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Li JY, Zhou CM, Jin RL, Song JH, Yang KC, Li SL, Tan BH, Li YC. The detection methods currently available for protein aggregation in neurological diseases. J Chem Neuroanat 2024; 138:102420. [PMID: 38626816 DOI: 10.1016/j.jchemneu.2024.102420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 03/30/2024] [Accepted: 04/13/2024] [Indexed: 04/21/2024]
Abstract
Protein aggregation is a pathological feature in various neurodegenerative diseases and is thought to play a crucial role in the onset and progression of neurological disorders. This pathological phenomenon has attracted increasing attention from researchers, but the underlying mechanism has not been fully elucidated yet. Researchers are increasingly interested in identifying chemicals or methods that can effectively detect protein aggregation or maintain protein stability to prevent aggregation formation. To date, several methods are available for detecting protein aggregates, including fluorescence correlation spectroscopy, electron microscopy, and molecular detection methods. Unfortunately, there is still a lack of methods to observe protein aggregation in situ under a microscope. This article reviews the two main aspects of protein aggregation: the mechanisms and detection methods of protein aggregation. The aim is to provide clues for the development of new methods to study this pathological phenomenon.
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Affiliation(s)
- Jing-Yi Li
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Cheng-Mei Zhou
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Rui-Lin Jin
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Jia-Hui Song
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China; Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, PR China
| | - Ke-Chao Yang
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Shu-Lei Li
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Bai-Hong Tan
- Laboratory Teaching Center of Basic Medicine, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Yan-Chao Li
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China; Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, PR China.
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2
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Juković M, Ratkaj I, Kalafatovic D, Bradshaw NJ. Amyloids, amorphous aggregates and assemblies of peptides - Assessing aggregation. Biophys Chem 2024; 308:107202. [PMID: 38382283 DOI: 10.1016/j.bpc.2024.107202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/31/2024] [Accepted: 02/14/2024] [Indexed: 02/23/2024]
Abstract
Amyloid and amorphous aggregates represent the two major categories of aggregates associated with diseases, and although exhibiting distinct features, researchers often treat them as equivalent, which demonstrates the need for more thorough characterization. Here, we compare amyloid and amorphous aggregates based on their biochemical properties, kinetics, and morphological features. To further decipher this issue, we propose the use of peptide self-assemblies as minimalistic models for understanding the aggregation process. Peptide building blocks are significantly smaller than proteins that participate in aggregation, however, they make a plausible means to bridge the gap in discerning the aggregation process at the more complex, protein level. Additionally, we explore the potential use of peptide-inspired models to research the liquid-liquid phase separation as a feasible mechanism preceding amyloid formation. Connecting these concepts can help clarify our understanding of aggregation-related disorders and potentially provide novel drug targets to impede and reverse these serious illnesses.
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Affiliation(s)
- Maja Juković
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia
| | - Ivana Ratkaj
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia
| | - Daniela Kalafatovic
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia.
| | - Nicholas J Bradshaw
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia.
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3
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Solov'eva TF, Bakholdina SI, Khomenko VA, Sidorin EV, Kim NY, Novikova OD, Shnyrov VL, Stenkova AM, Eremeev VI, Bystritskaya EP, Isaeva MP. Expression of membrane beta-barrel protein in E. coli at low temperatures: Structure of Yersinia pseudotuberculosis OmpF porin inclusion bodies. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183971. [PMID: 35643329 DOI: 10.1016/j.bbamem.2022.183971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 04/14/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
The recombinant OmpF porin of Yersinia pseudotuberculosis as a model of transmembrane protein of the β-barrel structural family was used to study low growth temperature effect on the structure of the produced inclusion bodies (IBs). This porin showed a very low expression level in E. coli at a growth temperature below optimal 37 °C. The introduction of a N-terminal hexahistidine tag into the mature porin molecule significantly increased the biosynthesis of the protein at low cultivation temperatures. The recombinant His-tagged porin (rOmpF-His) was expressed in E. coli at 30 and 18 °C as inclusion bodies (IB-30 and IB-18). The properties and structural organization of IBs, as well as the structure of rOmpF-His solubilized from the IBs with urea and SDS, were studied using turbidimetry, electron microscopy, dynamic light scattering, optical spectroscopy, and amyloid-specific dyes. IB-18, in comparison with IB-30, has a higher solubility in denaturants, suggesting a difference between IBs in the conformation of the associated polypeptide chains. The spectroscopic analysis revealed that rOmpF-His IBs have a high content of secondary structure with a tertiary-structure elements, including a native-like conformation, the proportion of which in IB-18 is higher than in IB-30. Solubilization of the porin from IBs is accompanied by a modification of its secondary structure. The studied IBs also contain amyloid-like structures. The results obtained in this study expand our knowledge of the structural organization of IBs formed by proteins of different structural classes and also have a contribution into the new approaches development of producing functionally active recombinant membrane proteins.
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Affiliation(s)
- Tamara F Solov'eva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Prospekt 100-let Vladivostoku 159, 690022 Vladivostok, Russia
| | - Svetlana I Bakholdina
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Prospekt 100-let Vladivostoku 159, 690022 Vladivostok, Russia.
| | - Valentina A Khomenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Prospekt 100-let Vladivostoku 159, 690022 Vladivostok, Russia
| | - Evgeniy V Sidorin
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Prospekt 100-let Vladivostoku 159, 690022 Vladivostok, Russia
| | - Natalya Yu Kim
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Prospekt 100-let Vladivostoku 159, 690022 Vladivostok, Russia
| | - Olga D Novikova
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Prospekt 100-let Vladivostoku 159, 690022 Vladivostok, Russia
| | - Valery L Shnyrov
- Departamento de Bioquimica y Biologia Molecular, Universidad de Salamanca, Plaza Doctores de la Reina s/n, 37007 Salamanca, Spain
| | - Anna M Stenkova
- Far Eastern Federal University School of Biomedicine, Russky Island Ajax Bay 10, 690922 Vladivostok, Russia
| | - Vyacheslav I Eremeev
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Prospekt 100-let Vladivostoku 159, 690022 Vladivostok, Russia
| | - Evgenia P Bystritskaya
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Prospekt 100-let Vladivostoku 159, 690022 Vladivostok, Russia
| | - Marina P Isaeva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-Eastern Branch of the Russian Academy of Sciences, Prospekt 100-let Vladivostoku 159, 690022 Vladivostok, Russia
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4
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Zaidi FK, Bhat R. Two polyphenols with diverse mechanisms towards amyloidosis: differential modulation of the fibrillation pathway of human lysozyme by curcumin and EGCG. J Biomol Struct Dyn 2022; 40:4593-4611. [DOI: 10.1080/07391102.2020.1860824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Fatima Kamal Zaidi
- Biophysical Chemistry Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Rajiv Bhat
- Biophysical Chemistry Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
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5
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Gustafsson C, Shirani H, Leira P, Rehn DR, Linares M, Nilsson KPR, Norman P, Lindgren M. Deciphering the Electronic Transitions of Thiophene-Based Donor-Acceptor-Donor Pentameric Ligands Utilized for Multimodal Fluorescence Microscopy of Protein Aggregates. Chemphyschem 2021; 22:323-335. [PMID: 33219724 PMCID: PMC7898931 DOI: 10.1002/cphc.202000669] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/28/2020] [Indexed: 12/23/2022]
Abstract
Anionic pentameric thiophene acetates can be used for fluorescence detection and diagnosis of protein amyloid aggregates. Replacing the central thiophene unit by benzothiadiazole (BTD) or quinoxaline (QX) leads to large emission shifts and basic spectral features have been reported [Chem. Eur. J. 2015, 21, 15133-13137]. Here we present new detailed experimental results of solvent effects, time-resolved fluorescence and examples employing multi-photon microscopy and lifetime imaging. Quantum chemical response calculations elucidate how the introduction of the BTD/QX groups changes the electronic states and emissions. The dramatic red-shift follows an increased conjugation and quinoid character of the π-electrons of the thiophene backbone. An efficient charge transfer in the excited states S1 and S2 compared to the all-thiophene analogue makes these more sensitive to the polarity and quenching by the solvent. Taken together, the results guide in the interpretation of images of stained Alzheimer disease brain sections employing advanced fluorescence microscopy and lifetime imaging, and can aid in optimizing future fluorescent ligand development.
