1
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Olgenblum GI, Hutcheson BO, Pielak GJ, Harries D. Protecting Proteins from Desiccation Stress Using Molecular Glasses and Gels. Chem Rev 2024; 124:5668-5694. [PMID: 38635951 PMCID: PMC11082905 DOI: 10.1021/acs.chemrev.3c00752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 02/18/2024] [Accepted: 02/22/2024] [Indexed: 04/20/2024]
Abstract
Faced with desiccation stress, many organisms deploy strategies to maintain the integrity of their cellular components. Amorphous glassy media composed of small molecular solutes or protein gels present general strategies for protecting against drying. We review these strategies and the proposed molecular mechanisms to explain protein protection in a vitreous matrix under conditions of low hydration. We also describe efforts to exploit similar strategies in technological applications for protecting proteins in dry or highly desiccated states. Finally, we outline open questions and possibilities for future explorations.
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Affiliation(s)
- Gil I. Olgenblum
- Institute
of Chemistry, Fritz Haber Research Center, and The Harvey M. Krueger
Family Center for Nanoscience & Nanotechnology, The Hebrew University, Jerusalem 9190401, Israel
| | - Brent O. Hutcheson
- Department
of Chemistry, University of North Carolina
at Chapel Hill (UNC-CH), Chapel
Hill, North Carolina 27599, United States
| | - Gary J. Pielak
- Department
of Chemistry, University of North Carolina
at Chapel Hill (UNC-CH), Chapel
Hill, North Carolina 27599, United States
- Department
of Chemistry, Department of Biochemistry & Biophysics, Integrated
Program for Biological & Genome Sciences, Lineberger Comprehensive
Cancer Center, University of North Carolina
at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Daniel Harries
- Institute
of Chemistry, Fritz Haber Research Center, and The Harvey M. Krueger
Family Center for Nanoscience & Nanotechnology, The Hebrew University, Jerusalem 9190401, Israel
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2
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Malik A, Alhomida A, Khan JM. SDBS induces multiple catalase conformations in a dose-dependent manner. Int J Biol Macromol 2023; 253:127606. [PMID: 37871717 DOI: 10.1016/j.ijbiomac.2023.127606] [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: 05/07/2023] [Revised: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 10/25/2023]
Abstract
Amyloid fibrils have been linked to several incurable diseases. They are long and thin fibrous proteins that self-assemble into fibrils. Small molecules can stimulate amyloid fibrillation, but the mechanism by which this happens is not well understood. This study examined how a negatively charged benzene ring containing surfactant, sodium dodecylbenzene sulphonate (SDBS), affects the fibrillation of bovine liver catalase (BLC). After SDBS treatment, BLC conformational changes were examined in vitro using turbidity, RLS kinetics, intrinsic fluorescence, ThT fluorescence, far-UV CD, and TEM. BLC in the native state was alpha-helical at pH 7.4, while it was converted to a random coil structure at pH 2.0. Far-UV CD and intrinsic fluorescence data showed that at concentrations <0.1 mM of SDBS, randomly coiled BLC assumed a native-like alpha-helical structure. However, between 0.1 and 1.0 mM SDBS, BLC was aggregated. ThT fluorescence and far-UV CD measurements showed the amyloid-like structures in the aggregated BLC. At higher SDBS concentrations (>1.0 mM) at pH 2.0, BLC again attains a native-like alpha-helical structure. It is essential for therapeutic purposes to clearly understand the process underlying surfactant- or lipid-induced fibrillation.
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Affiliation(s)
- Ajamaluddin Malik
- Department of Biochemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh, Saudi Arabia.
| | - Abdullah Alhomida
- Department of Biochemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh, Saudi Arabia
| | - Javed Masood Khan
- Department of Food Science and Nutrition, Faculty of Food and Agriculture Science, King Saud University, P.O. Box 2460, Riyadh, Saudi Arabia
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3
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Martínez-Rodríguez S, Cámara-Artigas A, Gavira JA. First 3-D structural evidence of a native-like intertwined dimer in the acylphosphatase family. Biochem Biophys Res Commun 2023; 682:85-90. [PMID: 37804591 DOI: 10.1016/j.bbrc.2023.09.053] [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: 09/11/2023] [Accepted: 09/20/2023] [Indexed: 10/09/2023]
Abstract
Acylphosphatase (AcP, EC 3.6.1.7) is a small model protein conformed by a ferredoxin-like fold, profoundly studied to get insights into protein folding and aggregation processes. Numerous studies focused on the aggregation and/or amyloidogenic properties of AcPs suggest the importance of edge-β-strands in the process. In this work, we present the first crystallographic structure of Escherichia coli AcP (EcoAcP), showing notable differences with the only available NMR structure for this enzyme. EcoAcP is crystalised as an intertwined dimer formed by replacing a single C-terminal β-strand between two protomers, suggesting a flexible character of the C-terminal edge of EcoAcP. Despite numerous works where AcP from different sources have been used as a model system for protein aggregation, our domain-swapped EcoAcP structure is the first 3-D structural evidence of native-like aggregated species for any AcP reported to date, providing clues on molecular determinants unleashing aggregation.
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Affiliation(s)
- Sergio Martínez-Rodríguez
- Department of Biochemistry and Molecular Biology III and Immunology, University of Granada, Avenida de La Investigación 11, Granada, 18071, Spain; Laboratorio de Estudios Cristalográficos, CSIC-UGR, Avda. de Las Palmeras 4, Armilla, Granada, 18100, Spain.
| | - Ana Cámara-Artigas
- Department of Chemistry and Physics, University of Almería, Agrifood Campus of International Excellence (ceiA3), Centro de Investigación en Agrosistemas Intensivos Mediterráneos y Biotecnología Agroalimentaria (CIAMBITAL), Carretera de Sacramento S/n, Almería, 04120, Spain
| | - Jose Antonio Gavira
- Laboratorio de Estudios Cristalográficos, CSIC-UGR, Avda. de Las Palmeras 4, Armilla, Granada, 18100, Spain
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4
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Garfagnini T, Bemporad F, Harries D, Chiti F, Friedler A. Amyloid Aggregation Is Potently Slowed Down by Osmolytes Due to Compaction of Partially Folded State. J Mol Biol 2023; 435:168281. [PMID: 37734431 DOI: 10.1016/j.jmb.2023.168281] [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: 03/25/2023] [Revised: 07/30/2023] [Accepted: 09/11/2023] [Indexed: 09/23/2023]
Abstract
Amyloid aggregation is a key process in amyloidoses and neurodegenerative diseases. Hydrophobicity is one of the major driving forces for this type of aggregation, as an increase in hydrophobicity generally correlates with aggregation susceptibility and rate. However, most experimental systems in vitro and prediction tools in silico neglect the contribution of protective osmolytes present in the cellular environment. Here, we assessed the role of hydrophobic mutations in amyloid aggregation in the presence of osmolytes. To achieve this goal, we used the model protein human muscle acylphosphatase (mAcP) and mutations to leucine that increased its hydrophobicity without affecting its thermodynamic stability. Osmolytes significantly slowed down the aggregation kinetics of the hydrophobic mutants, with an effect larger than that observed on the wild-type protein. The effect increased as the mutation site was closer to the middle of the protein sequence. We propose that the preferential exclusion of osmolytes from mutation-introduced hydrophobic side-chains quenches the aggregation potential of the ensemble of partially unfolded states of the protein by inducing its compaction and inhibiting its self-assembly with other proteins. Our results suggest that including the effect of the cellular environment in experimental setups and predictive softwares, for both mechanistic studies and drug design, is essential in order to obtain a more complete combination of the driving forces of amyloid aggregation.
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Affiliation(s)
- Tommaso Garfagnini
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 9190401, Israel
| | - Francesco Bemporad
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence 50134, Italy
| | - Daniel Harries
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 9190401, Israel; The Fritz Haber Research Center, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 9190401, Israel
| | - Fabrizio Chiti
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence 50134, Italy
| | - Assaf Friedler
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 9190401, Israel.
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5
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Malik A, Al-Amri AM, Alhomida A, Khan JM. Bovine liver catalase turns into three conformational states after exposure to an anionic surfactant. Colloids Surf B Biointerfaces 2023; 229:113481. [PMID: 37536170 DOI: 10.1016/j.colsurfb.2023.113481] [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: 02/08/2023] [Revised: 07/24/2023] [Accepted: 07/26/2023] [Indexed: 08/05/2023]
Abstract
The mechanism by which anionic surfactants promote amyloid fibril is not well understood. Here, we investigated how sodium dodecyl sulfate (SDS), a negatively charged surfactant, affects the fibrillation of the partially unfolded random-coiled bovine liver catalase (BLC) at a pH of 2.0. We used several methods, including turbidity, RLS kinetics, intrinsic fluorescence, ThT fluorescence, far-UV CD, and TEM imaging, to evaluate the conformational changes of BLC in vitro in response to SDS treatment. BLC is a multimeric protein and well folded at physiological pH but forms a random coil structure at pH 2.0. Intrinsic fluorescence and far-UV CD data showed that below 0.1 mM SDS, random coiled BLC turned into a native-like structure. BLC incubated with an SDS concentration ranging from 0.1 to 2.0 mM led to the formation of aggregates. The ThT fluorescence intensity was enhanced in the aggregated BLC samples (0.1-2.0 mM SDS), and cross beta-sheeted structure was detected by the far UV CD measurements. BLC adopts a complete alpha-helical structure upon interacting with SDS at a more than 2.0 mM concentration at pH 2.0. Understanding the mechanism of surfactant- or lipid-induced fibrillation is important for therapeutic purposes.
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Affiliation(s)
- Ajamaluddin Malik
- Department of Biochemistry, Collage of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia.
| | - Abdulaziz M Al-Amri
- Department of Biochemistry, Collage of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Abdullah Alhomida
- Department of Biochemistry, Collage of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Javed Masood Khan
- Department of Food and Nutrition, Facility of Food and Agriculture Science, King Saud University, P.O. Box 2460, Riyadh, 11451, Saudi Arabia
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6
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Eliaz D, Paul S, Benyamin D, Cernescu A, Cohen SR, Rosenhek-Goldian I, Brookstein O, Miali ME, Solomonov A, Greenblatt M, Levy Y, Raviv U, Barth A, Shimanovich U. Micro and nano-scale compartments guide the structural transition of silk protein monomers into silk fibers. Nat Commun 2022; 13:7856. [PMID: 36543800 PMCID: PMC9772184 DOI: 10.1038/s41467-022-35505-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
Silk is a unique, remarkably strong biomaterial made of simple protein building blocks. To date, no synthetic method has come close to reproducing the properties of natural silk, due to the complexity and insufficient understanding of the mechanism of the silk fiber formation. Here, we use a combination of bulk analytical techniques and nanoscale analytical methods, including nano-infrared spectroscopy coupled with atomic force microscopy, to probe the structural characteristics directly, transitions, and evolution of the associated mechanical properties of silk protein species corresponding to the supramolecular phase states inside the silkworm's silk gland. We found that the key step in silk-fiber production is the formation of nanoscale compartments that guide the structural transition of proteins from their native fold into crystalline β-sheets. Remarkably, this process is reversible. Such reversibility enables the remodeling of the final mechanical characteristics of silk materials. These results open a new route for tailoring silk processing for a wide range of new material formats by controlling the structural transitions and self-assembly of the silk protein's supramolecular phases.
