moreover, exposure to modern nanosurfaces via nanomedicines and other sources potentially invokes beneficial or deleterious biological response that needs rigorous investigation. Mounting evidences indicate that nanoparticles can either promote or impede amyloid aggregation, spurring efforts to tune their interactions for developing effective anti-amyloid strategies. Mechanistic insights into nanoparticle mediated aggregation pathways are therefore crucial for engineering anti-amyloid nanoparticle strategies that are biocompatible and sustainable. This review is a compilation of studies that contribute to the current understanding of the altering effects of molecular crowding as well as natural and artificial surfaces on protein amyloidogenesis.
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24
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TIAN L, HUANG J. Antioxidant effects of tea catechins on the shelf life of raw minced duck meat. FOOD SCIENCE AND TECHNOLOGY 2019. [DOI: 10.1590/fst.25217] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Lili TIAN
- Hunan Agricultural University, China; Hunan Agricultural University, China; Shandong Academy of Agricultural Sciences, China
| | - Jian’an HUANG
- Hunan Agricultural University, China; Hunan Agricultural University, China
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25
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W. Pilkington IV A, Legleiter J. Challenges in understanding the structure/activity relationship of Aβ oligomers. AIMS BIOPHYSICS 2019. [DOI: 10.3934/biophy.2019.1.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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26
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Gong S, Liu J, Tian M, Wang K, Cai S, Wang W, Shen L. Unravelling the mechanism of amyloid-β peptide oligomerization and fibrillation at chiral interfaces. Chem Commun (Camb) 2019; 55:13725-13728. [DOI: 10.1039/c9cc06980a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The mechanism of how surface chirality affects amyloid-β peptide oligomerization and fibrillation was firstly unravelled at the molecular level.
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Affiliation(s)
- Shuai Gong
- School of Chemistry
- Chemical Engineering and Life Science
- Wuhan University of Technology
- Wuhan 430074
- China
| | - Jingjing Liu
- School of Chemistry
- Chemical Engineering and Life Science
- Wuhan University of Technology
- Wuhan 430074
- China
| | - Mengting Tian
- School of Chemistry
- Chemical Engineering and Life Science
- Wuhan University of Technology
- Wuhan 430074
- China
| | - Kang Wang
- School of Chemistry
- Chemical Engineering and Life Science
- Wuhan University of Technology
- Wuhan 430074
- China
| | - Shali Cai
- School of Chemistry
- Chemical Engineering and Life Science
- Wuhan University of Technology
- Wuhan 430074
- China
| | - Weiyan Wang
- School of Chemistry
- Chemical Engineering and Life Science
- Wuhan University of Technology
- Wuhan 430074
- China
| | - Lei Shen
- School of Chemistry
- Chemical Engineering and Life Science
- Wuhan University of Technology
- Wuhan 430074
- China
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27
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Zhang J, Mao X, Xu W. Fibril Nucleation Kinetics of a Pharmaceutical Peptide: The Role of Conformation Stability, Formulation Factors, and Temperature Effect. Mol Pharm 2018; 15:5591-5601. [PMID: 30350639 DOI: 10.1021/acs.molpharmaceut.8b00769] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Peptide aggregation, such as the formation of fibrils, could pose a significant challenge for the stability of parenteral peptide drugs. To ensure a robust peptide formulation, a thorough understanding of aggregation kinetics and the development of appropriate accelerated testing conditions are necessary. The present research investigated factors that impact the fibrillation kinetics of a helical 29mer pharmaceutical peptide (peptide A) and attempts to correlate results of accelerated kinetic studies with real time kinetics. Conformational flexibility of the peptide and its potential impact on aggregation kinetics were thoroughly evaluated. Three orthogonal approaches to evaluate aggregation kinetics were assessed, thioflavin T fluorescence, turbidity, and soluble peptide concentration. The results from the methods demonstrated that peptide A showed nucleated polymerization kinetics. The lag time of the fibrillation process depends heavily on pH, ionic strength, temperature, agitation, and substrate interface. The temperature-dependent fibril nucleation kinetics follow Arrhenius behavior, despite a helical fold in the peptide structure. This finding suggests a potential opportunity to leverage accelerated testing conditions to project the long-term performance at storage temperatures. The present study provides both fundamental understanding and practical approaches to mitigate the aggregation risk for pharmaceutical peptides with a strong tendency to form fibrils.
