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Singh S, Navale GR, Agrawal S, Singh HK, Singla L, Sarkar D, Sarma M, Choudhury AR, Ghosh K. Design and synthesis of ruthenium complexes and their studies on the inhibition of amyloid β (1-42) peptide aggregation. Int J Biol Macromol 2023; 239:124197. [PMID: 36972817 DOI: 10.1016/j.ijbiomac.2023.124197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 03/07/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023]
Abstract
Misfolding and protein aggregation have been linked to numerous human neurodegenerative disorders such as Alzheimer's, prions, and Parkinson's. Due to their interesting photophysical properties, ruthenium (Ru) complexes have received considerable attention in studying protein aggregation. In this study, we synthesized the novel Ru complexes ([Ru(p-cymene)Cl(L-1)][PF6](Ru-1), and [Ru(p-cymene)Cl(L-2)][PF6](Ru-2)) and investigated their inhibitory activity against the bovine serum albumin (BSA) aggregation and the Aβ1-42 peptides amyloid formation. Several spectroscopic methods were used to characterize the complexes, and the molecular structure was determined by X-ray crystallography. Amyloid aggregation and inhibition activity were examined using the Thioflavin-T (ThT) assay, and secondary structures were analyzed by circular dichroism (CD) spectroscopy and transmission electron microscopy (TEM). The cell viability assay was carried out on the neuroblastoma cell line, revealing that the Ru-2 complex showed better protective effects against Aβ1-42 peptide toxicity on neuro-2a cells than the Ru-1 complex. Molecular docking studies elucidate binding sites and interactions between the Ru-complexes and the Aβ1-42 fibrils. The experimental studies revealed that these complexes significantly inhibited BSA aggregation and Aβ1-42 amyloid fibril formation at 1:3 and 1:1 equimolar concentrations, respectively. Antioxidant assays demonstrated that these complexes act as antioxidants, protecting from amyloid-induced oxidative stress. Molecular docking studies with the monomeric Aβ1-42 (PDB: 1IYT) show hydrophobic interaction, and both complexes bind preferably in the central region of the peptide and coordinate with two binding sites of the peptide. Hence, we suggest that the Ru-based complexes could be applied as a potential agent in metallopharmaceutical research against Alzheimer's disease.
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Affiliation(s)
- Sain Singh
- Department of Chemistry, Indian Institute of Technology, Roorkee 247667, India
| | - Govinda R Navale
- Department of Chemistry, Indian Institute of Technology, Roorkee 247667, India
| | - Sonia Agrawal
- Department of Organic Chemistry, CSIR-National Chemical Laboratory, Pune 411 008, India
| | - Haobam Kisan Singh
- Department of Chemistry, Indian Institute of Technology, Guwahati 781039, India
| | - Labhini Singla
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Mohali, India
| | - Dhiman Sarkar
- Department of Organic Chemistry, CSIR-National Chemical Laboratory, Pune 411 008, India
| | - Manabendra Sarma
- Department of Chemistry, Indian Institute of Technology, Guwahati 781039, India
| | - Anghuman Roy Choudhury
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Mohali, India
| | - Kaushik Ghosh
- Department of Chemistry, Indian Institute of Technology, Roorkee 247667, India; Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee 247667, India.
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Vekilov PG, Wolynes PG. Time-Resolved In Situ AFM Measurement of Growth Rates of Aβ40 Fibrils. Methods Mol Biol 2023; 2551:63-77. [PMID: 36310197 DOI: 10.1007/978-1-0716-2597-2_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
We employ time-resolved in situ atomic force microcopy to monitor the growth of individual Aβ40 fibrils and thereby directly measure the fibril growth rates. We describe procedures to express and purify the Aβ peptide and verify its identity, prepare solutions and seeds, quantify the displacements of the growing tips of individual fibrils, and determine their respective growth rates. We discuss approaches to evaluate and minimize the impact of the scanning tip on the monitored processes. We use the distribution of fibril thickness to characterize approximately the fibril structure. The ability to quantify faithfully the growth kinetics of amyloid fibrils empowers exploration of the molecular-level processes of fibril growth that relate to behaviors of amyloid species of laboratory and clinical interest.
