1
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Murumulla L, Bandaru LJM, Challa S. Heavy Metal Mediated Progressive Degeneration and Its Noxious Effects on Brain Microenvironment. Biol Trace Elem Res 2024; 202:1411-1427. [PMID: 37462849 DOI: 10.1007/s12011-023-03778-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/13/2023] [Indexed: 02/13/2024]
Abstract
Heavy metals, including lead (Pb), cadmium (Cd), arsenic (As), cobalt (Co), copper (Cu), manganese (Mn), zinc (Zn), and others, have a significant impact on the development and progression of neurodegenerative diseases in the human brain. This comprehensive review aims to consolidate the recent research on the harmful effects of different metals on specific brain cells such as neurons, microglia, astrocytes, and oligodendrocytes. Understanding the potential influence of these metals in neurodegeneration is crucial for effectively combating the ongoing advancement of these diseases. Metal-induced neurodegeneration involves molecular mechanisms such as apoptosis induction, dysregulation of metabolic and signaling pathways, metal imbalance, oxidative stress, loss of synaptic transmission, pathogenic peptide aggregation, and neuroinflammation. This review provides valuable insights by compiling the supportive evidence from recent research findings. Additionally, we briefly discuss the modes of action of natural neuroprotective compounds. While this comprehensive review aims to consolidate the recent research on the harmful effects of various metals on specific brain cells, it may not cover all studies and findings related to metal-induced neurodegeneration. Studies that are done using bioinformatics tools, microRNAs, long non-coding RNAs, emerging disease models, and studies based on the modes of exposure to toxic metals are a future prospect to be explored.
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Affiliation(s)
- Lokesh Murumulla
- Cell Biology Division, National Institute of Nutrition, Indian Council of Medical Research (ICMR), Hyderabad-500007, Hyderabad, Telangana, India
| | - Lakshmi Jaya Madhuri Bandaru
- Cell Biology Division, National Institute of Nutrition, Indian Council of Medical Research (ICMR), Hyderabad-500007, Hyderabad, Telangana, India
| | - Suresh Challa
- Cell Biology Division, National Institute of Nutrition, Indian Council of Medical Research (ICMR), Hyderabad-500007, Hyderabad, Telangana, India.
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2
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Bajaj M, Muddassir M, Choi B, Singh P, Park JB, Singh S, Yadav M, Kumar R, Eom K, Sharma D. Single-molecule analysis of osmolyte-mediated nanomechanical unfolding behavior of a protein domain. Int J Biol Macromol 2023; 253:126849. [PMID: 37717878 DOI: 10.1016/j.ijbiomac.2023.126849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/25/2023] [Accepted: 09/09/2023] [Indexed: 09/19/2023]
Abstract
The small organic molecules, known as osmolytes being ubiquitously present in different cell types, affect protein folding, stability and aggregation. However, it is unknown how the osmolytes affect the nanomechanical unfolding behavior of protein domain. Here, we show the osmolyte-dependent mechanical unfolding properties of protein titin immunoglobulin-27 (I27) domain using an atomic force microscopy (AFM)-based single-molecule force spectroscopy. We found that amines and methylamines improved the mechanical stability of I27 domain, whereas polyols had no effect. Interestingly, glycine betaine (GB) or trimethylamine-N-oxide (TMAO) increased the average unfolding force of the protein domain. The kinetic parameters analyzed at single-molecule level reveal that stabilizing effect of osmolytes is due to a decrease in the unfolding rate constant of I27, which was confirmed by molecular dynamics simulations. Our study reveals different effects that diverse osmolytes have on the mechanical properties of the protein, and suggests the potential use of osmolytes in modulating the mechanical stability of proteins required for various nano-biotechnological applications.
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Affiliation(s)
- Manish Bajaj
- Council of Scientific and Industrial Research - Institute of Microbial Technology, Sector-39A, Chandigarh, India
| | - Mohd Muddassir
- Council of Scientific and Industrial Research - Institute of Microbial Technology, Sector-39A, Chandigarh, India; Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Bumjoon Choi
- Biomechanics Laboratory, College of Sport Science, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea; Digial Bio R&D Center, Mediazen, Seoul 07789, Republic of Korea
| | - Priyanka Singh
- Council of Scientific and Industrial Research - Institute of Microbial Technology, Sector-39A, Chandigarh, India
| | - Jong Bum Park
- Biomechanics Laboratory, College of Sport Science, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
| | - Surjeet Singh
- Council of Scientific and Industrial Research - Institute of Microbial Technology, Sector-39A, Chandigarh, India
| | - Manisha Yadav
- School of Basic and Applied Sciences, Central University of Punjab, Bathinda, India
| | - Rajesh Kumar
- School of Basic and Applied Sciences, Central University of Punjab, Bathinda, India
| | - Kilho Eom
- Biomechanics Laboratory, College of Sport Science, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea.
| | - Deepak Sharma
- Council of Scientific and Industrial Research - Institute of Microbial Technology, Sector-39A, Chandigarh, India; Academy of Scientific & Innovative Research, India.
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3
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Kuila S, Dey S, Singh P, Shrivastava A, Nanda J. Phenylalanine-based fibrillar systems. Chem Commun (Camb) 2023; 59:14509-14523. [PMID: 37987167 DOI: 10.1039/d3cc04138g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Phenylketonuria (PKU) is an inborn metabolic disorder characterized by excess accumulation of phenylalanine (Phe) and its fibril formation, resulting in progressive intellectual disability. Several research groups have approached from various directions to understand the formation of toxic amyloid fibrils from the essential amino acid Phe. Different parameters like the nature of the solvent, pH, Phe concentration, temperature, etc. influence the fibril formation kinetics. In this article, we have summarized all major findings regarding the formation of Phe-based fibrils in aqueous and organic media and discussed how non-covalent interactions are involved in the self-assembly process using spectroscopic and microscopic techniques. The toxicity of Phe-based fibrils is compared with other neurodegenerative peptides. It is noted that the Phe-based fibrils can also induce various globular proteins into toxic fibrils. Later, we discuss the different approaches to inhibit fibril formation and reduce its toxicity. The presence of polyphenolic compounds, drugs, amino acids, nanoparticles, metal ions, crown ethers, and others showed a remarkable inhibitory effect on fibril formation. To the best of our knowledge, this is the first-ever etymological analysis of the Phe-fibrillar system and its inhibition to create a strong database against PKU.
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Affiliation(s)
- Soumen Kuila
- Department of Chemistry, University of North Bengal, Raja Rammohanpur, Siliguri 734013, West Bengal, India.
| | - Sukantha Dey
- Department of Chemistry, University of North Bengal, Raja Rammohanpur, Siliguri 734013, West Bengal, India.
| | - Pijush Singh
- Department of Chemistry, University of North Bengal, Raja Rammohanpur, Siliguri 734013, West Bengal, India.
