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Zhang W, Smith N, Zhou Y, McGee CM, Bartoli M, Fu S, Chen J, Domena JB, Joji A, Burr H, Lv G, Cilingir EK, Bedendo S, Claure ML, Tagliaferro A, Eliezer D, Veliz EA, Zhang F, Wang C, Leblanc RM. Carbon dots as dual inhibitors of tau and amyloid-beta aggregation for the treatment of Alzheimer's disease. Acta Biomater 2024:S1742-7061(24)00306-4. [PMID: 38849023 DOI: 10.1016/j.actbio.2024.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 05/27/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024]
Abstract
Alzheimer's disease (AD) is the most common form of senile dementia, presenting a significant challenge for the development of effective treatments. AD is characterized by extracellular amyloid plaques and intraneuronal neurofibrillary tangles. Therefore, targeting both hallmarks through inhibition of amyloid beta (Aβ) and tau aggregation presents a promising approach for drug development. Carbon dots (CD), with their high biocompatibility, minimal cytotoxicity, and blood-brain barrier (BBB) permeability, have emerged as promising drug nanocarriers. Congo red, an azo dye, has gathered significant attention for inhibiting amyloid-beta and tau aggregation. However, Congo red's inability to cross the BBB limits its potential to be used as a drug candidate for central nervous system (CNS) diseases. Furthermore, current studies only focus on using Congo red to target single disease hallmarks, without investigating dual inhibition capabilities. In this study, we synthesized Congo red-derived CD (CRCD) by using Congo red and citric acid as precursors, resulting in three variants, CRCD1, CRCD2 and CRCD3, based on different mass ratios of precursors. CRCD2 and CRCD3 exhibited sustained low cytotoxicity, and CRCD3 demonstrated the ability to traverse the BBB in a zebrafish model. Moreover, thioflavin T (ThT) aggregation assays and AFM imaging revealed CRCD as potent inhibitors against both tau and Aβ aggregation. Notably, CRCD1 emerged as the most robust inhibitor, displaying IC50 values of 0.2 ± 0.1 and 2.1 ± 0.5 µg/mL against tau and Aβ aggregation, respectively. Our findings underscore the dual inhibitory role of CRCD against tau and Aβ aggregation, showcasing effective BBB penetration and positioning CRCD as potential nanodrugs and nanocarriers for the CNS. Hence, CRCD-based compounds represent a promising candidate in the realm of multi-functional AD therapeutics, offering an innovative formulation component for future developments in this area. STATEMENT OF SIGNIFICANCE: This article reports Congo red-derived carbon dots (CRCD) as dual inhibitors of tau and amyloid-beta (Aβ) aggregation for the treatment of Alzheimer's disease (AD). The CRCD are biocompatible and show strong fluorescence, high stability, the ability to cross the blood-brain barrier, and the function of addressing two major pathological features of AD.
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Affiliation(s)
- Wei Zhang
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA
| | - Nathan Smith
- Department of Biological Sciences, Rensselaer Polytechnic Institute, NY 12180, USA
| | - Yiqun Zhou
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA; Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
| | - Caitlin M McGee
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA
| | - Mattia Bartoli
- Department of Applied Science and Technology, Politecnico di Torino, Italy; Center for Sustainable Future Technologies (CSFT), Istituto Italiano di Technologia (IIT), Via Livorno 60, 10144 Turin, Italy
| | - Shiwei Fu
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA
| | - Jiuyan Chen
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA
| | - Justin B Domena
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA
| | - Annu Joji
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA
| | - Hannah Burr
- Department of Biological Sciences, Rensselaer Polytechnic Institute, NY 12180, USA
| | - Guohua Lv
- Department of Biochemistry, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Emel K Cilingir
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA
| | - Susanna Bedendo
- Department of Applied Science and Technology, Politecnico di Torino, Italy
| | - Matteo L Claure
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA
| | | | - David Eliezer
- Department of Biochemistry, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Eduardo A Veliz
- Department of Natural Sciences, Miami Dade Collage, Miami, FL 33132, USA
| | - Fuwu Zhang
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA
| | - Chunyu Wang
- Department of Biological Sciences, Rensselaer Polytechnic Institute, NY 12180, USA.
| | - Roger M Leblanc
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
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Tao Y, Xia W, Zhao Q, Xiang H, Han C, Zhang S, Gu W, Tang W, Li Y, Tan L, Li D, Liu C. Structural mechanism for specific binding of chemical compounds to amyloid fibrils. Nat Chem Biol 2023; 19:1235-1245. [PMID: 37400537 DOI: 10.1038/s41589-023-01370-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 05/26/2023] [Indexed: 07/05/2023]
Abstract
Amyloid fibril is an important pharmaceutical target for diagnostic and therapeutic treatment of neurodegenerative diseases. However, rational design of chemical compounds that interact with amyloid fibrils is unachievable due to the lack of mechanistic understanding of the ligand-fibril interaction. Here we used cryoelectron microscopy to survey the amyloid fibril-binding mechanism of a series of compounds including classic dyes, (pre)clinical imaging tracers and newly identified binders from high-throughput screening. We obtained clear densities of several compounds in complex with an α-synuclein fibril. These structures unveil the basic mechanism of the ligand-fibril interaction, which exhibits remarkable difference from the canonical ligand-protein interaction. In addition, we discovered a druggable pocket that is also conserved in the ex vivo α-synuclein fibrils from multiple system atrophy. Collectively, these findings expand our knowledge of protein-ligand interaction in the amyloid fibril state, which will enable rational design of amyloid binders in a medicinally beneficial way.
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Affiliation(s)
- Youqi Tao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, China
| | - Wencheng Xia
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Qinyue Zhao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, China
| | - Huaijiang Xiang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Chao Han
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Shenqing Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Gu
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Wenjun Tang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Ying Li
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Li Tan
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Dan Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China.
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai, China.
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China.
- University of the Chinese Academy of Sciences, Beijing, China.
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China.
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Zhang L, Xia Y, Gui Y. Neuronal ApoE4 in Alzheimer's disease and potential therapeutic targets. Front Aging Neurosci 2023; 15:1199434. [PMID: 37333457 PMCID: PMC10272394 DOI: 10.3389/fnagi.2023.1199434] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/16/2023] [Indexed: 06/20/2023] Open
Abstract
The most prevalent genetic risk factor for Alzheimer's disease (AD) is Apolipoprotein E (ApoE), a gene located on chromosome 19 that encodes three alleles (e2, e3, and e4) that give rise to the ApoE subtypes E2, E3, and E4, respectively. E2 and E4 have been linked to increased plasma triglyceride concentrations and are known to play a critical role in lipoprotein metabolism. The prominent pathological features of AD mainly include senile plaques formed by amyloid β (Aβ42) aggregation and neuronal fibrous tangles (NFTs), and the deposited plaques are mainly composed of Aβ hyperphosphorylation and truncated head. In the central nervous system, the ApoE protein is primarily derived from astrocytes, but ApoE is also produced when neurons are stressed or affected by certain stress, injury, and aging conditions. ApoE4 in neurons induces Aβ and tau protein pathologies, leading to neuroinflammation and neuronal damage, impairing learning and memory functions. However, how neuronal ApoE4 mediates AD pathology remains unclear. Recent studies have shown that neuronal ApoE4 may lead to greater neurotoxicity, which increases the risk of AD development. This review focuses on the pathophysiology of neuronal ApoE4 and explains how neuronal ApoE4 mediates Aβ deposition, pathological mechanisms of tau protein hyperphosphorylation, and potential therapeutic targets.