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Affiliation(s)
- Peter G Vekilov
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA.
- Department of Chemistry, University of Houston, Houston, TX, USA.
| | - Peter G Wolynes
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
- Department of Chemistry, Rice University, Houston, TX, USA
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Tabatabaei F, Gelin A, Rasoulianboroujeni M, Tayebi L. Coating of 3D printed PCL/TCP scaffolds using homogenized-fibrillated collagen. Colloids Surf B Biointerfaces 2022; 217:112670. [PMID: 35779329 DOI: 10.1016/j.colsurfb.2022.112670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/26/2022] [Accepted: 06/27/2022] [Indexed: 11/15/2022]
Abstract
BACKGROUND Poly(3-caprolactone) (PCL)/β-tricalcium phosphate (β-TCP) composite scaffolds fabricated by three-dimensional (3D) printing are one of the common scaffolds for bone tissue regeneration. However, the main challenge of these 3D printed PCL/β-TCP scaffolds is the fact that many cells pass from porosities during in vitro cell seeding, leading to poor initial cell attachment. This study aimed to demonstrate the fabrication of a new collagen coating process for optimizing the hydrophilic property and cell-substrate interactions. This method may be used for coating collagen on any relevant biomedical constructs made of synthetic polymers to increase their biocompatibility and cell attachment. MATERIALS AND METHODS Porous composite scaffolds fabricated by 3D printing were coated with collagen by a novel method and compared to traditional methods. After plasma treatment, samples were inverted in a homogenized collagen solution, freeze-dried, stabilized by crosslinking, freeze-dried again, and fibrillated using a defined salt concentration. Samples were characterized by a 3D laser microscope, cytocompatibility assay, attenuated total reflectance Fourier-transform infrared (ATR-FTIR) spectroscopy, water absorption, protein absorption, and bioactivity assay. RESULTS Homogenized collagen at pH= 7 resulted in a very uniform layer on the surface of scaffolds with significantly higher cell proliferation (p < 0.05). Collagen-coated scaffolds showed significantly higher water absorption, protein absorption, and bioactivity compared to non-coated samples (p < 0.05). CONCLUSION The results demonstrate that both the pH and collagen structure influence the coating of scaffolds, while the concentrations used in this study do not have a significant difference in this aspect. The combination of homogenization and fibrillization makes scaffolds more biocompatible and desirable for bone tissue engineering.
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Affiliation(s)
| | - Alexandra Gelin
- School of Dentistry, Marquette University, Milwaukee, WI 53233, USA
| | | | - Lobat Tayebi
- School of Dentistry, Marquette University, Milwaukee, WI 53233, USA.
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4
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Yan C, Zhou Z. Ellagic acid and pentagalloylglucose are potential inhibitors of prion protein fibrillization. Int J Biol Macromol 2021; 172:371-380. [PMID: 33460657 DOI: 10.1016/j.ijbiomac.2021.01.045] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/19/2020] [Accepted: 01/07/2021] [Indexed: 01/29/2023]
Abstract
Prion diseases are fatal neurodegenerative diseases caused by the conformational transition of the cellular prion protein (PrPC) to the abnormal pathological prion protein (PrPSc). In this work, the effects of ellagic acid (EA) and pentagalloylglucose (PGG) on prion protein (PrP) fibrillization were investigated. Fluorescence quenching experiments indicated that both EA and PGG could specifically interact with native human PrP with binding affinities of 1.92 × 105 and 2.36 × 105 L·mol-1, respectively. Thioflavin-T (ThT) fluorescence assays showed that the binding of EA or PPG could effectively inhibit the nucleation and elongation of PrP fibrilization and reduce the amount of PrP fibrils generated. EA and PGG could also lead to a significant disaggregation of PrP fibrils. Circular dichroism (CD) measurements suggested that EA- or PPG-bound PrP could preserve a higher content of α-helical structures than β-sheet-rich PrP fibrils. The PrP aggregates formed in the presence of EA or PGG showed lower resistance to proteinase K (PK) digestion. Overall, the present work reported the inhibitory effect of EA and PGG on PrP fibrillization. These two natural polyphenols could be potential prodrug molecules for the prevention and treatment of prion diseases.
