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Ghosh S, Prabhu NP. Heterogeneous Macromolecular crowding effect on nucleation-independent fibril formation of Lysozyme: Spectroscopic analysis of Structure, Stability, and fibrillation rate. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 315:124276. [PMID: 38626673 DOI: 10.1016/j.saa.2024.124276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 04/05/2024] [Accepted: 04/09/2024] [Indexed: 04/18/2024]
Affiliation(s)
- Subhasree Ghosh
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - N Prakash Prabhu
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India.
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2
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Panda C, Kumar S, Gupta S, Pandey LM. Structural, kinetic, and thermodynamic aspects of insulin aggregation. Phys Chem Chem Phys 2023; 25:24195-24213. [PMID: 37674360 DOI: 10.1039/d3cp03103a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Given the significance of protein aggregation in proteinopathies and the development of therapeutic protein pharmaceuticals, revamped interest in assessing and modelling the aggregation kinetics has been observed. Quantitative analysis of aggregation includes data of gradual monomeric depletion followed by the formation of subvisible particles. Kinetic and thermodynamic studies are essential to gain key insights into the aggregation process. Despite being the medical marvel in the world of diabetes, insulin suffers from the challenge of aggregation. Physicochemical stresses are experienced by insulin during industrial formulation, storage, delivery, and transport, considerably impacting product quality, efficacy, and effectiveness. The present review briefly describes the pathways, mathematical kinetic models, and thermodynamics of protein misfolding and aggregation. With a specific focus on insulin, further discussions include the structural heterogeneity and modifications of the intermediates incurred during insulin fibrillation. Finally, different model equations to fit the kinetic data of insulin fibrillation are discussed. We believe that this review will shed light on the conditions that induce structural changes in insulin during the lag phase of fibrillation and will motivate scientists to devise strategies to block the initialization of the aggregation cascade. Subsequent abrogation of insulin fibrillation during bioprocessing will ensure stable and globally accessible insulin for efficient management of diabetes.
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Affiliation(s)
- Chinmaya Panda
- Bio-interface & Environmental Engineering Lab Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam, 781039, India.
| | - Sachin Kumar
- Viral Immunology Lab Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam, 781039, India
| | - Sharad Gupta
- Neurodegeneration and Peptide Engineering Research Lab Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Gujarat, 382355, India
| | - Lalit M Pandey
- Bio-interface & Environmental Engineering Lab Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam, 781039, India.
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3
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Lathuiliere A, Jo Y, Perbet R, Donahue C, Commins C, Quittot N, Fan Z, Bennett RE, Hyman BT. Specific detection of tau seeding activity in Alzheimer's disease using rationally designed biosensor cells. Mol Neurodegener 2023; 18:53. [PMID: 37553663 PMCID: PMC10408046 DOI: 10.1186/s13024-023-00643-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 07/28/2023] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND The prion-like propagation of tau in neurodegenerative disorders implies that misfolded pathological tau can recruit the normal protein and template its aggregation. Here, we report the methods for the development of sensitive biosensor cell lines for the detection of tau seeding activity. RESULTS We performed the rational design of novel tau probes based on the current structural knowledge of pathological tau aggregates in Alzheimer's disease. We generated Förster resonance energy transfer (FRET)-based biosensor stable cell lines and characterized their sensitivity, specificity, and overall ability to detect bioactive tau in human samples. As compared to the reference biosensor line, the optimized probe design resulted in an increased efficiency in the detection of tau seeding. The increased sensitivity allowed for the detection of lower amount of tau seeding competency in human brain samples, while preserving specificity for tau seeds found in Alzheimer's disease. CONCLUSIONS This next generation of FRET-based biosensor cells is a novel tool to study tau seeding activity in Alzheimer's disease human samples, especially in samples with low levels of seeding activity, which may help studying early tau-related pathological events.
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Affiliation(s)
- Aurelien Lathuiliere
- Department of Neurology, Massachusetts General Hospital/Harvard Medical School, 114 16Th Street, Charlestown, MA, 02129, USA
- Harvard Medical School, Boston, MA, USA
- Memory Center, Department of Rehabilitation and Geriatrics, Geneva University Hospital and University of Geneva, Geneva, Switzerland
| | - Youhwa Jo
- Department of Neurology, Massachusetts General Hospital/Harvard Medical School, 114 16Th Street, Charlestown, MA, 02129, USA
| | - Romain Perbet
- Department of Neurology, Massachusetts General Hospital/Harvard Medical School, 114 16Th Street, Charlestown, MA, 02129, USA
- Harvard Medical School, Boston, MA, USA
| | - Cameron Donahue
- Department of Neurology, Massachusetts General Hospital/Harvard Medical School, 114 16Th Street, Charlestown, MA, 02129, USA
| | - Caitlin Commins
- Department of Neurology, Massachusetts General Hospital/Harvard Medical School, 114 16Th Street, Charlestown, MA, 02129, USA
| | - Noé Quittot
- Department of Neurology, Massachusetts General Hospital/Harvard Medical School, 114 16Th Street, Charlestown, MA, 02129, USA
- Harvard Medical School, Boston, MA, USA
| | - Zhanyun Fan
- Department of Neurology, Massachusetts General Hospital/Harvard Medical School, 114 16Th Street, Charlestown, MA, 02129, USA
| | - Rachel E Bennett
- Department of Neurology, Massachusetts General Hospital/Harvard Medical School, 114 16Th Street, Charlestown, MA, 02129, USA
- Harvard Medical School, Boston, MA, USA
| | - Bradley T Hyman
- Department of Neurology, Massachusetts General Hospital/Harvard Medical School, 114 16Th Street, Charlestown, MA, 02129, USA.
- Harvard Medical School, Boston, MA, USA.
