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Kobayashi R, Nabika H. Liquid-liquid phase separation induced by crowding condition affects amyloid-β aggregation mechanism. SOFT MATTER 2024; 20:5331-5342. [PMID: 38847095 DOI: 10.1039/d4sm00470a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
Liquid-liquid phase separation (LLPS) is common in the aggregation of proteins associated with neurodegenerative diseases. Many efforts have been made to reproduce crowded conditions with artificial polymeric materials to understand the effect of LLPS in physiological conditions with significantly highly concentrated proteins, such as intrinsically disordered proteins. Although the possibility that LLPS is involved in intracellular amyloid-β (Aβ) aggregation, a protein related to the pathogenesis of Alzheimer's disease, has been investigated, the relationship between LLPS and the aggregation of Aβ is poorly characterized. Thus, in this study, we mimicked the intracellular crowding environment using polyethylene glycol and dextran, used commonly as model polymers, to examine the relationship of Aβ with LLPS and aggregation dynamics in vitro. We confirmed that Aβ undergoes LLPS under specific polymer coexistence conditions. Moreover, the addition of different electrolytes modulated LLPS and fibril formation. These results suggest that hydrophobic and electrostatic interactions are the driving forces for the LLPS of Aβ. Similar to the role of the liposome interface, the interface of droplets induced by LLPS functioned as the site for heterogeneous nucleation. These findings offer valuable insights into the complex mechanisms of Aβ aggregation in vivo and may be useful in establishing therapeutic methods for Alzheimer's disease.
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Affiliation(s)
- Ryuki Kobayashi
- Department of Science, Graduate School of Science and Engineering, Yamagata University, 1-4-12, Kojirakawa, Yamagata 990-8560, Japan
| | - Hideki Nabika
- Faculty of Science, Yamagata University, 1-4-12 Kojirakawa, Yamagata 990-8560, Japan.
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2
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Dey A, Verma A, Bhaskar U, Sarkar B, Kallianpur M, Vishvakarma V, Das AK, Garai K, Mukherjee O, Ishii K, Tahara T, Maiti S. A Toxicogenic Interaction between Intracellular Amyloid-β and Apolipoprotein-E. ACS Chem Neurosci 2024; 15:1265-1275. [PMID: 38421952 DOI: 10.1021/acschemneuro.4c00048] [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] [Indexed: 03/02/2024] Open
Abstract
Alzheimer's disease (AD) is associated with the aggregation of amyloid β (Aβ) and tau proteins. Why ApoE variants are significant genetic risk factors remains a major unsolved puzzle in understanding AD, although intracellular interactions with ApoE are suspected to play a role. Here, we show that specific changes in the fluorescence lifetime of fluorescently tagged small Aβ oligomers in rat brain cells correlate with the cellular ApoE content. An inhibitor of the Aβ-ApoE interaction suppresses these changes and concomitantly reduces Aβ toxicity in a dose-dependent manner. Single-molecule techniques show changes both in the conformation and in the stoichiometry of the oligomers. Neural stem cells derived from hiPSCs of Alzheimer's patients also exhibit these fluorescence lifetime changes. We infer that intracellular interaction with ApoE modifies the N-terminus of the Aβ oligomers, inducing changes in their stoichiometry, membrane affinity, and toxicity. These changes can be directly imaged in live cells and can potentially be used as a rapid and quantitative cellular assay for AD drug discovery.
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Affiliation(s)
- Arpan Dey
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Aditi Verma
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Uchit Bhaskar
- Institute of Stem Cell Science and Regenerative Medicine, Bangalore 560065, India
| | - Bidyut Sarkar
- Molecular Spectroscopy Laboratory, RIKEN, Wako, Saitama 3510198, Japan
| | - Mamata Kallianpur
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Vicky Vishvakarma
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Anand Kant Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Kanchan Garai
- Tata Institute of Fundamental Research, Hyderabad 500107, India
| | - Odity Mukherjee
- Institute of Stem Cell Science and Regenerative Medicine, Bangalore 560065, India
| | - Kunihiko Ishii
- Molecular Spectroscopy Laboratory, RIKEN, Wako, Saitama 3510198, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN, Wako, Saitama 3510198, Japan
| | - Sudipta Maiti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
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3
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Cheung See Kit M, Cropley TC, Bleiholder C, Chouinard CD, Sobott F, Webb IK. The role of solvation on the conformational landscape of α-synuclein. Analyst 2023; 149:125-136. [PMID: 37982746 PMCID: PMC10760066 DOI: 10.1039/d3an01680c] [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] [Indexed: 11/21/2023]
Abstract
Native ion mobility mass spectrometry has been used extensively to characterize ensembles of intrinsically disordered protein (IDP) conformers, but the extent to which the gaseous measurements provide realistic pictures of the solution conformations for such flexible proteins remains unclear. Therefore, we systematically studied the relationship between the solution and gaseous structural ensembles by measuring electrospray charge state and collision cross section (CCS) distributions for cationic and anionic forms of α-synuclein (αSN), an anionic protein in solution, as well as directly probed gas phase residue to residue distances via ion/ion reactions between gaseous α-synuclein cations and disulfonic acid linkers that form strong electrostatic bonds. We also combined results from in-solution protein crosslinking identified from native tandem mass spectrometry (MS/MS) with an initial αSN ensemble generated computationally by IDPConformerGenerator to generate an experimentally restrained solution ensemble of αSN. CCS distributions were directly calculated for the solution ensembles determined by NMR and compared to predicted gaseous conformers. While charge state and collision cross section distributions are useful for qualitatively describing the relative structural dynamics of proteins and major conformational changes induced by changes to solution states, the predicted and measured gas phase conformers include subpopulations that are significantly different than those expected from completely "freezing" solution conformations and preserving them in the gas phase. However, insights were gained on the various roles of solvent in stabilizing various conformers for extremely dynamic proteins like α-synuclein.