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Affiliation(s)
- Chunjun Yan
- School of Food Science and Bioengineering, Xihua University, Chengdu 610039, China
| | - Zheng Zhou
- School of Food Science and Bioengineering, Xihua University, Chengdu 610039, China.
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5
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Marvian AT, Aliakbari F, Mohammad-Beigi H, Ahmadi ZA, Mehrpooyan S, Lermyte F, Nasouti M, Collingwood JF, Otzen DE, Morshedi D. The status of the terminal regions of α-synuclein in different forms of aggregates during fibrillization. Int J Biol Macromol 2020; 155:543-550. [PMID: 32240735 DOI: 10.1016/j.ijbiomac.2020.03.238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/26/2020] [Accepted: 03/27/2020] [Indexed: 10/24/2022]
Abstract
The α-synuclein (αSN) amyloid fibrillization process is known to be a crucial phenomenon associated with neuronal loss in various neurodegenerative diseases, most famously Parkinson's disease. The process involves different aggregated species and ultimately leads to formation of β-sheet rich fibrillar structures. Despite the essential role of αSN aggregation in the pathoetiology of various neurological disorders, the characteristics of various assemblies are not fully understood. Here, we established a fluorescence-based model for studying the end-parts of αSN to decipher the structural aspects of aggregates during the fibrillization. Our model proved highly sensitive to the events at the early stage of the fibrillization process, which are hardly detectable with routine techniques. Combining fluorescent and PAGE analysis, we found different oligomeric aggregates in the nucleation phase of fibrillization with different sensitivity to SDS and different structures based on αSN termini. Moreover, we found that these oligomers are highly dynamic: after reaching peak levels during fibrillization, they decline and eventually disappear, suggesting their transformation into other αSN aggregated species. These findings shed light on the structural features of various αSN aggregates and their dynamics in synucleinopathies.
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Affiliation(s)
- Amir Tayaranian Marvian
- Bioprocess Engineering Department, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran; Department of Neurology, School of Medicine, Technical University of Munich, Munich, Germany; Department of Translational Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Farhang Aliakbari
- Bioprocess Engineering Department, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran; Interdisciplinary Nanoscience Centre (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Hossein Mohammad-Beigi
- Interdisciplinary Nanoscience Centre (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Zeinab Alsadat Ahmadi
- Bioprocess Engineering Department, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Sina Mehrpooyan
- Bioprocess Engineering Department, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | | | - Mahour Nasouti
- Bioprocess Engineering Department, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | | | - Daniel E Otzen
- Interdisciplinary Nanoscience Centre (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, DK-8000 Aarhus C, Denmark
| | - Dina Morshedi
- Bioprocess Engineering Department, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran.