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani 741235, West Bengal, India
| | - Akash Shrivastava
- Department of Chemistry, University of North Bengal, Raja Rammohanpur, Siliguri 734013, West Bengal, India.
| | - Jayanta Nanda
- Department of Chemistry, University of North Bengal, Raja Rammohanpur, Siliguri 734013, West Bengal, India.
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4
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Gao W, Liu W, Dong X, Sun Y. Albumin-manganese dioxide nanocomposites: a potent inhibitor and ROS scavenger against Alzheimer's β-amyloid fibrillogenesis and neuroinflammation. J Mater Chem B 2023; 11:10482-10496. [PMID: 37909060 DOI: 10.1039/d3tb01763j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Alzheimer's disease (AD) is the most prevalent neurodegenerative disease pathologically caused by amyloid-β protein (Aβ) aggregation, oxidative stress, and neuroinflammation. The pathogenesis of AD is still uncertain and intricate, and helpful therapy has rarely been recorded. So, discovering amyloid modulators is deemed a promising avenue for preventing and treating AD. In this study, human serum albumin (HSA), a protein-based Aβ inhibitor, was utilized as a template to guide the synthesis of HSA-manganese dioxide nanocomposites (HMn NCs) through biomineralization. The in situ formed MnO2 in HSA endows this nano-platform with outstanding reactive oxygen species (ROS) scavenging capability, including superoxide dismutase-mimetic and catalase-mimetic activities, which could scavenge the plethora of superoxide anion radicals and hydrogen peroxide. More importantly, the HMn NCs show enhanced potency in suppressing Aβ fibrillization compared with HSA, which further alleviates Aβ-mediated SH-SY5Y neurotoxicity by scavenging excessive ROS. Moreover, it is demonstrated that HMn NCs reduce Aβ-related inflammation in BV-2 cells by lowering tumor necrosis factor-α and interleukin-6. Furthermore, transgenic C. elegans studies showed that HMn NCs could remove Aβ plaques, reduce ROS in CL2006 worms, and promote the lifespan extension of worms. Thus, HMn NCs provide a promising tactic to facilitate the application of multifunctional nanocomposites in AD treatment.
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Affiliation(s)
- Weiqun Gao
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China.
| | - Wei Liu
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, China
| | - Xiaoyan Dong
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China.
| | - Yan Sun
- Department of Biochemical Engineering, School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China.
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5
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Bagchi D, Maity A, De SK, Chakraborty A. Metal-Ion-Induced Evolution of Phenylalanine Self-Assembly: Structural Polymorphism of Novel Metastable Intermediates. J Phys Chem Lett 2022; 13:10409-10417. [PMID: 36322139 DOI: 10.1021/acs.jpclett.2c02882] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The self-assembly of aromatic amino acids has been widely studied due to their ability to form well-defined amyloid-like fibrillar structures. Herein, for the first time, we report the existence of different metastable intermediate states of diverse morphologies, for example, droplets, spheres, vesicles, flowers, and toroids, that are sequentially formed in aqueous medium during the self-assembly process of phenylalanine in the presence of different divalent (Zn2+, Cd2+, and Hg2+) and trivalent (Al3+, Ga3+, and In3+) metal ions having low pKa values. Due to metal ion-amino acid coordination and strong hydrophobic interaction induced by these metal ions, spherical aggregates are obtained at the initial stage of the structural evolution and further transformed into other intermediate states. Our work may facilitate understanding of the role of metal ions in the amino acid self-assembly process and broaden future applications of the obtained nanostructures in drug delivery, tissue engineering, bioimaging, biocatalysis, and other fields.
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Affiliation(s)
- Debanjan Bagchi
- Indian Institute of Technology Indore, Department of Chemistry, Indore, 453552 Madhya Pradesh, India
| | - Avijit Maity
- Indian Institute of Technology Indore, Department of Chemistry, Indore, 453552 Madhya Pradesh, India
| | - Soumya Kanti De
- Indian Institute of Technology Indore, Department of Chemistry, Indore, 453552 Madhya Pradesh, India
| | - Anjan Chakraborty
- Indian Institute of Technology Indore, Department of Chemistry, Indore, 453552 Madhya Pradesh, India
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6
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Mandal PK, Roy RG, Samkaria A. Oxidative Stress: Glutathione and Its Potential to Protect Methionine-35 of Aβ Peptide from Oxidation. ACS OMEGA 2022; 7:27052-27061. [PMID: 35967059 PMCID: PMC9366984 DOI: 10.1021/acsomega.2c02760] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 07/07/2022] [Indexed: 05/15/2023]
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disorder with heterogeneous etiology. Intracellular neurofibrillary tangles caused by tau (τ) protein phosphorylation and extracellular senile plaques caused by aggregation of amyloid-beta (Aβ) peptide are characteristic histopathological hallmarks of AD. Oxidative stress (OS) is also suggested to play a role in the pathophysiology of AD. The antioxidant glutathione (GSH) is able to mitigate OS through the detoxification of free radicals. The clearance of these free radicals is reported to be affected when there is a decline in GSH levels in AD. These radicals further react with the methionine-35 (M-35) residue of Aβ and facilitate its subsequent oligomerization. This review presents a plausible model indicating the role of master antioxidant GSH to protect M35 of Aβ1-40/Aβ1-42 from oxidation in pathological conditions as compared to healthy controls.
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Affiliation(s)
- Pravat K. Mandal
- Neuroimaging
and Neurospectroscopy (NINS) Laboratory, National Brain Research Centre, Gurgaon Haryana 122051, India
- Florey
Institute of Neuroscience and Mental Health, Melbourne School of Medicine Campus, Parkville, VIC 3052, Australia
- , , and
| | - Rimil Guha Roy
- Neuroimaging
and Neurospectroscopy (NINS) Laboratory, National Brain Research Centre, Gurgaon Haryana 122051, India
| | - Avantika Samkaria
- Neuroimaging
and Neurospectroscopy (NINS) Laboratory, National Brain Research Centre, Gurgaon Haryana 122051, India
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7
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Wu B, Hanay SB, Kimmins SD, Cryan SA, Hermida Merino D, Heise A. Ion-Triggered Hydrogels Self-Assembled from Statistical Copolypeptides. ACS Macro Lett 2022; 11:323-328. [PMID: 35575374 PMCID: PMC8928472 DOI: 10.1021/acsmacrolett.1c00774] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
Statistical copolypeptides
comprising lysine and tyrosine with
unprecedented ion-induced gelation behavior are reported. Copolypeptides
are obtained by one-step N-carboxyanhydride (NCA)
ring-opening polymerization. The gelation mechanism is studied by
in situ SAXS analyses, in addition to optical spectroscopy and transmission
electron microscopy (TEM). It is found that the gelation of these
statistically polymerized polypeptides is due to the formation of
stable intermolecular β-sheet secondary structures induced by
the presence of salt ions as well as the aggregation of an α-helix
between the copolypeptides. This behavior is unique to the statistical
lysine/tyrosine copolypeptides and was not observed in any other amino
acid combination or arrangement. Furthermore, the diffusion and mechanical
properties of these hydrogels can be tuned through tailoring the polypeptide
chain length and ion strength.