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Cerón R, Peimbert M, Rojo-Domínguez A, Nájera H. Hen lysozyme fibrillogenesis, molten globule intermediate and effect of copper salts. J Biomol Struct Dyn 2023; 41:423-434. [PMID: 34821199 DOI: 10.1080/07391102.2021.2006090] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The amyloid fibres have been related to many diseases. The molten globule intermediate has been proposed to form part of the folding pathway of many proteins. In the present study, we investigated the mechanism of amyloid-fibres formation of hen egg-white lysozyme (HEWL) incubated in a potassium phosphate buffer, pH 11.8, 100 mM, at 37 °C for 30 h, and evaluated the influence of Cu(II) present in two salts (CuSO4 and CuCl2) during fibrillogenesis. Co-incubation and post-incubation of lysozyme with copper salts reduced the fluorescence signal of thioflavin T with an increment in the intrinsic fluorescence of the protein. The ANS fluorescence test showed that incubation of HEWL for 6 h generated a molten globule intermediate state that formed amyloid fibres when incubation was carried out for a 30-h timespan. Dynamic light scattering showed a heterogeneous population of states in samples incubated in the absence or the presence of salts during the fibrillation process. The existence of a reducing potential was verified during the formation of HEWL amyloid fibres with the bathocuproine disulphonate test. Transmission electron microscopy confirmed the presence and absence of fibres in solutions incubated with and without Cu(II). This work demonstrated that lysozyme formed amyloid fibres at 37 °C and copper inhibited its formation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ricardo Cerón
- Posgrado en Ciencias Naturales e Ingeniería, Universidad Autónoma Metropolitana-Cuajimalpa, Mexico City, Mexico.,Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa, Mexico City, Mexico
| | - Mariana Peimbert
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa, Mexico City, Mexico
| | - Arturo Rojo-Domínguez
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa, Mexico City, Mexico
| | - Hugo Nájera
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa, Mexico City, Mexico
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Kolasa M, Galita G, Majsterek I, Kucharska E, Czerczak K, Wasko J, Becht A, Fraczyk J, Gajda A, Pietrzak L, Szymanski L, Krakowiak A, Draczynski Z, Kolesinska B. Screening of Self-Assembling of Collagen IV Fragments into Stable Structures Potentially Useful in Regenerative Medicine. Int J Mol Sci 2021; 22:13584. [PMID: 34948383 PMCID: PMC8708666 DOI: 10.3390/ijms222413584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/03/2021] [Accepted: 12/14/2021] [Indexed: 11/17/2022] Open
Abstract
The aim of the research was to check whether it is possible to use fragments of type IV collagen to obtain, as a result of self-assembling, stable spatial structures that could be used to prepare new materials useful in regenerative medicine. Collagen IV fragments were obtained by using DMT/NMM/TosO- as a coupling reagent. The ability to self-organize and form stable spatial structures was tested by the CD method and microscopic techniques. Biological studies covered: resazurin assay (cytotoxicity assessment) on BJ, BJ-5TA and C2C12 cell lines; an alkaline version of the comet assay (genotoxicity), Biolegend Legendplex human inflammation panel 1 assay (SC cell lines, assessment of the inflammation activity) and MTT test to determine the cytotoxicity of the porous materials based on collagen IV fragments. It was found that out of the pool of 37 fragments (peptides 1-33 and 2.1-2.4) reconstructing the outer sphere of collagen IV, nine fragments (peptides: 2, 4, 5, 6, 14, 15, 25, 26 and 30), as a result of self-assembling, form structures mimicking the structure of the triple helix of native collagens. The stability of spatial structures formed as a result of self-organization at temperatures of 4 °C, 20 °C, and 40 °C was found. The application of the MST method allowed us to determine the Kd of binding of selected fragments of collagen IV to ITGα1β1. The stability of the spatial structures of selected peptides made it possible to obtain porous materials based on their equimolar mixture. The formation of the porous materials was found for cross-linked structures and the material stabilized only by weak interactions. All tested peptides are non-cytotoxic against all tested cell lines. Selected peptides also showed no genotoxicity and no induction of immune system responses. Research on the use of porous materials based on fragments of type IV collagen, able to form stable spatial structures as scaffolds useful in regenerative medicine, will be continued.
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Affiliation(s)
- Marcin Kolasa
- General Command of the Polish Armed Forces, Medical Division, Zwirki i Wigury 103/105, 00-912 Warsaw, Poland;
| | - Grzegorz Galita
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, Narutowicza 60, 90-136 Lodz, Poland; (G.G.); (I.M.)
| | - Ireneusz Majsterek
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, Narutowicza 60, 90-136 Lodz, Poland; (G.G.); (I.M.)
| | - Ewa Kucharska
- Department Geriatrics and Social Work, Jesuit University Ignatianum in Cracow, Kopernika 26, 31-501 Krakow, Poland;
| | - Katarzyna Czerczak
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland; (K.C.); (J.W.); (A.B.); (J.F.); (A.G.)
| | - Joanna Wasko
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland; (K.C.); (J.W.); (A.B.); (J.F.); (A.G.)
| | - Angelika Becht
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland; (K.C.); (J.W.); (A.B.); (J.F.); (A.G.)
| | - Justyna Fraczyk
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland; (K.C.); (J.W.); (A.B.); (J.F.); (A.G.)
| | - Anna Gajda
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland; (K.C.); (J.W.); (A.B.); (J.F.); (A.G.)
| | - Lukasz Pietrzak
- Institute of Mechatronics and Information Systems, Faculty of Electrical, Electronic, Computer and Control Engineering, Lodz University of Technology, Stefanowskiego 18/22, 90-924 Lodz, Poland; (L.P.); (L.S.)
| | - Lukasz Szymanski
- Institute of Mechatronics and Information Systems, Faculty of Electrical, Electronic, Computer and Control Engineering, Lodz University of Technology, Stefanowskiego 18/22, 90-924 Lodz, Poland; (L.P.); (L.S.)
| | - Agnieszka Krakowiak
- Centre of Molecular and Macromolecular Studies Polish Academy of Sciences, Department of Bioorganic Chemistry, Sienkiewicza 112, 90-363 Lodz, Poland;
| | - Zbigniew Draczynski
- Institute of Material Sciences of Textiles and Polymer Composites, Faculty of Material Technologies and Textile Design, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland;
| | - Beata Kolesinska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland; (K.C.); (J.W.); (A.B.); (J.F.); (A.G.)
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Khanna S, Singh AK, Behera SP, Gupta S. Thermoresponsive BSA hydrogels with phase tunability. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2020; 119:111590. [PMID: 33321635 DOI: 10.1016/j.msec.2020.111590] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 09/22/2020] [Accepted: 09/26/2020] [Indexed: 12/26/2022]
Abstract
Amyloids are fibrillar structures formed due to protein aggregation or misfolding when the molecules undergo a conformational change from α-helix to β-sheet. Although this self-assembly is associated with many neurodegenerative diseases in vivo, the highly ordered amyloidic structures formed in vitro are ideal scaffolds for many bionanotechnological applications. Amyloid fibrillar networks under specific stimuli can also form stable hydrogels. We have used bovine serum albumin (BSA) as a model amyloidogenic protein to obtain thermally-induced hydrogels that display tunable sol-gel-sol transitions spanning over minutes to days. High concentrations of BSA (14-22% w/v) were heated at 65 °C for less than 3 min without any cross-linking agent to yield soft, injectable gels that were non-toxic to mammalian cells. A detailed investigation of temperature, concentration, incubation time and ionic strength on the formation and reversal of these gels was carried out using visual inspection, rheology, electron microscopy, fluorescence spectroscopy, UV-visible spectroscopy and circular dichroism spectroscopy. The optimum gelation temperature (Tg) for phase reversal of BSA gels was found to lie between 60 and 70 °C. An increase in protein concentration led to a reduction in the gelation time and increase in the gel-to-rev sol transition time. Gels heated for longer duration than their minimum gelation time yielded irreversible gels suggesting that low incubation periods were favourable for partial protein denaturation and hydrogel formation. This was supported by time-resolved secondary and tertiary structural ensemble studies. Further, the hydrogel networks demonstrated a zero-order drug release kinetics and the rev sol was found to be cytocompatible with HaCaT skin cell lines. Overall, our approach demonstrates rapid, crosslinker-free thermoresponsive BSA gelation with wide tunability and control on the time and material property, ideal for topical drug delivery applications.
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Affiliation(s)
- Shruti Khanna
- Dept. of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Ajay Kumar Singh
- Dept. of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Soumya Prakash Behera
- Dept. of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Shalini Gupta
- Dept. of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India.