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Affiliation(s)
- Jingtao Zhang
- Department of Pharmaceutical Sciences, MRL , Merck & Co., Inc. , West Point , Pennsylvania 19486 , United States
| | - Xinpei Mao
- Department of Pharmaceutical Sciences, MRL , Merck & Co., Inc. , West Point , Pennsylvania 19486 , United States
| | - Wei Xu
- Department of Pharmaceutical Sciences, MRL , Merck & Co., Inc. , West Point , Pennsylvania 19486 , United States
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28
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Rangachari V, Dean DN, Rana P, Vaidya A, Ghosh P. Cause and consequence of Aβ - Lipid interactions in Alzheimer disease pathogenesis. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2018; 1860:1652-1662. [PMID: 29526709 PMCID: PMC6133763 DOI: 10.1016/j.bbamem.2018.03.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 02/28/2018] [Accepted: 03/02/2018] [Indexed: 12/14/2022]
Abstract
Self-templating propagation of protein aggregate conformations is increasingly becoming a significant factor in many neurological diseases. In Alzheimer disease (AD), intrinsically disordered amyloid-β (Aβ) peptides undergo aggregation that is sensitive to environmental conditions. High-molecular weight aggregates of Aβ that form insoluble fibrils are deposited as senile plaques in AD brains. However, low-molecular weight aggregates called soluble oligomers are known to be the primary toxic agents responsible for neuronal dysfunction. The aggregation process is highly stochastic involving both homotypic (Aβ-Aβ) and heterotypic (Aβ with interacting partners) interactions. Two of the important members of interacting partners are membrane lipids and surfactants, to which Aβ shows a perpetual association. Aβ-membrane interactions have been widely investigated for more than two decades, and this research has provided a wealth of information. Although this has greatly enriched our understanding, the objective of this review is to consolidate the information from the literature that collectively showcases the unique phenomenon of lipid-mediated Aβ oligomer generation, which has largely remained inconspicuous. This is especially important because Aβ aggregate "strains" are increasingly becoming relevant in light of the correlations between the structure of aggregates and AD phenotypes. Here, we will focus on aspects of Aβ-lipid interactions specifically from the context of how lipid modulation generates a wide variety of biophysically and biochemically distinct oligomer sub-types. This, we believe, will refocus our thinking on the influence of lipids and open new approaches in delineating the mechanisms of AD pathogenesis. This article is part of a Special Issue entitled: Protein Aggregation and Misfolding at the Cell Membrane Interface edited by Ayyalusamy Ramamoorthy.
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Affiliation(s)
- Vijayaraghavan Rangachari
- Department of Chemistry & Biochemistry, University of Southern Mississippi, Hattiesburg, MS 39406, USA.
| | - Dexter N Dean
- Department of Chemistry & Biochemistry, University of Southern Mississippi, Hattiesburg, MS 39406, USA
| | - Pratip Rana
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Ashwin Vaidya
- Department of Mathematical Science, Montclair State University, Montclair, NJ 07043, USA
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284, USA
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29
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Cheng Q, Hu ZW, Doherty KE, Tobin-Miyaji YJ, Qiang W. The on-fibrillation-pathway membrane content leakage and off-fibrillation-pathway lipid mixing induced by 40-residue β-amyloid peptides in biologically relevant model liposomes. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2018; 1860:1670-1680. [PMID: 29548698 PMCID: PMC6295276 DOI: 10.1016/j.bbamem.2018.03.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 03/08/2018] [Accepted: 03/10/2018] [Indexed: 02/06/2023]
Abstract
Disruption of the synaptic plasma membrane (SPM) induced by the aggregation of β-amyloid (Aβ) peptides has been considered as a potential mechanism for the neurotoxicity of Aβ in Alzheimer's disease (AD). However, the molecular basis of such membrane disruption process remains unclear, mainly because of the severe systematic heterogeneity problem that prevents the high-resolution studies. Our previous studies using a two-component phosphatidylcholine (PC)/phosphatidylglycerol (PG) model liposome showed the presence of Aβ-induced membrane disruptions that were either on the pathway or off the pathway of fibril formation. The present study focuses on a more biologically relevant model membrane with compositions that mimic the outer leaflet of SPMs. The main findings are: (1) the two competing membrane disruption effects discovered in PC/PG liposomes and their general peptide-to-lipid-molar-ratio dependence persist in the more complicated membrane models; (2) the SPM-mimic membrane promotes the formation of certain "on-fibrillation-pathway" intermediates with higher α-helical structural population, which lead to more rapid and significant of membrane content leakage; (3) although the "on-fibrillation-pathway" intermediate structures show dependence on membrane compositions, there seems to be a common final fibril structure grown from different liposomes, suggesting that there may be a predominant fibril structure for 40-residue Aβ (i.e. Aβ40) peptides in biologically-relevant membranes. This article is part of a Special Issue entitled: Protein Aggregation and Misfolding at the Cell Membrane Interface edited by Ayyalusamy Ramamoorthy.
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Affiliation(s)
- Qinghui Cheng
- Department of Chemistry, State University of New York at Binghamton, Binghamton, NY 13902, United States
| | - Zhi-Wen Hu
- Department of Chemistry, State University of New York at Binghamton, Binghamton, NY 13902, United States
| | - Katelynne E Doherty
- Department of Chemistry, State University of New York at Binghamton, Binghamton, NY 13902, United States
| | - Yuto J Tobin-Miyaji
- Department of Chemistry, State University of New York at Binghamton, Binghamton, NY 13902, United States
| | - Wei Qiang
- Department of Chemistry, State University of New York at Binghamton, Binghamton, NY 13902, United States.