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Affiliation(s)
- Bing Wu
- Department of Chemistry, RCSI University of Medicine and Health Sciences, Dublin 2, Ireland
- Dutch-Belgian Beamline (DUBBLE), ESRF - The European Synchrotron Radiation Facility, CS 40220, Grenoble 38043 Cedex 9, France
| | - Saltuk B. Hanay
- Department of Chemistry, RCSI University of Medicine and Health Sciences, Dublin 2, Ireland
| | - Scott D. Kimmins
- Instituto de Química, Pontificia Universidad Católica de Valparaíso, Avda. Universidad 330, Curauma, Placilla 2950, Valparaíso, Chile
| | - Sally-Ann Cryan
- School of Pharmacy and Biomolecular Sciences and Tissue Engineering Research Group, RCSI University of Medicine and Health Sciences, Dublin 2, Ireland
- Science Foundation Ireland (SFI) Centre for Research in Medical Devices (CURAM), RCSI, Dublin 2, Ireland
- AMBER, The SFI Advanced Materials and Bioengineering Research Centre, RCSI, Dublin 2, Ireland
| | - Daniel Hermida Merino
- Dutch-Belgian Beamline (DUBBLE), ESRF - The European Synchrotron Radiation Facility, CS 40220, Grenoble 38043 Cedex 9, France
| | - Andreas Heise
- Department of Chemistry, RCSI University of Medicine and Health Sciences, Dublin 2, Ireland
- Science Foundation Ireland (SFI) Centre for Research in Medical Devices (CURAM), RCSI, Dublin 2, Ireland
- AMBER, The SFI Advanced Materials and Bioengineering Research Centre, RCSI, Dublin 2, Ireland
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8
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Zhang M, Wang Y, Wong RMS, Yung KKL, Li R. Fine particulate matter induces endoplasmic reticulum stress-mediated apoptosis in human SH-SY5Y cells. Neurotoxicology 2021; 88:187-195. [PMID: 34813867 DOI: 10.1016/j.neuro.2021.11.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 11/10/2021] [Accepted: 11/18/2021] [Indexed: 02/08/2023]
Abstract
Exposure to ambient fine particulate matter (PM2.5) may contribute to brain injury, however, the molecular mechanisms have not yet been fully described. In this study, the human SH-SY5Y cells were treated with PM2.5 with different concentrations (0, 25, 100, and 250 μg/mL) for 24 h to investigate the cell apoptosis mediated by endoplasmic reticulum (ER) stress. The ratio of apoptosis, Ca2+ level, biomarkers of ER stress and apoptosis were determined. The results revealed that PM2.5 triggered the increase of apoptosis ratio and cellular Ca2+ levels. Compared with control, the expression of GRP78 and phosphorylation of IER1α and p38 were enhanced significantly in the cells under the conditions of PM2.5 exposure for activating ER stress signals. Besides, the key genes (CHOP/DR5/Caspase8/Caspase12) in ER stress-induced apoptosis signals were up-regulated after the PM2.5 treatment compared to the control. The results suggested PM2.5 induced apoptosis in SH-SY5Y cells by the stimulation of ER stress, which may be the potential mechanism of neurological diseases incurred by PM2.5.
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Affiliation(s)
- Mei Zhang
- Institute of Environmental Science, Shanxi University, Taiyuan, PR China
| | - Ying Wang
- Institute of Environmental Science, Shanxi University, Taiyuan, PR China
| | - Ricky M S Wong
- Institute of Environmental Science, Shanxi University, Taiyuan, PR China; Department of Chemistry, Hong Kong Baptist University, Hong Kong, China
| | - Ken Kin Lam Yung
- Institute of Environmental Science, Shanxi University, Taiyuan, PR China; Department of Biology, Hong Kong Baptist University, Hong Kong, China; Golden Meditech Center for NeuroRegeneration Sciences, Hong Kong Baptist University, Hong Kong, China.
| | - Ruijin Li
- Institute of Environmental Science, Shanxi University, Taiyuan, PR China.
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9
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Bagchi D, Maity A, De SK, Chakraborty A. Effect of Metal Ions on the Intrinsic Blue Fluorescence Property and Morphology of Aromatic Amino Acid Self-Assembly. J Phys Chem B 2021; 125:12436-12445. [PMID: 34734524 DOI: 10.1021/acs.jpcb.1c07392] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Metal ions are known to strongly bind with different proteins and peptides, resulting in alteration of their different physicochemical properties. In this work, we investigate the effect of metal ions of different nuclear charges and sizes on the intrinsic blue luminescence of the self-assembled structures formed by aromatic amino acids, namely, phenylalanine and tryptophan, using spectroscopic and imaging techniques. The study reveals that the intrinsic blue fluorescence of amino acid assemblies is influenced by metal ions and the pH of the medium. The metal ions with a higher charge to radius ratio promote clusterization which results in the enhancement of the intrinsic fluorescence, an effect known as "clusteroluminescence" of the amino acids aggregates. The imaging study reveals that metal ions with a higher charge to size ratio inhibit the large fibrillation of aromatic amino acids by promoting the formation of small nonfibrillar aggregates through increased hydrophobicity in the medium. The nanoaggregates are assumed to be responsible for the enhancement in the blue "clusteroluminescence".
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Affiliation(s)
- Debanjan Bagchi
- Indian Institute of Technology Indore, Discipline of Chemistry, Indore 453552, Madhya Pradesh, India
| | - Avijit Maity
- Indian Institute of Technology Indore, Discipline of Chemistry, Indore 453552, Madhya Pradesh, India
| | - Soumya Kanti De
- Indian Institute of Technology Indore, Discipline of Chemistry, Indore 453552, Madhya Pradesh, India
| | - Anjan Chakraborty
- Indian Institute of Technology Indore, Discipline of Chemistry, Indore 453552, Madhya Pradesh, India
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10
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Matuszyk MM, Garwood CJ, Ferraiuolo L, Simpson JE, Staniforth RA, Wharton SB. Biological and methodological complexities of beta-amyloid peptide: Implications for Alzheimer's disease research. J Neurochem 2021; 160:434-453. [PMID: 34767256 DOI: 10.1111/jnc.15538] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/29/2021] [Accepted: 11/09/2021] [Indexed: 01/01/2023]
Abstract
Although controversial, the amyloid cascade hypothesis remains central to the Alzheimer's disease (AD) field and posits amyloid-beta (Aβ) as the central factor initiating disease onset. In recent years, there has been an increase in emphasis on studying the role of low molecular weight aggregates, such as oligomers, which are suggested to be more neurotoxic than fibrillary Aβ. Other Aβ isoforms, such as truncated Aβ, have also been implicated in disease. However, developing a clear understanding of AD pathogenesis has been hampered by the complexity of Aβ biochemistry in vitro and in vivo. This review explores factors contributing to the lack of consistency in experimental approaches taken to model Aβ aggregation and toxicity and provides an overview of the different techniques available to analyse Aβ, such as electron and atomic force microscopy, nuclear magnetic resonance spectroscopy, dye-based assays, size exclusion chromatography, mass spectrometry and SDS-PAGE. The review also explores how different types of Aβ can influence Aβ aggregation and toxicity, leading to variation in experimental outcomes, further highlighting the need for standardisation in Aβ preparations and methods used in current research.