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Affiliation(s)
- D. Eliaz
- grid.13992.300000 0004 0604 7563Department of Molecular Chemistry and Materials Science, Faculty of Chemistry, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - S. Paul
- grid.10548.380000 0004 1936 9377Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 10691 Stockholm, Sweden
| | - D. Benyamin
- grid.9619.70000 0004 1937 0538Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 9190401 Israel
| | - A. Cernescu
- grid.431971.9Neaspec—Attocube Systems AG, Eglfinger Weg 2, Haar, 85540 Munich Germany
| | - S. R. Cohen
- grid.13992.300000 0004 0604 7563Department of Chemical Research Support, Weizmann Institute of Science, 7610001 Re-hovot, Israel
| | - I. Rosenhek-Goldian
- grid.13992.300000 0004 0604 7563Department of Chemical Research Support, Weizmann Institute of Science, 7610001 Re-hovot, Israel
| | - O. Brookstein
- grid.13992.300000 0004 0604 7563Department of Molecular Chemistry and Materials Science, Faculty of Chemistry, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - M. E. Miali
- grid.13992.300000 0004 0604 7563Department of Molecular Chemistry and Materials Science, Faculty of Chemistry, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - A. Solomonov
- grid.13992.300000 0004 0604 7563Department of Molecular Chemistry and Materials Science, Faculty of Chemistry, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - M. Greenblatt
- grid.13992.300000 0004 0604 7563Department of Chemical and Structural Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Y. Levy
- grid.13992.300000 0004 0604 7563Department of Chemical and Structural Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - U. Raviv
- grid.9619.70000 0004 1937 0538Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 9190401 Israel
| | - A. Barth
- grid.10548.380000 0004 1936 9377Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, 10691 Stockholm, Sweden
| | - U. Shimanovich
- grid.13992.300000 0004 0604 7563Department of Molecular Chemistry and Materials Science, Faculty of Chemistry, Weizmann Institute of Science, 7610001 Rehovot, Israel
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7
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Fidan GS, Parlar S, Tarikogullari AH, Alptuzun V, Alpan AS. Design, synthesis, acetylcholinesterase, butyrylcholinesterase, and amyloid-β aggregation inhibition studies of substituted 4,4'-diimine/4,4'-diazobiphenyl derivatives. Arch Pharm (Weinheim) 2022; 355:e2200152. [PMID: 35976708 DOI: 10.1002/ardp.202200152] [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: 03/25/2022] [Revised: 07/01/2022] [Accepted: 07/23/2022] [Indexed: 11/11/2022]
Abstract
A series of 4,4'-diimine/4,4'-diazobiphenyl derivatives were designed, synthesized, and evaluated for their ability to inhibit both the acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) enzymes, as well as Aβ1-42 aggregation, in vitro. The AChE and BChE inhibition assays demonstrated that all compounds displayed moderate AChE inhibitory activity in the range of IC50 = 5.77-16.22 μM, while they displayed weak or no BChE inhibition. Among the title compounds, compound 2l, 4,4'-bis(quinolin-8-yldiazenyl)-1,1'-biphenyl, having a diazo-quinoline moiety demonstrated the most potent inhibition against AChE with an IC50 value of 5.77 μM. Furthermore, diazo derivatives 2d, 4,4'-bis[(4-methoxyphenyl)diazenyl]-1,1'-biphenyl, and 2i, 4,4'-bis(pyridin-3-yldiazenyl)-1,1'-biphenyl, provided better potency on Aβ1-42 aggregation, with an inhibition value of 74.08% and 78.39% at 100 μM and 55.35% and 61.36% at 25 μM, respectively. Molecular modeling studies were carried out for the most active compound against AChE, compound 2l. All the results suggested that compounds 2d and 2i have better inhibitory potencies on Aβ1-42 aggregation and moderate AChE enzyme activity, and therefore can be highlighted as promising compounds.
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Affiliation(s)
- Görkem S Fidan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ege University, Izmir, Turkey
| | - Sulunay Parlar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ege University, Izmir, Turkey
| | - Ayse H Tarikogullari
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ege University, Izmir, Turkey
| | - Vildan Alptuzun
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ege University, Izmir, Turkey
| | - Ayşe S Alpan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ege University, Izmir, Turkey
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8
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Park H, Jeon H, Lee MY, Jeon H, Kwon S, Hong S, Kang K. Designed Amyloid Fibers with Emergent Melanosomal Functions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:7077-7084. [PMID: 35608255 DOI: 10.1021/acs.langmuir.2c00904] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Short peptides designed to self-associate into amyloid fibers with metal ion-binding ability have been used to catalyze various types of chemical reactions. This manuscript demonstrates that one of these short-peptide fibers coordinated with CuII can exhibit melanosomal functions. The coordinated CuII and the amyloid structure itself are differentially functional in accelerating oxidative self-association of dopamine into melanin-like species and in regulating their material properties (e.g., water dispersion, morphology, and the density of unpaired electrons). The results have implications for the role of functional amyloids in melanin biosynthesis and for designing peptide-based supramolecular structures with various emergent functions.
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Affiliation(s)
- Hyeyeon Park
- Department of Applied Chemistry, Kyung Hee University, 1732 Deogyoung-daero, Yongin, Gyeonggi 17104, South Korea
| | - Hyeri Jeon
- Department of Chemistry, Sookmyung Women's University, Seoul 04310, South Korea
| | - Min Young Lee
- Department of Applied Chemistry, Kyung Hee University, 1732 Deogyoung-daero, Yongin, Gyeonggi 17104, South Korea
| | - Hyojae Jeon
- Department of Applied Chemistry, Kyung Hee University, 1732 Deogyoung-daero, Yongin, Gyeonggi 17104, South Korea
| | - Sunbum Kwon
- Department of Chemistry, Chung-Ang University, Seoul 06974, South Korea
| | - Seungwoo Hong
- Department of Chemistry, Sookmyung Women's University, Seoul 04310, South Korea
| | - Kyungtae Kang
- Department of Applied Chemistry, Kyung Hee University, 1732 Deogyoung-daero, Yongin, Gyeonggi 17104, South Korea
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9
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Aprile FA, Temussi PA, Pastore A. Man does not live by intrinsically unstructured proteins alone: The role of structured regions in aggregation. Bioessays 2021; 43:e2100178. [PMID: 34674273 DOI: 10.1002/bies.202100178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/11/2021] [Accepted: 09/13/2021] [Indexed: 12/30/2022]
Abstract
Protein misfolding is a topic that is of primary interest both in biology and medicine because of its impact on fundamental processes and disease. In this review, we revisit the concept of protein misfolding and discuss how the field has evolved from the study of globular folded proteins to focusing mainly on intrinsically unstructured and often disordered regions. We argue that this shift of paradigm reflects the more recent realisation that misfolding may not only be an adverse event, as originally considered, but also may fulfil a basic biological need to compartmentalise the cell with transient reversible granules. We nevertheless provide examples in which structure is an important component of a much more complex aggregation behaviour that involves both structured and unstructured regions of a protein. We thus suggest that a more comprehensive evaluation of the mechanisms that lead to aggregation might be necessary.
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Affiliation(s)
- Francesco A Aprile
- Department of Chemistry, Imperial College London, White City Campus, 82 Wood Lane, London, W12 0BZ, UK
| | - Piero Andrea Temussi
- UK Dementia Research Institute at the Maurice Wohl Institute of King's College London, London, UK
| | - Annalisa Pastore
- UK Dementia Research Institute at the Maurice Wohl Institute of King's College London, London, UK
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10
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Olgenblum GI, Wien F, Sapir L, Harries D. β-Hairpin Miniprotein Stabilization in Trehalose Glass Is Facilitated by an Emergent Compact Non-Native State. J Phys Chem Lett 2021; 12:7659-7664. [PMID: 34351767 DOI: 10.1021/acs.jpclett.1c02379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
From stem cell freeze-drying to organ storage, considerable recent efforts have been directed toward the development of new preservation technologies. A prominent protein stabilizing strategy involves vitrification in glassy matrices, most notably those formed of sugars such as the biologically relevant preservative trehalose. Here, we compare the folding thermodynamics of a model miniprotein in solution and in the glassy state of the sugars trehalose and glucose. Using synchrotron radiation circular dichroism (SRCD), we find that the same native structure persists in solution and glass. However, upon transition to the glass, a completely different, conformationally restricted unfolded state replaces the disordered denatured state found in solution, potentially inhibiting misfolding. Concomitantly, a large exothermic contribution is observed in glass, exposing the stabilizing effect of interactions with the sugar matrix on the native state. Our results shed light on the mechanism of protein stabilization in sugar glass and should aid in future preservation technologies.
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Affiliation(s)
- Gil I Olgenblum
- Institute of Chemistry, the Fritz Haber Research Center, and the Harvey M. Kruger Center for Nanoscience & Nanotechnology, The Hebrew University, Jerusalem, 9190401, Israel
| | - Frank Wien
- DISCO Beamline, Synchrotron SOLEIL, 91192 Gif-sur-Yvette, France
| | - Liel Sapir
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Daniel Harries
- Institute of Chemistry, the Fritz Haber Research Center, and the Harvey M. Kruger Center for Nanoscience & Nanotechnology, The Hebrew University, Jerusalem, 9190401, Israel
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11
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Al-Shabib NA, Khan JM, Malik A, Rehman MT, Husain FM, AlAjmi MF, Hamdan Ali Alghamdi O, Khan A. Quinoline yellow dye stimulates whey protein fibrillation via electrostatic and hydrophobic interaction: A biophysical study. J Dairy Sci 2021; 104:5141-5151. [PMID: 33685710 DOI: 10.3168/jds.2020-19766] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 11/28/2020] [Indexed: 01/14/2023]
Abstract
Amyloid fibril formation of proteins is associated with a number of neurodegenerative diseases. Several small molecules can accelerate the amyloid fibril formation in vitro and in vivo. However, the molecular mechanism of amyloid fibrillation is still unclear. In this study, we investigated how the food dye quinoline yellow (QY) induces amyloid fibrillation in α-lactalbumin (α-LA), a major whey protein, at pH 2.0. We used several spectroscopy techniques and a microscopy technique to explore how QY provokes amyloid fibrillation in α-LA. From turbidity and Rayleigh light scattering experiments, we found that QY promotes α-LA aggregation in a concentration-dependent manner; the optimal concentration for α-LA aggregation was 0.15 to 10.00 mM. Below 0.1 mM, no aggregation occurred. Quinoline yellow-induced aggregation was a rapid process that escaped the lag phase, but it depended on the concentrations of both α-LA and QY. We also demonstrated that aggregation switched the secondary structure of α-LA from α-helices to cross-β-sheets. We then confirmed the amyloid-like structure of aggregated α-LA by transmission electron microscopy measurements. Molecular docking and simulation confirmed the stability of the α-LA-QY complex due to the formation of 1 hydrogen bond with Lys99 and 2 electrostatic interactions with Arg70 and Lys99, along with hydrophobic interactions with Leu59 and Tyr103. This study will aid in our understanding of how small molecules induce aggregation of proteins inside the stomach (low pH) and affect the digestive process.