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Affiliation(s)
- Camilla Gustafsson
- Department of Theoretical Chemistry and BiologySchool of Engineering Sciences in Chemistry, Biotechnology and Health KTH Royal Institute of Technology106 91StockholmSweden
| | - Hamid Shirani
- Division of Chemistry, Department of PhysicsChemistry and Biology Linköping University581 83LinköpingSweden
| | - Petter Leira
- Department of Physics-Faculty of Natural SciencesNorwegian University of Science and Technology (NTNU)7491TrondheimNorway
| | - Dirk R. Rehn
- Department of Theoretical Chemistry and BiologySchool of Engineering Sciences in Chemistry, Biotechnology and Health KTH Royal Institute of Technology106 91StockholmSweden
| | - Mathieu Linares
- Department of Theoretical Chemistry and BiologySchool of Engineering Sciences in Chemistry, Biotechnology and Health KTH Royal Institute of Technology106 91StockholmSweden
- Laboratory of Organic Electronics and Scientific Visualization GroupITN and Swedish e-Science Research Center (SeRC) Linköping University581 83LinköpingSweden
| | - K. Peter R. Nilsson
- Division of Chemistry, Department of PhysicsChemistry and Biology Linköping University581 83LinköpingSweden
| | - Patrick Norman
- Department of Theoretical Chemistry and BiologySchool of Engineering Sciences in Chemistry, Biotechnology and Health KTH Royal Institute of Technology106 91StockholmSweden
| | - Mikael Lindgren
- Department of Physics-Faculty of Natural SciencesNorwegian University of Science and Technology (NTNU)7491TrondheimNorway
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6
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Advanced Characterization of Silicone Oil Droplets in Protein Therapeutics Using Artificial Intelligence Analysis of Imaging Flow Cytometry Data. J Pharm Sci 2020; 109:2996-3005. [DOI: 10.1016/j.xphs.2020.07.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 07/07/2020] [Accepted: 07/07/2020] [Indexed: 12/21/2022]
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7
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L. Almeida Z, M. M. Brito R. Structure and Aggregation Mechanisms in Amyloids. Molecules 2020; 25:molecules25051195. [PMID: 32155822 PMCID: PMC7179426 DOI: 10.3390/molecules25051195] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/17/2020] [Accepted: 02/19/2020] [Indexed: 12/27/2022] Open
Abstract
The aggregation of a polypeptide chain into amyloid fibrils and their accumulation and deposition into insoluble plaques and intracellular inclusions is the hallmark of several misfolding diseases known as amyloidoses. Alzheimer′s, Parkinson′s and Huntington’s diseases are some of the approximately 50 amyloid diseases described to date. The identification and characterization of the molecular species critical for amyloid formation and disease development have been the focus of intense scrutiny. Methods such as X-ray and electron diffraction, solid-state nuclear magnetic resonance spectroscopy (ssNMR) and cryo-electron microscopy (cryo-EM) have been extensively used and they have contributed to shed a new light onto the structure of amyloid, revealing a multiplicity of polymorphic structures that generally fit the cross-β amyloid motif. The development of rational therapeutic approaches against these debilitating and increasingly frequent misfolding diseases requires a thorough understanding of the molecular mechanisms underlying the amyloid cascade. Here, we review the current knowledge on amyloid fibril formation for several proteins and peptides from a kinetic and thermodynamic point of view, the structure of the molecular species involved in the amyloidogenic process, and the origin of their cytotoxicity.
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8
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Karmakar S, Chakraborty S, Gautam S, Chowdhury PK. Exploring the potency of the naturally occurring polyphenol curcumin as a probe for protein aggregation in crowded environments. Int J Biol Macromol 2019; 141:1088-1101. [DOI: 10.1016/j.ijbiomac.2019.09.049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/03/2019] [Accepted: 09/06/2019] [Indexed: 01/12/2023]
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9
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Picking WD, Barta ML. The Tip Complex: From Host Cell Sensing to Translocon Formation. Curr Top Microbiol Immunol 2019; 427:173-199. [PMID: 31218507 DOI: 10.1007/82_2019_171] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Type III secretion systems are used by some Gram-negative bacteria to inject effector proteins into targeted eukaryotic cells for the benefit of the bacterium. The type III secretion injectisome is a complex nanomachine comprised of four main substructures including a cytoplasmic sorting platform, an envelope-spanning basal body, an extracellular needle and an exposed needle tip complex. Upon contact with a host cell, secretion is induced, resulting in the formation of a translocon pore in the host membrane. Translocon formation completes the conduit needed for effector secretion into the host cell. Control of type III secretion occurs in response to environmental signals, with the final signal being host cell contact. Secretion control occurs primarily at two sites-the cytoplasmic sorting platform, which determines secretion hierarchy, and the needle tip complex, which is critical for sensing and responding to environmental signals. The best-characterized injectisomes are those from Yersinia, Shigella and Salmonella species where there is a wealth of information on the tip complex and the two translocator proteins. Of these systems, the best characterized from a secretion regulation standpoint is Shigella. In the Shigella system, the tip complex and the first secreted translocon both contribute to secretion control and, thus, both are considered components of the tip complex. In this review, all three of these type III secretion systems are described with discussion focused on the structure and formation of the injectisome tip complex and what is known of the transition from nascent tip complex to assembled translocon pore.