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Ghosh P, De P. Modulation of Amyloid Protein Fibrillation by Synthetic Polymers: Recent Advances in the Context of Neurodegenerative Diseases. ACS APPLIED BIO MATERIALS 2020; 3:6598-6625. [DOI: 10.1021/acsabm.0c01021] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Pooja Ghosh
- Polymer Research Centre and Centre for Advanced Functional Materials, Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, 741246 Nadia, West Bengal, India
| | - Priyadarsi De
- Polymer Research Centre and Centre for Advanced Functional Materials, Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, 741246 Nadia, West Bengal, India
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Acylguanidine-BACE1 complex: Insights of intermolecular interactions and dynamics. J Theor Biol 2019; 464:33-49. [DOI: 10.1016/j.jtbi.2018.12.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 12/09/2018] [Accepted: 12/15/2018] [Indexed: 12/14/2022]
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9
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Dapson RW. Amyloid from a histochemical perspective. A review of the structure, properties and types of amyloid, and a proposed staining mechanism for Congo red staining. Biotech Histochem 2018; 93:543-556. [PMID: 30403893 DOI: 10.1080/10520295.2018.1528385] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Amyloid is a diverse group of unrelated peptides or proteins that have positive functionality or are associated with various pathologies. Despite vast differences, all amyloids share several features that together uniquely define the group. 1) All amyloids possess a characteristic cross-ß pattern with X-ray diffraction typical of ß-sheet secondary protein structures. 2) All amyloids are birefringent and dichroic under polarizing microscopy after staining with Congo red, which indicates a crystalline-like (ordered) structure. 3) All amyloids cause a spectral shift in the peak wavelength of Congo red with conventional light microscopy due to perturbation of π electrons of the dye. 4) All amyloids show heightened intensity of fluorescence with Congo red, which suggests an unusual degree of packing of the dye onto the substrate. The ß portion of amyloid molecules, the only logical substrate for specific Congo red staining under histochemical conditions, consists of a stack of ß-sheets laminated by hydrophilic and hydrophobic interactions between adjacent pairs. Only the first and last ß-sheets are accessible to dyes. Each sheet is composed of numerous identical peptides running across the width of the sheet and arranged in parallel with side chains in register over the length of the fibril. Two sets of grooves are bordered by side chains. X grooves run perpendicular to the long axis of the fibril; these grooves are short (the width of the sheet) and number in the hundreds or thousands. Y grooves are parallel with the long axis. Each groove runs the entire length of the fibril, but there are very few of them. While Congo red is capable of ionic bonding with proteins via two sulfonic acid groups, physical constraints on the staining solution preclude ionic interactions. Hydrogen bonding between dye amine groups and peptide carbonyls is the most likely primary bonding mechanism, because all ß-sheets possess backbone carbonyls. Various amino acid residues may form secondary bonds to the dye via any of three van der Waals forces. It is possible that Congo red binds within the Y grooves, but that would not produce the characteristic staining features that are the diagnostic hallmarks of amyloid. Binding in the X grooves would produce a tightly packed series of dye molecules over the entire length of the fibril. This would account for the signature staining of amyloid by Congo red: dichroic birefringence, enhanced intensity of fluorescence and a shift in visible absorption wavelength.
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Exploration of synthetic multifunctional amides as new therapeutic agents for Alzheimer's disease through enzyme inhibition, chemoinformatic properties, molecular docking and dynamic simulation insights. J Theor Biol 2018; 458:169-183. [PMID: 30243565 DOI: 10.1016/j.jtbi.2018.09.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/06/2018] [Accepted: 09/17/2018] [Indexed: 12/12/2022]
Abstract
A new series of multifunctional amides has been synthesized having moderate enzyme inhibitory potentials and mild cytotoxicity. 2-Furyl(1-piperazinyl)methanone (1) was coupled with 3,5-dichloro-2-hydroxybenzenesulfonyl chloride (2) to form {4-[(3,5-dichloro-2-hydroxyphenyl)sulfonyl]-1-piperazinyl}(2-furyl)methanone (3). Different elecrophiles were synthesized by the reaction of various un/substituted anilines (4a-o) with 2-bromoacetylbromide (5), 2‑bromo‑N-(un/substituted-phenyl)acetamides (6a-o). Further, equimolar ratios of 3 and 6a-o were allowed to react in the presence of K2CO3 in acetonitrile to form desired multifunctional amides (7a-o). The structural confirmation of all the synthesized compounds was carried out by their EI-MS, IR, 1H NMR and 13C NMR spectral data. Enzyme inhibition activity was performed against acetyl and butyrylcholinestrase enzymes, whereby 7e showed very good activity having IC50 value of 5.54 ± 0.03 and 9.15 ± 0.01 μM, respectively, relative to eserine, a reference standard. Hemolytic activity of the molecules was checked to asertain their cytotoxicity towards red blood cell membrance and it was observed that most of the compounds were not toxic up to certain range. Moreover, chemoinformatic protepties and docking simulation results also showed the significance of 7e as compared to other compounds. Based on in vitro and in silico analysis 7e could be used as a template for the development of new drugs against Alzheimer's disease.
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Cao M, Lu S, Zhao W, Deng L, Wang M, Wang J, Zhou P, Wang D, Xu H, Lu JR. Peptide Self-Assembled Nanostructures with Distinct Morphologies and Properties Fabricated by Molecular Design. ACS APPLIED MATERIALS & INTERFACES 2017; 9:39174-39184. [PMID: 29067798 DOI: 10.1021/acsami.7b11681] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Six surfactant-like peptides with the same amino acid composition but different primary sequences are designed, including G3A3V3I3K3, K3I3V3A3G3, I3V3A3G3K3, K3G3A3V3I3, V3G3I3A3K3, and K3A3I3G3V3. These peptides form antiparallel β-sheets during self-assembly. Because the constituent residues have different side chain size and hydrophobicity, sequence changes adjust group distribution and hydrophobicity on the two sides of a given β-sheet. This consequently tunes the binding energy of the side-to-side pairing conformations and leads to different self-assembled structures. G3A3V3I3K3 and K3I3V3A3G3 form short nanorods with diameters of 8.5 ± 1.0 nm and lengths <150 nm. I3V3A3G3K3 and K3G3A3V3I3 form nanosheets with heights of 4.0 ± 0.5 nm and limited lengths and widths. V3G3I3A3K3 and K3A3I3G3V3 form long fibrils with diameters of 7.0 ± 1.0 nm and lengths of micrometer scale. These nanostructures exhibit different capacity in encapsulating insoluble hydrophobic drug molecules and delivering them into the cells. The nanosheets of I3V3A3G3K3 and K3G3A3V3I3 can encapsulate both nile red and doxorubicin molecules to an extent of up to 17-23% in mole ratio. Moreover, the shape and size of the nanostructures affect the drug delivery into cells greatly, with the nanosheets and short rods exhibiting higher efficiency than the long fibrils. The study provides new insights into programmed peptide self-assembly toward specific functionalities.
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Affiliation(s)
- Meiwen Cao
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China) , 66 Changjiang West Road, Qingdao 266580, China
| | - Sha Lu
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China) , 66 Changjiang West Road, Qingdao 266580, China
| | - Wenjing Zhao
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China) , 66 Changjiang West Road, Qingdao 266580, China
| | - Li Deng
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China) , 66 Changjiang West Road, Qingdao 266580, China
| | - Meng Wang
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China) , 66 Changjiang West Road, Qingdao 266580, China
| | - Jiqian Wang
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China) , 66 Changjiang West Road, Qingdao 266580, China
| | - Peng Zhou
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China) , 66 Changjiang West Road, Qingdao 266580, China
| | - Dong Wang
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China) , 66 Changjiang West Road, Qingdao 266580, China
| | - Hai Xu
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China) , 66 Changjiang West Road, Qingdao 266580, China
| | - Jian R Lu
- Biological Physics Laboratory, School of Physics and Astronomy, University of Manchester , Schuster Building, Oxford Road, Manchester M13 9PL, U.K
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12
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Niu B, Zhang M, Du P, Jiang L, Qin R, Su Q, Chen F, Du D, Shu Y, Chou KC. Small molecular floribundiquinone B derived from medicinal plants inhibits acetylcholinesterase activity. Oncotarget 2017; 8:57149-57162. [PMID: 28915661 PMCID: PMC5593632 DOI: 10.18632/oncotarget.19169] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Accepted: 06/28/2017] [Indexed: 12/12/2022] Open
Abstract
Being a neurodegenerative disorder, Alzheimer's disease (AD) is the one of the most terrible diseases. And acetylcholinesterase (AChE) is considered as an important target for treating AD. Acetylcholinesterase inhibitors (AChEI) are considered to be one of the effective drugs for the treatment of AD. The aim of this study is to find a novel potential AChEI as a drug for the treatment of AD. In this study, instead of using the synthetic compounds, we used those extracted from plants to investigate the interaction between floribundiquinone B (FB) and AChE by means of both the experimental approach such as fluorescence spectra, ultraviolet-visible (UV-vis) absorption spectrometry, circular dichroism (CD) and the theoretical approaches such as molecular docking. The findings reported here have provided many useful clues and hints for designing more effective and less toxic drugs against Alzheimer's disease.