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Affiliation(s)
- Nasser A Al-Shabib
- Department of Food Science and Nutrition, Faculty of Food and Agricultural Sciences, King Saud University, 2460, Riyadh 11451, Saudi Arabia.
| | - Javed Masood Khan
- Department of Food Science and Nutrition, Faculty of Food and Agricultural Sciences, King Saud University, 2460, Riyadh 11451, Saudi Arabia.
| | - Ajamaluddin Malik
- Department of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Md Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Fohad Mabood Husain
- Department of Food Science and Nutrition, Faculty of Food and Agricultural Sciences, King Saud University, 2460, Riyadh 11451, Saudi Arabia
| | - Mohamed F AlAjmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | | | - Altaf Khan
- Department of Pharmacology and Toxicology, Central Laboratory, College of Pharmacy, King Saud University, 2460, Riyadh 11451, Saudi Arabia
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12
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Khan JM, Malik A, Ahmed A, Alghamdi OHA, Ahmed M. SDS induces cross beta-sheet amyloid as well as alpha-helical structure in conconavalin A. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.114154] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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13
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Pignataro MF, Herrera MG, Dodero VI. Evaluation of Peptide/Protein Self-Assembly and Aggregation by Spectroscopic Methods. Molecules 2020; 25:E4854. [PMID: 33096797 PMCID: PMC7587993 DOI: 10.3390/molecules25204854] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/17/2020] [Accepted: 10/19/2020] [Indexed: 01/08/2023] Open
Abstract
The self-assembly of proteins is an essential process for a variety of cellular functions including cell respiration, mobility and division. On the other hand, protein or peptide misfolding and aggregation is related to the development of Parkinson's disease and Alzheimer's disease, among other aggregopathies. As a consequence, significant research efforts are directed towards the understanding of this process. In this review, we are focused on the use of UV-Visible Absorption Spectroscopy, Fluorescence Spectroscopy and Circular Dichroism to evaluate the self-organization of proteins and peptides in solution. These spectroscopic techniques are commonly available in most chemistry and biochemistry research laboratories, and together they are a powerful approach for initial as well as routine evaluation of protein and peptide self-assembly and aggregation under different environmental stimulus. Furthermore, these spectroscopic techniques are even suitable for studying complex systems like those in the food industry or pharmaceutical formulations, providing an overall idea of the folding, self-assembly, and aggregation processes, which is challenging to obtain with high-resolution methods. Here, we compiled and discussed selected examples, together with our results and those that helped us better to understand the process of protein and peptide aggregation. We put particular emphasis on the basic description of the methods as well as on the experimental considerations needed to obtain meaningful information, to help those who are just getting into this exciting area of research. Moreover, this review is particularly useful to those out of the field who would like to improve reproducibility in their cellular and biomedical experiments, especially while working with peptide and protein systems as an external stimulus. Our final aim is to show the power of these low-resolution techniques to improve our understanding of the self-assembly of peptides and proteins and translate this fundamental knowledge in biomedical research or food applications.
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Affiliation(s)
- María Florencia Pignataro
- Department of Physiology and Molecular and Cellular Biology, Institute of Biosciences, Biotechnology and Translational Biology (iB3), Faculty of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires C1428EG, Argentina;
- Institute of Biological Chemistry and Physical Chemistry, Dr. Alejandro Paladini, University of Buenos Aires-CONICET, Buenos Aires C1113AAD, Argentina
| | - María Georgina Herrera
- Department of Physiology and Molecular and Cellular Biology, Institute of Biosciences, Biotechnology and Translational Biology (iB3), Faculty of Exact and Natural Sciences, University of Buenos Aires, Buenos Aires C1428EG, Argentina;
- Institute of Biological Chemistry and Physical Chemistry, Dr. Alejandro Paladini, University of Buenos Aires-CONICET, Buenos Aires C1113AAD, Argentina
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Verónica Isabel Dodero
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
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14
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Garcia AM, Giorgiutti C, El Khoury Y, Bauer V, Spiegelhalter C, Leize-Wagner E, Hellwig P, Potier N, Torbeev V. Aggregation and Amyloidogenicity of the Nuclear Coactivator Binding Domain of CREB-Binding Protein. Chemistry 2020; 26:9889-9899. [PMID: 32364648 DOI: 10.1002/chem.202001847] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 04/30/2020] [Indexed: 12/28/2022]
Abstract
The nuclear coactivator binding domain (NCBD) of transcriptional co-regulator CREB-binding protein (CBP) is an example of conformationally malleable proteins that can bind to structurally unrelated protein targets and adopt distinct folds in the respective protein complexes. Here, we show that the folding landscape of NCBD contains an alternative pathway that results in protein aggregation and self-assembly into amyloid fibers. The initial steps of such protein misfolding are driven by intermolecular interactions of its N-terminal α-helix bringing multiple NCBD molecules into contact. These oligomers then undergo slow but progressive interconversion into β-sheet-containing aggregates. To reveal the concealed aggregation potential of NCBD we used a chemically synthesized mirror-image d-NCBD form. The addition of d-NCBD promoted self-assembly into amyloid precipitates presumably due to formation of thermodynamically more stable racemic β-sheet structures. The unexpected aggregation of NCBD needs to be taken into consideration given the multitude of protein-protein interactions and resulting biological functions mediated by CBP.
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Affiliation(s)
- Ana Maria Garcia
- ISIS (Institut de Science et d'Ingénierie Supramoléculaires) and, icFRC (International Center for Frontier Research in Chemistry), University of Strasbourg, CNRS-UMR 7006, 8 allée Gaspard Monge, 67083, Strasbourg, France
| | - Christophe Giorgiutti
- Laboratory of Mass-Spectrometry of Interactions and Systems, University of Strasbourg, CNRS-UMR 7140, 1 rue Blaise Pascal, 67070, Strasbourg, France
| | - Youssef El Khoury
- Laboratory of Bioelectrochemistry and Spectroscopy, University of Strasbourg, CNRS-UMR 7140, 1 rue Blaise Pascal, 67070, Strasbourg, France
| | - Valentin Bauer
- ISIS (Institut de Science et d'Ingénierie Supramoléculaires) and, icFRC (International Center for Frontier Research in Chemistry), University of Strasbourg, CNRS-UMR 7006, 8 allée Gaspard Monge, 67083, Strasbourg, France
| | - Coralie Spiegelhalter
- Imaging Center, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), INSERM-U964, University of Strasbourg, CNRS-UMR 7104, 1 rue Laurent Fries, 67404, Illkirch, France
| | - Emmanuelle Leize-Wagner
- Laboratory of Mass-Spectrometry of Interactions and Systems, University of Strasbourg, CNRS-UMR 7140, 1 rue Blaise Pascal, 67070, Strasbourg, France
| | - Petra Hellwig
- Laboratory of Bioelectrochemistry and Spectroscopy, University of Strasbourg, CNRS-UMR 7140, 1 rue Blaise Pascal, 67070, Strasbourg, France
- Institute for Advanced Study, USIAS University of Strasbourg, 5 allée du Général Rouvillois, 67083, Strasbourg, France
| | - Noelle Potier
- Laboratory of Mass-Spectrometry of Interactions and Systems, University of Strasbourg, CNRS-UMR 7140, 1 rue Blaise Pascal, 67070, Strasbourg, France
| | - Vladimir Torbeev
- ISIS (Institut de Science et d'Ingénierie Supramoléculaires) and, icFRC (International Center for Frontier Research in Chemistry), University of Strasbourg, CNRS-UMR 7006, 8 allée Gaspard Monge, 67083, Strasbourg, France
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15
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Claes F, Rudyak S, Laird AS, Louros N, Beerten J, Debulpaep M, Michiels E, van der Kant R, Van Durme J, De Baets G, Houben B, Ramakers M, Yuan K, Gwee SSL, Hernandez S, Broersen K, Oliveberg M, Moahamed B, Kirstein J, Robberecht W, Rousseau F, Schymkowitz J. Exposure of a cryptic Hsp70 binding site determines the cytotoxicity of the ALS-associated SOD1-mutant A4V. Protein Eng Des Sel 2020; 32:443-457. [PMID: 32399571 DOI: 10.1093/protein/gzaa008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 04/21/2020] [Indexed: 12/11/2022] Open
Abstract
The accumulation of toxic protein aggregates is thought to play a key role in a range of degenerative pathologies, but it remains unclear why aggregation of polypeptides into non-native assemblies is toxic and why cellular clearance pathways offer ineffective protection. We here study the A4V mutant of SOD1, which forms toxic aggregates in motor neurons of patients with familial amyotrophic lateral sclerosis (ALS). A comparison of the location of aggregation prone regions (APRs) and Hsp70 binding sites in the denatured state of SOD1 reveals that ALS-associated mutations promote exposure of the APRs more than the strongest Hsc/Hsp70 binding site that we could detect. Mutations designed to increase the exposure of this Hsp70 interaction site in the denatured state promote aggregation but also display an increased interaction with Hsp70 chaperones. Depending on the cell type, in vitro this resulted in cellular inclusion body formation or increased clearance, accompanied with a suppression of cytotoxicity. The latter was also observed in a zebrafish model in vivo. Our results suggest that the uncontrolled accumulation of toxic SOD1A4V aggregates results from insufficient detection by the cellular surveillance network.