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Affiliation(s)
- William D Picking
- Department of Pharmaceutical Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, 66047, KS, USA.
| | - Michael L Barta
- Higuchi Biosciences, 2099 Constant Ave., Lawrence, 66047, KS, USA.,Catalent Pharma Solutions, 10245 Hickman Mills Drive, Kansas City, 64137, MO, USA
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10
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Effect of amino acid mutations on the conformational dynamics of amyloidogenic immunoglobulin light-chains: A combined NMR and in silico study. Sci Rep 2017; 7:10339. [PMID: 28871194 PMCID: PMC5583243 DOI: 10.1038/s41598-017-10906-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 08/16/2017] [Indexed: 12/19/2022] Open
Abstract
The conformational dynamics of a pathogenic κ4 human immunoglobulin light-chain variable domain, SMA, associated with AL amyloidosis, were investigated by 15N relaxation dispersion NMR spectroscopy. Compared to a homologous light-chain, LEN, which differs from SMA at eight positions but is non-amyloidogenic in vivo, we find that multiple residues in SMA clustered around the N-terminus and CDR loops experience considerable conformational exchange broadening caused by millisecond timescale protein motions, consistent with a destabilized dimer interface. To evaluate the contribution of each amino acid substitution to shaping the dynamic conformational landscape of SMA, NMR studies were performed for each SMA-like point mutant of LEN followed by in silico analysis for a subset of these proteins. These studies show that a combination of only three mutations located within or directly adjacent to CDR3 loop at the dimer interface, which remarkably include both destabilizing (Q89H and Y96Q) and stabilizing (T94H) mutations, largely accounts for the differences in conformational flexibility between LEN and SMA. Collectively, our studies indicate that a correct combination of stabilizing and destabilizing mutations is key for immunoglobulin light-chains populating unfolded intermediates that result in amyloid formation, and underscore the complex nature of correlations between light-chain conformational flexibility, thermodynamic stability and amyloidogenicity.
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11
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Zhang J, Sandberg A, Wu X, Nyström S, Lindgren M, Konradsson P, Hammarström P. trans-Stilbenoids with Extended Fluorescence Lifetimes for the Characterization of Amyloid Fibrils. ACS OMEGA 2017; 2:4693-4704. [PMID: 31457755 PMCID: PMC6641930 DOI: 10.1021/acsomega.7b00535] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 07/13/2017] [Indexed: 05/29/2023]
Abstract
It was previously reported that two naphthyl-based trans-stilbene probes, (E)-4-(2-(naphthalen-1-yl)vinyl)benzene-1,2-diol (1) and (E)-4-(2-(naphthalen-2-yl)vinyl)benzene-1,2-diol (3), can bind to both native transthyretin (TTR) and misfolded protofibrillar TTR at physiological concentrations, displaying distinct emission maxima bound to the different conformational states (>100 nm difference). To further explore this amyloid probe scaffold to obtain extended fluorescence lifetimes, two new analogues with expanded aromatic ring systems (anthracene and pyrene), (E)-4-(2-(anthracen-2-yl)vinyl)benzene-1,2-diol (4) and (E)-4-(2-(pyren-2-yl)vinyl)benzene-1,2-diol (5), were synthesized employing the palladium-catalyzed Mizoroki-Heck reaction. (E)-4-Styrylbenzene-1,2-diol (2), 3, 4, and 5 were investigated with respect to their photophysical properties in methanol and when bound to insulin, lysozyme, and Aβ1-42 fibrils, including time-resolved fluorescence measurements. In conclusion, 4 and 5 can bind to both native and fibrillar TTR, becoming highly fluorescent. Compounds 2-5 bind specifically to insulin, lysozyme, and Aβ1-42 fibrils with an apparent fluorescence intensity increase and moderate binding affinities. The average fluorescence lifetimes of the probes bound to Aβ1-42 fibrils are 1.3 ns (2), 1.5 ns (3), 5.7 ns (4), and 29.8 ns (5). In summary, the variable aromatic moieties of the para-positioned trans-stilbenoid vinyl-benzene-1,2-diol with benzene, naphthalene, anthracene, and pyrene showed that the extended conjugated systems retained the amyloid targeting properties of the probes. Furthermore, both the anthracene and pyrene moieties extensively enhanced the fluorescence intensity and prolonged lifetimes. These attractive probe properties should improve amyloid detection and characterization by fluorescence-based techniques.
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Affiliation(s)
- Jun Zhang
- IFM-Department
of Chemistry, Linköping University, Linköping 581 83, Sweden
| | - Alexander Sandberg
- IFM-Department
of Chemistry, Linköping University, Linköping 581 83, Sweden
| | - Xiongyu Wu
- IFM-Department
of Chemistry, Linköping University, Linköping 581 83, Sweden
| | - Sofie Nyström
- IFM-Department
of Chemistry, Linköping University, Linköping 581 83, Sweden
| | - Mikael Lindgren
- Department
of Physics, The Norwegian University of
Science and Technology, 7491 Trondheim, Norway
| | - Peter Konradsson
- IFM-Department
of Chemistry, Linköping University, Linköping 581 83, Sweden
| | - Per Hammarström
- IFM-Department
of Chemistry, Linköping University, Linköping 581 83, Sweden
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12
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Correlating the Effects of Antimicrobial Preservatives on Conformational Stability, Aggregation Propensity, and Backbone Flexibility of an IgG1 mAb. J Pharm Sci 2017; 106:1508-1518. [DOI: 10.1016/j.xphs.2017.02.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 02/02/2017] [Accepted: 02/06/2017] [Indexed: 11/23/2022]
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13
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Paikar A, Debnath M, Podder D, Sasmal S, Haldar D. Synthesis and structural investigation of 2-aminomethyl-3-(4-methoxy-phenyl)-propionic acid containing a peptide analogue of the amyloidogenic AS(6–7) sequence: inhibition of fibril formation. Org Biomol Chem 2017; 15:4218-4225. [DOI: 10.1039/c7ob00797c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The incorporation of a β-amino acid, namely 2-aminomethyl-3-(4-methoxy-phenyl)-propionic acid, inhibits amyloid-like fibril formation.
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Affiliation(s)
- Arpita Paikar
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- Mohanpur
- India
| | - Mintu Debnath
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- Mohanpur
- India
| | - Debasish Podder
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- Mohanpur
- India
| | - Supriya Sasmal
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- Mohanpur
- India
| | - Debasish Haldar
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- Mohanpur
- India
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14
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Khan MV, Ishtikhar M, Rabbani G, Zaman M, Abdelhameed AS, Khan RH. Polyols (Glycerol and Ethylene glycol) mediated amorphous aggregate inhibition and secondary structure restoration of metalloproteinase-conalbumin (ovotransferrin). Int J Biol Macromol 2016; 94:290-300. [PMID: 27744055 PMCID: PMC7112414 DOI: 10.1016/j.ijbiomac.2016.10.023] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 10/10/2016] [Indexed: 11/24/2022]
Abstract
Conalbumin aggregates at 65 °C and denaturation occur at above this temperature. The nature of aggregates was identified as amorphous. The polyols inhibits the aggregation of conalbumin via protecting the secondary structure. Glycerol is found to be more protective than ethylene glycol.
Under physical or chemical stress, proteins tend to form aggregates either highly ordered (amyloid) or unordered (amorphous) causing many pathological disorders in human and loss of proteins functionality in both laboratory conditions and industries during production and storage at commercial level. We investigated the effect of increasing temperature on Conalbumin (CA) and induced aggregation at 65 °C. The enhanced Thioflavin T (ThT) and ANS (1-anilinonaphtalene 8-sulfonic acid) fluorescence intensity, show no shift on Congo red binding, additionally, transmission and scanning electron microscopy (TEM) (SEM) reveal amorphous morphology of the aggregate. Our investigation clearly demonstrated that polyols namely Glycerol (GL) and Ethylene glycol (EG) are so staunch to inhibit amorphous aggregates via restoring secondary conformation. Addition of polyols (15% GL and 35% EG) significantly decrease the turbidity, Rayleigh scattering ThT and ANS fluorescence intensity. The dynamic light scattering (DLS) data show that hydrodynamic radii (Rh) of the aggregates is ∼20 times higher than native CA while nearly similar for GL and EG protected CA due to condensation of core size with little difference.