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4
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Ohgita T, Kono H, Morita I, Oyama H, Shimanouchi T, Kobayashi N, Saito H. Intramolecular interaction kinetically regulates fibril formation by human and mouse α-synuclein. Sci Rep 2023; 13:10885. [PMID: 37407638 DOI: 10.1038/s41598-023-38070-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 07/02/2023] [Indexed: 07/07/2023] Open
Abstract
Regulation of α-synuclein (αS) fibril formation is a potent therapeutic strategy for αS-related neurodegenerative disorders. αS, an intrinsically disordered 140-residue intraneural protein, comprises positively charged N-terminal, hydrophobic non-amyloid β component (NAC), and negatively charged C-terminal regions. Although mouse and human αS share 95% sequence identity, mouse αS forms amyloid fibrils faster than human αS. To evaluate the kinetic regulation of αS fibrillation, we examined the effects of mismatched residues in human and mouse αS on fibril formation and intramolecular interactions. Thioflavin T fluorescence assay using domain-swapped or C-terminal-truncated αS variants revealed that mouse αS exhibited higher nucleation and fibril elongation than human αS. In mouse αS, S87N substitution in the NAC region rather than A53T substitution is dominant for enhanced fibril formation. Fӧrester resonance energy transfer analysis demonstrated that the intramolecular interaction of the C-terminal region with the N-terminal and NAC regions observed in human αS is perturbed in mouse αS. In mouse αS, S87N substitution is responsible for the perturbed interaction. These results indicate that the interaction of the C-terminal region with the N-terminal and NAC regions suppresses αS fibril formation and that the human-to-mouse S87N substitution in the NAC region accelerates αS fibril formation by perturbing intramolecular interaction.
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Affiliation(s)
- Takashi Ohgita
- Laboratory of Biophysical Chemistry, Kyoto Pharmaceutical University, 5 Misasagi-Nakauchi-cho, Yamashina-ku, Kyoto, 607-8414, Japan.
| | - Hiroki Kono
- Laboratory of Biophysical Chemistry, Kyoto Pharmaceutical University, 5 Misasagi-Nakauchi-cho, Yamashina-ku, Kyoto, 607-8414, Japan
| | - Izumi Morita
- Department of Bioanalytical Chemistry, Kobe Pharmaceutical University, 4-19-1 Motoyama-Kitamachi, Higashinada-ku, Kobe, 658-8558, Japan
| | - Hiroyuki Oyama
- Department of Bioanalytical Chemistry, Kobe Pharmaceutical University, 4-19-1 Motoyama-Kitamachi, Higashinada-ku, Kobe, 658-8558, Japan
| | - Toshinori Shimanouchi
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
| | - Norihiro Kobayashi
- Department of Bioanalytical Chemistry, Kobe Pharmaceutical University, 4-19-1 Motoyama-Kitamachi, Higashinada-ku, Kobe, 658-8558, Japan
| | - Hiroyuki Saito
- Laboratory of Biophysical Chemistry, Kyoto Pharmaceutical University, 5 Misasagi-Nakauchi-cho, Yamashina-ku, Kyoto, 607-8414, Japan
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5
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Oxidative Damages on the Alzheimer's Related-Aβ Peptide Alters Its Ability to Assemble. Antioxidants (Basel) 2023; 12:antiox12020472. [PMID: 36830030 PMCID: PMC9951946 DOI: 10.3390/antiox12020472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/27/2023] [Accepted: 02/07/2023] [Indexed: 02/15/2023] Open
Abstract
Oxidative stress that can lead to oxidation of the amyloid-β (Aβ) peptide is considered a key feature in Alzheimer's disease (AD), influencing the ability of Aβ to assemble into β-sheet rich fibrils that are commonly found in senile plaques of AD patients. The present study aims at investigating the fallouts of Aβ oxidation on the assembly properties of the Aβ peptide. To accomplish this, we performed kinetics and analysis on an oxidized Aβ (oxAβ) peptide, resulting from the attack of reactive oxygen species (ROS) that are formed by the biologically relevant Cu/Aβ/dioxygen/ascorbate system. oxAβ was still able to assemble but displayed ill-defined and small oligomeric assemblies compared to the long and thick β-sheet rich fibrils from the non-oxidized counterpart. In addition, oxAβ does affect the assembly of the parent Aβ peptide. In a mixture of the two peptides, oxAβ has a mainly kinetic effect on the assembly of the Aβ peptide and was able to slow down the formation of Aβ fibril in a wide pH range [6.0-7.4]. However, oxAβ does not change the quantity and morphology of the Aβ fibrils formed to a significant extent. In the presence of copper or zinc di-cations, oxAβ assembled into weakly-structured aggregates rather than short, untangled Cu-Aβ fibrils and long untangled Zn-Aβ fibrils. The delaying effect of oxAβ on metal altered Aβ assembly was also observed. Hence, our results obtained here bring new insights regarding the tight interconnection between (i) ROS production leading to Aβ oxidation and (ii) Aβ assembly, in particular via the modulation of the Aβ assembly by oxAβ. It is the first time that co-assembly of oxAβ and Aβ under various environmental conditions (pH, metal ions …) are reported.
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6
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Unveiling the Metal-Dependent Aggregation Properties of the C-terminal Region of Amyloidogenic Intrinsically Disordered Protein Isoforms DPF3b and DPF3a. Int J Mol Sci 2022; 23:ijms232315291. [PMID: 36499617 PMCID: PMC9738585 DOI: 10.3390/ijms232315291] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/24/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Double-PHD fingers 3 (DPF3) is a BAF-associated human epigenetic regulator, which is increasingly recognised as a major contributor to various pathological contexts, such as cardiac defects, cancer, and neurodegenerative diseases. Recently, we unveiled that its two isoforms (DPF3b and DPF3a) are amyloidogenic intrinsically disordered proteins. DPF3 isoforms differ from their C-terminal region (C-TERb and C-TERa), containing zinc fingers and disordered domains. Herein, we investigated the disorder aggregation properties of C-TER isoforms. In agreement with the predictions, spectroscopy highlighted a lack of a highly ordered structure, especially for C-TERa. Over a few days, both C-TERs were shown to spontaneously assemble into similar antiparallel and parallel β-sheet-rich fibrils. Altered metal homeostasis being a neurodegeneration hallmark, we also assessed the influence of divalent metal cations, namely Cu2+, Mg2+, Ni2+, and Zn2+, on the C-TER aggregation pathway. Circular dichroism revealed that metal binding does not impair the formation of β-sheets, though metal-specific tertiary structure modifications were observed. Through intrinsic and extrinsic fluorescence, we found that metal cations differently affect C-TERb and C-TERa. Cu2+ and Ni2+ have a strong inhibitory effect on the aggregation of both isoforms, whereas Mg2+ impedes C-TERb fibrillation and, on the contrary, enhances that of C-TERa. Upon Zn2+ binding, C-TERb aggregation is also hindered, and the amyloid autofluorescence of C-TERa is remarkably red-shifted. Using electron microscopy, we confirmed that the metal-induced spectral changes are related to the morphological diversity of the aggregates. While metal-treated C-TERb formed breakable and fragmented filaments, C-TERa fibrils retained their flexibility and packing properties in the presence of Mg2+ and Zn2+ cations.