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Affiliation(s)
- Martyna M Matuszyk
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Claire J Garwood
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Laura Ferraiuolo
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Julie E Simpson
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | | | - Stephen B Wharton
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
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11
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Choi B, Kim NH, Jin GY, Kim YS, Kim YH, Eom K. Sequence-dependent aggregation-prone conformations of islet amyloid polypeptide. Phys Chem Chem Phys 2021; 23:22532-22542. [PMID: 34590645 DOI: 10.1039/d1cp01061a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Amyloid proteins, which aggregate to form highly ordered structures, play a crucial role in various disease pathologies. Despite many previous studies on amyloid fibrils, which are an end product of protein aggregation, the structural characteristics of amyloid proteins in the early stage of aggregation and their related aggregation mechanism still remain elusive. The role of the amino acid sequence in the aggregation-prone structures of amyloid proteins at such a stage is not understood. Here, we have studied the sequence-dependent structural characteristics of islet amyloid polypeptide based on atomistic simulations and spectroscopic experiments. We show that the amino acid sequence determines non-bonded interactions that play a leading role in the formation of aggregation-prone conformations. Specifically, a single point mutation critically changes the population of aggregation-prone conformations, resulting in a change of the aggregation mechanism. Our simulation results were supported by experimental results suggesting that mutation affects the kinetics of aggregation and the structural characteristics of amyloid aggregates. Our study provides an insight into the role of sequence-dependent aggregation-prone conformations in the underlying mechanisms of amyloid aggregation.
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Affiliation(s)
- Bumjoon Choi
- Biomechanics Laboratory, College of Sport Science, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea.
| | - Nam Hyeong Kim
- SKKU Advanced Institute of Nano Technology (SAINT), Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea.
| | - Geun Young Jin
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Yung Sam Kim
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Yong Ho Kim
- SKKU Advanced Institute of Nano Technology (SAINT), Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea. .,Department of Nano Engineering, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea.,Center for Neuroscience Imaging Research, Institute for Basic Science (IBS), Suwon 16419, Republic of Korea
| | - Kilho Eom
- Biomechanics Laboratory, College of Sport Science, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea.
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12
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Boopathi S, Poma AB, Garduño-Juárez R. An Overview of Several Inhibitors for Alzheimer's Disease: Characterization and Failure. Int J Mol Sci 2021; 22:10798. [PMID: 34639140 PMCID: PMC8509255 DOI: 10.3390/ijms221910798] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 10/01/2021] [Accepted: 10/03/2021] [Indexed: 01/04/2023] Open
Abstract
Amyloid beta (Aβ) oligomers are the most neurotoxic aggregates causing neuronal death and cognitive damage. A detailed elucidation of the aggregation pathways from oligomers to fibril formation is crucial to develop therapeutic strategies for Alzheimer's disease (AD). Although experimental techniques rely on the measure of time- and space-average properties, they face severe difficulties in the investigation of Aβ peptide aggregation due to their intrinsically disorder character. Computer simulation is a tool that allows tracing the molecular motion of molecules; hence it complements Aβ experiments, as it allows to explore the binding mechanism between metal ions and Aβ oligomers close to the cellular membrane at the atomic resolution. In this context, integrated studies of experiments and computer simulations can assist in mapping the complete pathways of aggregation and toxicity of Aβ peptides. Aβ oligomers are disordered proteins, and due to a rapid exploration of their intrinsic conformational space in real-time, they are challenging therapeutic targets. Therefore, no good drug candidate could have been identified for clinical use. Our previous investigations identified two small molecules, M30 (2-Octahydroisoquinolin-2(1H)-ylethanamine) and Gabapentin, capable of Aβ binding and inhibiting molecular aggregation, synaptotoxicity, intracellular calcium signaling, cellular toxicity and memory losses induced by Aβ. Thus, we recommend these molecules as novel candidates to assist anti-AD drug discovery in the near future. This review discusses the most recent research investigations about the Aβ dynamics in water, close contact with cell membranes, and several therapeutic strategies to remove plaque formation.
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Affiliation(s)
- Subramanian Boopathi
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico;
| | - Adolfo B. Poma
- Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research Polish Academy of Science, Pawińskiego 5B, 02-106 Warsaw, Poland
- International Center for Research on Innovative Biobased Materials (ICRI-BioM)—International Research Agenda, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland;
| | - Ramón Garduño-Juárez
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico;
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13
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Chien HM, Lee CC, Huang JJT. The Different Faces of the TDP-43 Low-Complexity Domain: The Formation of Liquid Droplets and Amyloid Fibrils. Int J Mol Sci 2021; 22:ijms22158213. [PMID: 34360978 PMCID: PMC8348237 DOI: 10.3390/ijms22158213] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/22/2021] [Accepted: 07/27/2021] [Indexed: 12/17/2022] Open
Abstract
Transactive response DNA-binding protein 43 (TDP-43) is a nucleic acid-binding protein that is involved in transcription and translation regulation, non-coding RNA processing, and stress granule assembly. Aside from its multiple functions, it is also known as the signature protein in the hallmark inclusions of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) patients. TDP-43 is built of four domains, but its low-complexity domain (LCD) has become an intense research focus that brings to light its possible role in TDP-43 functions and involvement in the pathogenesis of these neurodegenerative diseases. Recent endeavors have further uncovered the distinct biophysical properties of TDP-43 under various circumstances. In this review, we summarize the multiple structural and biochemical properties of LCD in either promoting the liquid droplets or inducing fibrillar aggregates. We also revisit the roles of the LCD in paraspeckles, stress granules, and cytoplasmic inclusions to date.
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Affiliation(s)
- Hung-Ming Chien
- Institute of Chemistry, Academia Sinica, Nangang, Taipei City 115, Taiwan; (H.-M.C.); (C.-C.L.)