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Affiliation(s)
- Bing Niu
- Shanghai Key Laboratory of Bio-Energy Crops, College of Life Science, Shanghai University, Shanghai, 200444, China.,Gordon Life Science Institute, Boston, MA 02478, USA
| | - Mengying Zhang
- Shanghai Key Laboratory of Bio-Energy Crops, College of Life Science, Shanghai University, Shanghai, 200444, China
| | - Pu Du
- Department of Neurology, The First People's Hospital of Foshan, Foshan, 528000, China
| | - Li Jiang
- Shanghai Key Laboratory of Bio-Energy Crops, College of Life Science, Shanghai University, Shanghai, 200444, China
| | - Rui Qin
- Department of Gynecology, Affiliated Minzu Hospital of Guangxi Medical University, Minzu Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530001, China
| | - Qiang Su
- Shanghai Key Laboratory of Bio-Energy Crops, College of Life Science, Shanghai University, Shanghai, 200444, China
| | - Fuxue Chen
- Shanghai Key Laboratory of Bio-Energy Crops, College of Life Science, Shanghai University, Shanghai, 200444, China
| | - Dongshu Du
- Shanghai Key Laboratory of Bio-Energy Crops, College of Life Science, Shanghai University, Shanghai, 200444, China.,Department of Life Science, Heze University, Heze, Shandong, 274500, China
| | - Yilai Shu
- Department of Otolaryngology-Head and Neck Surgery, Eye and Ear, Nose, Throat, Hospital, Shanghai Medical College, Fudan University, Shanghai, 200031, China
| | - Kuo-Chen Chou
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China.,Gordon Life Science Institute, Boston, MA 02478, USA
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13
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Pickhardt M, Biernat J, Hübschmann S, Dennissen FJA, Timm T, Aho A, Mandelkow EM, Mandelkow E. Time course of Tau toxicity and pharmacologic prevention in a cell model of Tauopathy. Neurobiol Aging 2017; 57:47-63. [PMID: 28600952 DOI: 10.1016/j.neurobiolaging.2017.04.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 03/29/2017] [Accepted: 04/23/2017] [Indexed: 10/19/2022]
Abstract
The aggregation of Tau protein is a hallmark of neurodegenerative diseases including Alzheimer's disease. Previously, we generated a cell model of tauopathy based on the 4-repeat domain with the FTDP-17 mutation ΔK280 (Tau4RDΔK) which is expressed in a regulatable fashion (tet-on). The deletion variant ΔK280 is highly amyloidogenic and forms fibrous aggregates in neuroblastoma N2a cells staining with the reporter dye Thioflavin S. The aggregation of Tau4RDΔK is toxic, contrary to wildtype or anti-aggregant variants of the protein. Using a novel approach for monitoring in situ Tau aggregation and toxicity by combination of microscopic analysis with FACS and biochemical analysis of cells enabled the dissection of the aggregating species which cause a time-dependent increase of toxicity. The dominant initiating step is the dimerization of Tau4RDΔK which leads to further aggregation and induces a strong increase in reactive oxygen species (ROS) and cytoplasmic Ca2+ which damage the membranes and cause cell death. Tau-based treatments using Tau aggregation inhibitors reduce both soluble oligomeric and fully aggregated Tau species and decrease their toxicity.
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Affiliation(s)
- Marcus Pickhardt
- DZNE, German Center for Neurodegenerative Diseases, Bonn, Germany; CAESAR Research Institute, Bonn, Germany
| | - Jacek Biernat
- DZNE, German Center for Neurodegenerative Diseases, Bonn, Germany; CAESAR Research Institute, Bonn, Germany.
| | - Sabrina Hübschmann
- DZNE, German Center for Neurodegenerative Diseases, Bonn, Germany; CAESAR Research Institute, Bonn, Germany
| | - Frank J A Dennissen
- DZNE, German Center for Neurodegenerative Diseases, Bonn, Germany; CAESAR Research Institute, Bonn, Germany
| | - Thomas Timm
- Institute of Biochemistry, Justus-Liebig-University, Giessen, Germany
| | | | - Eva-Maria Mandelkow
- DZNE, German Center for Neurodegenerative Diseases, Bonn, Germany; CAESAR Research Institute, Bonn, Germany; Max-Planck-Institute for Metabolism Research, Köln, Germany
| | - Eckhard Mandelkow
- DZNE, German Center for Neurodegenerative Diseases, Bonn, Germany; CAESAR Research Institute, Bonn, Germany; Max-Planck-Institute for Metabolism Research, Köln, Germany.
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14
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Save SN, Choudhary S. Effects of triphala and guggul aqueous extracts on inhibition of protein fibrillation and dissolution of preformed fibrils. RSC Adv 2017. [DOI: 10.1039/c6ra28440j] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Herbal preparations such as triphala and guggul aqueous extracts have ability to inhibit protein fibrillation which is known to be an important process responsible for many neurodegenerative and other diseases.
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Affiliation(s)
- S. N. Save
- UM-DAE Centre for Excellence in Basic Sciences
- University of Mumbai
- Mumbai 400098
- India
| | - S. Choudhary
- UM-DAE Centre for Excellence in Basic Sciences
- University of Mumbai
- Mumbai 400098
- India
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15
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Liu J, Costantino I, Venugopalan N, Fischetti RF, Hyman BT, Frosch MP, Gomez-Isla T, Makowski L. Amyloid structure exhibits polymorphism on multiple length scales in human brain tissue. Sci Rep 2016; 6:33079. [PMID: 27629394 PMCID: PMC5024092 DOI: 10.1038/srep33079] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 08/15/2016] [Indexed: 12/31/2022] Open
Abstract
Aggregation of Aβ amyloid fibrils into plaques in the brain is a universal hallmark of Alzheimer's Disease (AD), but whether plaques in different individuals are equivalent is unknown. One possibility is that amyloid fibrils exhibit different structures and different structures may contribute differentially to disease, either within an individual brain or between individuals. However, the occurrence and distribution of structural polymorphisms of amyloid in human brain is poorly documented. Here we use X-ray microdiffraction of histological sections of human tissue to map the abundance, orientation and structural heterogeneities of amyloid. Our observations indicate that (i) tissue derived from subjects with different clinical histories may contain different ensembles of fibrillar structures; (ii) plaques harboring distinct amyloid structures can coexist within a single tissue section and (iii) within individual plaques there is a gradient of fibrillar structure from core to margins. These observations have immediate implications for existing theories on the inception and progression of AD.
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Affiliation(s)
- Jiliang Liu
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Isabel Costantino
- Massachusetts Alzheimer's Disease Research Center, Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Bradley T Hyman
- Massachusetts Alzheimer's Disease Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Matthew P Frosch
- Massachusetts Alzheimer's Disease Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Teresa Gomez-Isla
- Massachusetts Alzheimer's Disease Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Lee Makowski
- Department of Bioengineering, Northeastern University, Boston, MA, USA
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16
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Girych M, Gorbenko G, Maliyov I, Trusova V, Mizuguchi C, Saito H, Kinnunen P. Combined thioflavin T-Congo red fluorescence assay for amyloid fibril detection. Methods Appl Fluoresc 2016; 4:034010. [PMID: 28355156 DOI: 10.1088/2050-6120/4/3/034010] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Fluorescence represents one of the most powerful tools for the detection and structural characterization of the pathogenic protein aggregates, amyloid fibrils. The traditional approaches to the identification and quantification of amyloid fibrils are based on monitoring the fluorescence changes of the benzothiazole dye thioflavin T (ThT) and absorbance changes of the azo dye Congo red (CR). In routine screening it is usually sufficient to perform only the ThT and CR assays, but both of them, when used separately, could give false results. Moreover, fibrillization kinetics can be measured only by ThT fluorescence, while the characteristic absorption spectra and birefringence of CR represent more rigid criteria for the presence of amyloid fibrils. Therefore, it seemed reasonable to use both these dyes simultaneously, combining the advantages of each technique. To this end, we undertook a detailed analysis of the fluorescence spectral behavior of these unique amyloid tracers upon their binding to amyloid fibrils from lysozyme, insulin and an N-terminal fragment of apolipoprotein A-I with Iowa mutation. The fluorescence measurements revealed several criteria for distinguishing between fibrillar and monomeric protein states: (i) a common drastic increase in ThT fluorescence intensity; (ii) a sharp decrease in ThT fluorescence upon addition of CR; (iii) an appearance of the maximum at 535-540 nm in the CR excitation spectra; (iv) increase in CR fluorescence intensity at 610 nm. Based on these findings we designed a novel combined ThT-CR fluorescence assay for amyloid identification. Such an approach not only strengthens the reliability of the ThT assay, but also provides new opportunities for structural characterization of amyloid fibrils.