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7
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Rezaei M, Kalhor HR. Amyloid fibril reduction through covalently modified lysine in HEWL and insulin. Arch Biochem Biophys 2022; 727:109350. [PMID: 35830943 DOI: 10.1016/j.abb.2022.109350] [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: 03/16/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 11/28/2022]
Abstract
Proteins possess a variety of nucleophiles, which can carry out different reactions in the functioning cells. Proteins endogenously and synthetically can be modified through their nucleophilic sites. The roles of these chemical modifications have not been completely revealed. These modifications can alter the protein folding process. Protein folding directly affects the function of proteins. If an error in protein folding occurs, it may cause protein malfunction leading to several neurodegenerative disorders such as Alzheimer's and Parkinson's. In this study, Hen Egg White Lysozyme (HEWL) and bovine insulin, as model proteins for studying the amyloid formation, were covalently attached with 5(6)-thiophenolfluorescein. The amyloid formation of the covalently labeled lysozyme and insulin were compared with the native proteins. Interestingly, the results indicated that the covalent attachment of fluorescein slowed down the amyloid formation of HEWL and insulin significantly. The amyloid formation was examined using Thioflavin T (ThT) fluorescence assay, circular dichroism, FTIR, and gel electrophoresis. Tandem mass spectrometry was employed to identify the sites of covalent modifications in HEWL. It turned out that two surface lysine residues (K97 and K 116) in HEWL were modified. Computational studies, including docking and molecular simulations, revealed that 5(6)-thiophenolfluorescein makes several non-covalent interactions with HEWL residues, including Lys 97, leading to the reduction of the β-sheet in the protein. Additionally, AFM analysis confirmed the amyloid fibril reduction of lysine-modified bovine insulin and HEWL. Altogether, our results expand mechanistic insights into preventing amyloid formation by providing an approach for reducing amyloid formation by modifying specific lysine residues in the proteins.
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Affiliation(s)
- Mohsen Rezaei
- Biochemistry and Chemical Biology Research Laboratory, Chemistry Department, Sharif University of Technology, P.O. Box 11155-3516, Tehran, Iran
| | - Hamid Reza Kalhor
- Biochemistry and Chemical Biology Research Laboratory, Chemistry Department, Sharif University of Technology, P.O. Box 11155-3516, Tehran, Iran.
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8
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Gharb M, Nouralishahi A, Riazi A, Riazi G. Inhibition Of Tau Protein Aggregation By a Chaperone-like β-Boswellic Acid Conjugated To Gold Nanoparticles. ACS OMEGA 2022; 7:30347-30358. [PMID: 36061732 PMCID: PMC9434627 DOI: 10.1021/acsomega.2c03616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
A potential therapeutic strategy to inhibit tau protein aggregation in neurons has substantial effects on preventing or controlling Alzheimer's disease (AD). In this work, we designed a covalent and noncovalent conjugation of β-boswellic acid (BA) to gold nanoparticles (GNPs). We provided the opportunity to investigate the effect of the surface composition of BA-GNPs on the aggregation of the tau protein 1N/4R isoform in vitro. HR-TEM and FESEM micrographs revealed that GNPs were spherical and uniform, smaller than 25 nm. According to UV-visible and FTIR data, BA was successfully conjugated to GNPs. The finding illustrates the effect of the surface charge, size, and hydrophobicity of BA-GNPs on the kinetics of tau protein aggregation. The size and surface area of U-G-BA demonstrated that inhibited tau aggregation more effectively than covalently linked BA. The proposed method for preventing tau aggregation was monomer reduction. At the same time, a chaperone-like feature of GNP-BA while sustaining a tau native structure prevented the additional formation of fibrils. Overall, this study provides insight into the interaction of GNP-BAs with a monomer of tau protein and may suggest novel future therapies for AD.
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Affiliation(s)
- Masoumeh Gharb
- Institute
of Biochemistry and Biophysics, University
of Tehran, Tehran 14176-14335, Iran
- Caspian
Factually of Engineering, University of
Tehran, Rezvanshahr 4386191836, Gilan Iran
| | - Amideddin Nouralishahi
- Caspian
Factually of Engineering, University of
Tehran, Rezvanshahr 4386191836, Gilan Iran
| | - Ali Riazi
- Kondor
Pharma Inc., Mississauga, Ontario L4V 1T4, Canada
| | - Gholamhossein Riazi
- Institute
of Biochemistry and Biophysics, University
of Tehran, Tehran 14176-14335, Iran
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9
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Tran CH, Saha R, Blanco C, Bagchi D, Chen IA. Modulation of α-Synuclein Aggregation In Vitro by a DNA Aptamer. Biochemistry 2022; 61:1757-1765. [PMID: 35994742 PMCID: PMC9454088 DOI: 10.1021/acs.biochem.2c00207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein aggregation is an important problem for human health and biotechnology, with consequences in areas ranging from neurodegenerative diseases to protein production yields. Methods to modulate protein aggregation are therefore essential. One suggested method to modulate protein aggregation is the use of nucleic acid aptamers, that is, single-stranded nucleic acids that have been selected to specifically bind to a target. Previous studies in some systems have demonstrated that aptamers may inhibit protein aggregation, including for α-synuclein, a protein implicated in synucleinopathies. However, the mechanisms by which aptamers might affect or modulate aggregation have not been fully determined. In this study, we investigated the effect of an aptamer that binds α-synuclein oligomer, T-SO508, on α-synuclein aggregation in vitro using thioflavin T to monitor aggregation kinetics, and we performed atomic force microscopy, transmission electron microscopy, and analytical ultracentrifugation to characterize intermediate structures. The results indicated that T-SO508, but not control DNA sequences, extends the lag phase of aggregation and stabilizes formation of a small non-fibrillar aggregate complex. Attempts to use the aptamer-induced complexes to seed fibril formation did not in fact accelerate aggregation, indicating that these structures are off-pathway for aggregation. This study highlights a potential mechanism by which aptamers may modulate the aggregation properties of proteins.