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Affiliation(s)
- Filip Claes
- VIB Center for Brain & Disease Research, Switch Laboratory, Herestraat 49, Leuven, Belgium.,KU Leuven, Department of Cellular and Molecular Medicine, Switch Laboratory, Herestraat 49, Leuven, Belgium
| | - Stanislav Rudyak
- VIB Center for Brain & Disease Research, Switch Laboratory, Herestraat 49, Leuven, Belgium.,KU Leuven, Department of Cellular and Molecular Medicine, Switch Laboratory, Herestraat 49, Leuven, Belgium.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Leninskiy Prospekt, 14, Moscow 119991, Russia
| | - Angela S Laird
- VIB, Center for Brain and Disease Research, Laboratory of Neurobiology, Herestraat 49, Leuven, Belgium.,Center for Motor Neuron Disease Research, Department of Biomedical Science, Faculty of Medicine, Macquarie University, Balaclava Rd, Macquarie Park, Sydney NSW 2109, Australia
| | - Nikolaos Louros
- VIB Center for Brain & Disease Research, Switch Laboratory, Herestraat 49, Leuven, Belgium.,KU Leuven, Department of Cellular and Molecular Medicine, Switch Laboratory, Herestraat 49, Leuven, Belgium
| | - Jacinte Beerten
- VIB Center for Brain & Disease Research, Switch Laboratory, Herestraat 49, Leuven, Belgium.,Applied Stem Cell Technologies, University of Twente, Technical Medical Centre, Drienerlolaan 5, Enschede, The Netherlands
| | - Maja Debulpaep
- VIB Center for Brain & Disease Research, Switch Laboratory, Herestraat 49, Leuven, Belgium.,Applied Stem Cell Technologies, University of Twente, Technical Medical Centre, Drienerlolaan 5, Enschede, The Netherlands
| | - Emiel Michiels
- VIB Center for Brain & Disease Research, Switch Laboratory, Herestraat 49, Leuven, Belgium.,KU Leuven, Department of Cellular and Molecular Medicine, Switch Laboratory, Herestraat 49, Leuven, Belgium
| | - Rob van der Kant
- VIB Center for Brain & Disease Research, Switch Laboratory, Herestraat 49, Leuven, Belgium.,KU Leuven, Department of Cellular and Molecular Medicine, Switch Laboratory, Herestraat 49, Leuven, Belgium
| | - Joost Van Durme
- VIB Center for Brain & Disease Research, Switch Laboratory, Herestraat 49, Leuven, Belgium.,KU Leuven, Department of Cellular and Molecular Medicine, Switch Laboratory, Herestraat 49, Leuven, Belgium.,Applied Stem Cell Technologies, University of Twente, Technical Medical Centre, Drienerlolaan 5, Enschede, The Netherlands
| | - Greet De Baets
- VIB Center for Brain & Disease Research, Switch Laboratory, Herestraat 49, Leuven, Belgium.,KU Leuven, Department of Cellular and Molecular Medicine, Switch Laboratory, Herestraat 49, Leuven, Belgium.,Applied Stem Cell Technologies, University of Twente, Technical Medical Centre, Drienerlolaan 5, Enschede, The Netherlands
| | - Bert Houben
- VIB Center for Brain & Disease Research, Switch Laboratory, Herestraat 49, Leuven, Belgium.,KU Leuven, Department of Cellular and Molecular Medicine, Switch Laboratory, Herestraat 49, Leuven, Belgium
| | - Meine Ramakers
- VIB Center for Brain & Disease Research, Switch Laboratory, Herestraat 49, Leuven, Belgium.,KU Leuven, Department of Cellular and Molecular Medicine, Switch Laboratory, Herestraat 49, Leuven, Belgium
| | - Kristy Yuan
- Center for Motor Neuron Disease Research, Department of Biomedical Science, Faculty of Medicine, Macquarie University, Balaclava Rd, Macquarie Park, Sydney NSW 2109, Australia
| | - Serene S L Gwee
- Center for Motor Neuron Disease Research, Department of Biomedical Science, Faculty of Medicine, Macquarie University, Balaclava Rd, Macquarie Park, Sydney NSW 2109, Australia
| | - Sara Hernandez
- VIB, Center for Brain and Disease Research, Laboratory of Neurobiology, Herestraat 49, Leuven, Belgium
| | - Kerensa Broersen
- VIB Center for Brain & Disease Research, Switch Laboratory, Herestraat 49, Leuven, Belgium.,Applied Stem Cell Technologies, University of Twente, Technical Medical Centre, Drienerlolaan 5, Enschede, The Netherlands
| | - Mikael Oliveberg
- Stockholm University, Department of Biochemistry and Biophysics, Frescativägen, 114 19 Stockholm, Sweden
| | - Barbara Moahamed
- Universität Bremen, Fachbereich 2 Biologie/ Chemie, Postfach 330 440, Bremen, Germany
| | - Janine Kirstein
- Universität Bremen, Fachbereich 2 Biologie/ Chemie, Postfach 330 440, Bremen, Germany
| | - Wim Robberecht
- VIB, Center for Brain and Disease Research, Laboratory of Neurobiology, Herestraat 49, Leuven, Belgium
| | - Frederic Rousseau
- VIB Center for Brain & Disease Research, Switch Laboratory, Herestraat 49, Leuven, Belgium.,KU Leuven, Department of Cellular and Molecular Medicine, Switch Laboratory, Herestraat 49, Leuven, Belgium
| | - Joost Schymkowitz
- VIB Center for Brain & Disease Research, Switch Laboratory, Herestraat 49, Leuven, Belgium.,KU Leuven, Department of Cellular and Molecular Medicine, Switch Laboratory, Herestraat 49, Leuven, Belgium
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16
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Kundu D, Prerna K, Chaurasia R, Bharty MK, Dubey VK. Advances in protein misfolding, amyloidosis and its correlation with human diseases. 3 Biotech 2020; 10:193. [PMID: 32269898 PMCID: PMC7128022 DOI: 10.1007/s13205-020-2166-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/11/2020] [Indexed: 12/24/2022] Open
Abstract
Protein aggregation, their mechanisms and trends in the field of neurodegenerative diseases is still far from completely being decoded. It is mainly attributed to the complexity surrounding the interaction between proteins which includes various regulatory mechanisms involved with the presentation of abnormal conditions. Although most proteins are functional in their soluble form, they have also been reported to convert themselves into insoluble aggregates under certain conditions naturally. Misfolded protein forms aggregates which are mostly unwanted by the cellular system and are mostly involved in various pathophysiologies including Alzheimer's, Type II Diabetes mellitus, Kurus's etc. Challenges lie in understanding the complex mechanism of protein misfolding and its correlation with clinical evidence. It is often understood that due to the slowness of the process and its association with ageing, timely intervention with drugs or preventive measures will play an essential role in lowering the rate of dementia causing diseases and associated ailments in the future. Today approximately more than 35 proteins have been identified capable of forming amyloids under defined conditions, and nearly all of them have been associated with disease outcomes. This review incorporates a major understanding from the history of diseases associated with protein misfolding, to the current state of neurodegenerative diseases globally, highlighting challenges in drug development and current state of research in a comprehensive manner in the field of protein misfolding diseases. There is increasing clinical association of protein misfolding with regards to amyloids compelling us to thread questions solved and further helping us design possible solutions by generating a pathway-based research on which future work in this field could be driven.
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Affiliation(s)
- Debanjan Kundu
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, UP 221005 India
| | - Kumari Prerna
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, UP 221005 India
| | - Rahul Chaurasia
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, UP 221005 India
| | - Manoj Kumar Bharty
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, UP 221005 India
| | - Vikash Kumar Dubey
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, UP 221005 India
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17
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Khan JM, Malik A, Ahmad Khan M, Sharma P, Sen P. Pre-micellar concentrations of sodium dodecylbenzene sulphonate induce amyloid-like fibril formation in myoglobin at pH 4.5. Colloids Surf A Physicochem Eng Asp 2020. [DOI: 10.1016/j.colsurfa.2019.124240] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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18
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Devitt G, Rice W, Crisford A, Nandhakumar I, Mudher A, Mahajan S. Conformational Evolution of Molecular Signatures during Amyloidogenic Protein Aggregation. ACS Chem Neurosci 2019; 10:4593-4611. [PMID: 31661242 DOI: 10.1021/acschemneuro.9b00451] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Aggregation is a pathological hallmark of proteinopathies such as Alzheimer's disease and results in the deposition of β-sheet-rich amyloidogenic protein aggregates. Such proteinopathies can be classified by the identity of one or more aggregated proteins, with recent evidence also suggesting that distinct molecular conformers (strains) of the same protein can be observed in different diseases, as well is in subtypes of the same disease. Therefore, methods for the quantification of pathological changes in protein conformation are central to understanding and treating proteinopathies. In this work, the evolution of Raman spectroscopic molecular signatures of three conformationally distinct proteins, bovine serum albumin (α-helical-rich), β2-microglobulin (β-sheet-rich), and tau (natively disordered), was assessed during aggregation into oligomers and fibrils. The morphological evolution was tracked using atomic force microscopy and corresponding conformational changes were assessed by their Raman signatures acquired in both wet and dried conditions. A deconvolution model was developed which allowed us to quantify the conformation of the nonregular protein tau, as well as for the oligomeric and fibrillar species of each of the proteins. Principle component analysis of the fingerprint region allowed further identification of the distinguishing spectral features and unsupervised distinction. While an increase in β-sheet is seen on aggregation, crucially, however, each protein also retains a significant proportion of its native monomeric structure after aggregation. Thus, spectral analysis of each aggregated species, oligomeric, as well as fibrillar, for each protein resulted in a unique and quantitative "conformational fingerprint". This approach allowed us to provide the first differential detection of both oligomers and fibrils of the three different amyloidogenic proteins, including tau, whose aggregates have never before been interrogated using spontaneous Raman spectroscopy. Quantitative "conformational fingerprinting" by Raman spectroscopy thus demonstrates its huge potential and utility in understanding proteinopathic disease mechanisms and for providing strain-specific early diagnostic markers and targets for disease-modifying therapies.
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19
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Lin Y, Sahoo BR, Ozawa D, Kinoshita M, Kang J, Lim MH, Okumura M, Huh YH, Moon E, Jang JH, Lee HJ, Ryu KY, Ham S, Won HS, Ryu KS, Sugiki T, Bang JK, Hoe HS, Fujiwara T, Ramamoorthy A, Lee YH. Diverse Structural Conversion and Aggregation Pathways of Alzheimer's Amyloid-β (1-40). ACS NANO 2019; 13:8766-8783. [PMID: 31310506 DOI: 10.1021/acsnano.9b01578] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Complex amyloid aggregation of amyloid-β (1-40) (Aβ1-40) in terms of monomer structures has not been fully understood. Herein, we report the microscopic mechanism and pathways of Aβ1-40 aggregation with macroscopic viewpoints through tuning its initial structure and solubility. Partial helical structures of Aβ1-40 induced by low solvent polarity accelerated cytotoxic Aβ1-40 amyloid fibrillation, while predominantly helical folds did not aggregate. Changes in the solvent polarity caused a rapid formation of β-structure-rich protofibrils or oligomers via aggregation-prone helical structures. Modulation of the pH and salt concentration transformed oligomers to protofibrils, which proceeded to amyloid formation. We reveal diverse molecular mechanisms underlying Aβ1-40 aggregation with conceptual energy diagrams and propose that aggregation-prone partial helical structures are key to inducing amyloidogenesis. We demonstrate that context-dependent protein aggregation is comprehensively understood using the macroscopic phase diagram, which provides general insights into differentiation of amyloid formation and phase separation from unfolded and folded structures.