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Affiliation(s)
- Mykhailo Girych
- Department of Nuclear and Medical Physics, V.N. Karazin Kharkiv National University, 4 Svobody Sq., Kharkiv 61022, Ukraine. Department of Neuroscience and Biomedical Engineering, School of Science and Technology, Aalto University, FI-00076, Espoo, Finland. Author to whom any correspondence should be addressed. 19/2 Tankopiya Str., ap. 47, Kharkov 61091, Ukraine
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17
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Discriminate protein decoys from native by using a scoring function based on ubiquitous Phi and Psi angles computed for all atom. J Theor Biol 2016; 398:112-21. [DOI: 10.1016/j.jtbi.2016.03.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Revised: 02/26/2016] [Accepted: 03/17/2016] [Indexed: 12/20/2022]
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18
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Amyloid-like ribbons of amelogenins in enamel mineralization. Sci Rep 2016; 6:23105. [PMID: 27009419 PMCID: PMC4806362 DOI: 10.1038/srep23105] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 02/29/2016] [Indexed: 12/27/2022] Open
Abstract
Enamel, the outermost layer of teeth, is an acellular mineralized tissue that cannot regenerate; the mature tissue is composed of high aspect ratio apatite nanocrystals organized into rods and inter-rod regions. Amelogenin constitutes 90% of the protein matrix in developing enamel and plays a central role in guiding the hierarchical organization of apatite crystals observed in mature enamel. To date, a convincing link between amelogenin supramolecular structures and mature enamel has yet to be described, in part because the protein matrix is degraded during tissue maturation. Here we show compelling evidence that amelogenin self-assembles into an amyloid-like structure in vitro and in vivo. We show that enamel matrices stain positive for amyloids and we identify a specific region within amelogenin that self-assembles into β-sheets. We propose that amelogenin nanoribbons template the growth of apatite mineral in human enamel. This is a paradigm shift from the current model of enamel development.
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19
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Jagusiak A, Konieczny L, Krol M, Marszalek P, Piekarska B, Piwowar P, Roterman I, Rybarska J, Stopa B, Zemanek G. Intramolecular immunological signal hypothesis revived--structural background of signalling revealed by using Congo Red as a specific tool. Mini Rev Med Chem 2015; 14:1104-13. [PMID: 25429660 PMCID: PMC4440395 DOI: 10.2174/1389557514666141127150803] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 10/11/2014] [Accepted: 11/11/2014] [Indexed: 11/22/2022]
Abstract
Micellar structures formed by self-assembling Congo red molecules bind to proteins penetrating into functionrelated
unstable packing areas. Here, we have used Congo red - a supramolecular protein ligand to investigate how the
intramolecular structural changes that take place in antibodies following antigen binding lead to complement activation.
According to our findings, Congo red binding significantly enhances the formation of antigen-antibody complexes. As a
result, even low-affinity transiently binding antibodies can participate in immune complexes in the presence of Congo
red, although immune complexes formed by these antibodies fail to trigger the complement cascade. This indicates that
binding of antibodies to the antigen may not, by itself, fulfill the necessary conditions to generate the signal which
triggers effector activity. These findings, together with the results of molecular dynamics simulation studies, enable us to
conclude that, apart from the necessary assembling of antibodies, intramolecular structural changes generated by
strains which associate high- affinity bivalent antibody fitting to antigen determinants are also required to cross the
complement activation threshold.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - G Zemanek
- Department of Bioinformatics and Telemedicine, Jagiellonian University, Medical College, Lazarza 16, 31- 530 Krakow, Poland..
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20
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In silico analysis of binding of neurotoxic venom ligands with acetylcholinesterase for therapeutic use in treatment of Alzheimer’s disease. J Theor Biol 2015; 372:107-17. [DOI: 10.1016/j.jtbi.2015.02.028] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 02/22/2015] [Accepted: 02/25/2015] [Indexed: 01/08/2023]
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21
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Bäcklund FG, Solin N. Tuning the aqueous self-assembly process of insulin by a hydrophobic additive. RSC Adv 2015. [DOI: 10.1039/c5ra16144d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The presence of a fluorescent hydrophobic oligothiophene (6T) dramatically influences the process where insulin self-assembles into spherulites, resulting in large (up to 1.4 mm) fluorescent spherulites.
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Affiliation(s)
- Fredrik G. Bäcklund
- Department of Physics, Chemistry, and Biology
- Biomolecular and Organic Electronics
- Linköping University
- 581 83 Linköping
- Sweden
| | - Niclas Solin
- Department of Physics, Chemistry, and Biology
- Biomolecular and Organic Electronics
- Linköping University
- 581 83 Linköping
- Sweden
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22
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Congo red modulates ACh-induced Ca(2+) oscillations in single pancreatic acinar cells of mice. Acta Pharmacol Sin 2014; 35:1514-20. [PMID: 25345744 DOI: 10.1038/aps.2014.94] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Accepted: 08/19/2014] [Indexed: 12/16/2022] Open
Abstract
AIM Congo red, a secondary diazo dye, is usually used as an indicator for the presence of amyloid fibrils. Recent studies show that congo red exerts neuroprotective effects in a variety of models of neurodegenerative diseases. However, its pharmacological profile remains unknown. In this study, we investigated the effects of congo red on ACh-induced Ca(2+) oscillations in mouse pancreatic acinar cells in vitro. METHODS Acutely dissociated pancreatic acinar cells of mice were prepared. A U-tube drug application system was used to deliver drugs into the bath. Intracellular Ca(2+) oscillations were monitored by whole-cell recording of Ca(2+)-activated Cl(-) currents and by using confocal Ca(2+) imaging. For intracellular drug application, the drug was added in pipette solution and diffused into cell after the whole-cell configuration was established. RESULTS Bath application of ACh (10 nmol/L) induced typical Ca(2+) oscillations in dissociated pancreatic acinar cells. Addition of congo red (1, 10, 100 μmol/L) dose-dependently enhanced Ach-induced Ca(2+) oscillations, but congo red alone did not induce any detectable response. Furthermore, this enhancement depended on the concentrations of ACh: congo red markedly enhanced the Ca(2+) oscillations induced by ACh (10-30 nmol/L), but did not alter the Ca(2+) oscillations induced by ACh (100-10000 nmol/L). Congo red also enhanced the Ca(2+) oscillations induced by bath application of IP3 (30 μmol/L). Intracellular application of congo red failed to alter ACh-induced Ca(2+) oscillations. CONCLUSION Congo red significantly modulates intracellular Ca(2+) signaling in pancreatic acinar cells, and this pharmacological effect should be fully considered when developing congo red as a novel therapeutic drug.
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23
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Hoffner G, Djian P. Polyglutamine Aggregation in Huntington Disease: Does Structure Determine Toxicity? Mol Neurobiol 2014; 52:1297-1314. [PMID: 25336039 DOI: 10.1007/s12035-014-8932-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 10/09/2014] [Indexed: 01/14/2023]
Abstract
Huntington disease is a dominantly inherited disease of the central nervous system. The mutational expansion of polyglutamine beyond a critical length produces a toxic gain of function in huntingtin and results in neuronal death. In the course of the disease, expanded huntingtin is proteolyzed, becomes abnormally folded, and accumulates in oligomers, fibrils, and microscopic inclusions. The aggregated forms of the expanded protein are structurally diverse. Structural heterogeneity may explain why polyglutamine-containing aggregates could paradoxically be either toxic or neuroprotective. When defined, the toxic structures could then specifically be targeted by prophylactic or therapeutic drugs aimed at inhibiting polyglutamine aggregation.
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Affiliation(s)
- Guylaine Hoffner
- Laboratoire de Physiologie Cérébrale, Centre National de la Recherche Scientifique, Université Paris Descartes, 45 rue des Saints Pères, 75006, Paris, France
| | - Philippe Djian
- Laboratoire de Physiologie Cérébrale, Centre National de la Recherche Scientifique, Université Paris Descartes, 45 rue des Saints Pères, 75006, Paris, France.
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24
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Structure of N-terminal sequence Asp-Ala-Glu-Phe-Arg-His-Asp-Ser of Aβ-peptide with phospholipase A2 from venom of Andaman Cobra sub-species Naja naja sagittifera at 2.0 Å resolution. Int J Mol Sci 2014; 15:4221-36. [PMID: 24619194 PMCID: PMC3975393 DOI: 10.3390/ijms15034221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 02/20/2014] [Accepted: 03/05/2014] [Indexed: 01/13/2023] Open
Abstract
Alzheimer’s disease (AD) is one of the most significant social and health burdens of the present century. Plaques formed by extracellular deposits of amyloid β (Aβ) are the prime player of AD’s neuropathology. Studies have implicated the varied role of phospholipase A2 (PLA2) in brain where it contributes to neuronal growth and inflammatory response. Overall contour and chemical nature of the substrate-binding channel in the low molecular weight PLA2s are similar. This study involves the reductionist fragment-based approach to understand the structure adopted by N-terminal fragment of Alzheimer’s Aβ peptide in its complex with PLA2. In the current communication, we report the structure determined by X-ray crystallography of N-terminal sequence Asp-Ala-Glu-Phe-Arg-His-Asp-Ser (DAEFRHDS) of Aβ-peptide with a Group I PLA2 purified from venom of Andaman Cobra sub-species Naja naja sagittifera at 2.0 Å resolution (Protein Data Bank (PDB) Code: 3JQ5). This is probably the first attempt to structurally establish interaction between amyloid-β peptide fragment and hydrophobic substrate binding site of PLA2 involving H bond and van der Waals interactions. We speculate that higher affinity between Aβ and PLA2 has the therapeutic potential of decreasing the Aβ–Aβ interaction, thereby reducing the amyloid aggregation and plaque formation in AD.