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30
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Martial B, Lefèvre T, Auger M. Understanding amyloid fibril formation using protein fragments: structural investigations via vibrational spectroscopy and solid-state NMR. Biophys Rev 2018; 10:1133-1149. [PMID: 29855812 PMCID: PMC6082320 DOI: 10.1007/s12551-018-0427-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 05/17/2018] [Indexed: 12/11/2022] Open
Abstract
It is well established that amyloid proteins play a primary role in neurodegenerative diseases. Alzheimer's, Parkinson's, type II diabetes, and Creutzfeldt-Jakob's diseases are part of a wider family encompassing more than 50 human pathologies related to aggregation of proteins. Although this field of research is thoroughly investigated, several aspects of fibrillization remain misunderstood, which in turn slows down, or even impedes, advances in treating and curing amyloidoses. To solve this problem, several research groups have chosen to focus on short fragments of amyloid proteins, sequences that have been found to be of great importance for the amyloid formation process. Studying short peptides allows bypassing the complexity of working with full-length proteins and may provide important information relative to critical segments of amyloid proteins. To this end, efficient biophysical tools are required. In this review, we focus on two essential types of spectroscopic techniques, i.e., vibrational spectroscopy and its derivatives (conventional Raman scattering, deep-UV resonance Raman (DUVRR), Raman optical activity (ROA), surface-enhanced Raman spectroscopy (SERS), tip-enhanced Raman spectroscopy (TERS), infrared (IR) absorption spectroscopy, vibrational circular dichroism (VCD)) and solid-state nuclear magnetic resonance (ssNMR). These techniques revealed powerful to provide a better atomic and molecular comprehension of the amyloidogenic process and fibril structure. This review aims at underlining the information that these techniques can provide and at highlighting their strengths and weaknesses when studying amyloid fragments. Meaningful examples from the literature are provided for each technique, and their complementarity is stressed for the kinetic and structural characterization of amyloid fibril formation.
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Affiliation(s)
- Benjamin Martial
- Department of Chemistry, Regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines (PROTEO), Centre de recherche sur les matériaux avancés (CERMA), Centre québécois sur les matériaux fonctionnels (CQMF), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Thierry Lefèvre
- Department of Chemistry, Regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines (PROTEO), Centre de recherche sur les matériaux avancés (CERMA), Centre québécois sur les matériaux fonctionnels (CQMF), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Michèle Auger
- Department of Chemistry, Regroupement québécois de recherche sur la fonction, l'ingénierie et les applications des protéines (PROTEO), Centre de recherche sur les matériaux avancés (CERMA), Centre québécois sur les matériaux fonctionnels (CQMF), Université Laval, Québec, QC, G1V 0A6, Canada.
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31
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Yang M, Wang K, Lin J, Wang L, Wei F, Zhu J, Zheng W, Shen L. Gel Phase Membrane Retards Amyloid β-Peptide (1-42) Fibrillation by Restricting Slaved Diffusion of Peptides on Lipid Bilayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:8408-8414. [PMID: 29925241 DOI: 10.1021/acs.langmuir.8b01315] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Plasma membranes in the human brain can interact with amyloid β-peptide (1-42; Aβ42) and induce Aβ42 fibrillation, which is considered to be a crucial process underlying the neurotoxicity of Aβ42 and the pathogenesis of Alzheimer's disease (AD). However, the mechanism of membrane-mediated Aβ42 fibrillation at the molecular level remains elusive. Here we study the role of adsorbed Aβ42 peptides on membrane-mediated fibrillation using supported lipid bilayers of varying phase structures (gel and fluid). Using total internal reflection fluorescence microscopy and interfacial specific second-order nonlinear optical spectroscopy, we show that the dynamics of 2D-mobile Aβ42 molecules, facilitated by the highly mobile lipids underneath the peptides, are critical to Aβ42 fibrillation on liquid phase membranes. This growth mechanism is retarded on gel phase membranes where the dynamics of 2D-mobile peptides are restricted by the "frozen" lipids with less mobility.
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Affiliation(s)
- Mengting Yang
- School of Chemistry and Chemical Engineering , Huazhong University of Science and Technology , Wuhan 430070 , China
| | - Kang Wang
- School of Chemistry, Chemical Engineering and Life Science , Wuhan University of Technology , Wuhan 430074 , China
| | - Jiake Lin
- School of Chemistry, Chemical Engineering and Life Science , Wuhan University of Technology , Wuhan 430074 , China
| | - Liqun Wang
- Institute for Interdisciplinary Research & Key Laboratory of Optoelectronic Chemical Materials and Devices of Education , Jianghan University , Wuhan 430056 , China
| | - Feng Wei
- Institute for Interdisciplinary Research & Key Laboratory of Optoelectronic Chemical Materials and Devices of Education , Jianghan University , Wuhan 430056 , China
| | - Jintao Zhu
- School of Chemistry and Chemical Engineering , Huazhong University of Science and Technology , Wuhan 430070 , China
| | - Wanquan Zheng
- Institute for Interdisciplinary Research & Key Laboratory of Optoelectronic Chemical Materials and Devices of Education , Jianghan University , Wuhan 430056 , China
- Institute des Sciences Moléculaires d'Orsay, Université Paris-Sud , 91405 Orsay Cedex , France
| | - Lei Shen
- School of Chemistry, Chemical Engineering and Life Science , Wuhan University of Technology , Wuhan 430074 , China
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32
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Lee TH, Hirst DJ, Kulkarni K, Del Borgo MP, Aguilar MI. Exploring Molecular-Biomembrane Interactions with Surface Plasmon Resonance and Dual Polarization Interferometry Technology: Expanding the Spotlight onto Biomembrane Structure. Chem Rev 2018; 118:5392-5487. [PMID: 29793341 DOI: 10.1021/acs.chemrev.7b00729] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The molecular analysis of biomolecular-membrane interactions is central to understanding most cellular systems but has emerged as a complex technical challenge given the complexities of membrane structure and composition across all living cells. We present a review of the application of surface plasmon resonance and dual polarization interferometry-based biosensors to the study of biomembrane-based systems using both planar mono- or bilayers or liposomes. We first describe the optical principals and instrumentation of surface plasmon resonance, including both linear and extraordinary transmission modes and dual polarization interferometry. We then describe the wide range of model membrane systems that have been developed for deposition on the chips surfaces that include planar, polymer cushioned, tethered bilayers, and liposomes. This is followed by a description of the different chemical immobilization or physisorption techniques. The application of this broad range of engineered membrane surfaces to biomolecular-membrane interactions is then overviewed and how the information obtained using these techniques enhance our molecular understanding of membrane-mediated peptide and protein function. We first discuss experiments where SPR alone has been used to characterize membrane binding and describe how these studies yielded novel insight into the molecular events associated with membrane interactions and how they provided a significant impetus to more recent studies that focus on coincident membrane structure changes during binding of peptides and proteins. We then discuss the emerging limitations of not monitoring the effects on membrane structure and how SPR data can be combined with DPI to provide significant new information on how a membrane responds to the binding of peptides and proteins.