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Affiliation(s)
- Yuxi Lin
- Department of Chemistry , Sookmyung Women's University , Cheongpa-ro 47-gil 100 , Yongsan-gu, Seoul 04310 , South Korea
| | - Bikash R Sahoo
- Biophysics Program and Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering , University of Michigan , Ann Arbor , Michigan 48109-1055 , United States
| | - Daisaku Ozawa
- Department of Neurotherapeutics , Osaka University Graduate School of Medicine , 2-2 Yamadaoka , Suita , Osaka 565-0871 , Japan
| | - Misaki Kinoshita
- Frontier Research Institute for Interdisciplinary Sciences , Tohoku University , 6-3 Aramaki-Aza-Aoba , Aoba-ku, Sendai 980-8578 , Japan
| | - Juhye Kang
- Department of Chemistry , Korea Advanced Institute of Science and Technology , Daejeon 34141 , South Korea
- Department of Chemistry , Ulsan National Institute of Science and Technology , Ulsan 44919 , South Korea
| | - Mi Hee Lim
- Department of Chemistry , Korea Advanced Institute of Science and Technology , Daejeon 34141 , South Korea
| | - Masaki Okumura
- Frontier Research Institute for Interdisciplinary Sciences , Tohoku University , 6-3 Aramaki-Aza-Aoba , Aoba-ku, Sendai 980-8578 , Japan
| | | | | | | | - Hyun-Ju Lee
- Department of Neural Development and Disease , Korea Brain Research Institute , 61 Cheomdan-ro , Dong-gu, Daegu 41068 , South Korea
| | - Ka-Young Ryu
- Department of Neural Development and Disease , Korea Brain Research Institute , 61 Cheomdan-ro , Dong-gu, Daegu 41068 , South Korea
| | - Sihyun Ham
- Department of Chemistry , Sookmyung Women's University , Cheongpa-ro 47-gil 100 , Yongsan-gu, Seoul 04310 , South Korea
| | - Hyung-Sik Won
- Department of Biotechnology, Research Institute and College of Biomedical and Health Science , Konkuk University , Chungju , Chungbuk 27478 , South Korea
| | | | - Toshihiko Sugiki
- Institute for Protein Research , Osaka University , Yamadaoka 3-2 , Suita , Osaka 565-0871 , Japan
| | | | - Hyang-Sook Hoe
- Department of Neural Development and Disease , Korea Brain Research Institute , 61 Cheomdan-ro , Dong-gu, Daegu 41068 , South Korea
| | - Toshimichi Fujiwara
- Institute for Protein Research , Osaka University , Yamadaoka 3-2 , Suita , Osaka 565-0871 , Japan
| | - Ayyalusamy Ramamoorthy
- Biophysics Program and Department of Chemistry, Biomedical Engineering, and Macromolecular Science and Engineering , University of Michigan , Ann Arbor , Michigan 48109-1055 , United States
| | - Young-Ho Lee
- Institute for Protein Research , Osaka University , Yamadaoka 3-2 , Suita , Osaka 565-0871 , Japan
- Bio-Analytical Science , University of Science and Technology , Daejeon 34113 , South Korea
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20
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Przybyłowska M, Kowalski S, Dzierzbicka K, Inkielewicz-Stepniak I. Therapeutic Potential of Multifunctional Tacrine Analogues. Curr Neuropharmacol 2019; 17:472-490. [PMID: 29651948 PMCID: PMC6520589 DOI: 10.2174/1570159x16666180412091908] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 03/25/2018] [Accepted: 04/04/2018] [Indexed: 12/12/2022] Open
Abstract
Abstract: Tacrine is a potent inhibitor of cholinesterases (acetylcholinesterase and butyrylcholinesterase) that shows limiting clinical application by liver toxicity. In spite of this, analogues of tacrine are considered as a model inhibitor of cholinesterases in the therapy of Alzheimer’s disease. The interest in these compounds is mainly related to a high variety of their structure and biological properties. In the present review, we have described the role of cholinergic transmission and treatment strategies in Alzheimer’s disease as well as the synthesis and biological activity of several recently developed classes of multifunctional tacrine analogues and hybrids, which consist of a new paradigm to treat Alzheimer’s disease. We have also reported potential of these analogues in the treatment of Alzheimer’s diseases in various experimental systems.
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Affiliation(s)
- Maja Przybyłowska
- Department of Organic Chemistry, Gdansk University of Technology, 11/12 G. Narutowicza Street, 80-233, Gdansk, Poland
| | - Szymon Kowalski
- Department of Medical Chemistry, Medical University of Gdansk, Debinki 1 Street, 80-211 Gdansk, Poland
| | - Krystyna Dzierzbicka
- Department of Organic Chemistry, Gdansk University of Technology, 11/12 G. Narutowicza Street, 80-233, Gdansk, Poland
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21
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Sun X, Zhao D, Lu F, Peng S, Yu M, Liu N, Sun Y, Du H, Wang B, Chen J, Dong S, Lu F, Zhang W. Hydrogen sulfide regulates muscle RING finger-1 protein S-sulfhydration at Cys 44 to prevent cardiac structural damage in diabetic cardiomyopathy. Br J Pharmacol 2019; 177:836-856. [PMID: 30734268 DOI: 10.1111/bph.14601] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 12/04/2018] [Accepted: 12/19/2018] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND AND PURPOSE Hydrogen sulfide (H2 S) plays important roles as a gasotransmitter in pathologies. Increased expression of the E3 ubiquitin ligase, muscle RING finger-1 (MuRF1), may be involved in diabetic cardiomyopathy. Here we have investigated whether and how exogenous H2 S alleviates cardiac muscle degradation through modifications of MuRF1 S-sulfhydration in db/db mice. EXPERIMENTAL APPROACH Neonatal rat cardiomyocytes were treated with high glucose (40 mM), oleate (100 μM), palmitate (400 μM), and NaHS (100 μM) for 72 hr. MuRF1 was silenced with siRNA technology and mutation at Cys44 . Endoplasmic reticulum stress markers, MuRF1 expression, and ubiquitination level were measured. db/db mice were injected with NaHS (39 μmol·kg-1 ) for 20 weeks. Echocardiography, cardiac ultrastructure, cystathionine-γ-lyase, cardiac structure proteins expression, and S-sulfhydration production were measured. KEY RESULTS H2 S levels and cystathionine-γ-lyase protein expression in myocardium were decreased in db/db mice. Exogenous H2 S reversed endoplasmic reticulum stress, including impairment of the function of cardiomyocytes and structural damage in db/db mice. Exogenous H2 S could suppress the levels of myosin heavy chain 6 and myosin light chain 2 ubiquitination in cardiac tissues of db/db mice, and MuRF1 was modified by S-sulfhydration, following treatment with exogenous H2 S, to reduce the interaction between MuRF1 and myosin heavy chain 6 and myosin light chain 2. CONCLUSIONS AND IMPLICATIONS Our findings suggest that H2 S regulates MuRF1 S-sulfhydration at Cys44 to prevent myocardial degradation in the cardiac tissues of db/db mice. LINKED ARTICLES This article is part of a themed section on Hydrogen Sulfide in Biology & Medicine. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v177.4/issuetoc.
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Affiliation(s)
- Xiaojiao Sun
- Department of Pathophysiology, Harbin Medical University, Harbin, China
| | - Dechao Zhao
- Department of Cardiology, First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Fangping Lu
- Department of Pathophysiology, Harbin Medical University, Harbin, China
| | - Shuo Peng
- Department of Pathophysiology, Harbin Medical University, Harbin, China
| | - Miao Yu
- Department of Pathophysiology, Harbin Medical University, Harbin, China
| | - Ning Liu
- Department of Pathophysiology, Harbin Medical University, Harbin, China
| | - Yu Sun
- Department of Pathophysiology, Harbin Medical University, Harbin, China
| | - Haining Du
- Department of Pathophysiology, Harbin Medical University, Harbin, China
| | - Bingzhu Wang
- Department of Pathophysiology, Harbin Medical University, Harbin, China
| | - Jian Chen
- Department of Pathophysiology, Harbin Medical University, Harbin, China
| | - Shiyun Dong
- Department of Pathophysiology, Harbin Medical University, Harbin, China
| | - Fanghao Lu
- Department of Pathophysiology, Harbin Medical University, Harbin, China
| | - Weihua Zhang
- Department of Pathophysiology, Harbin Medical University, Harbin, China.,Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University Ministry of Education, Harbin, China
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22
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Detection/quantification of amyloid aggregation in solution using the novel fluorescent benzofuranone-derivative compounds as amyloid fluorescent probes: synthesis and in vitro characterization. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2019. [DOI: 10.1007/s13738-019-01599-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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23
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Bobrovnik SA, Demchenko MO, Komisarenko SV. Effect of trifluoroethanol on antibody reactivity against corresponding and nonrelated antigens. UKRAINIAN BIOCHEMICAL JOURNAL 2018. [DOI: 10.15407/ubj90.04.080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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24
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Barinov NA, Protopopova AD, Dubrovin EV, Klinov DV. Thermal denaturation of fibrinogen visualized by single-molecule atomic force microscopy. Colloids Surf B Biointerfaces 2018; 167:370-376. [DOI: 10.1016/j.colsurfb.2018.04.037] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 04/08/2018] [Accepted: 04/17/2018] [Indexed: 01/27/2023]
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25
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Gull N, Khan JM, Rukhsana, Khan RH. Spectroscopic studies on the gemini surfactant mediated refolding of human serum albumin. Int J Biol Macromol 2017; 102:331-335. [DOI: 10.1016/j.ijbiomac.2017.03.134] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 03/21/2017] [Accepted: 03/24/2017] [Indexed: 11/26/2022]
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26
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Kiran Kumar E, Prasad DK, Prakash Prabhu N. Concentration dependent switch in the kinetic pathway of lysozyme fibrillation: Spectroscopic and microscopic analysis. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 183:187-194. [PMID: 28448956 DOI: 10.1016/j.saa.2017.04.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 03/09/2017] [Accepted: 04/14/2017] [Indexed: 06/07/2023]
Abstract
Formation of amyloid fibrils is found to be a general tendency of many proteins. Investigating the kinetic mechanisms and structural features of the intermediates and the final fibrillar state is essential to understand their role in amyloid diseases. Lysozyme, a notable model protein for amyloidogenic studies, readily formed fibrils in vitro at neutral pH in the presence of urea. It, however, showed two different kinetic pathways under varying urea concentrations when probed with thioflavin T (ThT) fluorescence. In 2M urea, lysozyme followed a nucleation-dependent fibril formation pathway which was not altered by varying the protein concentration from 2mg/ml to 8mg/ml. In 4M urea, the protein exhibited concentration dependent change in the mechanism. At lower protein concentrations, lysozyme formed fibrils without any detectable nuclei (nucleation-independent polymerization pathway). When the concentration of the protein was increased above 3mg/ml, the protein followed nucleation-dependent polymerization pathway as observed in the case of 2M urea condition. This was further verified using microscopic images of the fibrils. The kinetic parameters such as lag time, elongation rate, and fibrillation half-time, which were derived from ThT fluorescence changes, showed linear dependency against the initial protein concentration suggested that under the nucleation-dependent pathway conditions, the protein followed primary-nucleation mechanism without any significant secondary nucleation events. The results also suggested that the differences in the initial protein conformation might alter the mechanism of fibrillation; however, at the higher protein concentrations lysozyme shifted to nucleation-dependent pathway.
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Affiliation(s)
- E Kiran Kumar
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India
| | - Deepak Kumar Prasad
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India
| | - N Prakash Prabhu
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India.