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25
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Xu Y, Shao XJ, Wu LY, Deng NY, Chou KC. iSNO-AAPair: incorporating amino acid pairwise coupling into PseAAC for predicting cysteine S-nitrosylation sites in proteins. PeerJ 2013; 1:e171. [PMID: 24109555 PMCID: PMC3792191 DOI: 10.7717/peerj.171] [Citation(s) in RCA: 228] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 09/06/2013] [Indexed: 11/20/2022] Open
Abstract
As one of the most important and universal posttranslational modifications (PTMs) of proteins, S-nitrosylation (SNO) plays crucial roles in a variety of biological processes, including the regulation of cellular dynamics and many signaling events. Knowledge of SNO sites in proteins is very useful for drug development and basic research as well. Unfortunately, it is both time-consuming and costly to determine the SNO sites purely based on biological experiments. Facing the explosive protein sequence data generated in the post-genomic era, we are challenged to develop automated vehicles for timely and effectively determining the SNO sites for uncharacterized proteins. To address the challenge, a new predictor called iSNO-AAPair was developed by taking into account the coupling effects for all the pairs formed by the nearest residues and the pairs by the next nearest residues along protein chains. The cross-validation results on a state-of-the-art benchmark have shown that the new predictor outperformed the existing predictors. The same was true when tested by the independent proteins whose experimental SNO sites were known. A user-friendly web-server for iSNO-AAPair was established at http://app.aporc.org/iSNO-AAPair/, by which users can easily obtain their desired results without the need to follow the mathematical equations involved during its development.
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Affiliation(s)
- Yan Xu
- Department of Information and Computer Science, University of Science and Technology Beijing , Beijing , China ; Gordon Life Science Institute , Belmont, MA , USA
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26
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Computational studies on Alzheimer’s disease associated pathways and regulatory patterns using microarray gene expression and network data: Revealed association with aging and other diseases. J Theor Biol 2013; 334:109-21. [DOI: 10.1016/j.jtbi.2013.06.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 06/07/2013] [Accepted: 06/10/2013] [Indexed: 12/31/2022]
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27
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Temperature dependence of Congo red binding to amyloid β12–28. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2013; 42:495-501. [DOI: 10.1007/s00249-013-0902-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 04/06/2013] [Indexed: 10/26/2022]
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28
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Wu Y, Wang K, Buschle-Diller G, Liles MR. Fiber formation by dehydration-induced aggregation of albumin. J Appl Polym Sci 2013. [DOI: 10.1002/app.38771] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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29
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Duboisset J, Ferrand P, He W, Wang X, Rigneault H, Brasselet S. Thioflavine-T and Congo Red reveal the polymorphism of insulin amyloid fibrils when probed by polarization-resolved fluorescence microscopy. J Phys Chem B 2013; 117:784-8. [PMID: 23289901 DOI: 10.1021/jp309528f] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Amyloid fibrils are protein misfolding structures that involve a β-sheet structure and are associated with the pathologies of various neurodegenerative diseases. Here we show that Thioflavine-T and Congo Red, two major dyes used to image fibrils by fluorescence assays, can provide deep structural information when probed by means of polarization-resolved fluorescence microscopy. Unlike fluorescence anisotropy or fluorescence detected linear dichroism imaging, this technique allows to retrieve simultaneously both mean orientation and orientation dispersion of the dye, used here as a reporter of the fibril structure. We have observed that insulin amyloid fibrils exhibit a homogeneous behavior over the fibrils' length, confirming their structural uniformity. In addition, these results reveal the existence of various structures among the observed fibrils' population, in spite of a similar aspect when imaged with conventional fluorescence microscopy. This optical nondestructive technique opens perspectives for in vivo structural analyses or high throughput screening.
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Affiliation(s)
- Julien Duboisset
- Aix Marseille Université, CNRS, Ecole Centrale Marseille, Institut Fresnel, 13013 Marseille, France.
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30
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Gan C, Zhou L, Zhao Z, Wang H. Benzothiazole Schiff-bases as potential imaging agents for β-amyloid plaques in Alzheimer’s disease. Med Chem Res 2012. [DOI: 10.1007/s00044-012-0416-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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31
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Remya C, Dileep KV, Tintu I, Variyar EJ, Sadasivan C. Design of potent inhibitors of acetylcholinesterase using morin as the starting compound. FRONTIERS IN LIFE SCIENCE 2012. [DOI: 10.1080/21553769.2013.815137] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Cinar G, Ceylan H, Urel M, Erkal TS, Deniz Tekin E, Tekinay AB, Dâna A, Guler MO. Amyloid inspired self-assembled peptide nanofibers. Biomacromolecules 2012; 13:3377-87. [PMID: 22984884 DOI: 10.1021/bm301141h] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amyloid peptides are important components in many degenerative diseases as well as in maintaining cellular metabolism. Their unique stable structure provides new insights in developing new materials. Designing bioinspired self-assembling peptides is essential to generate new forms of hierarchical nanostructures. Here we present oppositely charged amyloid inspired peptides (AIPs), which rapidly self-assemble into nanofibers at pH 7 upon mixing in water caused by noncovalent interactions. Mechanical properties of the gels formed by self-assembled AIP nanofibers were analyzed with oscillatory rheology. AIP gels exhibited strong mechanical characteristics superior to gels formed by self-assembly of previously reported synthetic short peptides. Rheological studies of gels composed of oppositely charged mixed AIP molecules (AIP-1 + 2) revealed superior mechanical stability compared to individual peptide networks (AIP-1 and AIP-2) formed by neutralization of net charges through pH change. Adhesion and elasticity properties of AIP mixed nanofibers and charge neutralized AIP-1, AIP-2 nanofibers were analyzed by high resolution force-distance mapping using atomic force microscopy (AFM). Nanomechanical characterization of self-assembled AIP-1 + 2, AIP-1, and AIP-2 nanofibers also confirmed macroscopic rheology results, and mechanical stability of AIP mixed nanofibers was higher compared to individual AIP-1 and AIP-2 nanofibers self-assembled at acidic and basic pH, respectively. Experimental results were supported with molecular dynamics simulations by considering potential noncovalent interactions between the amino acid residues and possible aggregate forms. In addition, HUVEC cells were cultured on AIP mixed nanofibers at pH 7 and biocompatibility and collagen mimetic scaffold properties of the nanofibrous system were observed. Encapsulation of a zwitterionic dye (rhodamine B) within AIP nanofiber network was accomplished at physiological conditions to demonstrate that this network can be utilized for inclusion of soluble factors as a scaffold for cell culture studies.
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Hamley IW. The Amyloid Beta Peptide: A Chemist’s Perspective. Role in Alzheimer’s and Fibrillization. Chem Rev 2012; 112:5147-92. [DOI: 10.1021/cr3000994] [Citation(s) in RCA: 670] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- I. W. Hamley
- Department
of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD,
U.K
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34
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Wang CC, Huang HB, Tsay HJ, Shiao MS, Wu WJW, Cheng YC, Lin TH. Characterization of Aβ aggregation mechanism probed by congo red. J Biomol Struct Dyn 2012; 30:160-9. [DOI: 10.1080/07391102.2012.677767] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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35
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Partovi-Nia R, Beheshti S, Qin Z, Mandal HS, Long YT, Girault HH, Kraatz HB. Study of amyloid β-peptide (Aβ12-28-Cys) interactions with Congo red and β-sheet breaker peptides using electrochemical impedance spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:6377-6385. [PMID: 22449117 DOI: 10.1021/la300093h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
A surface-based approach is presented to study the interactions of Aβ12-28-Cys assembled on gold surfaces with Congo red (CR) and a β-sheet breaker (BSB) peptide. The various aspects of the peptide film have been examined using different electrochemical and surface analytical techniques. Cyclic voltammetry and electrochemical impedance spectroscopy (EIS) results using redox probes [Fe(CN)(6)](3-/4-) show that Aβ12-28-Cys on gold forms a stable and reproducible blocking film. EIS analysis shows that CR and BSB have different effects on the electrochemical properties of Aβ12-28-Cys films, presumably due to changes in the interactions between the film and CR and BSB. EIS results indicate that in the case of CR film resistance decreases significantly presumably due to better penetration of the solution-based redox probe into the film, whereas in the case of BSB, the film resistance increases. We interpret this difference to BSB being able to interact with the Aβ12-28-Cys on the surface and presumably forming a film that presents a higher resistance for electron transfer from the redox probe to the solution.