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Affiliation(s)
- Mohsin Vahid Khan
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Mohd Ishtikhar
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Gulam Rabbani
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Masihuz Zaman
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Ali Saber Abdelhameed
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Rizwan Hasan Khan
- Molecular Biophysics and Biophysical Chemistry Group, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India.
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15
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Zaman M, Zakariya SM, Nusrat S, Khan MV, Qadeer A, Ajmal MR, Khan RH. Surfactant-mediated amyloidogenesis behavior of stem bromelain; a biophysical insight. J Biomol Struct Dyn 2016; 35:1407-1419. [DOI: 10.1080/07391102.2016.1185040] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Masihuz Zaman
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, UP 202002, India
| | - Syed Mohammad Zakariya
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, UP 202002, India
| | - Saima Nusrat
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, UP 202002, India
| | - Mohsin Vahid Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, UP 202002, India
| | - Atiyatul Qadeer
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, UP 202002, India
| | - Mohammad Rehan Ajmal
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, UP 202002, India
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, UP 202002, India
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16
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Al-Thabaiti SA, Aazam ES, Khan Z, Bashir O. Aggregation of Congo red with surfactants and Ag-nanoparticles in an aqueous solution. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 156:28-35. [PMID: 26641283 DOI: 10.1016/j.saa.2015.11.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 11/13/2015] [Accepted: 11/18/2015] [Indexed: 06/05/2023]
Abstract
Self aggregation, sorption, and interaction of Congo red, with cetyltrimethylammonium bromide (CTAB), sodium dodecylsulfate (SDS), Ag(+) ions and silver nanoparticles have been determined spectrophotometrically. Congo red self-aggregation was identified from UV-visible spectra due to the shrinkage in an absorption band at 495 nm. The shape of the absorbance spectrum changed entirely with increasing [Congo red] but wavelength maxima remain unchanged. The molar absorptivity was found to be 9804 mol(-1) dm(3) cm(-1) at 495 nm. Absorption spectra of Congo red with Ag(+) ions show an isosbestic point. The complex formation constant and difference in absorption coefficients were found to be 8.5 × 10(4) mol(-1) dm(3) and 11,764 mol(-1) dm(3) cm(-1), respectively. Silver nano-particles could not be used for the catalytic degradation of Congo red because it results in the formation of a strong complex with them. Sodium dodecylsulfate did not show any significant interaction with this dye. Congo red was also used as a probe to determine the critical micellar concentration of CTAB.
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Affiliation(s)
- Shaeel Ahmed Al-Thabaiti
- Chemistry Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Elham Shafik Aazam
- Chemistry Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Zaheer Khan
- Chemistry Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia.
| | - Ommer Bashir
- Nanoscience Research Laboratory, Department of Chemistry, Jamia Millia Islamia (Central University), New Delhi 110025, India
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17
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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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18
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Sequence-dependent abnormal aggregation of human Tau fragment in an inducible cell model. Biochim Biophys Acta Mol Basis Dis 2015; 1852:1561-73. [DOI: 10.1016/j.bbadis.2015.04.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 03/27/2015] [Accepted: 04/14/2015] [Indexed: 11/15/2022]
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19
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Young LM, Saunders JC, Mahood RA, Revill CH, Foster RJ, Tu LH, Raleigh DP, Radford SE, Ashcroft AE. Screening and classifying small-molecule inhibitors of amyloid formation using ion mobility spectrometry-mass spectrometry. Nat Chem 2014; 7:73-81. [PMID: 25515893 PMCID: PMC4280571 DOI: 10.1038/nchem.2129] [Citation(s) in RCA: 223] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 11/05/2014] [Indexed: 12/28/2022]
Abstract
The search for therapeutic agents which bind specifically to precursor protein conformations and inhibit amyloid assembly is an important challenge. Identifying such inhibitors is difficult since many protein precursors of aggregation are partially folded or intrinsically disordered, ruling out structure-based design. Furthermore, inhibitors can act by a variety of mechanisms, including specific or non-specific binding, as well as colloidal inhibition. Here we report a high throughput method based on ion mobility spectrometry-mass spectrometry (IMS-MS) that is capable of rapidly detecting small molecules that bind to amyloid precursors, identifying the interacting protein species, and defining the mode of inhibition. Using this method we have classified a variety of small molecules that are potential inhibitors of human islet amyloid polypeptide (hIAPP) aggregation or amyloid-beta 1-40 (Aβ40) aggregation as either specific, non-specific, colloidal or non-interacting. We also demonstrate the ability of IMS-MS to screen for inhibitory small molecules in a 96-well plate format and use this to discover a new inhibitor of hIAPP amyloid assembly.
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Affiliation(s)
- Lydia M Young
- Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, UK.,School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK
| | - Janet C Saunders
- Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, UK.,School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK
| | - Rachel A Mahood
- Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, UK.,School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK
| | - Charlotte H Revill
- Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, UK.,School of Chemistry, University of Leeds, LS2 9JT, UK
| | - Richard J Foster
- Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, UK.,School of Chemistry, University of Leeds, LS2 9JT, UK
| | - Ling-Hsien Tu
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Daniel P Raleigh
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, UK.,School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK
| | - Alison E Ashcroft
- Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, UK.,School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK
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20
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Saluja A, Sadineni V, Mungikar A, Nashine V, Kroetsch A, Dahlheim C, Rao VM. Significance of Unfolding Thermodynamics for Predicting Aggregation Kinetics: A Case Study on High Concentration Solutions of a Multi-Domain Protein. Pharm Res 2014; 31:1575-87. [DOI: 10.1007/s11095-013-1263-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 12/09/2013] [Indexed: 11/29/2022]
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21
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Khan JM, Abdulrehman SA, Zaidi FK, Gourinath S, Khan RH. Hydrophobicity alone can not trigger aggregation in protonated mammalian serum albumins. Phys Chem Chem Phys 2014; 16:5150-61. [DOI: 10.1039/c3cp54941k] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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22
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Ramirez-Alvarado M. Amyloid formation in light chain amyloidosis. Curr Top Med Chem 2013; 12:2523-33. [PMID: 23339305 DOI: 10.2174/1568026611212220007] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 09/10/2012] [Accepted: 09/12/2012] [Indexed: 01/16/2023]
Abstract
Light chain amyloidosis is one of the unique examples within amyloid diseases where the amyloidogenic precursor is a protein that escapes the quality control machinery and is secreted from the cells to be circulated in the bloodstream. The immunoglobulin light chains are produced by an abnormally proliferative monoclonal population of plasma cells that under normal conditions produce immunoglobulin molecules such as IgG, IgM or IgA. Once the light chains are in circulation, the proteins misfold and deposit as amyloid fibrils in numerous tissues and organs, causing organ failure and death. While there is a correlation between the thermodynamic stability of the protein and the kinetics of amyloid formation, we have recently found that this correlation applies within a thermodynamic range, and it is only a helpful correlation when comparing mutants from the same protein. Light chain amyloidosis poses unique challenges because each patient has a unique protein sequence as a result of the selection of a germline gene and the incorporation of somatic mutations. The exact location of the misfolding process is unknown as well as the full characterization of all of the toxic species populated during the amyloid formation process in light chain amyloidosis.