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Xia H, Fu H, Zhang Y, Shih KC, Ren Y, Anuganti M, Nieh MP, Cheng J, Lin Y. Supramolecular Assembly of Comb-like Macromolecules Induced by Chemical Reactions that Modulate the Macromolecular Interactions In Situ. J Am Chem Soc 2017; 139:11106-11116. [DOI: 10.1021/jacs.7b04986] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | | | - Yanfeng Zhang
- Department
of Materials Science and Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | | | | | | | | | - Jianjun Cheng
- Department
of Materials Science and Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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28
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Bag S, Mitra R, DasGupta S, Dasgupta S. Inhibition of Human Serum Albumin Fibrillation by Two-Dimensional Nanoparticles. J Phys Chem B 2017; 121:5474-5482. [DOI: 10.1021/acs.jpcb.7b01289] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sudipta Bag
- Department of Chemistry and ‡Department of Chemical Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Rishav Mitra
- Department of Chemistry and ‡Department of Chemical Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Sunando DasGupta
- Department of Chemistry and ‡Department of Chemical Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Swagata Dasgupta
- Department of Chemistry and ‡Department of Chemical Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
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29
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Lavanya V, Anil Kumar B, Jamal S, Khan MKA, Ahmed N. Sub-Micellar Concentration of Sodium Dodecyl Sulphate Prevents Thermal Denaturation Induced Aggregation of Plant Lectin, Jacalin. Protein J 2017; 36:17-27. [PMID: 28133706 DOI: 10.1007/s10930-017-9694-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The irreversible thermal unfolding of jacalin, the lectin purified from jackfruit seeds was accompanied by aggregation, where intermolecular interactions among the subunits are favoured over intramolecular interactions. The extent of aggregation increased as a function of temperature, time and protein concentration. The anionic surfactant, sodium dodecyl sulphate (SDS) significantly suppressed the formation of aggregates as observed by turbidity measurements and Rayleigh scattering assay. Moreover, far UV-CD spectra indicate that the protein β sheet transforms into α helical structure, when denatured in the presence of 3 mM SDS. Further, jacalin when heated in the presence of SDS partially retained the hemagglutination activity when jacalin-SDS mixture was diluted to 1:8 factor since 3 mM SDS was found to lyse the red blood cells. Thus, SDS only altered the aggregation behaviour of jacalin by preventing intermolecular hydrogen bonding among the exposed residues but did not completely stabilize the native conformation.
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Affiliation(s)
- V Lavanya
- School of Life Sciences, B S Abdur Rahman University, GST Road, Vandalur, Chennai, Tamil Nadu, 600048, India
| | - B Anil Kumar
- School of Life Sciences, B S Abdur Rahman University, GST Road, Vandalur, Chennai, Tamil Nadu, 600048, India
| | - Shazia Jamal
- School of Life Sciences, B S Abdur Rahman University, GST Road, Vandalur, Chennai, Tamil Nadu, 600048, India
| | - Md Khurshid Alam Khan
- School of Life Sciences, B S Abdur Rahman University, GST Road, Vandalur, Chennai, Tamil Nadu, 600048, India
| | - Neesar Ahmed
- School of Life Sciences, B S Abdur Rahman University, GST Road, Vandalur, Chennai, Tamil Nadu, 600048, India.
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30
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Force Sensitivity in Saccharomyces cerevisiae Flocculins. mSphere 2016; 1:mSphere00128-16. [PMID: 27547825 PMCID: PMC4989244 DOI: 10.1128/msphere.00128-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 06/27/2016] [Indexed: 12/28/2022] Open
Abstract
The Saccharomyces cerevisiae flocculins mediate the formation of cellular aggregates and biofilm-like mats, useful in clearing yeast from fermentations. An important property of fungal adhesion proteins, including flocculins, is the ability to form catch bonds, i.e., bonds that strengthen under tension. This strengthening is based, at least in part, on increased avidity of binding due to clustering of adhesins in cell surface nanodomains. This clustering depends on amyloid-like β-aggregation of short amino acid sequences in the adhesins. In Candida albicans adhesin Als5, shear stress from vortex mixing can unfold part of the protein to expose aggregation-prone sequences, and then adhesins aggregate into nanodomains. We therefore tested whether shear stress from mixing can increase flocculation activity by potentiating similar protein remodeling and aggregation in the flocculins. The results demonstrate the applicability of the Als adhesin model and provide a rational framework for the enhancement or inhibition of flocculation in industrial applications. Many fungal adhesins have short, β-aggregation-prone sequences that play important functional roles, and in the Candida albicans adhesin Als5p, these sequences cluster the adhesins after exposure to shear force. Here, we report that Saccharomyces cerevisiae flocculins Flo11p and Flo1p have similar β-aggregation-prone sequences and are similarly stimulated by shear force, despite being nonhomologous. Shear from vortex mixing induced the formation of small flocs in cells expressing either adhesin. After the addition of Ca2+, yeast cells from vortex-sheared populations showed greatly enhanced flocculation and displayed more pronounced thioflavin-bright surface nanodomains. At high concentrations, amyloidophilic dyes inhibited Flo1p- and Flo11p-mediated agar invasion and the shear-induced increase in flocculation. Consistent with these results, atomic force microscopy of Flo11p showed successive force-distance peaks characteristic of sequentially unfolding tandem repeat domains, like Flo1p and Als5p. Flo11p-expressing cells bound together through homophilic interactions with adhesion forces of up to 700 pN and rupture lengths of up to 600 nm. These results are consistent with the potentiation of yeast flocculation by shear-induced formation of high-avidity domains of clustered adhesins at the cell surface, similar to the activation of Candida albicans adhesin Als5p. Thus, yeast adhesins from three independent gene families use similar force-dependent interactions to drive cell adhesion. IMPORTANCE The Saccharomyces cerevisiae flocculins mediate the formation of cellular aggregates and biofilm-like mats, useful in clearing yeast from fermentations. An important property of fungal adhesion proteins, including flocculins, is the ability to form catch bonds, i.e., bonds that strengthen under tension. This strengthening is based, at least in part, on increased avidity of binding due to clustering of adhesins in cell surface nanodomains. This clustering depends on amyloid-like β-aggregation of short amino acid sequences in the adhesins. In Candida albicans adhesin Als5, shear stress from vortex mixing can unfold part of the protein to expose aggregation-prone sequences, and then adhesins aggregate into nanodomains. We therefore tested whether shear stress from mixing can increase flocculation activity by potentiating similar protein remodeling and aggregation in the flocculins. The results demonstrate the applicability of the Als adhesin model and provide a rational framework for the enhancement or inhibition of flocculation in industrial applications.
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31
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Amyloid formation of growth hormone in presence of zinc: Relevance to its storage in secretory granules. Sci Rep 2016; 6:23370. [PMID: 27004850 PMCID: PMC4804206 DOI: 10.1038/srep23370] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 03/04/2016] [Indexed: 11/16/2022] Open
Abstract
Amyloids are cross-β-sheet fibrillar aggregates, associated with various human diseases and native functions such as protein/peptide hormone storage inside secretory granules of neuroendocrine cells. In the current study, using amyloid detecting agents, we show that growth hormone (GH) could be stored as amyloid in the pituitary of rat. Moreover, to demonstrate the formation of GH amyloid in vitro, we studied various conditions (solvents, glycosaminoglycans, salts and metal ions) and found that in presence of zinc metal ions (Zn(II)), GH formed short curvy fibrils. The amyloidogenic nature of these fibrils was examined by Thioflavin T binding, Congo Red binding, transmission electron microscopy and X-ray diffraction. Our biophysical studies also suggest that Zn(II) initiates the early oligomerization of GH that eventually facilitates the fibrillation process. Furthermore, using immunofluorescence study of pituitary tissue, we show that GH in pituitary significantly co-localizes with Zn(II), suggesting the probable role of zinc in GH aggregation within secretory granules. We also found that GH amyloid formed in vitro is capable of releasing monomers. The study will help to understand the possible mechanism of GH storage, its regulation and monomer release from the somatotrophs of anterior pituitary.
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Carcamo-Noriega EN, Saab-Rincon G. Identification of fibrillogenic regions in human triosephosphate isomerase. PeerJ 2016; 4:e1676. [PMID: 26870617 PMCID: PMC4748702 DOI: 10.7717/peerj.1676] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 01/20/2016] [Indexed: 12/31/2022] Open
Abstract
Background. Amyloid secondary structure relies on the intermolecular assembly of polypeptide chains through main-chain interaction. According to this, all proteins have the potential to form amyloid structure, nevertheless, in nature only few proteins aggregate into toxic or functional amyloids. Structural characteristics differ greatly among amyloid proteins reported, so it has been difficult to link the fibrillogenic propensity with structural topology. However, there are ubiquitous topologies not represented in the amyloidome that could be considered as amyloid-resistant attributable to structural features, such is the case of TIM barrel topology. Methods. This work was aimed to study the fibrillogenic propensity of human triosephosphate isomerase (HsTPI) as a model of TIM barrels. In order to do so, aggregation of HsTPI was evaluated under native-like and destabilizing conditions. Fibrillogenic regions were identified by bioinformatics approaches, protein fragmentation and peptide aggregation. Results. We identified four fibrillogenic regions in the HsTPI corresponding to the β3, β6, β7 y α8 of the TIM barrel. From these, the β3-strand region (residues 59–66) was highly fibrillogenic. In aggregation assays, HsTPI under native-like conditions led to amorphous assemblies while under partially denaturing conditions (urea 3.2 M) formed more structured aggregates. This slightly structured aggregates exhibited residual cross-β structure, as demonstrated by the recognition of the WO1 antibody and ATR-FTIR analysis. Discussion. Despite the fibrillogenic regions present in HsTPI, the enzyme maintained under native-favoring conditions displayed low fibrillogenic propensity. This amyloid-resistance can be attributed to the three-dimensional arrangement of the protein, where β-strands, susceptible to aggregation, are protected in the core of the molecule. Destabilization of the protein structure may expose inner regions promoting β-aggregation, as well as the formation of hydrophobic disordered aggregates. Being this last pathway kinetically favored over the thermodynamically more stable fibril aggregation pathway.
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Affiliation(s)
- Edson N Carcamo-Noriega
- Instituto de Biotecnología, Departamento de Ingeniería Celular y Biocatálisis, Universidad Nacional Autónoma de México , Cuernavaca, Morelos , Mexico
| | - Gloria Saab-Rincon
- Instituto de Biotecnología, Departamento de Ingeniería Celular y Biocatálisis, Universidad Nacional Autónoma de México , Cuernavaca, Morelos , Mexico
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33
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Awasthi M, Singh S, Pandey VP, Dwivedi UN. Alzheimer's disease: An overview of amyloid beta dependent pathogenesis and its therapeutic implications along with in silico approaches emphasizing the role of natural products. J Neurol Sci 2016; 361:256-71. [DOI: 10.1016/j.jns.2016.01.008] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 01/02/2016] [Accepted: 01/04/2016] [Indexed: 01/09/2023]
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34
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Khan JM, Khan MS, Ali MS, Al-Shabib NA, Khan RH. Cetyltrimethylammonium bromide (CTAB) promote amyloid fibril formation in carbohydrate binding protein (concanavalin A) at physiological pH. RSC Adv 2016. [DOI: 10.1039/c6ra03707k] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Low concentration of CTAB provoked cross β-sheet formation whereas high concentrations of CTAB direct to alpha helix induction in Con A.