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Affiliation(s)
- Raheleh Partovi-Nia
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street North, London, Ontario N6A 5B7, Canada
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36
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Wang C, Yang A, Li X, Li D, Zhang M, Du H, Li C, Guo Y, Mao X, Dong M, Besenbacher F, Yang Y, Wang C. Observation of molecular inhibition and binding structures of amyloid peptides. NANOSCALE 2012; 4:1895-909. [PMID: 22334382 DOI: 10.1039/c2nr11508e] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Unveiling interactions between labeling molecules and amyloid fibrils is essential to develop new detection methods for studying amyloid structures under various conditions. This review endeavours to reflect the progress in studying interactions between molecular inhibitors and amyloid peptides using a series of experimental approaches, such as X-ray diffraction, nuclear magnetic resonance, scanning probe microscopy, and electron microscopy. The revealed binding mechanisms of anti-amyloid drugs and target proteins could benefit the rational design of drugs for prevention or treatment of amyloidal diseases.
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Affiliation(s)
- Chenxuan Wang
- National Center for Nanoscience and Technology, Beijing, 100190, PR China
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37
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Le Droumaguet B, Souguir H, Brambilla D, Verpillot R, Nicolas J, Taverna M, Couvreur P, Andrieux K. Selegiline-functionalized, PEGylated poly(alkyl cyanoacrylate) nanoparticles: Investigation of interaction with amyloid-β peptide and surface reorganization. Int J Pharm 2011; 416:453-60. [DOI: 10.1016/j.ijpharm.2011.01.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Revised: 12/28/2010] [Accepted: 01/05/2011] [Indexed: 11/25/2022]
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38
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Zhang J, Gao DY, Yearwood J. A novel canonical dual computational approach for prion AGAAAAGA amyloid fibril molecular modeling. J Theor Biol 2011; 284:149-57. [PMID: 21723301 DOI: 10.1016/j.jtbi.2011.06.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Revised: 06/15/2011] [Accepted: 06/17/2011] [Indexed: 12/22/2022]
Abstract
Many experimental studies have shown that the prion AGAAAAGA palindrome hydrophobic region (113-120) has amyloid fibril forming properties and plays an important role in prion diseases. However, due to the unstable, noncrystalline and insoluble nature of the amyloid fibril, to date structural information on AGAAAAGA region (113-120) has been very limited. This region falls just within the N-terminal unstructured region PrP (1-123) of prion proteins. Traditional X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy experimental methods cannot be used to get its structural information. Under this background, this paper introduces a novel approach of the canonical dual theory to address the 3D atomic-resolution structure of prion AGAAAAGA amyloid fibrils. The novel and powerful canonical dual computational approach introduced in this paper is for the molecular modeling of prion AGAAAAGA amyloid fibrils, and that the optimal atomic-resolution structures of prion AGAAAAGA amyloid fibils presented in this paper are useful for the drive to find treatments for prion diseases in the field of medicinal chemistry. Overall, this paper presents an important method and provides useful information for treatments of prion diseases.
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Affiliation(s)
- Jiapu Zhang
- Centre in Informatics and Applied Optimization, Graduate School of Sciences, Informatics Technology and Engineering, University of Ballarat, Mount Helen, VIC 3353, Australia.
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39
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Mao X, Guo Y, Wang C, Zhang M, Ma X, Liu L, Niu L, Zeng Q, Yang Y, Wang C. Binding modes of thioflavin T molecules to prion peptide assemblies identified by using scanning tunneling microscopy. ACS Chem Neurosci 2011; 2:281-7. [PMID: 22778872 DOI: 10.1021/cn200006h] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Accepted: 03/30/2011] [Indexed: 11/30/2022] Open
Abstract
The widely used method to monitor the aggregation process of amyloid peptide is thioflavin T (ThT) assay, while the detailed molecular mechanism is still not clear. In this work, we report here the direct identification of the binding modes of ThT molecules with the prion peptide GNNQQNY by using scanning tunneling microscopy (STM). The assembly structures of GNNQQNY were first observed by STM on a graphite surface, and the introduction of ThT molecules to the surface facilitated the STM observations of the adsorption conformations of ThT with peptide strands. ThT molecules are apt to adsorb on the peptide assembly with β-sheet structure and oriented parallel with the peptide strands adopting four different binding modes. This effort could benefit the understanding of the mechanisms of the interactions between labeling species or inhibitory ligands and amyloid peptides, which is keenly needed for developing diagnostic and therapeutic approaches.
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Affiliation(s)
- Xiaobo Mao
- Key Laboratory for Biological Effects of Nanomaterials & Nanosafety and Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences) National Center for Nanoscience and Technology, 11 Beiyitiao, Zhongguancun, Beijing 100190, P. R. China
| | - Yuanyuan Guo
- Key Laboratory for Biological Effects of Nanomaterials & Nanosafety and Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences) National Center for Nanoscience and Technology, 11 Beiyitiao, Zhongguancun, Beijing 100190, P. R. China
| | - Chenxuan Wang
- Key Laboratory for Biological Effects of Nanomaterials & Nanosafety and Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences) National Center for Nanoscience and Technology, 11 Beiyitiao, Zhongguancun, Beijing 100190, P. R. China
| | - Min Zhang
- Key Laboratory for Biological Effects of Nanomaterials & Nanosafety and Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences) National Center for Nanoscience and Technology, 11 Beiyitiao, Zhongguancun, Beijing 100190, P. R. China
| | - Xiaojing Ma
- Key Laboratory for Biological Effects of Nanomaterials & Nanosafety and Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences) National Center for Nanoscience and Technology, 11 Beiyitiao, Zhongguancun, Beijing 100190, P. R. China
| | - Lei Liu
- Key Laboratory for Biological Effects of Nanomaterials & Nanosafety and Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences) National Center for Nanoscience and Technology, 11 Beiyitiao, Zhongguancun, Beijing 100190, P. R. China
| | - Lin Niu
- Key Laboratory for Biological Effects of Nanomaterials & Nanosafety and Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences) National Center for Nanoscience and Technology, 11 Beiyitiao, Zhongguancun, Beijing 100190, P. R. China
| | - Qingdao Zeng
- Key Laboratory for Biological Effects of Nanomaterials & Nanosafety and Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences) National Center for Nanoscience and Technology, 11 Beiyitiao, Zhongguancun, Beijing 100190, P. R. China
| | - Yanlian Yang
- Key Laboratory for Biological Effects of Nanomaterials & Nanosafety and Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences) National Center for Nanoscience and Technology, 11 Beiyitiao, Zhongguancun, Beijing 100190, P. R. China
| | - Chen Wang
- Key Laboratory for Biological Effects of Nanomaterials & Nanosafety and Key Laboratory of Standardization and Measurement for Nanotechnology (Chinese Academy of Sciences) National Center for Nanoscience and Technology, 11 Beiyitiao, Zhongguancun, Beijing 100190, P. R. China
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40
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Optimal atomic-resolution structures of prion AGAAAAGA amyloid fibrils. J Theor Biol 2011; 279:17-28. [DOI: 10.1016/j.jtbi.2011.02.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2010] [Revised: 02/05/2011] [Accepted: 02/16/2011] [Indexed: 11/20/2022]
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41
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Schütz AK, Soragni A, Hornemann S, Aguzzi A, Ernst M, Böckmann A, Meier BH. Die Amyloid-Kongorot-Bindungsstelle in atomarer Auflösung. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201008276] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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42
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Schütz AK, Soragni A, Hornemann S, Aguzzi A, Ernst M, Böckmann A, Meier BH. The amyloid-Congo red interface at atomic resolution. Angew Chem Int Ed Engl 2011; 50:5956-60. [PMID: 21591034 DOI: 10.1002/anie.201008276] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Revised: 03/03/2011] [Indexed: 11/07/2022]
Affiliation(s)
- Anne K Schütz
- Physikalische Chemie, ETH Zürich, 8093 Zürich, Switzerland
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43
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Mao X, Wang C, Ma X, Zhang M, Liu L, Zhang L, Niu L, Zeng Q, Yang Y, Wang C. Molecular level studies on binding modes of labeling molecules with polyalanine peptides. NANOSCALE 2011; 3:1592-1599. [PMID: 21283870 DOI: 10.1039/c0nr00782j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
In this work, the binding modes of typical labeling molecules (thioflavin T (ThT), Congo red (CR) and copper(II) phthalocyanine tetrasulfonic acid tetrasodium salt (PcCu(SO(3)Na)(4))) on pentaalanine, which is a model peptide segment of amyloid peptides, have been resolved at the molecular level by using scanning tunneling microscopy (STM). In the STM images, ThT molecules are predominantly adsorbed parallel to the peptide strands and two binding modes could be identified. It was found that ThT molecules are preferentially binding on top of the peptide strand, and the mode of intercalated between neighboring peptides also exists. The parallel binding mode of CR molecules can be observed with pentaalanine peptides. Besides the binding modes of labeling molecules, the CR and PcCu(SO(3)Na)(4) display different adsorption affinity with the pentaalanine peptides. The results could be beneficial for obtaining molecular level insight of the interactions between labeling molecules and peptides.