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Affiliation(s)
- Tzong-Hsien Lee
- Department of Biochemistry and Molecular Biology and Biomedicine Discovery Institute , Monash University , Clayton , VIC 3800 , Australia
| | - Daniel J Hirst
- Department of Biochemistry and Molecular Biology and Biomedicine Discovery Institute , Monash University , Clayton , VIC 3800 , Australia
| | - Ketav Kulkarni
- Department of Biochemistry and Molecular Biology and Biomedicine Discovery Institute , Monash University , Clayton , VIC 3800 , Australia
| | - Mark P Del Borgo
- Department of Biochemistry and Molecular Biology and Biomedicine Discovery Institute , Monash University , Clayton , VIC 3800 , Australia
| | - Marie-Isabel Aguilar
- Department of Biochemistry and Molecular Biology and Biomedicine Discovery Institute , Monash University , Clayton , VIC 3800 , Australia
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33
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Analysis of Physicochemical Interaction of Aβ40 with a GM1 Ganglioside-Containing Lipid Membrane. J Phys Chem B 2018. [DOI: 10.1021/acs.jpcb.8b00139] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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34
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Jamasbi E, Hossain MA, Tan M, Separovic F, Ciccotosto GD. Fluorescence imaging of the interaction of amyloid beta 40 peptides with live cells and model membrane. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1609-1615. [PMID: 29408451 DOI: 10.1016/j.bbamem.2018.01.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 01/23/2018] [Accepted: 01/27/2018] [Indexed: 11/30/2022]
Abstract
Amyloid beta peptides (Aβ) found in plaques in the brain have been widely recognised as a hallmark of Alzheimer's disease although the underlying mechanism is still unknown. Aβ40 and Aβ40(A2T) peptides were synthesized and their effects on neuronal cells are reported together with the effect of tetramer forms of the peptides. ThT assay revealed that mutation affected the lag time and aggregation and the presence of lipid vesicles changed the fibril formation profile for both peptides. The A2T mutation appeared to reduce cytotoxicity and lessen binding of Aβ40 peptides to neuronal cells. Fluorescence microscopy of the interaction between Aβ40 peptides and giant unilamellar vesicles revealed that both peptides led to formation of smaller vesicles although the tetramer of Aβ(A2T) appeared to promote vesicle aggregation. This article is part of a Special Issue entitled: Protein Aggregation and Misfolding at the Cell Membrane Interface edited by Ayyalusamy Ramamoorthy.
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Affiliation(s)
- Elaheh Jamasbi
- School of Chemistry, Bio21 Institute, The University of Melbourne, VIC 3010, Australia
| | - Mohammed Akhter Hossain
- School of Chemistry, Bio21 Institute, The University of Melbourne, VIC 3010, Australia; The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, VIC 3010, Australia
| | - Marsha Tan
- Department of Pathology, The University of Melbourne, VIC 3010, Australia
| | - Frances Separovic
- School of Chemistry, Bio21 Institute, The University of Melbourne, VIC 3010, Australia.