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Affiliation(s)
- Claire H Tran
- Program in Biomolecular Sciences and Engineering, Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Ranajay Saha
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90024, United States
| | - Celia Blanco
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90024, United States
| | - Damayanti Bagchi
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90024, United States
| | - Irene A Chen
- Program in Biomolecular Sciences and Engineering, Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States.,Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90024, United States
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10
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Miyagawa A, Ide R, Nagatomo S, Nakatani K. Distribution Behavior of Single-Stranded DNA Molecules in an Amino-Group-Functionalized Silica Microparticle. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:8462-8468. [PMID: 35767692 DOI: 10.1021/acs.langmuir.2c01062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In this study, we investigated the distribution behavior of single-stranded DNA molecules with 20 bases in silica particles (particle size: ∼30 μm) using confocal fluorescence microspectroscopy. The distribution kinetics was investigated under various conditions, such as the type of base (adenine, thymine, guanine, and cytosine), pore size of the particle (30 and 50 nm), and salt concentration (100, 200, and 500 mM), which changed the distribution behavior. At high salt concentrations, we observed sigmoidal kinetic behavior, which does not occur in the general distribution of small organic molecules but is often observed in protein aggregation and nuclear growth. An analytical model based on DNA aggregation explained the sigmoidal distribution behavior well, and this model also worked well when the number of DNA molecules involved in DNA aggregation was greater than two. The intraparticle diffusion of DNA molecules was analyzed using the pore and surface diffusion model. As a result, the intraparticle diffusion of DNA aggregates mainly occurs according to surface diffusion, and the surface diffusion coefficient has the same value ((2.4-6.7) × 10-9 cm2 s-1) independent of the pore size and type of base.
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Affiliation(s)
- Akihisa Miyagawa
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba 305-8571, Ibaraki, Japan
| | - Ryosuke Ide
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba 305-8571, Ibaraki, Japan
| | - Shigenori Nagatomo
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba 305-8571, Ibaraki, Japan
| | - Kiyoharu Nakatani
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba 305-8571, Ibaraki, Japan
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11
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Mechanisms of enhanced aggregation and fibril formation of Parkinson's disease-related variants of α-synuclein. Sci Rep 2022; 12:6770. [PMID: 35474118 PMCID: PMC9043213 DOI: 10.1038/s41598-022-10789-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 04/08/2022] [Indexed: 12/18/2022] Open
Abstract
Aggregation of α-synuclein (α-syn) into amyloid fibrils is closely associated with Parkinson’s disease (PD). Familial mutations or posttranslational truncations in α-syn are known as risk factor for PD. Here, we examined the effects of the PD-related A30P or A53T point mutation and C-terminal 123–140 or 104–140 truncation on the aggregating property of α-syn based on the kinetic and thermodynamic analyses. Thioflavin T fluorescence measurements indicated that A53T, Δ123‒140, and Δ104–140 variants aggregated faster than WT α-syn, in which the A53T mutation markedly increases nucleation rate whereas the Δ123‒140 or Δ104‒140 truncation significantly increases both nucleation and fibril elongation rates. Ultracentrifugation and western blotting analyses demonstrated that these mutations or truncations promote the conversion of monomer to aggregated forms of α-syn. Analysis of the dependence of aggregation reaction of α-syn variants on the monomer concentration suggested that the A53T mutation enhances conversion of monomers to amyloid nuclei whereas the C-terminal truncations, especially the Δ104–140, enhance autocatalytic aggregation on existing fibrils. In addition, thermodynamic analysis of the kinetics of nucleation and fibril elongation of α-syn variants indicated that both nucleation and fibril elongation of WT α-syn are enthalpically and entropically unfavorable. Interestingly, the unfavorable activation enthalpy of nucleation greatly decreases for the A53T and becomes reversed in sign for the C-terminally truncated variants. Taken together, our results indicate that the A53T mutation and the C-terminal truncation enhance α-syn aggregation by reducing unfavorable activation enthalpy of nucleation, and the C-terminal truncation further triggers the autocatalytic fibril elongation on the fibril surfaces.
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12
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Briner A, Götz J, Polanco JC. Fyn Kinase Controls Tau Aggregation In Vivo. Cell Rep 2021; 32:108045. [PMID: 32814048 DOI: 10.1016/j.celrep.2020.108045] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 06/14/2020] [Accepted: 07/27/2020] [Indexed: 12/27/2022] Open
Abstract
Alzheimer's disease (AD) is a proteinopathy exhibiting aggregation of β-amyloid (Aβ) as amyloid plaques and tau as neurofibrillary tangles (NFTs), whereas primary tauopathies display only a tau pathology. Aβ toxicity is mediated by Fyn kinase in a tau-dependent process; however, whether Fyn controls tau pathology in diseases that lack Aβ pathology remains unexplored. To address this, we generate the Tg/Fyn-/- mouse, which couples mutant tau overexpression with Fyn knockout. Surprisingly, Tg/Fyn-/- mice exhibit a near-complete ablation of NFTs, alongside reduced tau hyperphosphorylation, altered tau solubility, and diminished synaptic tau accumulation. Furthermore, Tg/Fyn-/- brain lysates elicit less tau seeding in tau biosensor cells. Lastly, the fibrillization of tau is boosted by its pseudophosphorylation at the Fyn epitope Y18. Together, this identifies Fyn as a key regulator of tau pathology independently of Aβ-induced toxicity and thereby represents a potentially valuable therapeutic target for not only AD but also tauopathies more generally.
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Affiliation(s)
- Adam Briner
- Clem Jones Centre for Ageing Dementia Research (CJCADR), Queensland Brain Institute (QBI), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jürgen Götz
- Clem Jones Centre for Ageing Dementia Research (CJCADR), Queensland Brain Institute (QBI), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Juan Carlos Polanco
- Clem Jones Centre for Ageing Dementia Research (CJCADR), Queensland Brain Institute (QBI), The University of Queensland, Brisbane, QLD 4072, Australia.