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Affiliation(s)
- Xiaobo Mao
- National Center for Nanoscience and Technology, Beijing, 100190, China
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44
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Liu Q, Wu WH, Fang CL, Li RW, Liu P, Lei P, Hu J, Sun X, Zheng YZ, Zhao YF, Li YM. Mapping ApoE/Aβ binding regions to guide inhibitor discovery. MOLECULAR BIOSYSTEMS 2011; 7:1693-700. [PMID: 21409287 DOI: 10.1039/c1mb05019b] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Blocking the interaction between the E4 isoform of apolipoprotein E (ApoE) and amyloid beta-peptide (Aβ) may be an avenue for pharmacological intervention in Alzheimer's disease (AD). The main regions of interaction of the two proteins are, respectively, ApoE244-272 and Aβ12-28. These protein segments are too large to facilitate the design of small molecule inhibitors. We mapped the primary components of ApoE/Aβ interaction to smaller peptide segments. Within the three motifs that are primarily responsible for ApoE/Aβ interaction, we identified four peptides that substantially block ApoE/Aβ interaction and further improved their inhibitory activity by rational hydrophobic amino acid substitution. Moreover, the mapping results provide the clue that the Aβ residues which interact with ApoE appear to be in the same region where Aβ self-interacts. According to this information, we found that Congo Red and X-34 could strongly inhibit ApoE/Aβ interaction. Our findings extend our understanding of ApoE/Aβ interaction and may guide the discovery of inhibitors that treat AD by antagonizing ApoE/Aβ interaction.
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Affiliation(s)
- Qian Liu
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, PR China
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45
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Wang HY, Ying YL, Li Y, Kraatz HB, Long YT. Nanopore Analysis of β-Amyloid Peptide Aggregation Transition Induced by Small Molecules. Anal Chem 2011; 83:1746-52. [DOI: 10.1021/ac1029874] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Hai-Yan Wang
- Shanghai Key Laboratory of Functional Materials Chemistry & Department of Chemistry, East China University of Science and Technology, Shanghai 200237, China
| | - Yi-Lun Ying
- Shanghai Key Laboratory of Functional Materials Chemistry & Department of Chemistry, East China University of Science and Technology, Shanghai 200237, China
| | - Yang Li
- Shanghai Key Laboratory of Functional Materials Chemistry & Department of Chemistry, East China University of Science and Technology, Shanghai 200237, China
| | - Heinz-Bernhard Kraatz
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario, N5A 5B9, Canada
| | - Yi-Tao Long
- Shanghai Key Laboratory of Functional Materials Chemistry & Department of Chemistry, East China University of Science and Technology, Shanghai 200237, China
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46
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Hu L, Huang T, Shi X, Lu WC, Cai YD, Chou KC. Predicting functions of proteins in mouse based on weighted protein-protein interaction network and protein hybrid properties. PLoS One 2011; 6:e14556. [PMID: 21283518 PMCID: PMC3023709 DOI: 10.1371/journal.pone.0014556] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2010] [Accepted: 12/21/2010] [Indexed: 11/27/2022] Open
Abstract
Background With the huge amount of uncharacterized protein sequences generated in the post-genomic age, it is highly desirable to develop effective computational methods for quickly and accurately predicting their functions. The information thus obtained would be very useful for both basic research and drug development in a timely manner. Methodology/Principal Findings Although many efforts have been made in this regard, most of them were based on either sequence similarity or protein-protein interaction (PPI) information. However, the former often fails to work if a query protein has no or very little sequence similarity to any function-known proteins, while the latter had similar problem if the relevant PPI information is not available. In view of this, a new approach is proposed by hybridizing the PPI information and the biochemical/physicochemical features of protein sequences. The overall first-order success rates by the new predictor for the functions of mouse proteins on training set and test set were 69.1% and 70.2%, respectively, and the success rate covered by the results of the top-4 order from a total of 24 orders was 65.2%. Conclusions/Significance The results indicate that the new approach is quite promising that may open a new avenue or direction for addressing the difficult and complicated problem.
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Affiliation(s)
- Lele Hu
- Institute of Systems Biology, Shanghai University, Shanghai, China
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai, China
| | - Tao Huang
- Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Shanghai Center for Bioinformation Technology, Shanghai, China
| | - Xiaohe Shi
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wen-Cong Lu
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai, China
| | - Yu-Dong Cai
- Institute of Systems Biology, Shanghai University, Shanghai, China
- Centre for Computational Systems Biology, Fudan University, Shanghai, China
- Gordon Life Science Institute, San Diego, California, United States of America
- * E-mail:
| | - Kuo-Chen Chou
- Gordon Life Science Institute, San Diego, California, United States of America
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47
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Guilbaud JB, Saiani A. Using small angle scattering (SAS) to structurally characterise peptide and protein self-assembled materials. Chem Soc Rev 2011; 40:1200-10. [DOI: 10.1039/c0cs00105h] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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48
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Komatsu H, Feingold-Link E, Sharp KA, Rastogi T, Axelsen PH. Intrinsic linear heterogeneity of amyloid β protein fibrils revealed by higher resolution mass-per-length determinations. J Biol Chem 2010; 285:41843-51. [PMID: 20940298 PMCID: PMC3009912 DOI: 10.1074/jbc.m110.165068] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Revised: 10/01/2010] [Indexed: 11/06/2022] Open
Abstract
Amyloid β proteins spontaneously form fibrils in vitro that vary in their thermodynamic stability and in morphological characteristics such as length, width, shape, longitudinal twist, and the number of component filaments. It is vitally important to determine which variant best represents the type of fibril that accumulates in Alzheimer disease. In the present study, the nature of morphological variation was examined by dark-field and transmission electron microscopy in a preparation of seeded amyloid β protein fibrils that formed at relatively low protein concentrations and exhibited remarkably high thermodynamic stability. The number of filaments comprising these fibrils changed frequently from two to six along their length, and these changes only became apparent when mass-per-length (MPL) determinations are made with sufficient resolution. The MPL results could be reproduced by a simple stochastic model with a single adjustable parameter. The presence of more than two primary filaments could not be discerned by transmission electron microscopy, and they had no apparent relationship to the longitudinal twist of the fibrils. However, the pitch of the twist was strongly affected by the pH of the negative stain. We conclude that highly stable amyloid fibrils may form in which a surprising amount of intrinsic linear heterogeneity may be obscured by MPL measurements of insufficient resolution, and by the negative stains used for imaging fibrils by electron microscopy.
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Affiliation(s)
| | | | | | | | - Paul H. Axelsen
- From the Departments of Pharmacology
- Biochemistry and Biophysics, and
- Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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49
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Cell-produced alpha-synuclein is secreted in a calcium-dependent manner by exosomes and impacts neuronal survival. J Neurosci 2010; 30:6838-51. [PMID: 20484626 DOI: 10.1523/jneurosci.5699-09.2010] [Citation(s) in RCA: 842] [Impact Index Per Article: 60.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
alpha-Synuclein is central in Parkinson's disease pathogenesis. Although initially alpha-synuclein was considered a purely intracellular protein, recent data suggest that it can be detected in the plasma and CSF of humans and in the culture media of neuronal cells. To address a role of secreted alpha-synuclein in neuronal homeostasis, we have generated wild-type alpha-synuclein and beta-galactosidase inducible SH-SY5Y cells. Soluble oligomeric and monomeric species of alpha-synuclein are readily detected in the conditioned media (CM) of these cells at concentrations similar to those observed in human CSF. We have found that, in this model, alpha-synuclein is secreted by externalized vesicles in a calcium-dependent manner. Electron microscopy and liquid chromatography-mass spectrometry proteomic analysis demonstrate that these vesicles have the characteristic hallmarks of exosomes, secreted intraluminar vesicles of multivesicular bodies. Application of CM containing secreted alpha-synuclein causes cell death of recipient neuronal cells, which can be reversed after alpha-synuclein immunodepletion from the CM. High- and low-molecular-weight alpha-synuclein species, isolated from this CM, significantly decrease cell viability. Importantly, treatment of the CM with oligomer-interfering compounds before application rescues the recipient neuronal cells from the observed toxicity. Our results show for the first time that cell-produced alpha-synuclein is secreted via an exosomal, calcium-dependent mechanism and suggest that alpha-synuclein secretion serves to amplify and propagate Parkinson's disease-related pathology.
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50
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Studies of Interaction Between Cyanine Dye T-284 and Fibrillar Alpha-Synuclein. J Fluoresc 2010; 20:1267-74. [DOI: 10.1007/s10895-010-0678-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Accepted: 05/05/2010] [Indexed: 12/24/2022]
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