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6
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Choi EY, Kang SS, Lee SK, Han BH. Polyphenolic Biflavonoids Inhibit Amyloid-Beta Fibrillation and Disaggregate Preformed Amyloid-Beta Fibrils. Biomol Ther (Seoul) 2020; 28:145-151. [PMID: 31697876 PMCID: PMC7059817 DOI: 10.4062/biomolther.2019.113] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/14/2019] [Accepted: 09/16/2019] [Indexed: 12/18/2022] Open
Abstract
Alzheimer’s disease (AD) is a devastating neurodegenerative disease and a major cause of dementia in elderly individuals world-wide. Increased deposition of insoluble amyloid β (Aβ) fibrils in the brain is thought be a key neuropathological hallmark of AD. Many recent studies show that natural products such as polyphenolic flavonoids inhibit the formation of insoluble Aβ fibrils and/or destabilize β-sheet-rich Aβ fibrils to form non-cytotoxic aggregates. In the present study, we explored the structure-activity relationship of naturally-occurring biflavonoids on Aβ amyloidogenesis utilizing an in vitro thioflavin T assay with Aβ1–42 peptide which is prone to aggregate more rapidly to fibrils than Aβ1–40 peptide. Among the biflavonoids we tested, we found amentoflavone revealed the most potent effects on inhibiting Aβ1–42 fibrillization (IC50: 0.26 μM), as well as on disassembling preformed Aβ1–42 fibrils (EC50: 0.59 μM). Our structure-activity relationship study suggests that the hydroxyl groups of biflavonoid compounds play an essential role in their molecular interaction with the dynamic process of Aβ1–42 fibrillization. Our atomic force microscopic imaging analysis demonstrates that amentoflavone directly disrupts the fibrillar structure of preformed Aβ1–42 fibrils, resulting in conversion of those fibrils to amorphous Aβ1–42 aggregates. These results indicate that amentoflavone affords the most potent anti-amyloidogenic effects on both inhibition of Aβ1–42 fibrillization and disaggregation of preformed mature Aβ1–42 fibrils.
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Affiliation(s)
- Erika Y Choi
- Department of Pharmacology, A.T. Still University of Health Sciences, Kirksville, MO 63501, USA
| | - Sam Sik Kang
- School of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang Kook Lee
- School of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Byung Hee Han
- Department of Pharmacology, A.T. Still University of Health Sciences, Kirksville, MO 63501, USA
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7
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Ding X, Sun F, Chen J, Chen L, Tobin-Miyaji Y, Xue S, Qiang W, Luo SZ. Amyloid-Forming Segment Induces Aggregation of FUS-LC Domain from Phase Separation Modulated by Site-Specific Phosphorylation. J Mol Biol 2019; 432:467-483. [PMID: 31805282 DOI: 10.1016/j.jmb.2019.11.017] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 11/19/2019] [Accepted: 11/19/2019] [Indexed: 11/28/2022]
Abstract
The RNA-binding protein fused in sarcoma (FUS) forms physiological granules and pathological fibrils, which facilitate RNA functions and cause neurodegenerative diseases, respectively. Phosphorylation at Ser/Thr residues may regulate the functional assembly of FUS and prevent pathological aggregation in cells. However, the low-complexity nature of the FUS sequence makes it challenging to characterize how phosphorylation of specific sites within the core amyloid-forming segment affects aggregation. Taking advantage of the recently solved molecular structures of the fibrillar core of the FUS low-complexity (FUS-LC) domain, we systematically investigated the aggregation of repeated segments within the core. We identified a segment with a strong amyloid-forming tendency that induced the aggregation of FUS-LC domain in phase-separated liquid droplets and further seeded the aggregation of full-length FUS. The aggregation propensity and seeding ability of this amyloid-forming segment were modulated by site-specific phosphorylation. Solid-state nuclear magnetic resonance (NMR) spectroscopy and computational modeling implied that site-specific phosphorylation at Ser61 plays key roles in FUS assembly by disrupting both intra- and intermolecular interactions that maintain the amyloid core structure.
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Affiliation(s)
- Xiufang Ding
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Fude Sun
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jialin Chen
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Long Chen
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yuto Tobin-Miyaji
- Department of Chemistry, Binghamton University, State University of New York, Vestal, NY 13902, USA
| | - Song Xue
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Wei Qiang
- Department of Chemistry, Binghamton University, State University of New York, Vestal, NY 13902, USA.
| | - Shi-Zhong Luo
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China.