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Chen X, Deng X, Han X, Liang Y, Meng Z, Liu R, Su W, Zhu H, Fu T. Inhibition of Lysozyme Amyloid Fibrillation by Silybin Diastereoisomers: The Effects of Stereochemistry. ACS OMEGA 2021; 6:3307-3318. [PMID: 33553948 PMCID: PMC7860231 DOI: 10.1021/acsomega.0c05788] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 01/08/2021] [Indexed: 05/24/2023]
Abstract
Silybin is a flavonoid lignin compound consisting of two diastereomers with nearly equal molar ratios. It has been reported that silybin can effectively inhibit the aggregation of amyloid protein, but the difference between the two silybin diastereomers has been rarely studied. In this work, the inhibitory ability of silybin to hen egg-white lysozyme (HEWL) was demonstrated, and the difference of kinetic parameters of two diastereomers was analyzed. Fluorescence quenching titration was utilized to analyze the binding differences to native HEWL between the diastereomers, and transmission electron microscopy (TEM) was utilized to analyze the characteristics of the surface of various samples. The differences between hydrophobicity and the secondary structure among several HEWL samples were measured by the 8-anilino-1-naphthalene sulfonic (ANS) acid fluorescence probe, Raman spectra, and far-UV circular dichroism. Moreover, the differences in the binding energy of these two diastereomers with HEWL were analyzed by molecular docking. Also, we have investigated the effect of silybin diastereomers on HEWL fibril-induced cytotoxicity in SH-SY5Y cells. Results show that silybin has a certain inhibitory effect on the HEWL fibrillogenesis process, while silybin B (SB) has a more significant inhibitory effect than silybin A (SA), especially at high concentrations. This work provides some insights into the screening of amyloid inhibitors from complicated natural products and indicates that SB has the prospect of further development as an amyloid inhibitor.
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Affiliation(s)
- Xuanyu Chen
- School
of Pharmacy, Nanjing University of Chinese
Medicine, Nanjing 210023, China
- Plant
Medicine Research and Technological Development Center of Jiangsu
Province, Nanjing 210023, China
| | - Xiaomin Deng
- School
of Pharmacy, Nanjing University of Chinese
Medicine, Nanjing 210023, China
- Plant
Medicine Research and Technological Development Center of Jiangsu
Province, Nanjing 210023, China
| | - Xingxing Han
- School
of Pharmacy, Nanjing University of Chinese
Medicine, Nanjing 210023, China
- Plant
Medicine Research and Technological Development Center of Jiangsu
Province, Nanjing 210023, China
| | - Yinmei Liang
- School
of Pharmacy, Nanjing University of Chinese
Medicine, Nanjing 210023, China
- Plant
Medicine Research and Technological Development Center of Jiangsu
Province, Nanjing 210023, China
| | - Zhiping Meng
- School
of Pharmacy, Nanjing University of Chinese
Medicine, Nanjing 210023, China
- Plant
Medicine Research and Technological Development Center of Jiangsu
Province, Nanjing 210023, China
| | - Rui Liu
- School
of Pharmacy, Nanjing University of Chinese
Medicine, Nanjing 210023, China
| | - Wenqiang Su
- School
of Pharmacy, Nanjing University of Chinese
Medicine, Nanjing 210023, China
- Plant
Medicine Research and Technological Development Center of Jiangsu
Province, Nanjing 210023, China
| | - Huaxu Zhu
- School
of Pharmacy, Nanjing University of Chinese
Medicine, Nanjing 210023, China
- Plant
Medicine Research and Technological Development Center of Jiangsu
Province, Nanjing 210023, China
- Separation
Engineering of Chinese Traditional Medicine Compound, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Tingming Fu
- School
of Pharmacy, Nanjing University of Chinese
Medicine, Nanjing 210023, China
- Plant
Medicine Research and Technological Development Center of Jiangsu
Province, Nanjing 210023, China
- Separation
Engineering of Chinese Traditional Medicine Compound, Nanjing University of Chinese Medicine, Nanjing 210023, China
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14
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The Aggregation Pattern of Aβ
1–40
is Altered by the Presence of
N
‐Truncated Aβ
4–40
and/or Cu
II
in a Similar Way through Ionic Interactions. Chemistry 2021; 27:2798-2809. [DOI: 10.1002/chem.202004484] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Indexed: 12/19/2022]
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15
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Faller P, Hureau C. Reproducibility Problems of Amyloid-β Self-Assembly and How to Deal With Them. Front Chem 2021; 8:611227. [PMID: 33520935 PMCID: PMC7841044 DOI: 10.3389/fchem.2020.611227] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/08/2020] [Indexed: 12/25/2022] Open
Abstract
The self-assembly of peptides and proteins into amyloid fibrils and other aggregates are linked to several diseases. One of the most studied cases is the peptide amyloid-β (Aβ), found self-assembled in Alzheimer's disease patients' brains. In test tubes, assays with chemically synthesized or recombinant Aβ are widely investigated to understand the aggregation process and to find modulators, which could be of therapeutic interest. Experience over more than a decade in our laboratory through discussions with colleagues, expertly studying the literature, and as reviewers revealed to us the widely encountered difficulty to control the aggregation and obtain reproducible results in the test tube. However, this issue is scarcely reported and discussed in the publications, which we think hampers strongly the progress in this field and can deceive newcomers. Here, we describe the difficulty and potential reasons to obtain reproducible aggregation data and propose some guidelines for working with it.
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Affiliation(s)
- Peter Faller
- Institut de Chimie, UMR 7177, CNRS-Université de Strasbourg, Strasbourg, France
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16
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Saghir AE, Farrugia G, Vassallo N. The human islet amyloid polypeptide in protein misfolding disorders: Mechanisms of aggregation and interaction with biomembranes. Chem Phys Lipids 2020; 234:105010. [PMID: 33227292 DOI: 10.1016/j.chemphyslip.2020.105010] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/06/2020] [Accepted: 11/09/2020] [Indexed: 02/09/2023]
Abstract
Human islet amyloid polypeptide (hIAPP), otherwise known as amylin, is a 37-residue peptide hormone which is reported to be a common factor in protein misfolding disorders such as type-2 diabetes mellitus, Alzheimer's disease and Parkinson's disease, due to deposition of insoluble hIAPP amyloid in the pancreas and brain. Multiple studies point to the importance of the peptide's interaction with biological membranes and the cytotoxicity of hIAPP species. Here, we discuss the aggregation pathways of hIAPP amyloid fibril formation and focus on the complex interplay between membrane-mediated assembly of hIAPP and the associated mechanisms of membrane damage caused by the peptide species. Mitochondrial membranes, which are unique in their lipid composition, are proposed as prime targets for the early intracellular formation of hIAPP toxic entities. We suggest that future studies should include more physiologically-relevant and in-cell studies to allow a more accurate model of in vivo interactions. Finally, we underscore an urgent need for developing effective therapeutic strategies aimed at hindering hIAPP-phospholipid interactions.