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35
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Oil Palm Phenolics Inhibit the In Vitro Aggregation of β-Amyloid Peptide into Oligomeric Complexes. Int J Alzheimers Dis 2018; 2018:7608038. [PMID: 29666700 PMCID: PMC5831689 DOI: 10.1155/2018/7608038] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 11/23/2017] [Accepted: 12/07/2017] [Indexed: 01/01/2023] Open
Abstract
Alzheimer's disease is a severe neurodegenerative disease characterized by the aggregation of amyloid-β peptide (Aβ) into toxic oligomers which activate microglia and astrocytes causing acute neuroinflammation. Multiple studies show that the soluble oligomers of Aβ42 are neurotoxic and proinflammatory, whereas the monomers and insoluble fibrils are relatively nontoxic. We show that Aβ42 aggregation is inhibited in vitro by oil palm phenolics (OPP), an aqueous extract from the oil palm tree (Elaeis guineensis). The data shows that OPP inhibits stacking of β-pleated sheets, which is essential for oligomerization. We demonstrate the inhibition of Aβ42 aggregation by (1) mass spectrometry; (2) Congo Red dye binding; (3) 2D-IR spectroscopy; (4) dynamic light scattering; (5) transmission electron microscopy; and (6) transgenic yeast rescue assay. In the yeast rescue assay, OPP significantly reduces the cytotoxicity of aggregating neuropeptides in yeast genetically engineered to overexpress these peptides. The data shows that OPP inhibits (1) the aggregation of Aβ into oligomers; (2) stacking of β-pleated sheets; and (3) fibrillar growth and coalescence. These inhibitory effects prevent the formation of neurotoxic oligomers and hold potential as a means to reduce neuroinflammation and neuronal death and thereby may play some role in the prevention or treatment of Alzheimer's disease.
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36
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Mancini O, Wellbrock T, Rolinski OJ, Kubiak-Ossowska K, Mulheran PA. Probing beta amyloid aggregation using fluorescence anisotropy: experiments and simulation. Phys Chem Chem Phys 2018; 20:4216-4225. [DOI: 10.1039/c7cp08217g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Simulated fluorescence anisotropy from Tyr residues distinguishes a beta amyloid monomer (black) from oligomers (coloured).
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Affiliation(s)
- Onorio Mancini
- Department of Chemical Engineering and Process Engineering
- University of Strathclyde
- Glasgow
- UK
| | | | | | | | - Paul A. Mulheran
- Department of Chemical Engineering and Process Engineering
- University of Strathclyde
- Glasgow
- UK
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37
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Inferring Mechanistic Parameters from Amyloid Formation Kinetics by Approximate Bayesian Computation. Biophys J 2017; 112:868-880. [PMID: 28297646 DOI: 10.1016/j.bpj.2017.01.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 01/12/2017] [Accepted: 01/17/2017] [Indexed: 11/23/2022] Open
Abstract
Amyloid formation is implicated in a number of human diseases, and is thought to proceed via a nucleation-dependent polymerization mechanism. Experimenters often wish to relate changes in amyloid formation kinetics, for example, in response to small molecules to specific mechanistic steps along this pathway. However, fitting kinetic fibril formation data to a complex model including explicit rate constants results in an ill-posed problem with a vast number of potential solutions. The levels of uncertainty remaining in parameters calculated from these models, arising both from experimental noise and high levels of degeneracy or codependency in parameters, is often unclear. Here, we demonstrate that a combination of explicit mathematical models with an approximate Bayesian computation approach can be used to assign the mechanistic effects of modulators on amyloid fibril formation. We show that even when exact rate constants cannot be extracted, parameters derived from these rate constants can be recovered and used to assign mechanistic effects and their relative magnitudes with a great deal of confidence. Furthermore, approximate Bayesian computation provides a robust method for visualizing uncertainty remaining in the model parameters, regardless of its origin. We apply these methods to the problem of heparin-mediated tau polymerization, which displays complex kinetic behavior not amenable to analysis by more traditional methods. Our analysis indicates that the role of heparin cannot be explained by enhancement of nucleation alone, as has been previously proposed. The methods described here are applicable to a wide range of systems, as models can be easily adapted to account for new reactions and reversibility.
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38
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Young LM, Tu LH, Raleigh DP, Ashcroft AE, Radford SE. Understanding co-polymerization in amyloid formation by direct observation of mixed oligomers. Chem Sci 2017; 8:5030-5040. [PMID: 28970890 PMCID: PMC5613229 DOI: 10.1039/c7sc00620a] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 05/03/2017] [Indexed: 12/15/2022] Open
Abstract
Although amyloid assembly in vitro is commonly investigated using single protein sequences, fibril formation in vivo can be more heterogeneous, involving co-assembly of proteins of different length, sequence and/or post-translational modifications. Emerging evidence suggests that co-polymerization can alter the rate and/or mechanism of aggregation and can contribute to pathogenicity. Electrospray ionization-ion mobility spectrometry-mass spectrometry (ESI-IMS-MS) is uniquely suited to the study of these heterogeneous ensembles. Here, ESI-IMS-MS combined with analysis of fibrillation rates using thioflavin T (ThT) fluorescence, is used to track the course of aggregation of variants of islet-amyloid polypeptide (IAPP) in isolation and in pairwise mixtures. We identify a sub-population of extended monomers as the key precursors of amyloid assembly, and reveal that the fastest aggregating sequence in peptide mixtures determines the lag time of fibrillation, despite being unable to cross-seed polymerization. The results demonstrate that co-polymerization of IAPP sequences radically alters the rate of amyloid assembly by altering the conformational properties of the mixed oligomers that form.