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8
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Abdolvahabi A, Rasouli S, Croom CM, Plewman DL. High-Throughput Microplate-Based Fluorescence Assays for Studying Stochastic Aggregation of Superoxide Dismutase-1. Methods Mol Biol 2019; 1873:93-108. [PMID: 30341605 DOI: 10.1007/978-1-4939-8820-4_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Investigating in vitro kinetics of superoxide dismutase-1 (SOD1) aggregation with high-throughput microplate-based assays provides valuable information regarding SOD1 pathogenesis in amyotrophic lateral sclerosis (ALS) and opens venues for the development of effective therapies. In this chapter, we first explain the step-by-step purification and demetallation of wild-type (WT) and ALS-variant SOD1 proteins from Saccharomyces cerevisiae (baker's yeast). We then describe the methodology for a microplate-based fluorescence assay that is used to study real-time kinetics of metal-free (apo)-SOD1 aggregation. This technique is highly sensitive, semiautomated, requires minimum modifications to protein, and produces a plethora of data in a short period of time. We also describe a new approach for extracting clinically relevant information from SOD1 aggregation data using Kaplan-Meier estimators.
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Affiliation(s)
- Alireza Abdolvahabi
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Sanaz Rasouli
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
- Institute of Biomedical Studies, Baylor University, Waco, TX, USA
| | - Corbin M Croom
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - Devon L Plewman
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
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9
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Qi X, McGuirl M. Revisit the effect of fibrillization on functions of prion protein from the perspective of Cu(II) binding. Biochem Biophys Res Commun 2018; 503:32-7. [PMID: 29807014 DOI: 10.1016/j.bbrc.2018.05.118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 05/16/2018] [Indexed: 01/01/2023]
Abstract
Conversion of prion protein (PrP) from its α-helical form to a β-sheet rich scrapie form constitutes the key event of the etiology of prion diseases. Fundamental questions remain concerning the functions of prion protein and the mechanisms leading to the formation of misfolded forms. A wealth of evidence links physiological functions of PrP to its ability to bind Cu(II), suggesting that it may act as a copper buffer or be part of the copper transportation system. In contrast, much less attention has been devoted to understanding Cu(II) binding to the scrapie forms. The goal of this work is to comparatively investigate the coordination geometries among PrP conformers at different pH values using continuous X-band electron paramagnetic resonance (EPR) spectroscopy. We have found that while both α-helical monomeric and fibrillar forms of PrP bind Cu(II) similarly, the multi-His configuration is more favored in the fibrillar form. Our results have provided insights into the effect of fibrillization on the functions of prion protein.
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10
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Huang RYC, Iacob RE, Sankaranarayanan S, Yang L, Ahlijanian M, Tao L, Tymiak AA, Chen G. Probing Conformational Dynamics of Tau Protein by Hydrogen/Deuterium Exchange Mass Spectrometry. J Am Soc Mass Spectrom 2018; 29:174-182. [PMID: 28971440 DOI: 10.1007/s13361-017-1815-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/12/2017] [Accepted: 09/13/2017] [Indexed: 06/07/2023]
Abstract
Fibrillization of the microtubule-associated protein tau has been recognized as one of the signature pathologies of the nervous system in Alzheimer's disease, progressive supranuclear palsy, and other tauopathies. The conformational transition of tau in the fibrillization process, tau monomer to soluble aggregates to fibrils in particular, remains unclear. Here we report on the use of hydrogen/deuterium exchange mass spectrometry (HDX-MS) in combination with other biochemical approaches, including Thioflavin S fluorescence measurements, enzyme-linked immunosorbent assay (ELISA), and Western blotting to understand the heparin-induced tau's fibrillization. HDX-MS studies including anti-tau antibody epitope mapping experiments provided molecular level details of the full-length tau's conformational dynamics and its regional solvent accessibility upon soluble aggregates formation. The results demonstrate that R3 region in the full-length tau's microtubule binding repeat region (MTBR) is stabilized in the aggregation process, leaving both N and C terminal regions to be solvent exposed in the soluble aggregates and fibrils. The findings also illustrate the practical utility of orthogonal analytical methodologies for the characterization of protein higher order structure. Graphical Abstract ᅟ.