- Department of Chemistry, National Taiwan University, Taipei City 115, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan University, Taipei City 115, Taiwan
| | - Chi-Chang Lee
- Institute of Chemistry, Academia Sinica, Nangang, Taipei City 115, Taiwan; (H.-M.C.); (C.-C.L.)
| | - Joseph Jen-Tse Huang
- Institute of Chemistry, Academia Sinica, Nangang, Taipei City 115, Taiwan; (H.-M.C.); (C.-C.L.)
- Department of Applied Chemistry, National Chiayi University, Chiayi City 600, Taiwan
- Neuroscience Program of Academia Sinica, Academia Sinica, Taipei City 115, Taiwan
- Correspondence: ; Tel.: +886-2-5572-8652
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14
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Badhe RV, Akinfosile O, Bijukumar D, Barba M, Mathew MT. Systemic toxicity eliciting metal ion levels from metallic implants and orthopedic devices - A mini review. Toxicol Lett 2021; 350:213-224. [PMID: 34252509 DOI: 10.1016/j.toxlet.2021.07.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 06/19/2021] [Accepted: 07/07/2021] [Indexed: 12/28/2022]
Abstract
The metal/metal alloy-based implants and prostheses are in use for over a century, and the rejections, revisions, and metal particle-based toxicities were reported concurrently. Complications developed due to metal ions, metal debris, and organo-metallic particles in orthopedic patients have been a growing concern in recent years. It was reported that local and systemic toxicity caused by such released products from the implants is one of the major reasons for implant rejection and revision. Even though the description of environmental metal toxicants and safety limits for their exposure to humans were well established in the literature, an effort was not adequately performed in the case of implant-based metal toxicology. Since the metal ion concentration in serum acts as a possible indicator of the systemic toxicity, this review summarizes the reported human serum safe limits, toxic limits, and concentration range (μg/L, ppb, etc.) for mild to severe symptoms of six (cardiac, hepatic, neuro, nephron, dermal and endocrine) systemic toxicities for twelve most commonly used metallic implants. It also covers the widely used metal ion quantification techniques and systemic toxicity treatments reported.
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Affiliation(s)
- Ravindra V Badhe
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL, USA
| | - Obakanyin Akinfosile
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL, USA
| | - Divya Bijukumar
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL, USA
| | | | - Mathew T Mathew
- Department of Biomedical Sciences, University of Illinois College of Medicine at Rockford, Rockford, IL, USA.
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15
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Heterologous Expression and Characterization of Plant Lipase LIP2 from Elaeis guineensis Jacq. Oil Palm Mesocarp in Escherichia coli. Catalysts 2021. [DOI: 10.3390/catal11020244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
In order to determine the potential of biochemical and structural features of Elaeis guineensis Jacq. oil palm mesocarp lipases, the LIP2 gene was isolated, expressed, purified and characterized through the Escherichia coli microbial recombinant system. Gene analysis of LIP2 revealed that it is composed of 1584 base pairs which are encoded in 528 amino acid residues with a molecular weight of around 57 kDa. LIP2 has distinctive lipolytic properties in terms of α/β fold and the catalytic triad for lipase. The LIP2 lipase was successfully expressed and purified from E. coli Rosetta (DE3) via affinity chromatography. The optimal temperature and pH for the lipase activity was 30 °C and a pH of 9, respectively. Stability was profoundly increased with the addition of metal ions (Ca2+, Mg2+, Mn+, and Ni+), along with organic solvents (ethanol and octanol). pNP myristate was the most suitable among all pNP esters. In biophysical characterization analysis, LIP2 has a thermal denaturing point at 66 °C, which mostly consists of random patterns (39.8%) followed by α-helix (30.3%), turns (23.8%) and β-sheet (6.2%). From the successful purification and characterization, the potential of oil palm mesocarp lipase was able to be further explored.
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16
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Pounot K, Grime GW, Longo A, Zamponi M, Noferini D, Cristiglio V, Seydel T, Garman EF, Weik M, Foderà V, Schirò G. Zinc determines dynamical properties and aggregation kinetics of human insulin. Biophys J 2021; 120:886-898. [PMID: 33545104 DOI: 10.1016/j.bpj.2020.11.2280] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 11/08/2020] [Accepted: 11/30/2020] [Indexed: 12/26/2022] Open
Abstract
Protein aggregation is a widespread process leading to deleterious consequences in the organism, with amyloid aggregates being important not only in biology but also for drug design and biomaterial production. Insulin is a protein largely used in diabetes treatment, and its amyloid aggregation is at the basis of the so-called insulin-derived amyloidosis. Here, we uncover the major role of zinc in both insulin dynamics and aggregation kinetics at low pH, in which the formation of different amyloid superstructures (fibrils and spherulites) can be thermally induced. Amyloid aggregation is accompanied by zinc release and the suppression of water-sustained insulin dynamics, as shown by particle-induced x-ray emission and x-ray absorption spectroscopy and by neutron spectroscopy, respectively. Our study shows that zinc binding stabilizes the native form of insulin by facilitating hydration of this hydrophobic protein and suggests that introducing new binding sites for zinc can improve insulin stability and tune its aggregation propensity.
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Affiliation(s)
- Kevin Pounot
- Applied Physics, University of Tübingen, Tübingen, Baden-Würtemberg, Germany.
| | | | - Alessandro Longo
- Istituto per lo Studio dei Materiali Nanostrutturati, CNR, Palermo, Italy
| | - Michaela Zamponi
- Jülich Centre for Neutron Science JCNS, Forschungszentrum Jülich GmbH Outstation at MLZ, Garching, Germany
| | - Daria Noferini
- Jülich Centre for Neutron Science JCNS, Forschungszentrum Jülich GmbH Outstation at MLZ, Garching, Germany
| | | | - Tilo Seydel
- Science Division, Institut Max von Laue-Paul Langevin, Grenoble, France
| | | | - Martin Weik
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38000 Grenoble, France
| | - Vito Foderà
- Pharmacy, University of Copenhagen, Copenhagen, Denmark.
| | - Giorgio Schirò
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38000 Grenoble, France.
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17
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Ben-Shushan S, Miller Y. Insulin fibrillation control by specific zinc binding sites. Inorg Chem Front 2021. [DOI: 10.1039/d1qi01054a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, we present for the first time a study that identifies the morphology of full-length insulin fibrils in the absence and in the presence of Zn2+ ions.