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Affiliation(s)
- Marina Ramirez-Alvarado
- Department of Biochemistry and Molecular Biology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA.
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23
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Filipe V, Hawe A, Carpenter JF, Jiskoot W. Analytical approaches to assess the degradation of therapeutic proteins. Trends Analyt Chem 2013. [DOI: 10.1016/j.trac.2013.05.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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24
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Skeby KK, Sørensen J, Schiøtt B. Identification of a Common Binding Mode for Imaging Agents to Amyloid Fibrils from Molecular Dynamics Simulations. J Am Chem Soc 2013; 135:15114-28. [DOI: 10.1021/ja405530p] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Katrine Kirkeby Skeby
- The Center
for Insoluble Protein Structures (inSPIN), the Interdisciplinary
Nanoscience Center (iNANO), and Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C
| | - Jesper Sørensen
- The Center
for Insoluble Protein Structures (inSPIN), the Interdisciplinary
Nanoscience Center (iNANO), and Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C
| | - Birgit Schiøtt
- The Center
for Insoluble Protein Structures (inSPIN), the Interdisciplinary
Nanoscience Center (iNANO), and Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C
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25
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Gerson JE, Kayed R. Formation and propagation of tau oligomeric seeds. Front Neurol 2013; 4:93. [PMID: 23882255 PMCID: PMC3713404 DOI: 10.3389/fneur.2013.00093] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 07/01/2013] [Indexed: 12/14/2022] Open
Abstract
Tau misfolding and aggregation leads to the formation of neurofibrillary tangles (NFTs), which have long been considered one of the main pathological hallmarks for numerous neurodegenerative diseases known as tauopathies, including Alzheimer’s Disease (AD) and Parkinson’s Disease (PD). However, recent studies completed both in vitro and in vivo suggest that intermediate forms of tau, known as tau oligomers, between the monomeric form and NFTs are the true toxic species in disease and the best targets for anti-tau therapies. However, the exact mechanism by which the spread of pathology occurs is unknown. Evidence suggests that tau oligomers may act as templates for the misfolding of native tau, thereby seeding the spread of the toxic forms of the protein. Recently, researchers have reported the ability of tau oligomers to enter and exit cells, propagating from disease-affected regions to unaffected areas. While the mechanism by which the spreading of misfolded tau occurs has yet to be elucidated, there are a few different models which have been proposed, including cell membrane stress and pore-formation, endocytosis and exocytosis, and non-traditional secretion of protein not enclosed by a membrane. Coming to an understanding of how toxic tau species seed and spread through the brain will be crucial to finding effective treatments for neurodegenerative tauopathies.
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Affiliation(s)
- Julia E Gerson
- George P. and Cynthia Woods Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch , Galveston, TX , USA ; Department of Neurology, University of Texas Medical Branch , Galveston, TX , USA ; Department of Neuroscience and Cell Biology, University of Texas Medical Branch , Galveston, TX , USA
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26
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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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27
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Stopa B, Jagusiak A, Konieczny L, Piekarska B, Rybarska J, Zemanek G, Król M, Piwowar P, Roterman I. The use of supramolecular structures as protein ligands. J Mol Model 2013; 19:4731-40. [PMID: 23296569 PMCID: PMC3825278 DOI: 10.1007/s00894-012-1744-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2012] [Accepted: 12/17/2012] [Indexed: 11/30/2022]
Abstract
Congo red dye as well as other eagerly self-assembling organic molecules which form rod-like or ribbon-like supramolecular structures in water solutions, appears to represent a new class of protein ligands with possible wide-ranging medical applications. Such molecules associate with proteins as integral clusters and preferentially penetrate into areas of low molecular stability. Abnormal, partly unfolded proteins are the main binding target for such ligands, while well packed molecules are generally inaccessible. Of particular interest is the observation that local susceptibility for binding supramolecular ligands may be promoted in some proteins as a consequence of function-derived structural changes, and that such complexation may alter the activity profile of target proteins. Examples are presented in this paper.
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Affiliation(s)
- Barbara Stopa
- Medical Biochemistry, Jagiellonian University - Medical College, Kopernika 7, 31-034, Kraków, Poland
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28
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Huy PDQ, Yu YC, Ngo ST, Thao TV, Chen CP, Li MS, Chen YC. In silico and in vitro characterization of anti-amyloidogenic activity of vitamin K3 analogues for Alzheimer's disease. Biochim Biophys Acta Gen Subj 2013; 1830:2960-9. [PMID: 23295971 DOI: 10.1016/j.bbagen.2012.12.026] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 12/19/2012] [Accepted: 12/21/2012] [Indexed: 11/29/2022]
Abstract
BACKGROUND Aggregation of amyloid-beta (Aβ) has been proposed as the main cause of Alzheimer's disease (AD). Vitamin K deficiency has been linked to the pathogenesis of AD. Therefore, 15 synthesized vitamin K3 (VK3) analogues were studied for their anti-amyloidogenic activity. METHODS Biological and spectroscopic assays were used to characterize the effect of VK3 analogues on amyloidogenic properties of Aβ, such as aggregation, free radical formation, and cell viability. Molecular dynamics simulation was used to calculate the binding affinity and mode of VK3 analogue binding to Aβ. RESULTS Both numerical and experimental results showed that several VK3 analogues, including VK3-6, VK3-8, VK3-9, VK3-10, and VK3-224 could effectively inhibit Aβ aggregation and conformational conversion. The calculated inhibition constants were in the μM range for VK3-10, VK3-6, and VK3-9 which was similar to the IC50 of curcumin. Cell viability assays indicated that VK3-9 could effectively reduce free radicals and had a protective effect on cytotoxicity induced by Aβ. CONCLUSIONS The results clearly demonstrated that VK3 analogues could effectively inhibit Aβ aggregation and protect cells against Aβ induced toxicity. Modified VK3 analogues can possibly be developed as effective anti-amyloidogenic drugs for the treatment of AD. GENERAL SIGNIFICANCE VK3 analogues effectively inhibit Aβ aggregation and are highly potent as anti-amyloidogenic drugs for therapeutic treatment of AD.
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Affiliation(s)
- Pham Dinh Quoc Huy
- Institute for Computational Science and Technology, 6 Quarter, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Viet Nam
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29
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Maity S, Kumar R, Maity SK, Jana P, Bera S, Haldar D. Synthesis and study of 2-acetyl amino-3-[4-(2-amino-5-sulfo-phenylazo)-phenyl]-propionic acid: a new class of inhibitor for hen egg white lysozyme amyloidogenesis. MEDCHEMCOMM 2013. [DOI: 10.1039/c2md20236k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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30
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Lee YH, Goto Y. Kinetic intermediates of amyloid fibrillation studied by hydrogen exchange methods with nuclear magnetic resonance. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:1307-23. [DOI: 10.1016/j.bbapap.2012.07.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Revised: 07/24/2012] [Accepted: 07/26/2012] [Indexed: 01/28/2023]
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31
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Jameson LP, Smith NW, Dzyuba SV. Dye-binding assays for evaluation of the effects of small molecule inhibitors on amyloid (aβ) self-assembly. ACS Chem Neurosci 2012; 3:807-19. [PMID: 23173064 DOI: 10.1021/cn300076x] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 08/06/2012] [Indexed: 01/07/2023] Open
Abstract
Dye-binding assays, such as those utilizing Congo red and thioflavin T, are among the most widely used tools to probe the aggregation of amyloidogenic biomolecules and for the evaluation of small molecule inhibitors of amyloid aggregation and fibrillization. A number of recent reports have indicated that these dye-binding assays could be prone to false positive effects when assessing inhibitors' potential toward Aβ peptides, species involved in Alzheimer's disease. Specifically, this review focuses on the application of thioflavin T for determining the efficiency of small molecule inhibitors of Aβ aggregation and addresses potential reasons that might be associated with the false positive effects in an effort to increase reliability of dye-binding assays.