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Affiliation(s)
- Richard Y-C Huang
- Bioanalytical and Discovery Analytical Sciences, Pharmaceutical Candidate Optimization, Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Roxana E Iacob
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Sethu Sankaranarayanan
- Discovery Biology, Research and Development, Bristol-Myers Squibb Company, Wallingford, CT, USA
| | - Ling Yang
- Discovery Biology, Research and Development, Bristol-Myers Squibb Company, Wallingford, CT, USA
| | - Michael Ahlijanian
- Discovery Biology, Research and Development, Bristol-Myers Squibb Company, Wallingford, CT, USA
| | - Li Tao
- Biologics Development, Global Product Development and Supply, Bristol-Myers Squibb Company, Hopewell, NJ, USA
| | - Adrienne A Tymiak
- Bioanalytical and Discovery Analytical Sciences, Pharmaceutical Candidate Optimization, Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Guodong Chen
- Bioanalytical and Discovery Analytical Sciences, Pharmaceutical Candidate Optimization, Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA.
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11
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Mučibabić M, Apetri MM, Canters GW, Aartsma TJ. The effect of fluorescent labeling on α-synuclein fibril morphology. Biochim Biophys Acta 2016; 1864:1419-27. [PMID: 27475048 DOI: 10.1016/j.bbapap.2016.07.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 07/06/2016] [Accepted: 07/21/2016] [Indexed: 11/15/2022]
Abstract
The misfolding and aggregation of a small, natively unfolded protein α-synuclein (α-syn) is presumably an important factor in the development of Parkinson's disease. However, the mechanism of α-syn aggregation into amyloid fibrils and their morphology are not well understood. To elucidate the aggregation kinetics and the morphology of aggregates by the use of fluorescent techniques the protein needs to be suitably labeled. In this study, using atomic force microscopy, we demonstrate a significant effect of fluorescent labels on the α-syn fibrillization process. We studied in detail the morphology of α-syn aggregates as a function of the composition of mixtures of labeled and wild type (WT) α-syn in solution using different types of fluorescent dyes. Although the overall charge of the fluorophores we used and their chemical structure varied significantly, the morphology of α-syn fibrils changed in a similar way in all cases. The increase in the fraction of labeled α-syn in solution led to shortening of the fibrils as compared to those from WT-only α-syn, whereas the height of the fibrils remained mainly unaffected. The twisted fibril morphology observed in the WT and A140C α-syn mutant completely disappeared when the A140C α-syn mutant was 100% fluorescently labeled.
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Affiliation(s)
- M Mučibabić
- Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - M M Apetri
- Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - G W Canters
- Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - T J Aartsma
- Leiden Institute of Physics, Leiden University, Leiden, The Netherlands.
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12
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Sosnowska M, Skibiszewska S, Kamińska E, Wieczerzak E, Jankowska E. Designing peptidic inhibitors of serum amyloid A aggregation process. Amino Acids 2016; 48:1069-1078. [PMID: 26759015 DOI: 10.1007/s00726-015-2167-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 12/26/2015] [Indexed: 02/05/2023]
Abstract
Amyloid A amyloidosis is a life-threatening complication of a wide range of chronic inflammatory, infectious and neoplastic diseases, and the most common form of systemic amyloidosis worldwide. It is characterized by extracellular tissue deposition of fibrils that are composed of fragments of serum amyloid A protein (SAA), a major acute-phase reactant protein, produced predominantly by hepatocytes. Currently, there are no approved therapeutic agents directed against the formation of fibrillar SAA assemblies. We attempted to develop peptidic inhibitors based on their similarity and complementarity to the regions critical for SAA self-association, which they should interact with and block their assembly into amyloid fibrils. Inh1 and inh4 which are comprised of the residues from the amyloidogenic region of SAA1.1 protein and Aβ peptide, respectively, were found by us as capable to significantly suppress aggregation of the SAA1-12 peptide. It was chosen as an aggregation model that mimicks the amyloidogenic nucleus of SAA protein. We suppose that aromatic interactions may be responsible for inhibitory activity of both compounds. We also recognized that aromatic residues are involved in self-association of SAA1-12.