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Affiliation(s)
- Shira Ben-Shushan
- Department of Chemistry, Ben-Gurion University of the Negev, P.O. Box 653, Beér Sheva 84105, Israel
- Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beér-Sheva 84105, Israel
| | - Yifat Miller
- Department of Chemistry, Ben-Gurion University of the Negev, P.O. Box 653, Beér Sheva 84105, Israel
- Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beér-Sheva 84105, Israel
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18
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Prasanna G, Jing P. Self-assembly of N-terminal Alzheimer's β-amyloid and its inhibition. Biochem Biophys Res Commun 2020; 534:950-956. [PMID: 33143872 DOI: 10.1016/j.bbrc.2020.10.065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 10/23/2020] [Indexed: 10/23/2022]
Abstract
Peptide sequence modulates amyloid fibril formation and triggers Alzheimer's disease. The N-terminal region of amyloid peptide is disordered and lack any specific secondary structure. An ionic interaction of Aβ1-11 with factor XII is critical for the activation of the contact system in Alzheimer's disease. In this study, we report the self-assembly of fluctuating N-terminal Aβ1-11 into nanotubes using atomic force micrography, transmission electron microscopy, circular dichroism studies and molecular modeling studies. The effect of four polyphenols: baicalein, rutin, vanillin and cyanidin-3-O-glucoside (C3G) was also explored on the amyloid fibril inhibitor perspective using amyloid specific dye Thioflavin T (ThT). AFM micrographs suggested the self-assembly of Aβ1-11 into nanotubes after three weeks of incubation. Microwave treatment results in the conformational variation of disordered structure to β-sheet rich amyloid fibrils. The presence of salts (sodium and potassium chloride) induces the structural transformation of Aβ1-11 to super-helix. Fluorescence spectroscopy studies using ThT suggested differential inhibition of amyloid fibrils formation in the presence of polyphenols. Molecular modeling studies suggested that binding of polyphenols to Aβ1-11 through hydrophobic interaction (Phe4 and Tyr 10) and hydrogen bonding (Glu3 and Arg5) play a substantial role in stabilizing Aβ1-11-polyphenols complex. In the presence of polyphenols, Aβ1-11 transforms to hybrid nanostructures thus hindering amyloid fibril formation. These results provide structural insights and importance of the N-terminal residues in the Aβ1-42 self-assembly mechanism.
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Affiliation(s)
- Govindarajan Prasanna
- Shanghai Food Safety and Engineering Technology Research Center, Key Lab of Urban Agriculture (South), Bor S. Luh Food Safety Research Center, School of Agriculture & Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Pu Jing
- Shanghai Food Safety and Engineering Technology Research Center, Key Lab of Urban Agriculture (South), Bor S. Luh Food Safety Research Center, School of Agriculture & Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
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19
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Ejaz HW, Wang W, Lang M. Copper Toxicity Links to Pathogenesis of Alzheimer's Disease and Therapeutics Approaches. Int J Mol Sci 2020; 21:E7660. [PMID: 33081348 PMCID: PMC7589751 DOI: 10.3390/ijms21207660] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/24/2020] [Accepted: 09/29/2020] [Indexed: 02/07/2023] Open
Abstract
Alzheimer's disease (AD) is an irreversible, age-related progressive neurological disorder, and the most common type of dementia in aged people. Neuropathological lesions of AD are neurofibrillary tangles (NFTs), and senile plaques comprise the accumulated amyloid-beta (Aβ), loaded with metal ions including Cu, Fe, or Zn. Some reports have identified metal dyshomeostasis as a neurotoxic factor of AD, among which Cu ions seem to be a central cationic metal in the formation of plaque and soluble oligomers, and have an essential role in the AD pathology. Cu-Aβ complex catalyzes the generation of reactive oxygen species (ROS) and results in oxidative damage. Several studies have indicated that oxidative stress plays a crucial role in the pathogenesis of AD. The connection of copper levels in AD is still ambiguous, as some researches indicate a Cu deficiency, while others show its higher content in AD, and therefore there is a need to increase and decrease its levels in animal models, respectively, to study which one is the cause. For more than twenty years, many in vitro studies have been devoted to identifying metals' roles in Aβ accumulation, oxidative damage, and neurotoxicity. Towards the end, a short review of the modern therapeutic approach in chelation therapy, with the main focus on Cu ions, is discussed. Despite the lack of strong proofs of clinical advantage so far, the conjecture that using a therapeutic metal chelator is an effective strategy for AD remains popular. However, some recent reports of genetic-regulating copper transporters in AD models have shed light on treating this refractory disease. This review aims to succinctly present a better understanding of Cu ions' current status in several AD features, and some conflicting reports are present herein.
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Affiliation(s)
- Hafza Wajeeha Ejaz
- CAS Center for Excellence in Biotic Interactions, College of Life Science, University of Chinese Academy of Sciences, Yuquan Road 19, Beijing 100049, China;
| | - Wei Wang
- School of Medical and Health Sciences, Edith Cowan University, Perth WA6027, Australia;
| | - Minglin Lang
- CAS Center for Excellence in Biotic Interactions, College of Life Science, University of Chinese Academy of Sciences, Yuquan Road 19, Beijing 100049, China;
- College of Life Science, Agricultural University of Hebei, Baoding 071000, China
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20
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Spider silk with weaker bonding resulting in higher strength and toughness through progressive unfolding and load transfer. J Mech Behav Biomed Mater 2020; 108:103773. [DOI: 10.1016/j.jmbbm.2020.103773] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/27/2020] [Accepted: 04/04/2020] [Indexed: 11/20/2022]
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21
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Lucas MJ, Pan HS, Verbeke EJ, Webb LJ, Taylor DW, Keitz BK. Functionalized Mesoporous Silicas Direct Structural Polymorphism of Amyloid-β Fibrils. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:7345-7355. [PMID: 32482072 DOI: 10.1021/acs.langmuir.0c00827] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The aggregation of amyloid-β (Aβ) is associated with the onset of Alzheimer's disease (AD) and involves a complex kinetic pathway as monomers self-assemble into fibrils. A central feature of amyloid fibrils is the existence of multiple structural polymorphs, which complicates the development of disease-relevant structure-function relationships. Developing these relationships requires new methods to control fibril structure. In this work, we evaluated the effect that mesoporous silicas (SBA-15) functionalized with hydrophobic (SBA-PFDTS) and hydrophilic groups (SBA-PEG) have on the aggregation kinetics and resulting structure of Aβ1-40 fibrils. The hydrophilic SBA-PEG had little effect on amyloid kinetics, while as-synthesized and hydrophobic SBA-PFDTS accelerated aggregation kinetics. Subsequently, we quantified the relative population of fibril structures formed in the presence of each material using electron microscopy. Fibrils formed from Aβ1-40 exposed to SBA-PEG were structurally similar to control fibrils. In contrast, Aβ1-40 incubated with SBA-15 or SBA-PFDTS formed fibrils with shorter crossover distances that were more structurally representative of fibrils found in AD patient derived samples. Overall, our results suggest that mesoporous silicas and other exogenous materials are promising scaffolds for the de novo production of specific fibril polymorphs of Aβ1-40 and other amyloidogenic proteins.