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Affiliation(s)
- Laramie P. Jameson
- Department of Chemistry, Texas Christian University, Fort Worth, Texas 76129, United States
| | - Nicholas W. Smith
- Department of Chemistry, Texas Christian University, Fort Worth, Texas 76129, United States
| | - Sergei V. Dzyuba
- Department of Chemistry, Texas Christian University, Fort Worth, Texas 76129, United States
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32
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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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Maltsev AS, Grishaev A, Bax A. Monomeric α-synuclein binds Congo Red micelles in a disordered manner. Biochemistry 2012; 51:631-42. [PMID: 22242826 PMCID: PMC3260784 DOI: 10.1021/bi201435d] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
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The histological dye Congo Red (CR) previously has been shown to inhibit α-synuclein (aS) fibrillation, but the mode of this inhibition remained unclear. Because of favorable exchange kinetics, interaction between CR and aS lends itself to a detailed nuclear magnetic resonance study, and relaxation dispersion measurements yield the bound fraction and time scales for the interaction of aS with CR. We find that at pH 6, CR exists as a micelle, and at a CR:aS molar ratio of ∼1, only a small fraction of aS (∼2%) is bound to these micelles. Rapid exchange (kex ∼ 3000 s–1) between the free and CR-bound states broadens and strongly attenuates resonances of aS by two processes: a magnetic field-dependent contribution, caused by the chemical shift difference between the two states, and a nearly field-independent contribution caused by slower tumbling of aS bound to the CR micelle. The salt dependence of the interaction suggests a predominantly electrostatic mechanism for the 60 N-terminal residues, while the weaker interaction between residues 61–100 and CR is mostly hydrophobic. Chemical shift and transferred NOE data indicate that aS becomes slightly more helical but remains largely disordered when bound to CR. Results indicate that inhibition of fibril formation does not result from binding of CR to free aS and, therefore, must result from interaction of aS fibrils or protofibrils with CR micelles.
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Affiliation(s)
- Alexander S Maltsev
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
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34
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Abelein A, Bolognesi B, Dobson CM, Gräslund A, Lendel C. Hydrophobicity and conformational change as mechanistic determinants for nonspecific modulators of amyloid β self-assembly. Biochemistry 2011; 51:126-37. [PMID: 22133042 DOI: 10.1021/bi201745g] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The link between many neurodegenerative disorders, including Alzheimer's and Parkinson's diseases, and the aberrant folding and aggregation of proteins has prompted a comprehensive search for small organic molecules that have the potential to inhibit such processes. Although many compounds have been reported to affect the formation of amyloid fibrils and/or other types of protein aggregates, the mechanisms by which they act are not well understood. A large number of compounds appear to act in a nonspecific way affecting several different amyloidogenic proteins. We describe here a detailed study of the mechanism of action of one representative compound, lacmoid, in the context of the inhibition of the aggregation of the amyloid β-peptide (Aβ) associated with Alzheimer's disease. We show that lacmoid binds Aβ(1-40) in a surfactant-like manner and counteracts the formation of all types of Aβ(1-40) and Aβ(1-42) aggregates. On the basis of these and previous findings, we are able to rationalize the molecular mechanisms of action of nonspecific modulators of protein self-assembly in terms of hydrophobic attraction and the conformational preferences of the polypeptide.
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Affiliation(s)
- Axel Abelein
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius v. 16, SE-106 91 Stockholm, Sweden
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Mahalka AK, Maury CPJ, Kinnunen PKJ. 1-Palmitoyl-2-(9′-oxononanoyl)-sn-glycero-3-phosphocholine, an Oxidized Phospholipid, Accelerates Finnish Type Familial Gelsolin Amyloidosis in Vitro. Biochemistry 2011; 50:4877-89. [DOI: 10.1021/bi200195s] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ajay K. Mahalka
- Helsinki Biophysics and Biomembrane Group, Department of Biomedical Engineering and Computational Science, Aalto University, Espoo, Finland
| | | | - Paavo K. J. Kinnunen
- Helsinki Biophysics and Biomembrane Group, Department of Biomedical Engineering and Computational Science, Aalto University, Espoo, Finland
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Tao K, Wang J, Zhou P, Wang C, Xu H, Zhao X, Lu JR. Self-assembly of short aβ(16-22) peptides: effect of terminal capping and the role of electrostatic interaction. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:2723-2730. [PMID: 21309606 DOI: 10.1021/la1034273] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We report the characterization of self-assembly of two short β-amyloid (Aβ) peptides (16-22), KLVFFAE and Ac-KLVFFAE-NH2, focusing on examining the effect of terminal capping. At pH 2.0, TEM and AFM imaging revealed that the uncapped peptide self-assembled into long, straight, and unbranched nanofibrils with a diameter of 3.8 ± 1.0 nm while the capped one formed nanotapes with a width of 70.0 ± 25.0 nm. CD analysis indicated the formation of β-sheet structures in both aggregated systems, but the characteristic CD peaks were less intense and less red-shifted for the uncapped than the capped one, indicative of weaker hydrogen bonding and weaker π-π stacking. Fluorescence and rheological measurements also confirmed stronger intermolecular attraction associated with the capped nanotapes. At acidic pH 2, each uncapped KLVFFAE molecule carries two positive charges at the N-terminus, and the strong electrostatic repulsion favors interfacial curving and twisting within the β-sheet, causing weakening of hydrogen bonds and π-π stacking. In contrast, capping reduces the charge by half, and intermolecular electrostatic repulsion is drastically reduced. As a result, the lateral attraction of β-sheets favors stronger lamellar structuring, leading to the formation of rather flat nanotapes. Flat tapes with similar morphological structure were also formed by the capped peptide at pH 12.0 where the charge on the capping end was reversed. This study has thus demonstrated how self-assembled nanostructures of small peptides can be manipulated through simple molecular structure design and tuning of electrostatic interaction.