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Affiliation(s)
- Adam El Saghir
- Dept. of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta; Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Gianluca Farrugia
- Dept. of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta; Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Neville Vassallo
- Dept. of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta; Centre for Molecular Medicine and Biobanking, University of Malta, Msida, Malta.
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17
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Amadei F, Thoma J, Czajor J, Kimmle E, Yamamoto A, Abuillan W, Konovalov OV, Chushkin Y, Tanaka M. Ion-Mediated Cross-linking of Biopolymers Confined at Liquid/Liquid Interfaces Probed by In Situ High-Energy Grazing Incidence X-ray Photon Correlation Spectroscopy. J Phys Chem B 2020; 124:8937-8942. [PMID: 32876453 DOI: 10.1021/acs.jpcb.0c07056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
As manifested in biological cell membranes, the confinement of chemical reactions at the 2D interfaces significantly improves the reaction efficacy. The interface between two liquid phases is used in various key processes in industries, such as in food emulsification and floatation. However, monitoring the changes in the mechanics and dynamics of molecules confined at the liquid/liquid interfaces still remains a scientific challenge because it is nontrivial to access the interface buried under a liquid phase. Herein, we report the in situ monitoring of the cross-linking of polyalginate mediated by Ca2+ ions at the oil/water interface by grazing incidence X-ray photon correlation spectroscopy (GIXPCS). We first optimized the reaction conditions with the aid of interfacial shear rheology and then performed GIXPCS using a high-energy synchrotron X-ray beam (22 keV) that guarantees sufficiently high transmittance through the oil phase. The intensity autocorrelation functions implied that the formation of a percolated network of polyalginate is accompanied by increasing relaxation time. Moreover, the relaxation rate scales linearly with the momentum transfer parallel to the interface, suggesting that the process is driven by hyperdiffusive propagation but not by Brownian diffusion. Our data indicated that high-energy GIXPCS has potential for in situ monitoring of changes in the dynamics of polymers confined between two liquid phases.
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Affiliation(s)
- Federico Amadei
- Physical Chemistry of Biosystems, Institute of Physical Chemistry, Heidelberg University, Heidelberg 69120, Germany
| | - Judith Thoma
- Physical Chemistry of Biosystems, Institute of Physical Chemistry, Heidelberg University, Heidelberg 69120, Germany
| | - Julian Czajor
- Physical Chemistry of Biosystems, Institute of Physical Chemistry, Heidelberg University, Heidelberg 69120, Germany
| | - Esther Kimmle
- Physical Chemistry of Biosystems, Institute of Physical Chemistry, Heidelberg University, Heidelberg 69120, Germany
| | - Akihisa Yamamoto
- Center for Integrative Medicine and Physics, Institute for Advanced Study, Kyoto University, Kyoto 606-8501, Japan
| | - Wasim Abuillan
- Physical Chemistry of Biosystems, Institute of Physical Chemistry, Heidelberg University, Heidelberg 69120, Germany
| | - Oleg V Konovalov
- European Synchrotron Radiation Facility, CS 40220, Grenoble 38043, France
| | - Yuriy Chushkin
- European Synchrotron Radiation Facility, CS 40220, Grenoble 38043, France
| | - Motomu Tanaka
- Physical Chemistry of Biosystems, Institute of Physical Chemistry, Heidelberg University, Heidelberg 69120, Germany.,Center for Integrative Medicine and Physics, Institute for Advanced Study, Kyoto University, Kyoto 606-8501, Japan
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18
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Króliczewski J, Bartoszewska S, Dudkowska M, Janiszewska D, Biernatowska A, Crossman DK, Krzymiński K, Wysocka M, Romanowska A, Baginski M, Markuszewski M, Ochocka RJ, Collawn JF, Sikorski AF, Sikora E, Bartoszewski R. Utilizing Genome-Wide mRNA Profiling to Identify the Cytotoxic Chemotherapeutic Mechanism of Triazoloacridone C-1305 as Direct Microtubule Stabilization. Cancers (Basel) 2020; 12:cancers12040864. [PMID: 32252403 PMCID: PMC7226417 DOI: 10.3390/cancers12040864] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/21/2020] [Accepted: 03/31/2020] [Indexed: 12/12/2022] Open
Abstract
Rational drug design and in vitro pharmacology profiling constitute the gold standard in drug development pipelines. Problems arise, however, because this process is often difficult due to limited information regarding the complete identification of a molecule’s biological activities. The increasing affordability of genome-wide next-generation technologies now provides an excellent opportunity to understand a compound’s diverse effects on gene regulation. Here, we used an unbiased approach in lung and colon cancer cell lines to identify the early transcriptomic signatures of C-1305 cytotoxicity that highlight the novel pathways responsible for its biological activity. Our results demonstrate that C-1305 promotes direct microtubule stabilization as a part of its mechanism of action that leads to apoptosis. Furthermore, we show that C-1305 promotes G2 cell cycle arrest by modulating gene expression. The results indicate that C-1305 is the first microtubule stabilizing agent that also is a topoisomerase II inhibitor. This study provides a novel approach and methodology for delineating the antitumor mechanisms of other putative anticancer drug candidates.
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Affiliation(s)
- Jarosław Króliczewski
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, 80-416 Gdansk, Poland; (J.K.); (R.J.O.)
| | - Sylwia Bartoszewska
- Department of Inorganic Chemistry, Medical University of Gdansk, 80-416 Gdansk, Poland;
| | - Magdalena Dudkowska
- Laboratory of the Molecular Bases of Ageing, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, 02-093 Warsaw, Poland (D.J.); (E.S.)
| | - Dorota Janiszewska
- Laboratory of the Molecular Bases of Ageing, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, 02-093 Warsaw, Poland (D.J.); (E.S.)
| | - Agnieszka Biernatowska
- Department of Cytobiochemistry, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw Poland;
| | - David K. Crossman
- Department of Genetics, UAB Genomics Core Facility, University of Alabama at Birmingham, Birmingham, AL 35233, USA;
| | - Karol Krzymiński
- Faculty of Chemistry, University of Gdansk, 80-308 Gdansk, Poland; (K.K.); (M.W.); (A.R.)
| | - Małgorzata Wysocka
- Faculty of Chemistry, University of Gdansk, 80-308 Gdansk, Poland; (K.K.); (M.W.); (A.R.)
| | - Anna Romanowska
- Faculty of Chemistry, University of Gdansk, 80-308 Gdansk, Poland; (K.K.); (M.W.); (A.R.)
| | - Maciej Baginski
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, 80-233 Gdansk, Poland;
| | - Michal Markuszewski
- Department of Biopharmacy and Pharmacodynamics, Medical University of Gdansk, 80-416 Gdansk, Poland;
| | - Renata J. Ochocka
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, 80-416 Gdansk, Poland; (J.K.); (R.J.O.)
| | - James F. Collawn
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
| | | | - Ewa Sikora
- Laboratory of the Molecular Bases of Ageing, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, 02-093 Warsaw, Poland (D.J.); (E.S.)
| | - Rafal Bartoszewski
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, 80-416 Gdansk, Poland; (J.K.); (R.J.O.)