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Affiliation(s)
- Michael J Lucas
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Henry S Pan
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Eric J Verbeke
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Lauren J Webb
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - David W Taylor
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, United States
- LIVESTRONG Cancer Institutes, Dell Medical School, Austin, Texas 78712, United States
| | - Benjamin K Keitz
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
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22
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Saravanan KM, Zhang H, Zhang H, Xi W, Wei Y. On the Conformational Dynamics of β-Amyloid Forming Peptides: A Computational Perspective. Front Bioeng Biotechnol 2020; 8:532. [PMID: 32656188 PMCID: PMC7325929 DOI: 10.3389/fbioe.2020.00532] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 05/04/2020] [Indexed: 12/12/2022] Open
Abstract
Understanding the conformational dynamics of proteins and peptides involved in important functions is still a difficult task in computational structural biology. Because such conformational transitions in β-amyloid (Aβ) forming peptides play a crucial role in many neurological disorders, researchers from different scientific fields have been trying to address issues related to the folding of Aβ forming peptides together. Many theoretical models have been proposed in the recent years for studying Aβ peptides using mathematical, physicochemical, and molecular dynamics simulation, and machine learning approaches. In this article, we have comprehensively reviewed the developmental advances in the theoretical models for Aβ peptide folding and interactions, particularly in the context of neurological disorders. Furthermore, we have extensively reviewed the advances in molecular dynamics simulation as a tool used for studying the conversions between polymorphic amyloid forms and applications of using machine learning approaches in predicting Aβ peptides and aggregation-prone regions in proteins. We have also provided details on the theoretical advances in the study of Aβ peptides, which would enhance our understanding of these peptides at the molecular level and eventually lead to the development of targeted therapies for certain acute neurological disorders such as Alzheimer's disease in the future.
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Affiliation(s)
| | | | | | - Wenhui Xi
- Center for High Performance Computing, Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yanjie Wei
- Center for High Performance Computing, Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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23
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Liyanage SI, Weaver DF. Misfolded proteins as a therapeutic target in Alzheimer's disease. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 118:371-411. [PMID: 31928732 DOI: 10.1016/bs.apcsb.2019.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
For decades, Alzheimer's Disease (AD) was defined as a disorder of protein misfolding and aggregation. In particular, the extracellular peptide fragment: amyloid-β (Aβ), and the intracellular microtubule-associated protein: tau, were thought to initiate a neurodegenerative cascade which culminated in AD's progressive loss of memory and executive function. As such, both proteins became the focus of intense scrutiny, and served as the principal pathogenic target for hundreds of clinical trials. However, with varying efficacy, none of these investigations produced a disease-modifying therapy - offering patients with AD little recourse aside from transient, symptomatic medications. The near universal failure of clinical trials is unprecedented for a major research discipline. In part, this has motivated an increasing skepticism of the relevance of protein misfolding to AD's etiology. Several recent observations, principally the presence of significant protein pathologies in non-demented seniors, have lent credence to an apparent cursory role for Aβ and tau. Herein, we review both Aβ and tau, examining the processes from their biosynthesis to their pathogenesis and evaluate their vulnerability to medicinal intervention. We further attempt to reconcile the apparent failure of trials with the potential these targets hold. Ultimately, we seek to answer if protein misfolding is a viable platform in the pursuit of a disease-arresting strategy for AD.
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Affiliation(s)
- S Imindu Liyanage
- Krembil Research Institute, University Health Network, Toronto, ON, Canada
| | - Donald F Weaver
- Krembil Research Institute, University Health Network, Toronto, ON, Canada; Departments of Medicine (Neurology), Chemistry and Pharmaceutical Sciences, University of Toronto, Toronto, ON, Canada
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24
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Choi H, Lee W, Lee G, Yoon DS, Na S. The Formation Mechanism of Segmented Ring-Shaped Aβ Oligomers and Protofibrils. ACS Chem Neurosci 2019; 10:3830-3838. [PMID: 31313912 DOI: 10.1021/acschemneuro.9b00324] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A clear understanding of amyloid formation with diverse morphologies is critical to overcoming the fatal disease amyloidosis. Studies have revealed that monomer concentration is a crucial factor for determining amyloid morphologies, such as protofibrils, annular, or spherical oligomers. However, gaining a complete understanding of the mechanism of formation of the various amyloid morphologies has been limited by the lack of experimental devices and insufficient knowledge. In this study, we demonstrate that the monomer concentration is an essential factor in determining the morphology of beta-amyloid (Aβ) oligomers or protofibrils. By computational and experimental approaches, we investigated the strategies for structural stabilization of amyloid protein, the morphological changes, and amyloid aggregation. In particular, we found unprecedented conformations, e.g., single bent oligomers and segmented ring-shaped protofibrils, the formation of which was explained by the computational analysis. Our findings provide insight into the structural features of amyloid molecules formed at low concentrations of monomer, which will help determine the clinical targets (in therapy) to effectively inhibit amyloid formation in the early stages of the amyloid growth phase.
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Affiliation(s)
| | - Wonseok Lee
- Department of Control and Instrumentation Engineering , Korea University , Sejong 30019 , Republic of Korea
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25
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Zn 2+ Interaction with Amyloid-Β: Affinity and Speciation. Molecules 2019; 24:molecules24152796. [PMID: 31370315 PMCID: PMC6695645 DOI: 10.3390/molecules24152796] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 07/26/2019] [Accepted: 07/29/2019] [Indexed: 12/26/2022] Open
Abstract
Conflicting values, obtained by different techniques and often under different experimental conditions have been reported on the affinity of Zn2+ for amyloid-β, that is recognized as the major interaction responsible for Alzheimer’s disease. Here, we compare the approaches employed so far, i.e., the evaluation of Kd and the determination of the stability constants to quantitatively express the affinity of Zn2+ for the amyloid-β peptide, evidencing the pros and cons of the two approaches. We also comment on the different techniques and conditions employed that may lead to divergent data. Through the analysis of the species distribution obtained for two selected examples, we show the implications that the speciation, based on stoichiometric constants rather than on Kd, may have on data interpretation. The paper also demonstrates that the problem is further complicated by the occurrence of multiple equilibria over a relatively narrow pH range.
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26
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Maity S, Lyubchenko YL. Force clamp approach for characterization of nano-assembly in amyloid beta 42 dimer. NANOSCALE 2019; 11:12259-12265. [PMID: 31210224 PMCID: PMC6597289 DOI: 10.1039/c9nr01670h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Amyloid β (Aβ) oligomers are formed at the early stages of the amyloidogenesis process and exhibit neurotoxicity. Development of oligomer specific therapeutics requires a detailed understanding of oligomerization processes. Amyloid oligomers exist transiently and single-molecule approaches are capable of characterizing such species. In this paper, we describe the application of an AFM based force clamp approach for probing of Aβ42 dimers. Aβ42 monomers were tethered to the AFM tip and surface and the dimers are formed during the approaching the tip to the surface. AFM force clamp experiments were performed at different force clamps. They revealed two types of transient states for dissociating Aβ42 dimers. The analysis showed that these states have distinct lifetimes of 188 ± 52 milliseconds (type 1, short lived) and 317 ± 67 milliseconds (type 2, long lived). Type 1 state prevails over type 2 state as the value of the applied force increases. The rupture lengths analysis led to the models of the dimer dissociation pathways that are proposed.