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Affiliation(s)
- Kai Tao
- Centre for Bioengineering and Biotechnology, China University of Petroleum (East China) , 66 Changjiang West Road, Qingdao 266555, China
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37
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A role for amyloid in cell aggregation and biofilm formation. PLoS One 2011; 6:e17632. [PMID: 21408122 PMCID: PMC3050909 DOI: 10.1371/journal.pone.0017632] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Accepted: 02/04/2011] [Indexed: 01/09/2023] Open
Abstract
Cell adhesion molecules in Saccharomyces cerevisiae and Candida albicans contain amyloid-forming sequences that are highly conserved. We have now used site-specific mutagenesis and specific peptide perturbants to explore amyloid-dependent activity in the Candida albicans adhesin Als5p. A V326N substitution in the amyloid-forming region conserved secondary structure and ligand binding, but abrogated formation of amyloid fibrils in soluble Als5p and reduced cell surface thioflavin T fluorescence. When displayed on the cell surface, Als5p with this substitution prevented formation of adhesion nanodomains and formation of large cellular aggregates and model biofilms. In addition, amyloid nanodomains were regulated by exogenous peptides. An amyloid-forming homologous peptide rescued aggregation and biofilm activity of Als5pV326N cells, and V326N substitution peptide inhibited aggregation and biofilm activity in Als5pWT cells. Therefore, specific site mutation, inhibition by anti-amyloid peturbants, and sequence-specificity of pro-amyloid and anti-amyloid peptides showed that amyloid formation is essential for nanodomain formation and activation.
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Maity S, Kumar P, Haldar D. An amyloid-like fibril-forming supramolecular cross-β-structure of a model peptide: a crystallographic insight. Org Biomol Chem 2011; 9:3787-91. [DOI: 10.1039/c0ob01033b] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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Pedersen MØ, Mikkelsen K, Behrens MA, Pedersen JS, Enghild JJ, Skrydstrup T, Malmendal A, Nielsen NC. NMR Reveals Two-Step Association of Congo Red to Amyloid β in Low-Molecular-Weight Aggregates. J Phys Chem B 2010; 114:16003-10. [DOI: 10.1021/jp108035y] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marie Ø. Pedersen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, and Department of Molecular Biology, Aarhus University, Denmark
| | - Katrine Mikkelsen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, and Department of Molecular Biology, Aarhus University, Denmark
| | - Manja A. Behrens
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, and Department of Molecular Biology, Aarhus University, Denmark
| | - Jan S. Pedersen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, and Department of Molecular Biology, Aarhus University, Denmark
| | - Jan J. Enghild
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, and Department of Molecular Biology, Aarhus University, Denmark
| | - Troels Skrydstrup
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, and Department of Molecular Biology, Aarhus University, Denmark
| | - Anders Malmendal
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, and Department of Molecular Biology, Aarhus University, Denmark
| | - Niels Chr. Nielsen
- Center for Insoluble Protein Structures (inSPIN), Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, and Department of Molecular Biology, Aarhus University, Denmark
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von Berlepsch H, Brandenburg E, Koksch B, Böttcher C. Peptide adsorption to cyanine dye aggregates revealed by cryo-transmission electron microscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:11452-11460. [PMID: 20364866 DOI: 10.1021/la100944d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The binding interaction between aggregates of the 5-chloro-2-[[5-chloro-3-(3-sulfopropyl)-3H-benzothiazol-2-ylidene]methyl]-3-(3-sulfopropyl)benzothiazolium hydroxide inner salt ammonium salt (CD-1) and alpha-helix, as well as beta-sheet forming de novo designed peptides, was investigated by absorption spectroscopy, circular dichroism spectroscopy, and cryogenic transmission electron microscopy. Both pure dye and pure peptides self-assembled into well-defined supramolecular assemblies in acetate buffer at pH = 4. The dye formed sheetlike and tubular H- and J-aggregates and the peptides alpha-helical coiled-coil assemblies or beta-sheet rich fibrils. After mixing dye and peptide solutions, tubular aggregates with an unusual ultrastructure were found, most likely due to the decoration of dye tubes with monolayers of peptide assemblies based on the strong electrostatic attraction between the oppositely charged species. There was neither indication of a transfer of chirality from the peptides to the dye aggregates nor the opposite effect of a structural transfer from dye aggregates onto the peptides secondary structure.
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Affiliation(s)
- Hans von Berlepsch
- Forschungszentrum für Elektronenmikroskopie, Institut für Chemie und Biochemie, Freie Universität Berlin, Fabeckstrasse 36 a, D-14195 Berlin, Germany.
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41
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Yan C, Pattani V, Tunnell JW, Ren P. Temperature-induced unfolding of epidermal growth factor (EGF): insight from molecular dynamics simulation. J Mol Graph Model 2010; 29:2-12. [PMID: 20466569 DOI: 10.1016/j.jmgm.2010.03.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Revised: 03/15/2010] [Accepted: 03/29/2010] [Indexed: 10/19/2022]
Abstract
Thermal disruption of protein structure and function is a potentially powerful therapeutic vehicle. With the emerging nanoparticle-targeting and femtosecond laser technology, it is possible to deliver heating locally to specific molecules. It is therefore important to understand how fast a protein can unfold or lose its function at high temperatures, such as near the water boiling point. In this study, the thermal damage of EGF was investigated by combining the replica exchange (136 replicas) and conventional molecular dynamics simulations. The REMD simulation was employed to rigorously explore the free-energy landscape of EGF unfolding. Interestingly, besides the native and unfolded states, we also observed a distinct molten globule (MG) state that retained substantial amount of native contacts. Based on the understanding that which the unfolding of EGF is a three-state process, we have examined the unfolding kinetics of EGF (N-->MG and MG-->D) with multiple 20-ns conventional MD simulations. The Arrhenius prefactors and activation energy barriers determined from the simulation are within the range of previously studied proteins. In contrast to the thermal damage of cells and tissues which take place on the time scale of seconds to hours at relatively low temperatures, the denaturation of proteins occur in nanoseconds when the temperature of heat bath approaches the boiling point.
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Affiliation(s)
- Chunli Yan
- Department of Biomedical Engineering, University of Texas, Austin, TX 78712, USA
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42
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Groenning M. Binding mode of Thioflavin T and other molecular probes in the context of amyloid fibrils-current status. J Chem Biol 2010; 3:1-18. [PMID: 19693614 PMCID: PMC2816742 DOI: 10.1007/s12154-009-0027-5] [Citation(s) in RCA: 441] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Accepted: 08/04/2009] [Indexed: 10/20/2022] Open
Abstract
Because understanding amyloid fibrillation in molecular detail is essential for development of strategies to control amyloid formation and overcome neurodegenerative disorders, increased understanding of present molecular probes as well as development of new probes are of utmost importance. To date, the binding modes of these molecular probes to amyloid fibrils are by no means adequately described or understood, and the large number of studies on Thioflavin T (ThT) and Congo Red (CR) binding have resulted in models that are incomplete and conflicting. Different types of binding sites are likely to be present in amyloid fibrils with differences in binding modes. ThT may bind in channels running parallel to the long axis of the fibril. In the channels, ThT may bind in either a monomeric or dimeric form of which the molecular conformation is likely to be planar. CR may bind in grooves formed along the β-sheets as a planar molecule in either a monomeric or supramolecular form.