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Affiliation(s)
- Javed Masood Khan
- Department of Food Science and Nutrition
- Faculty of Food and Agricultural Sciences
- King Saud University
- 2460 Riyadh 11451
- Saudi Arabia
| | - Mohd Shahnawaz Khan
- Protein Research Chair
- Department of Biochemistry
- College of Science
- King Saud University
- Riyadh
| | - Mohd Sajid Ali
- Department of Chemistry
- King Saud University
- Riyadh 11451
- Saudi Arabia
| | - Nasser Abdulatif Al-Shabib
- Department of Food Science and Nutrition
- Faculty of Food and Agricultural Sciences
- King Saud University
- 2460 Riyadh 11451
- Saudi Arabia
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit
- Aligarh Muslim University
- Aligarh
- India
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35
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Chan CXJ, Joseph IG, Huang A, Jackson DN, Lipke PN. Quantitative Analyses of Force-Induced Amyloid Formation in Candida albicans Als5p: Activation by Standard Laboratory Procedures. PLoS One 2015; 10:e0129152. [PMID: 26047318 PMCID: PMC4457901 DOI: 10.1371/journal.pone.0129152] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 05/05/2015] [Indexed: 11/18/2022] Open
Abstract
Candida albicans adhesins have amyloid-forming sequences. In Als5p, these amyloid sequences cluster cell surface adhesins to create high avidity surface adhesion nanodomains. Such nanodomains form after force is applied to the cell surface by atomic force microscopy or laminar flow. Here we report centrifuging and resuspending S. cerevisiae cells expressing Als5p led to 1.7-fold increase in initial rate of adhesion to ligand coated beads. Furthermore, mechanical stress from vortex-mixing of Als5p cells or C. albicans cells also induced additional formation of amyloid nanodomains and consequent activation of adhesion. Vortex-mixing for 60 seconds increased the initial rate of adhesion 1.6-fold. The effects of vortex-mixing were replicated in heat-killed cells as well. Activation was accompanied by increases in thioflavin T cell surface fluorescence measured by flow cytometry or by confocal microscopy. There was no adhesion activation in cells expressing amyloid-impaired Als5pV326N or in cells incubated with inhibitory concentrations of anti-amyloid dyes. Together these results demonstrated the activation of cell surface amyloid nanodomains in yeast expressing Als adhesins, and further delineate the forces that can activate adhesion in vivo. Consequently there is quantitative support for the hypothesis that amyloid forming adhesins act as both force sensors and effectors.
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Affiliation(s)
- Cho X. J. Chan
- Biology Department, Brooklyn College City University of New York, New York, New York, United States of America
- The Graduate Center, City University of New York, New York, New York, United States of America
- Haskins Laboratories and the Department of Chemistry and Physical Sciences, Pace University, New York, New York, United States of America
| | - Ivor G. Joseph
- Biology Department, Brooklyn College City University of New York, New York, New York, United States of America
| | - Andy Huang
- Biology Department, Brooklyn College City University of New York, New York, New York, United States of America
| | - Desmond N. Jackson
- Biology Department, Brooklyn College City University of New York, New York, New York, United States of America
| | - Peter N. Lipke
- Biology Department, Brooklyn College City University of New York, New York, New York, United States of America
- The Graduate Center, City University of New York, New York, New York, United States of America
- * E-mail:
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36
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Jaganathan M, Dhathathreyan A, Selvaraju C, Miller R. Jones-Ray effect on the organization of lysozyme in the presence of NaNO3 at an air/water interface: is it a cause or consequence? RSC Adv 2015. [DOI: 10.1039/c5ra15444h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Interfacial rheology confirms the Jones-Ray effect resulting from a synergy between lysozyme and NaNO3 at an air/fluid interface.
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Affiliation(s)
| | | | | | - Reinhard Miller
- Max-Planck-Institut fuer Kolloid-und Grenzflaechenforschung
- Potsdam
- Germany
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37
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Effect of heat-induced formation of rice bran protein fibrils on morphological structure and physicochemical properties in solutions and gels. Food Sci Biotechnol 2014. [DOI: 10.1007/s10068-014-0194-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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38
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Direct single-molecule observation of calcium-dependent misfolding in human neuronal calcium sensor-1. Proc Natl Acad Sci U S A 2014; 111:13069-74. [PMID: 25157171 DOI: 10.1073/pnas.1401065111] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Neurodegenerative disorders are strongly linked to protein misfolding, and crucial to their explication is a detailed understanding of the underlying structural rearrangements and pathways that govern the formation of misfolded states. Here we use single-molecule optical tweezers to monitor misfolding reactions of the human neuronal calcium sensor-1, a multispecific EF-hand protein involved in neurotransmitter release and linked to severe neurological diseases. We directly observed two misfolding trajectories leading to distinct kinetically trapped misfolded conformations. Both trajectories originate from an on-pathway intermediate state and compete with native folding in a calcium-dependent manner. The relative probability of the different trajectories could be affected by modulating the relaxation rate of applied force, demonstrating an unprecedented real-time control over the free-energy landscape of a protein. Constant-force experiments in combination with hidden Markov analysis revealed the free-energy landscape of the misfolding transitions under both physiological and pathological calcium concentrations. Remarkably for a calcium sensor, we found that higher calcium concentrations increased the lifetimes of the misfolded conformations, slowing productive folding to the native state. We propose a rugged, multidimensional energy landscape for neuronal calcium sensor-1 and speculate on a direct link between protein misfolding and calcium dysregulation that could play a role in neurodegeneration.
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39
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Sant'Anna R, Braga C, Varejão N, Pimenta KM, Graña-Montes R, Alves A, Cortines J, Cordeiro Y, Ventura S, Foguel D. The importance of a gatekeeper residue on the aggregation of transthyretin: implications for transthyretin-related amyloidoses. J Biol Chem 2014; 289:28324-37. [PMID: 25086037 PMCID: PMC4192486 DOI: 10.1074/jbc.m114.563981] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Protein aggregation into β-sheet-enriched amyloid fibrils is associated with an increasing number of human disorders. The adoption of such amyloid conformations seems to constitute a generic property of polypeptide chains. Therefore, during evolution, proteins have adopted negative design strategies to diminish their intrinsic propensity to aggregate, including enrichment of gatekeeper charged residues at the flanks of hydrophobic aggregation-prone segments. Wild type transthyretin (TTR) is responsible for senile systemic amyloidosis, and more than 100 mutations in the TTR gene are involved in familial amyloid polyneuropathy. The TTR 26–57 segment bears many of these aggressive amyloidogenic mutations as well as the binding site for heparin. We demonstrate here that Lys-35 acts as a gatekeeper residue in TTR, strongly decreasing its amyloidogenic potential. This protective effect is sequence-specific because Lys-48 does not affect TTR aggregation. Lys-35 is part of the TTR basic heparin-binding motif. This glycosaminoglycan blocks the protective effect of Lys-35, probably by neutralization of its side chain positive charge. A K35L mutation emulates this effect and results in the rapid self-assembly of the TTR 26–57 region into amyloid fibrils. This mutation does not affect the tetrameric protein stability, but it strongly increases its aggregation propensity. Overall, we illustrate how TTR is yet another amyloidogenic protein exploiting negative design to prevent its massive aggregation, and we show how blockage of conserved protective features by endogenous factors or mutations might result in increased disease susceptibility.
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Affiliation(s)
- Ricardo Sant'Anna
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Estrutural
| | - Carolina Braga
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Estrutural
| | - Nathalia Varejão
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Estrutural
| | - Karinne M Pimenta
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Estrutural
| | - Ricardo Graña-Montes
- the Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Aline Alves
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Estrutural
| | - Juliana Cortines
- the Instituto de Microbiologia Professor Paulo de Goés, Universidade Federal do Rio de Janeiro, Rio de Janeiro CEP 21941-590, Brazil and
| | | | - Salvador Ventura
- the Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Debora Foguel
- From the Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Estrutural,
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40
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Potential therapeutic strategies for Alzheimer's disease targeting or beyond β-amyloid: insights from clinical trials. BIOMED RESEARCH INTERNATIONAL 2014; 2014:837157. [PMID: 25136630 PMCID: PMC4124758 DOI: 10.1155/2014/837157] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Revised: 06/23/2014] [Accepted: 06/25/2014] [Indexed: 01/25/2023]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder with two hallmarks: β-amyloid plagues and neurofibrillary tangles. It is one of the most alarming illnesses to elderly people. No effective drugs and therapies have been developed, while mechanism-based explorations of therapeutic approaches have been intensively investigated. Outcomes of clinical trials suggested several pitfalls in the choice of biomarkers, development of drug candidates, and interaction of drug-targeted molecules; however, they also aroused concerns on the potential deficiency in our understanding of pathogenesis of AD, and ultimately stimulated the advent of novel drug targets tests. The anticipated increase of AD patients in next few decades makes development of better therapy an urgent issue. Here we attempt to summarize and compare putative therapeutic strategies that have completed clinical trials or are currently being tested from various perspectives to provide insights for treatments of Alzheimer's disease.
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41
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Emadi S, Behzadi M. A comparative study on the aggregating effects of guanidine thiocyanate, guanidine hydrochloride and urea on lysozyme aggregation. Biochem Biophys Res Commun 2014; 450:1339-44. [PMID: 25003319 DOI: 10.1016/j.bbrc.2014.06.133] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 06/26/2014] [Indexed: 11/15/2022]
Abstract
Protein aggregation and its subsequent deposition in different tissues culminate in a diverse range of diseases collectively known as amyloidoses. Aggregation of hen or human lysozyme depends on certain conditions, namely acidic pH or the presence of additives. In the present study, the effects on the aggregation of hen egg-white lysozyme via incubation in concentrated solutions of three different chaotropic agents namely guanidine thiocyanate, guanidine hydrochloride and urea were investigated. Here we used three different methods for the detection of the aggregates, thioflavin T fluorescence, circular dichroism spectroscopy and atomic force microscopy. Our results showed that upon incubation with different concentrations (0.5, 1.0, 2.0, 3.0, 4.0, 5.0M) of the chemical denaturants, lysozyme was aggregated at low concentrations of guanidine thiocyanate (1.0 and 2.0M) and at high concentrations of guanidine hydrochloride (4 and 5M), although no fibril formation was detected. In the case of urea, no aggregation was observed at any concentration.
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Affiliation(s)
- Saeed Emadi
- Department of Biological Sciences, Institute in Advanced Studies in Basic Sciences (IASBS), Zanjan, Iran.
| | - Maliheh Behzadi
- Department of Biological Sciences, Institute in Advanced Studies in Basic Sciences (IASBS), Zanjan, Iran
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Takekiyo T, Fukudome K, Yamazaki K, Abe H, Yoshimura Y. Protein aggregation and partial globular state in aqueous 1-alkyl-3-methylimidazolium nitrate solutions. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.03.089] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Das S, Pal U, Das S, Bagga K, Roy A, Mrigwani A, Maiti NC. Sequence complexity of amyloidogenic regions in intrinsically disordered human proteins. PLoS One 2014; 9:e89781. [PMID: 24594841 PMCID: PMC3940659 DOI: 10.1371/journal.pone.0089781] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 01/26/2014] [Indexed: 01/03/2023] Open
Abstract
An amyloidogenic region (AR) in a protein sequence plays a significant role in protein aggregation and amyloid formation. We have investigated the sequence complexity of AR that is present in intrinsically disordered human proteins. More than 80% human proteins in the disordered protein databases (DisProt+IDEAL) contained one or more ARs. With decrease of protein disorder, AR content in the protein sequence was decreased. A probability density distribution analysis and discrete analysis of AR sequences showed that ∼8% residue in a protein sequence was in AR and the region was in average 8 residues long. The residues in the AR were high in sequence complexity and it seldom overlapped with low complexity regions (LCR), which was largely abundant in disorder proteins. The sequences in the AR showed mixed conformational adaptability towards α-helix, β-sheet/strand and coil conformations.