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Affiliation(s)
- Sibaprasad Maity
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA.
| | - Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA.
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27
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Wang Y, Zhang M, Li Z, Yue J, Xu M, Zhang Y, Yung KKL, Li R. Fine particulate matter induces mitochondrial dysfunction and oxidative stress in human SH-SY5Y cells. CHEMOSPHERE 2019; 218:577-588. [PMID: 30502696 DOI: 10.1016/j.chemosphere.2018.11.149] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 10/28/2018] [Accepted: 11/23/2018] [Indexed: 05/06/2023]
Abstract
Exposure to ambient fine particulate matter (PM2.5) is associated with neurodegenerative diseases. Mitochondrion is key to brain degeneration. However, the underlying mechanism of PM2.5-induced brain injury, especially mitochondrial damage, is still unclear. In this study, changes in mitochondrial dynamics, mitochondrial permeability transition pore (mPTP), mitochondrial DNA (mtDNA) and oxidative stress in human SH-SY5Y cells exposed to PM2.5 at different concentrations (0, 25, 100, and 250 μg mL-1) were investigated. The results showed that PM2.5 caused more mitochondrial swell, accompanied by the opening of mPTP and the decrease of ATP levels, mitochondrial membrane potential and mtDNA copy number in SH-SY5Y cells. PM2.5 significantly enhanced the expression of mitochondrial fission/fusion genes (Drp1 and OPA1) and affected the gene expression of CypD, SIRT3, and COX Ⅳ in SH-SY5Y cells. Besides, PM2.5 triggered the increase of cellular ROS, Ca2+ and Aβ-42 levels, inhibition of manganese-superoxide dismutase (SOD2) activities, reduction of GSH levels GSH/GSSG ratio, and elevation of mitochondrial malondialdehyde contents. It suggests that mitochondrial dysfunction and oxidative stress are the potential mechanisms underlying PM2.5-induced brain nerve cell injury, which may be related to neurological diseases. Additionally, our study elucidated that PM2.5 components trigger different cytotoxicity.
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Affiliation(s)
- Ying Wang
- Institute of Environmental Science, Shanxi University, Taiyuan, China
| | - Mei Zhang
- Institute of Environmental Science, Shanxi University, Taiyuan, China
| | - Zhiping Li
- Shanxi Unisdom Testing Technologies Co., Ltd, Taiyuan, China
| | - Jianwei Yue
- Shanxi Unisdom Testing Technologies Co., Ltd, Taiyuan, China
| | - Min Xu
- Shanxi Unisdom Testing Technologies Co., Ltd, Taiyuan, China
| | - Yanhao Zhang
- Department of Biology, State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong SAR, China
| | - Ken Kin Lam Yung
- Institute of Environmental Science, Shanxi University, Taiyuan, China; Department of Biology, State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong SAR, China.
| | - Ruijin Li
- Institute of Environmental Science, Shanxi University, Taiyuan, China.
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28
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Computer Simulation of Protein Materials at Multiple Length Scales: From Single Proteins to Protein Assemblies. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/s42493-018-00009-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Chen D, Li Y, Guo W, Li Y, Savidge T, Li X, Fan X. The shielding effect of metal complexes on the binding affinities of ligands to metalloproteins. Phys Chem Chem Phys 2019; 21:205-216. [DOI: 10.1039/c8cp06555a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The contributions of metal–ligand interactions to the ligand binding affinities are largely reduced by the shielding effects of metal complexes.
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Affiliation(s)
- Deliang Chen
- Jiangxi Key Laboratory of Organo-Pharmaceutical Chemistry
- Chemistry and Chemical Engineering College
- Gannan Normal University
- Ganzhou
- P. R. China
| | - Yibao Li
- Jiangxi Key Laboratory of Organo-Pharmaceutical Chemistry
- Chemistry and Chemical Engineering College
- Gannan Normal University
- Ganzhou
- P. R. China
| | - Wei Guo
- Jiangxi Key Laboratory of Organo-Pharmaceutical Chemistry
- Chemistry and Chemical Engineering College
- Gannan Normal University
- Ganzhou
- P. R. China
| | - Yongdong Li
- Jiangxi Key Laboratory of Organo-Pharmaceutical Chemistry
- Chemistry and Chemical Engineering College
- Gannan Normal University
- Ganzhou
- P. R. China
| | - Tor Savidge
- Department of Pathology & Immunology
- Baylor College of Medicine
- Houston
- USA
- Texas Children's Microbiome Center
| | - Xun Li
- Jiangxi Key Laboratory of Organo-Pharmaceutical Chemistry
- Chemistry and Chemical Engineering College
- Gannan Normal University
- Ganzhou
- P. R. China
| | - Xiaolin Fan
- Jiangxi Key Laboratory of Organo-Pharmaceutical Chemistry
- Chemistry and Chemical Engineering College
- Gannan Normal University
- Ganzhou
- P. R. China
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Lee G, Lee W, Baik S, Kim YH, Eom K, Kwon T. Correlation between the hierarchical structures and nanomechanical properties of amyloid fibrils. NANOTECHNOLOGY 2018; 29:295701. [PMID: 29644980 DOI: 10.1088/1361-6528/aabd8a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Amyloid fibrils have recently been highlighted due to their excellent mechanical properties, which not only play a role in their biological functions but also imply their applications in biomimetic material design. Despite recent efforts to unveil how the excellent mechanical properties of amyloid fibrils originate, it has remained elusive how the anisotropic nanomechanical properties of hierarchically structured amyloid fibrils are determined. Here, we characterize the anisotropic nanomechanical properties of hierarchically structured amyloid fibrils using atomic force microscopy experiments and atomistic simulations. It is shown that the hierarchical structure of amyloid fibrils plays a crucial role in determining their radial elastic property but does not make any effect on their bending elastic property. This is attributed to the role of intermolecular force acting between the filaments (constituting the fibril) on the radial elastic modulus of amyloid fibrils. Our finding illustrates how the hierarchical structure of amyloid fibrils encodes their anisotropic nanomechanical properties. Our study provides key design principles of amyloid fibrils, which endow valuable insight into the underlying mechanisms of amyloid mechanics.
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Affiliation(s)
- Gyudo Lee
- School of Public Health, Harvard University, Boston, MA 02115, United States of America
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