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Affiliation(s)
- Minna Groenning
- Department of Pharmaceutics and Analytical Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- IFM, Department of Chemistry, Linköping University, 581 83 Linköping, Sweden
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Dutt A, Spencer E, Howard J, Pramanik A. Studies of Amyloid-Like Fibrillogenesis throughβ-Sheet-Mediated Self-Assembly of Short Synthetic Peptides. Chem Biodivers 2010; 7:363-75. [DOI: 10.1002/cbdv.200900050] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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44
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Chang E, Honson NS, Bandyopadhyay B, Funk KE, Jensen JR, Kim S, Naphade S, Kuret J. Modulation and detection of tau aggregation with small-molecule ligands. Curr Alzheimer Res 2009; 6:409-14. [PMID: 19874263 DOI: 10.2174/156720509789207976] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2008] [Accepted: 01/16/2009] [Indexed: 11/22/2022]
Abstract
Recent results from high-throughput and other screening approaches reveal that small molecules can directly interact with recombinant full-length tau monomers and fibrillar tau aggregates in three distinct modes. First, in the high concentration regime (>10 micromolar), certain anionic molecules such as Congo red efficiently promote tau filament formation through a nucleation-elongation mechanism involving a dimeric nucleus and monomer-mediated elongation. These compounds are useful for modeling tau aggregation in vitro and in biological models. Second, in the low concentration regime (<1 micromolar), other ligands, including cyanine dyes, display aggregation antagonist activity. Compounds that can prevent or reverse fibrillization are candidate modifiers of disease pathology. Finally, certain compounds bind mature tau fibrils with varying affinities at multiple binding sites without modulating the aggregation reaction. For some ligands, >10-fold selectivity for tau aggregates relative to filaments composed of beta-amyloid or alpha-synuclein can be demonstrated at the level of binding affinity. Together these observations suggest that small-molecules have utility for interrogating the tau aggregation pathway, for inhibiting neuritic lesion formation, and for selective pre-mortem detection of neurofibrillary lesions through whole brain imaging.
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Affiliation(s)
- Edward Chang
- Center for Molecular Neurobiology, Department of Molecular and Cellular Biochemistry, The Ohio State University College of Medicine, Columbus, Ohio 43210, USA
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Lendel C, Bertoncini CW, Cremades N, Waudby CA, Vendruscolo M, Dobson CM, Schenk D, Christodoulou J, Toth G. On the Mechanism of Nonspecific Inhibitors of Protein Aggregation: Dissecting the Interactions of α-Synuclein with Congo Red and Lacmoid. Biochemistry 2009; 48:8322-34. [DOI: 10.1021/bi901285x] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Christofer Lendel
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Carlos W. Bertoncini
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Nunilo Cremades
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Christopher A. Waudby
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Christopher M. Dobson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Dale Schenk
- Elan Pharmaceuticals, 700 Gateway Boulevard, South San Francisco, California 94080
| | - John Christodoulou
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
- Department of Structural & Molecular Biology, University College London, Gower Street, London WC1E 6BT, U.K
| | - Gergely Toth
- Elan Pharmaceuticals, 700 Gateway Boulevard, South San Francisco, California 94080
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Hamill AC, Lee CT. Photocontrol of β-Amyloid Peptide (1−40) Fibril Growth in the Presence of a Photosurfactant. J Phys Chem B 2009; 113:6164-72. [DOI: 10.1021/jp8080113] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Andrea C. Hamill
- Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1211
| | - C. Ted Lee
- Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089-1211
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47
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Distinct Activities of Escherichia coli Small Heat Shock Proteins IbpA and IbpB Promote Efficient Protein Disaggregation. J Mol Biol 2009; 386:178-89. [DOI: 10.1016/j.jmb.2008.12.009] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2008] [Revised: 11/20/2008] [Accepted: 12/04/2008] [Indexed: 11/21/2022]
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48
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Blancas-Mejia LM, Tellez LA, del Pozo-Yauner L, Becerril B, Sanchez-Ruiz JM, Fernandez-Velasco DA. Thermodynamic and kinetic characterization of a germ line human lambda6 light-chain protein: the relation between unfolding and fibrillogenesis. J Mol Biol 2009; 386:1153-66. [PMID: 19154739 DOI: 10.1016/j.jmb.2008.12.069] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Revised: 11/21/2008] [Accepted: 12/21/2008] [Indexed: 11/16/2022]
Abstract
Proteins encoded by the gene segment 6a of the lambda variable light-chain repertoire are strongly associated with amyloid deposition. 6aJL2 is a model protein constructed with the predicted sequences encoded by the 6a and JL2 germ line genes. In this work, we characterized the urea- and temperature-induced unfolding of 6aJL2. In the short time scale, spectroscopic, hydrodynamic and calorimetric experiments were compatible with a two-state transition. Furthermore, DeltaG, m and the midpoint urea concentration obtained from equilibrium experiments were compatible with those obtained from kinetic experiments. Since fibril formation is a slow process, samples were also incubated for longer times. After incubation for several hours at 37 degrees C, spectroscopic, hydrodynamic and calorimetric experiments revealed the presence of a partially unfolded off-pathway intermediate around the midpoint urea concentration (1.5-3.0 M urea). In vitro fibrillogenesis assays show that the maximum growth rate for fibril formation and the minimum lag time were obtained at urea concentrations where the partially unfolded state was populated (2.5 M urea at 37 degrees C). This indicates that this partially unfolded state is critical for in vitro fibril formation. Concentration-dependent kinetics and hydrodynamic properties of the intermediate were consistent with a soluble oligomeric state. The intermediate is formed around the midpoint urea concentration, where the native and unfolded states are equally populated and their rate of interconversion is the slowest. This situation may promote the slow accumulation of an intermediate state that is prone to aggregate.
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Affiliation(s)
- Luis M Blancas-Mejia
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica Facultad de Medicina, Universidad Nacional Autónoma de México, Apartado Postal 70-159 D.F. 04510 México
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Hawe A, Sutter M, Jiskoot W. Extrinsic fluorescent dyes as tools for protein characterization. Pharm Res 2008; 25:1487-99. [PMID: 18172579 PMCID: PMC2440933 DOI: 10.1007/s11095-007-9516-9] [Citation(s) in RCA: 869] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2007] [Accepted: 12/05/2007] [Indexed: 11/16/2022]
Abstract
Noncovalent, extrinsic fluorescent dyes are applied in various fields of protein analysis, e.g. to characterize folding intermediates, measure surface hydrophobicity, and detect aggregation or fibrillation. The main underlying mechanisms, which explain the fluorescence properties of many extrinsic dyes, are solvent relaxation processes and (twisted) intramolecular charge transfer reactions, which are affected by the environment and by interactions of the dyes with proteins. In recent time, the use of extrinsic fluorescent dyes such as ANS, Bis-ANS, Nile Red, Thioflavin T and others has increased, because of their versatility, sensitivity and suitability for high-throughput screening. The intention of this review is to give an overview of available extrinsic dyes, explain their spectral properties, and show illustrative examples of their various applications in protein characterization.
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Affiliation(s)
- Andrea Hawe
- Division of Drug Delivery Technology, Leiden/Amsterdam Center for Drug Research, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Marc Sutter
- Division of Drug Delivery Technology, Leiden/Amsterdam Center for Drug Research, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
- Novartis Pharma AG, WSJ-316.4.14, CH-4056 Basel, Switzerland
| | - Wim Jiskoot
- Division of Drug Delivery Technology, Leiden/Amsterdam Center for Drug Research, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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50
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Carazzone C, Colombo R, Quaglia M, Mangione P, Raimondi S, Giorgetti S, Caccialanza G, Bellotti V, De Lorenzi E. Sulfonated molecules that bind a partially structured species of β2-microglobulin also influence refolding and fibrillogenesis. Electrophoresis 2008; 29:1502-10. [DOI: 10.1002/elps.200700677] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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