- Correspondence: ; Tel.: +48-58-349-32-14; Fax: +48-58-349-32-11
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19
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Mishra A, Korlepara DB, Balasubramanian S, George SJ. Bioinspired, ATP-driven co-operative supramolecular polymerization and its pathway dependence. Chem Commun (Camb) 2020; 56:1505-1508. [PMID: 31917382 DOI: 10.1039/c9cc08790g] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A bio-inspired, ATP-driven nucleation growth assembly is demonstrated using an amphiphilic naphthalene diimide (NDI) derivative appended with guanidinium receptors to promote specific salt-bridge type interaction with nucleotide phosphates. Detailed spectroscopic and microscopic probing revealed a pathway-dependent co-operative self-assembly to yield two-dimensional and scrolled nano-tubular bilayer assemblies under kinetic and thermodynamic conditions, respectively.
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Affiliation(s)
- Ananya Mishra
- Supramolecular Chemistry Laboratory, New Chemistry Unit, School of Advanced Materials, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore, 560064, India.
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20
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Lempart J, Tse E, Lauer JA, Ivanova MI, Sutter A, Yoo N, Huettemann P, Southworth D, Jakob U. Mechanistic insights into the protective roles of polyphosphate against amyloid cytotoxicity. Life Sci Alliance 2019; 2:2/5/e201900486. [PMID: 31533964 PMCID: PMC6751573 DOI: 10.26508/lsa.201900486] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 09/09/2019] [Accepted: 09/10/2019] [Indexed: 11/24/2022] Open
Abstract
This study provides novel insights into the mechanisms by which presence of polyP alters the formation, structural properties, and cytotoxic effects of α-synuclein fibers. The universally abundant polyphosphate (polyP) accelerates fibril formation of disease-related amyloids and protects against amyloid cytotoxicity. To gain insights into the mechanism(s) by which polyP exerts these effects, we focused on α-synuclein, a well-studied amyloid protein, which constitutes the major component of Lewy bodies found in Parkinson’s disease. Here, we demonstrate that polyP is unable to accelerate the rate-limiting step of α-synuclein fibril formation but effectively nucleates fibril assembly once α-synuclein oligomers are formed. Binding of polyP to α-synuclein either during fibril formation or upon fibril maturation substantially alters fibril morphology and effectively reduces the ability of α-synuclein fibrils to interact with cell membranes. The effect of polyP appears to be α-synuclein fibril specific and successfully prevents the uptake of fibrils into neuronal cells. These results suggest that altering the polyP levels in the extracellular space might be a potential therapeutic strategy to prevent the spreading of the disease.
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Affiliation(s)
- Justine Lempart
- Graduate Program in Biochemistry, Department of Chemistry, Technische Universität München, München, Germany.,Department of Molecular, Cellular and Developmental Biology University of Michigan, Ann Arbor, MI, USA
| | - Eric Tse
- Institute for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - James A Lauer
- Department of Molecular, Cellular and Developmental Biology University of Michigan, Ann Arbor, MI, USA
| | - Magdalena I Ivanova
- Biophysics Program, University of Michigan, Ann Arbor, MI, USA.,Department of Neurology, University of Michigan, Ann Arbor, MI, USA
| | | | - Nicholas Yoo
- Department of Molecular, Cellular and Developmental Biology University of Michigan, Ann Arbor, MI, USA
| | - Philipp Huettemann
- Department of Molecular, Cellular and Developmental Biology University of Michigan, Ann Arbor, MI, USA
| | - Daniel Southworth
- Institute for Neurodegenerative Diseases, Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Ursula Jakob
- Department of Molecular, Cellular and Developmental Biology University of Michigan, Ann Arbor, MI, USA .,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
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21
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Omojola T, Lukyanov DB, Cherkasov N, Zholobenko VL, van Veen AC. Influence of Precursors on the Induction Period and Transition Regime of Dimethyl Ether Conversion to Hydrocarbons over ZSM-5 Catalysts. Ind Eng Chem Res 2019. [DOI: 10.1021/acs.iecr.9b03344] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Toyin Omojola
- Department of Chemical Engineering, University of Bath, Claverton Down, Bath BA2 7AY, U.K
- School of Engineering, University of Warwick, Library Road, Coventry CV4 7AL, U.K
| | - Dmitry B. Lukyanov
- Department of Chemical Engineering, University of Bath, Claverton Down, Bath BA2 7AY, U.K
| | - Nikolay Cherkasov
- School of Engineering, University of Warwick, Library Road, Coventry CV4 7AL, U.K
| | | | - André C. van Veen
- School of Engineering, University of Warwick, Library Road, Coventry CV4 7AL, U.K
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22
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Niknaddaf F, Shahangian SS, Heydari A, Hosseinkhani S, Sajedi RH. Deep Eutectic Solvents as a New Generation of Chemical Chaperones. ChemistrySelect 2018. [DOI: 10.1002/slct.201802235] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Forouzan Niknaddaf
- Department of Biochemistry; Faculty of Biological Sciences, Tarbiat Modares University; Tehran Iran
| | | | - Akbar Heydari
- Department of Chemistry Faculty of Basic Sciences; Tarbiat Modares University Tehran; Iran
| | - Saman Hosseinkhani
- Department of Biochemistry; Faculty of Biological Sciences, Tarbiat Modares University; Tehran Iran
| | - Reza H. Sajedi
- Department of Biochemistry; Faculty of Biological Sciences, Tarbiat Modares University; Tehran Iran
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23
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Eilertsen J, Schnell S. A Kinetic Analysis of Coupled (or Auxiliary) Enzyme Reactions. Bull Math Biol 2018; 80:3154-3183. [DOI: 10.1007/s11538-018-0513-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 09/20/2018] [Indexed: 10/28/2022]
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24
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Mishra A, Korlepara DB, Kumar M, Jain A, Jonnalagadda N, Bejagam KK, Balasubramanian S, George SJ. Biomimetic temporal self-assembly via fuel-driven controlled supramolecular polymerization. Nat Commun 2018; 9:1295. [PMID: 29602946 PMCID: PMC5878180 DOI: 10.1038/s41467-018-03542-z] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 02/22/2018] [Indexed: 12/26/2022] Open
Abstract
Temporal control of supramolecular assemblies to modulate the structural and transient characteristics of synthetic nanostructures is an active field of research within supramolecular chemistry. Molecular designs to attain temporal control have often taken inspiration from biological assemblies. One such assembly in Nature which has been studied extensively, for its well-defined structure and programmable self-assembly, is the ATP-driven seeded self-assembly of actin. Here we show, in a synthetic manifestation of actin self-assembly, an ATP-selective and ATP-fuelled, controlled supramolecular polymerization of a phosphate receptor functionalised monomer. It undergoes fuel-driven nucleation and seeded growth that provide length control and narrow dispersity of the resultant assemblies. Furthermore, coupling via ATP-hydrolysing enzymes yielded its transient characteristics. These results will usher investigations into synthetic analogues of important biological self-assembly motifs and will prove to be a significant advancement toward biomimetic temporally programmed materials.