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Affiliation(s)
- Swagata Das
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB), Kolkata, India
| | - Uttam Pal
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB), Kolkata, India
| | - Supriya Das
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB), Kolkata, India
| | - Khyati Bagga
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB), Kolkata, India
| | - Anupam Roy
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB), Kolkata, India
| | - Arpita Mrigwani
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB), Kolkata, India
| | - Nakul C. Maiti
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology (IICB), Kolkata, India
- * E-mail:
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44
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Induction of amyloidogenicity in wild type HEWL by a dialdehyde: Analysis involving multi dimensional approach. Int J Biol Macromol 2014; 64:36-44. [DOI: 10.1016/j.ijbiomac.2013.11.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 11/17/2013] [Accepted: 11/18/2013] [Indexed: 11/23/2022]
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45
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Kunkel J, Asuri P. Function, structure, and stability of enzymes confined in agarose gels. PLoS One 2014; 9:e86785. [PMID: 24466239 PMCID: PMC3897775 DOI: 10.1371/journal.pone.0086785] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 12/13/2013] [Indexed: 01/21/2023] Open
Abstract
Research over the past few decades has attempted to answer how proteins behave in molecularly confined or crowded environments when compared to dilute buffer solutions. This information is vital to understanding in vivo protein behavior, as the average spacing between macromolecules in the cell cytosol is much smaller than the size of the macromolecules themselves. In our study, we attempt to address this question using three structurally and functionally different model enzymes encapsulated in agarose gels of different porosities. Our studies reveal that under standard buffer conditions, the initial reaction rates of the agarose-encapsulated enzymes are lower than that of the solution phase enzymes. However, the encapsulated enzymes retain a higher percentage of their activity in the presence of denaturants. Moreover, the concentration of agarose used for encapsulation had a significant effect on the enzyme functional stability; enzymes encapsulated in higher percentages of agarose were more stable than the enzymes encapsulated in lower percentages of agarose. Similar results were observed through structural measurements of enzyme denaturation using an 8-anilinonaphthalene-1-sulfonic acid fluorescence assay. Our work demonstrates the utility of hydrogels to study protein behavior in highly confined environments similar to those present in vivo; furthermore, the enhanced stability of gel-encapsulated enzymes may find use in the delivery of therapeutic proteins, as well as the design of novel strategies for biohybrid medical devices.
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Affiliation(s)
- Jeffrey Kunkel
- Department of Bioengineering, Santa Clara University, Santa Clara, California, United States of America
| | - Prashanth Asuri
- Department of Bioengineering, Santa Clara University, Santa Clara, California, United States of America
- * E-mail:
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46
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Bekard I, Dunstan DE. Electric field induced changes in protein conformation. SOFT MATTER 2014; 10:431-7. [PMID: 24652412 DOI: 10.1039/c3sm52653d] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The effect of a low strength oscillating electric field on the conformation of Bovine Serum Albumin (BSA) and Lysozyme in solution has been measured. A purpose built cell has been used to measure the real time autofluorescence and Circular Dichroism of the protein solutions exposed to electric fields of differing strength and frequency. Exposure to the electric fields results in protein unfolding for both Lysozyme and BSA. The applied field strengths are extremely small compared to the protein inter-chain intra-molecular forces. We propose a model whereby the electrophoretic motion of the proteins leads to a frictional force that results in protein unfolding. For BSA and Lysozyme in the electric fields used in this study, the shear rates at the protein surface under electrophoretic motion are of order 10(3) and 10(4) s(-1) respectively. Prolonged electric field exposure results in significant frictional energy dissipation in the proteins. The energy dissipated in the proteins results in protein unfolding, which is a critical initial step for protein aggregation and potentially amyloid fibril formation.
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Affiliation(s)
- Innocent Bekard
- CSL Behring, 189-209 Camp Road, Broadmeadows, Victoria, 3047, Australia
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47
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Minsky BB, Zheng B, Dubin PL. Inhibition of antithrombin and bovine serum albumin native state aggregation by heparin. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:278-287. [PMID: 24313340 DOI: 10.1021/la4039232] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Protein native state aggregation, a major problem in pharmaceutical and biological processes, has been addressed pharmacologically by the addition of protein-binding excipients. Heparin (Hp), a highly sulfated polysaccharide, interacts with numerous proteins with moderate to high affinity, but reports about its effect on protein aggregation are contradictory. We studied the pH dependence of the aggregation of antithrombin (AT) and bovine serum albumin (BSA) in the presence and absence of heparin. High-precision turbidimetry showed strong aggregation for both AT and BSA in I = 10 mM NaCl, conditions at which electrostatically driven Hp binding and aggregation both occur, with more obvious aggregation of heparin-free AT appearing as larger aggregate size. Aggregation of AT was dramatically inhibited at Hp: protein 6:1 (mole ratio); however, the effect at 0.5:1 Hp:protein was greater for BSA. Frontal analysis capillary electrophoresis showed a much larger equilibrium association constant Kobs between Hp and AT, in accord with the onset of Hp binding at a higher pH; both effects are explained by the higher charge density of the positive domain for AT as revealed by modeling with DelPhi. The corresponding modeling images showed that these domains persist at high salt only for AT, consistent with the 160-fold drop in Kobs at 100 mM salt for BSA-Hp binding. The smaller inhibition effect for AT arises from the tendency of its uncomplexed monomer to form larger aggregates more rapidly, but the stronger binding of Hp to AT does not facilitate Hp-induced aggregate dissolution which occurs more readily for BSA. This can be attributed to the higher density of AT aggregates evidenced by higher fractal dimensions. Differences between inhibition and reversal by Hp arise because the former may depend on the stage at which Hp enters the aggregation process and the latter on aggregate size and morphology.
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Affiliation(s)
- Burcu Baykal Minsky
- Department of Chemistry, University of Massachusetts , Amherst, Massachusetts, 01003, United States
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Ferrolino MC, Zhuravleva A, Budyak IL, Krishnan B, Gierasch LM. Delicate balance between functionally required flexibility and aggregation risk in a β-rich protein. Biochemistry 2013; 52:8843-54. [PMID: 24236614 DOI: 10.1021/bi4013462] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Susceptibility to aggregation is general to proteins because of the potential for intermolecular interactions between hydrophobic stretches in their amino acid sequences. Protein aggregation has been implicated in several catastrophic diseases, yet we still lack in-depth understanding about how proteins are channeled to this state. Using a predominantly β-sheet protein whose folding has been explored in detail, cellular retinoic acid-binding protein 1 (CRABP1), as a model, we have tackled the challenge of understanding the links between a protein's natural tendency to fold, 'breathe', and function with its propensity to misfold and aggregate. We identified near-native dynamic species that lead to aggregation and found that inherent structural fluctuations in the native protein, resulting in opening of the ligand-entry portal, expose hydrophobic residues on the most vulnerable aggregation-prone sequences in CRABP1. CRABP1 and related intracellullar lipid-binding proteins have not been reported to aggregate inside cells, and we speculate that the cellular concentration of their open, aggregation-prone conformations is sufficient for ligand binding but below the critical concentration for aggregation. Our finding provides an example of how nature fine-tunes a delicate balance between protein function, conformational variability, and aggregation vulnerability and implies that with the evolutionary requirement for proteins to fold and function, aggregation becomes an unavoidable but controllable risk.
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Affiliation(s)
- Mylene C Ferrolino
- Department of Biochemistry and Molecular Biology, ‡Program in Molecular and Cellular Biology, and §Department of Chemistry, University of Massachusetts , Amherst, Massachusetts 01003, United States
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Selvakumar P, Sharma N, Tomar PPS, Kumar P, Sharma AK. Structural insights into the aggregation behavior of Murraya koenigii miraculin-like protein below pH 7.5. Proteins 2013; 82:830-40. [PMID: 24265134 DOI: 10.1002/prot.24461] [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: 05/30/2013] [Revised: 10/03/2013] [Accepted: 10/21/2013] [Indexed: 11/07/2022]
Abstract
Murraya koenigii miraculin-like protein (MKMLP) gradually precipitates below pH 7.5. Here, we explore the basis for this aggregation by identifying the aggregation-prone regions via comparative analysis of crystal structures acquired at several pH values. The prediction of aggregation-prone regions showed the presence of four short peptides either in beta sheets or loops on surface of the protein. These peptides were distributed in two patches far apart on the surface. Comparison of crystal structures of MKMLP, determined at 2.2 Å resolution in pH 7.0 and 4.6 in the present study and determined at 2.9 Å in pH 8.0 in an earlier reported study, reveal subtle conformational differences resulting in gradual exposure of aggregation-prone regions. As the pH is lowered, there are alterations in ionic interactions within the protein interactions of the chain with water molecules and exposure of hydrophobic residues. The analysis of symmetry-related molecular interfaces involving one patch revealed shortening of nonpolar intermolecular contacts as the pH decreased. In particular, a decrease in the intermolecular distance between Trp103 of the aggregation-prone peptide WFITTG (103-108) unique to MLPs was observed. These results demonstrated that aggregation occurs due to the cumulative effect of the changes in interactions in two aggregation-prone defined regions.
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Affiliation(s)
- Purushotham Selvakumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247 667, India
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50
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Amani S, Nasim F, Khan TA, Fazili NA, Furkan M, Bhat IA, Khan JM, Khan RH, Naeem A. Detergent induces the formation of IgG aggregates: a multi-methodological approach. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 120:151-160. [PMID: 24184618 DOI: 10.1016/j.saa.2013.09.141] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 09/23/2013] [Accepted: 09/29/2013] [Indexed: 06/02/2023]
Abstract
Role of micellar environment created by Triton X-100 (TX-100) and CHAPSO on protein conformation using IgG as a model system has been studied in this paper. A substantial amount of secondary structure with the reduction in constant tertiary contacts was obtained in both bovine and human IgG in the presence of 0.12 mM TX-100 where as 6 and 8 mM CHAPSO concentration was required for this type of secondary structure. Further addition of either of the detergents result in the induction of α-helix in both the IgGs as evident by helix specific peaks in the amide I region of FTIR and circular dichroism spectra. Tryptophan and 8-anilino-1-naphthalene-sulphonic acid (ANS) fluorescence confirmed changes in protein conformation upon addition of detergents. Maximum ANS binding at 0.12 mM TX-100 in both while 6 and 8 mM CHAPSO in bovine and human IgG respectively, indicate a compact ''molten-globule''-like conformation. An increase addition of these detergents results in the burial of hydrophobic patches of both IgG owing to aggregation. Presence of aggregates at 0.2 and 0.16 mM TX-100 and 8 and 9 mM CHAPSO, for bovine and human IgG respectively, was further confirmed by reduction in ANS fluorescence, dynamic light scattering study, thioflavin T fluorescence and congo red absorbance.
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Affiliation(s)
- Samreen Amani
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - Faisal Nasim
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - Taqi Ahmed Khan
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - Naveed Ahmad Fazili
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - Mohammad Furkan
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - Imtiyaz Ahmad Bhat
- Department of Chemistry, Faculty of Science, Aligarh Muslim University, Aligarh 202002, India
| | - Javed Masood Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Aabgeena Naeem
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India.
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