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Affiliation(s)
- Lydia M Young
- Astbury Centre for Structural Molecular Biology , School of Molecular and Cellular Biology , University of Leeds , Leeds LS2 9JT , UK .
| | - Ling-Hsien Tu
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794-3400 , USA
- Genomics Research Center , Academia Sinica , 128 Academia , Taipei 11529 , Taiwan
| | - Daniel P Raleigh
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794-3400 , USA
| | - Alison E Ashcroft
- 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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39
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Di Martino RMC, Bisi A, Rampa A, Gobbi S, Belluti F. Recent progress on curcumin-based therapeutics: a patent review (2012-2016). Part II: curcumin derivatives in cancer and neurodegeneration. Expert Opin Ther Pat 2017; 27:953-965. [DOI: 10.1080/13543776.2017.1339793] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Rita Maria Concetta Di Martino
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-Bologna University, Bologna, Italy
- Department of Drug Discovery and Development, Istituto Italiano di Tecnologia, Genova, Italy
| | - Alessandra Bisi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-Bologna University, Bologna, Italy
| | - Angela Rampa
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-Bologna University, Bologna, Italy
| | - Silvia Gobbi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-Bologna University, Bologna, Italy
| | - Federica Belluti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum-Bologna University, Bologna, Italy
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40
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Michaels TCT, Liu LX, Meisl G, Knowles TPJ. Physical principles of filamentous protein self-assembly kinetics. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:153002. [PMID: 28170349 DOI: 10.1088/1361-648x/aa5f10] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The polymerization of proteins and peptides into filamentous supramolecular structures is an elementary form of self-organization of key importance to the functioning biological systems, as in the case of actin biofilaments that compose the cellular cytoskeleton. Aberrant filamentous protein self-assembly, however, is associated with undesired effects and severe clinical disorders, such as Alzheimer's and Parkinson's diseases, which, at the molecular level, are associated with the formation of certain forms of filamentous protein aggregates known as amyloids. Moreover, due to their unique physicochemical properties, protein filaments are finding extensive applications as biomaterials for nanotechnology. With all these different factors at play, the field of filamentous protein self-assembly has experienced tremendous activity in recent years. A key question in this area has been to elucidate the microscopic mechanisms through which filamentous aggregates emerge from dispersed proteins with the goal of uncovering the underlying physical principles. With the latest developments in the mathematical modeling of protein aggregation kinetics as well as the improvement of the available experimental techniques it is now possible to tackle many of these complex systems and carry out detailed analyses of the underlying microscopic steps involved in protein filament formation. In this paper, we review some classical and modern kinetic theories of protein filament formation, highlighting their use as a general strategy for quantifying the molecular-level mechanisms and transition states involved in these processes.
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Affiliation(s)
- Thomas C T Michaels
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, United States of America
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41
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El Gaamouch F, Jing P, Xia J, Cai D. Alzheimer's Disease Risk Genes and Lipid Regulators. J Alzheimers Dis 2017; 53:15-29. [PMID: 27128373 DOI: 10.3233/jad-160169] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Brain lipid homeostasis plays an important role in Alzheimer's disease (AD) and other neurodegenerative disorders. Aggregation of amyloid-β peptide is one of the major events in AD. The complex interplay between lipids and amyloid-β accumulation has been intensively investigated. The proportions of lipid components including phospholipids, sphingolipids, and cholesterol are roughly similar across different brain regions under physiological conditions. However, disruption of brain lipid homeostasis has been described in AD and implicated in disease pathogenesis. Moreover, studies suggest that analysis of lipid composition in plasma and cerebrospinal fluid could improve our understanding of the disease development and progression, which could potentially serve as disease biomarkers and prognostic indicators for AD therapies. Here, we summarize the functional roles of AD risk genes and lipid regulators that modulate brain lipid homeostasis including different lipid species, lipid complexes, and lipid transporters, particularly their effects on amyloid processing, clearance, and aggregation, as well as neuro-toxicities that contribute to AD pathogenesis.
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Affiliation(s)
- Farida El Gaamouch
- James J Peters VA Medical Center, Research & Development, Bronx, NY, USA.,Department of Neurology, Alzheimer Disease Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ping Jing
- The Central Hospital of Wuhan, China
| | | | - Dongming Cai
- James J Peters VA Medical Center, Research & Development, Bronx, NY, USA.,Department of Neurology, Alzheimer Disease Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,The Central Hospital of Wuhan, China
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42
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Goch W, Bal W. Numerical Simulations Reveal Randomness of Cu(II) Induced Aβ Peptide Dimerization under Conditions Present in Glutamatergic Synapses. PLoS One 2017; 12:e0170749. [PMID: 28125716 PMCID: PMC5268396 DOI: 10.1371/journal.pone.0170749] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 01/10/2017] [Indexed: 12/22/2022] Open
Abstract
The interactions between the Aβ1-40 molecules species and the copper ions (Cu(II)) were intensively investigated due to their potential role in the development of the Alzheimer Disease (AD). The rate and the mechanism of the Cu(II)-Aβ complexes formation determines the aggregation pathway of the Aβ species, starting from smaller but more cytotoxic oligomers and ending up in large Aβ plaques, being the main hallmark of the AD. In our study we exploit the existing knowledge on the Cu(II)-Aβ interactions and create the theoretical model of the initial phase of the copper- driven Aβ aggregation mechanism. The model is based on the direct solution of the Chemical Master Equations, which capture the inherent stochastics of the considered system. In our work we argue that due to a strong Cu(II) affinity to Aβ and temporal accessibility of the Cu(II) ions during normal synaptic activity the aggregation driven by Cu(II) dominates the pure Aβ aggregation. We also demonstrate the dependence of the formation of different Cu(II)-Aβ complexes on the concentrations of reagents and the synaptic activity. Our findings correspond to recent experimental results and give a sound hypothesis on the AD development mechanisms.