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Affiliation(s)
- Ananya Mishra
- Supramolecular Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore, 560064, India
| | - Divya B Korlepara
- Molecular Simulations Laboratory, Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore, 560064, India
| | - Mohit Kumar
- Supramolecular Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore, 560064, India
| | - Ankit Jain
- Supramolecular Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore, 560064, India
| | - Narendra Jonnalagadda
- Supramolecular Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore, 560064, India
| | - Karteek K Bejagam
- Molecular Simulations Laboratory, Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore, 560064, India
| | - Sundaram Balasubramanian
- Molecular Simulations Laboratory, Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore, 560064, India.
| | - Subi J George
- Supramolecular Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore, 560064, India.
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25
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Kamgar-Parsi K, Hong L, Naito A, Brooks CL, Ramamoorthy A. Growth-incompetent monomers of human calcitonin lead to a noncanonical direct relationship between peptide concentration and aggregation lag time. J Biol Chem 2017; 292:14963-14976. [PMID: 28739873 PMCID: PMC5592673 DOI: 10.1074/jbc.m117.791236] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 07/19/2017] [Indexed: 11/06/2022] Open
Abstract
The role of the peptide hormone calcitonin in skeletal protection has led to its use as a therapeutic for osteoporosis. However, calcitonin aggregation into amyloid fibrils limits its therapeutic efficacy, necessitating a modification of calcitonin's aggregation kinetics. Here, we report a direct relationship between human calcitonin (hCT) concentration and aggregation lag time. This kinetic trend was contrary to the conventional understanding of amyloid aggregation and persisted over a range of aggregation conditions, as confirmed by thioflavin-T kinetics assays, CD spectroscopy, and transmission EM. Dynamic light scattering, 1H NMR experiments, and seeded thioflavin-T assay results indicated that differences in initial peptide species contribute to this trend more than variations in the primary nucleus formation rate. On the basis of kinetics modeling results, we propose a mechanism whereby a structural conversion of hCT monomers is needed before incorporation into the fibril. Our kinetic mechanism recapitulates the experimentally observed relationship between peptide concentration and lag time and represents a novel mechanism in amyloid aggregation. Interestingly, hCT at low pH and salmon calcitonin (sCT) exhibited the canonical inverse relationship between concentration and lag time. Comparative studies of hCT and sCT with molecular dynamics simulations and CD indicated an increased α-helical structure in sCT and low-pH hCT monomers compared with neutral-pH hCT, suggesting that α-helical monomers represent a growth-competent species, whereas unstructured random coil monomers represent a growth-incompetent species. Our finding that initial monomer concentration is positively correlated with lag time in hCT aggregation could help inform future efforts for improving therapeutic applications of CT.
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Affiliation(s)
- Kian Kamgar-Parsi
- From the Applied Physics Program, University of Michigan, Ann Arbor, Michigan 48109
| | - Liu Hong
- Zhou Pei-Yuan Center for Applied Mathematics, Tsinghua University, Beijing 100084, China
| | - Akira Naito
- Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan, and
| | - Charles L Brooks
- Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109-1055
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109-1055
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26
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Crespo R, Villar-Alvarez E, Taboada P, Rocha FA, Damas AM, Martins PM. Insoluble Off-Pathway Aggregates as Crowding Agents during Amyloid Fibril Formation. J Phys Chem B 2017; 121:2288-2298. [DOI: 10.1021/acs.jpcb.7b01120] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Rosa Crespo
- LEPABE,
Laboratório de Engenharia de Processos, Ambiente, Biotecnologia
e Energia, Departamento de Engenharia Química, Faculdade de Engenharia da Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Eva Villar-Alvarez
- Área
de Física de la Materia Condensada, Facultad de Física, Universidad de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Pablo Taboada
- Área
de Física de la Materia Condensada, Facultad de Física, Universidad de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Fernando A. Rocha
- LEPABE,
Laboratório de Engenharia de Processos, Ambiente, Biotecnologia
e Energia, Departamento de Engenharia Química, Faculdade de Engenharia da Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Ana M. Damas
- ICBAS
− Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto 4050-313, Portugal
| | - Pedro M. Martins
- LEPABE,
Laboratório de Engenharia de Processos, Ambiente, Biotecnologia
e Energia, Departamento de Engenharia Química, Faculdade de Engenharia da Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ICBAS
− Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto 4050-313, Portugal
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27
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Marasini C, Foderà V, Vestergaard B. Sucrose modulates insulin amyloid-like fibril formation: effect on the aggregation mechanism and fibril morphology. RSC Adv 2017. [DOI: 10.1039/c6ra25872g] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Sucrose modifies the human insulin fibrillation pathways, affecting the fibril morphology.
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Affiliation(s)
- Carlotta Marasini
- Department of Drug Design and Pharmacology
- University of Copenhagen
- 2100 Copenhagen
- Denmark
| | - Vito Foderà
- Section for Biologics
- Department of Pharmacy
- University of Copenhagen
- 2100 Copenhagen
- Denmark
| | - Bente Vestergaard
- Department of Drug Design and Pharmacology
- University of Copenhagen
- 2100 Copenhagen
- Denmark
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