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Affiliation(s)
- Marta Sosnowska
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Sandra Skibiszewska
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Emilia Kamińska
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Ewa Wieczerzak
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Elżbieta Jankowska
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland.
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Tuttle MD, Courtney JM, Barclay AM, Rienstra CM. Preparation of Amyloid Fibrils for Magic-Angle Spinning Solid-State NMR Spectroscopy. Methods Mol Biol 2016; 1345:173-83. [PMID: 26453212 DOI: 10.1007/978-1-4939-2978-8_11] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Solid-state NMR spectroscopy (SSNMR) is an established and invaluable tool for the study of amyloid fibril structure with atomic-level detail. Optimization of the homogeneity and concentration of fibrils enhances the resolution and sensitivity of SSNMR spectra. Here, we present a fibrillization and fibril processing protocol, starting from purified monomeric α-synuclein, that enables the collection of high-resolution SSNMR spectra suitable for site-specific structural analysis. This protocol does not rely on any special features of α-synuclein and should be generalizable to any other amyloid protein.
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Banerjee R. Effect of Curcumin on the metal ion induced fibrillization of amyloid-β peptide. Spectrochim Acta A Mol Biomol Spectrosc 2014; 117:798-800. [PMID: 24119373 DOI: 10.1016/j.saa.2013.09.064] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 08/29/2013] [Accepted: 09/18/2013] [Indexed: 06/02/2023]
Abstract
The effect of Curcumin on Cu(II) and Zn(II) induced oligomerization and protofibrillization of the amyloid-beta (Aβ) peptide has been studied by spectroscopic and microscopic methods. Curcumin could significantly reduce the β-sheet content of the peptide in a time dependent manner. It also plays an antagonistic role in β-sheet formation that is promoted by metal ions like Cu(II) and Zn(II) as observed by Circular Dichroism (CD) spectroscopy. Atomic force microscopic (AFM) images show that spontaneous fibrillization of the peptide occurs in presence of Cu(II) and Zn(II) but is inhibited on incubation of the peptide with Curcumin indicating the beneficial role of Curcumin in preventing the aggregation of Aβ peptide.
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Affiliation(s)
- Rona Banerjee
- Department of Biotechnology, Indian Institute of Technology, Roorkee 247667, Uttaranchal, India.
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Fontanillo M, Angulo-Pachón CA, Escuder B, Miravet JF. In situ synthesis-gelation at room temperature vs. heating-cooling procedure. Fine tuning of molecular gels derived from succinic acid and L-valine. J Colloid Interface Sci 2013; 412:65-71. [PMID: 24144375 DOI: 10.1016/j.jcis.2013.08.055] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 08/30/2013] [Indexed: 10/26/2022]
Abstract
HYPOTHESIS The reaction between succinic anhydride and a diamine derived from L-valine should afford efficiently a molecular gelator. Based on this reaction, it should be feasible to prepare molecular gels at room temperature, avoiding the conventional thermal treatment required for the solubilization of the gelator, by in situ, simultaneous, synthesis and gelation. The gels prepared by in situ and conventional heating-cooling protocols could present important differences relevant for potential practical applications of these materials. EXPERIMENTAL The gelator was synthesized by reaction of succinic anhydride and a diamine derived from L-valine, affording two new amide bonds. The molecular gels were studied by IR, NMR, electron microscopy, X-ray diffraction and DSC. FINDINGS The results indicate that different polymorphic fibrillar networks are formed depending on the gel preparation method, highlighting how the properties of molecular gels can be tuned in this way. Significant differences between thermal and in situ gels were found in properties such as thermal stability, thixotropic behavior or release of an entrapped dye. In situ synthesis-gelation has also been shown to provide gels in media such as oleic acid which cannot be jellified by conventional heating-cooling procedures.
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Affiliation(s)
- Miriam Fontanillo
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, 12071 Castelló, Spain
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