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Affiliation(s)
- Wojciech Goch
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Wojciech Bal
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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43
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Tanaka M, Nishimura A, Takeshita H, Takase H, Yamada T, Mukai T. Effect of lipid environment on amyloid fibril formation of human serum amyloid A. Chem Phys Lipids 2017; 202:6-12. [DOI: 10.1016/j.chemphyslip.2016.11.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 11/14/2016] [Accepted: 11/14/2016] [Indexed: 10/20/2022]
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44
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Cenini G, Rüb C, Bruderek M, Voos W. Amyloid β-peptides interfere with mitochondrial preprotein import competence by a coaggregation process. Mol Biol Cell 2016; 27:3257-3272. [PMID: 27630262 PMCID: PMC5170859 DOI: 10.1091/mbc.e16-05-0313] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 08/25/2016] [Accepted: 09/06/2016] [Indexed: 12/03/2022] Open
Abstract
Aβ peptides play a central role in the etiology of Alzheimer disease (AD) by exerting cellular toxicity correlated with aggregate formation. Experimental evidence has shown intraneuronal accumulation of Aβ peptides and interference with mitochondrial functions. Nevertheless, the relevance of intracellular Aβ peptides in the pathophysiology of AD is controversial. Here we found that the two major species of Aβ peptides, in particular Aβ42, exhibited a strong inhibitory effect on the preprotein import reactions essential for mitochondrial biogenesis. However, Aβ peptides interacted only weakly with mitochondria and did not affect the inner membrane potential or the structure of the preprotein translocase complexes. Aβ peptides significantly decreased the import competence of mitochondrial precursor proteins via an extramitochondrial coaggregation mechanism. Coaggregation and import inhibition were significantly stronger for the longer peptide Aβ42, correlating with its importance in AD pathology. Our results demonstrate that direct interference of aggregation-prone Aβ peptides with mitochondrial protein biogenesis represents a crucial aspect of the pathobiochemical mechanisms contributing to cellular damage in AD.
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Affiliation(s)
- Giovanna Cenini
- Institut für Biochemie und Molekularbiologie, Universität Bonn, 53115 Bonn, Germany
| | - Cornelia Rüb
- Institut für Biochemie und Molekularbiologie, Universität Bonn, 53115 Bonn, Germany
| | - Michael Bruderek
- Institut für Biochemie und Molekularbiologie, Universität Bonn, 53115 Bonn, Germany
| | - Wolfgang Voos
- Institut für Biochemie und Molekularbiologie, Universität Bonn, 53115 Bonn, Germany
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45
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Malishev R, Nandi S, Kolusheva S, Shaham-Niv S, Gazit E, Jelinek R. Bacoside-A, an anti-amyloid natural substance, inhibits membrane disruption by the amyloidogenic determinant of prion protein through accelerating fibril formation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2208-2214. [DOI: 10.1016/j.bbamem.2016.06.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 06/20/2016] [Accepted: 06/22/2016] [Indexed: 12/29/2022]
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46
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Wang J, Liu K, Xing R, Yan X. Peptide self-assembly: thermodynamics and kinetics. Chem Soc Rev 2016; 45:5589-5604. [PMID: 27487936 DOI: 10.1039/c6cs00176a] [Citation(s) in RCA: 615] [Impact Index Per Article: 76.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Self-assembling systems play a significant role in physiological functions and have therefore attracted tremendous attention due to their great potential for applications in energy, biomedicine and nanotechnology. Peptides, consisting of amino acids, are among the most popular building blocks and programmable molecular motifs. Nanostructures and materials assembled using peptides exhibit important potential for green-life new technology and biomedical applications mostly because of their bio-friendliness and reversibility. The formation of these ordered nanostructures pertains to the synergistic effect of various intermolecular non-covalent interactions, including hydrogen-bonding, π-π stacking, electrostatic, hydrophobic, and van der Waals interactions. Therefore, the self-assembly process is mainly driven by thermodynamics; however, kinetics is also a critical factor in structural modulation and function integration. In this review, we focus on the influence of thermodynamic and kinetic factors on structural assembly and regulation based on different types of peptide building blocks, including aromatic dipeptides, amphiphilic peptides, polypeptides, and amyloid-relevant peptides.
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Affiliation(s)
- Juan Wang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
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47
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Membrane binding of peptide models for early stages of amyloid formation: Lipid packing counts more than charge. Chem Phys Lipids 2016; 198:28-38. [DOI: 10.1016/j.chemphyslip.2016.02.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 02/04/2016] [Accepted: 02/27/2016] [Indexed: 11/17/2022]
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48
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Ghobeh M, Ahmadian S, Meratan AA, Ebrahim-Habibi A, Ghasemi A, Shafizadeh M, Nemat-Gorgani M. Interaction of Aβ(25-35) fibrillation products with mitochondria: Effect of small-molecule natural products. Biopolymers 2016; 102:473-86. [PMID: 25297917 DOI: 10.1002/bip.22572] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 09/18/2014] [Accepted: 10/06/2014] [Indexed: 12/25/2022]
Abstract
The 25-35 fragment of the amyloid β (Aβ) peptide is a naturally occurring proteolytic by-product that retains the pathophysiology of its larger parent molecule, whose deposition has been shown to involve mitochondrial dysfunction. Hence, disruption of Aβ(25-35) aggregates could afford an effective remedial strategy for Alzheimer's disease (AD). In the present study, the effect of a number of selected small-molecule natural products (polyphenols: resveratrol, quercetin, biochanin A, and indoles: indole-3-acetic acid, indole-3-carbinol (I3C)) on Aβ(25-35) fibrillogenesis was explored under physiological conditions, and interaction of the resulting structures with rat brain mitochondria was investigated. Several techniques, including fluorescence, circular dichroism, and transmission electron microscopy were utilized to characterize the aggregation products, and possible mitochondrial membrane permeabilization was determined following release of marker enzymes. Results demonstrate the capacity of Aβ(25-35) fibrils to damage mitochondria and suggest how small molecules may afford protection. While I3C appeared more effective in inhibiting the fibrillation process, all natural products behaved similarly in destabilizing preformed aggregates. It is concluded that elucidation of such protection may provide important insights into the development of preventive and therapeutic agents for AD.
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Affiliation(s)
- Maryam Ghobeh
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
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49
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Paracha S, Hestekin C. Field amplified sample stacking of amyloid beta (1-42) oligomers using capillary electrophoresis. BIOMICROFLUIDICS 2016; 10:033105. [PMID: 27375814 PMCID: PMC4912557 DOI: 10.1063/1.4954051] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 06/01/2016] [Indexed: 05/12/2023]
Abstract
Oligomeric forms of the amyloid beta (Aβ) protein have been indicated to be an important factor in the development of Alzheimer's disease (AD). Since the oligomeric forms of Aβ can vary in size and conformation, it is vital to understand the early stages of Aβ aggregation in order to improve the care and treatment of patients with AD. This is the first study to determine the effect of field amplified sample stacking (FASS) on the separation of oligomeric forms of Aβ1-42 using capillary electrophoresis (CE) with ultraviolet (UV) detection. UV-CE was able to separate two different species of Aβ1-42 oligomers (<7 mers and 7-22 mers). Although FASS required the use of a higher ionic strength buffer, Aβ1-42 oligomers had the same aggregation behavior as under the non-FASS conditions with only small changes in the amounts of oligomers observed. In general, FASS provided smaller peak widths (>75% average reduction) and increased peak heights (>60% average increase) when compared to non-FASS conditions. UV-CE with FASS also provided higher resolution between the Aβ1-42 oligomers for all aggregation time points studied. In addition, Congo red and Orange G inhibition studies were used to help evaluate the conformation of the observed species. This work demonstrates the ability of UV-CE employing FASS to provide higher resolution between oligomeric forms of Aβ1-42 without significantly altering their aggregation.
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Affiliation(s)
- Sadia Paracha
- Ralph E. Martin Department of Chemical Engineering, University of Arkansas , Fayetteville, Arkansas 72701, USA
| | - Christa Hestekin
- Ralph E. Martin Department of Chemical Engineering, University of Arkansas , Fayetteville, Arkansas 72701, USA
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50
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Yoon SY, Kim DH. Alzheimer's disease genes and autophagy. Brain Res 2016; 1649:201-209. [PMID: 27016058 DOI: 10.1016/j.brainres.2016.03.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Revised: 03/09/2016] [Accepted: 03/13/2016] [Indexed: 11/15/2022]
Abstract
Autophagy is a process to degrade and recycle cellular constituents via the lysosome for regulating cellular homeostasis. Its dysfunction is now considered to be involved in many diseases, including neurodegenerative diseases. Many features reflecting autophagy impairment, such as autophagosome accumulation and lysosomal dysfunction, have been also revealed to be involved in Alzheimer's disease (AD). Recent genetic studies such as genome-wide association studies in AD have identified a number of novel genes associated with AD. Some of the identified genes have demonstrated dysfunction in autophagic processes in AD, while others remain under investigation. Since autophagy is strongly regarded to be one of the major pathogenic mechanisms of AD, it is necessary to review how the AD-associated genes are related to autophagy. We anticipate our current review to be a starting point for future studies regarding AD-associated genes and autophagy. This article is part of a Special Issue entitled SI:Autophagy.
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Affiliation(s)
- Seung-Yong Yoon
- Alzheimer's Disease Experts Lab (ADEL), Asan Institute of Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea; Department of Brain Science, University of Ulsan College of Medicine, Seoul, Republic of Korea; Bio-Medical Institute of Technology (BMIT), University of Ulsan College of Medicine, Seoul, Republic of Korea; Cell Dysfunction Research Center (CDRC), University of Ulsan College of Medicine, Seoul, Republic of Korea.
| | - Dong-Hou Kim
- Alzheimer's Disease Experts Lab (ADEL), Asan Institute of Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea; Department of Brain Science, University of Ulsan College of Medicine, Seoul, Republic of Korea; Bio-Medical Institute of Technology (BMIT), University of Ulsan College of Medicine, Seoul, Republic of Korea; Cell Dysfunction Research Center (CDRC), University of Ulsan College of Medicine, Seoul, Republic of Korea.
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