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Affiliation(s)
- Melanie Cheung See Kit
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, USA.
| | - Tyler C Cropley
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Christian Bleiholder
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
| | | | - Frank Sobott
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Ian K Webb
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, USA.
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
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4
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Das S, Rana G, Ali F, Datta A. Single particle level dynamics of photoactivation and suppression of Auger recombination in aqueous Cu-doped CdS quantum dots. NANOSCALE 2023; 15:4469-4476. [PMID: 36752332 DOI: 10.1039/d2nr06688b] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Cu-doped CdS quantum dots (QDs) have been synthesized in water using 3-mercaptopropionic acid (3-MPA) as the capping agent. They exhibit intense photoluminescence and excellent color tunability, unlike most of the QDs synthesized/dispersed in water so far. Complete characterization of these aqueous doped CdS QDs has been performed for the first time, along with a single particle level elucidation of their exciton dynamics using fluorescence correlation spectroscopy. Photoactivation via dim/dark to bright particle conversion is observed at higher excitation powers. Dispersive blinking kinetics in undoped QDs reflects the involvement of a broad distribution of trap states. A lesser extent of dispersity is observed for doped QDs, in which hole-capture by Cu-defect states predominates. Excitation fluence dependence of the blinking rate highlights the role of Auger recombination in undoped QDs, which is suppressed significantly upon doping, due to disruption of the electron-hole correlation.
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Affiliation(s)
- Sharmistha Das
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Gourab Rana
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Fariyad Ali
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Anindya Datta
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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5
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Alraawi Z, Banerjee N, Mohanty S, Kumar TKS. Amyloidogenesis: What Do We Know So Far? Int J Mol Sci 2022; 23:ijms232213970. [PMID: 36430450 PMCID: PMC9695042 DOI: 10.3390/ijms232213970] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/01/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
The study of protein aggregation, and amyloidosis in particular, has gained considerable interest in recent times. Several neurodegenerative diseases, such as Alzheimer's (AD) and Parkinson's (PD) show a characteristic buildup of proteinaceous aggregates in several organs, especially the brain. Despite the enormous upsurge in research articles in this arena, it would not be incorrect to say that we still lack a crystal-clear idea surrounding these notorious aggregates. In this review, we attempt to present a holistic picture on protein aggregation and amyloids in particular. Using a chronological order of discoveries, we present the case of amyloids right from the onset of their discovery, various biophysical techniques, including analysis of the structure, the mechanisms and kinetics of the formation of amyloids. We have discussed important questions on whether aggregation and amyloidosis are restricted to a subset of specific proteins or more broadly influenced by the biophysiochemical and cellular environment. The therapeutic strategies and the significant failure rate of drugs in clinical trials pertaining to these neurodegenerative diseases have been also discussed at length. At a time when the COVID-19 pandemic has hit the globe hard, the review also discusses the plausibility of the far-reaching consequences posed by the virus, such as triggering early onset of amyloidosis. Finally, the application(s) of amyloids as useful biomaterials has also been discussed briefly in this review.
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Affiliation(s)
- Zeina Alraawi
- Department of Chemistry and Biochemistry, Fulbright College of Art and Science, University of Arkansas, Fayetteville, AR 72701, USA
| | - Nayan Banerjee
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Srujana Mohanty
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Kolkata 741246, India
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6
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Davidson DS, Kraus JA, Montgomery JM, Lemkul JA. Effects of Familial Alzheimer's Disease Mutations on the Folding Free Energy and Dipole-Dipole Interactions of the Amyloid β-Peptide. J Phys Chem B 2022; 126:7552-7566. [PMID: 36150020 PMCID: PMC9547858 DOI: 10.1021/acs.jpcb.2c03520] [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] [Indexed: 11/30/2022]
Abstract
Familial Alzheimer's disease (FAD) mutations of the amyloid β-peptide (Aβ) are known to lead to early onset and more aggressive Alzheimer's disease. FAD mutations such as "Iowa" (D23N), "Arctic" (E22G), "Italian" (E22K), and "Dutch" (E22Q) have been shown to accelerate Aβ aggregation relative to the wild-type (WT). The mechanism by which these mutations facilitate increased aggregation is unknown, but each mutation results in a change in the net charge of the peptide. Previous studies have used nonpolarizable force fields to study Aβ, providing some insight into how this protein unfolds. However, nonpolarizable force fields have fixed charges that lack the ability to redistribute in response to changes in local electric fields. Here, we performed polarizable molecular dynamics simulations on the full-length Aβ42 of WT and FAD mutations and calculated folding free energies of the Aβ15-27 fragment via umbrella sampling. By studying both the full-length Aβ42 and a fragment containing mutations and the central hydrophobic cluster (residues 17-21), we were able to systematically study how these FAD mutations impact secondary and tertiary structure and the thermodynamics of folding. Electrostatic interactions, including those between permanent and induced dipoles, affected side-chain properties, salt bridges, and solvent interactions. The FAD mutations resulted in shifts in the electronic structure and solvent accessibility at the central hydrophobic cluster and the hydrophobic C-terminal region. Using umbrella sampling, we found that the folding of the WT and E22 mutants is enthalpically driven, whereas the D23N mutant is entropically driven, arising from a different unfolding pathway and peptide-bond dipole response. Together, the unbiased, full-length, and umbrella sampling simulations of fragments reveal that the FAD mutations perturb nearby residues and others in hydrophobic regions to potentially alter solubility. These results highlight the role electronic polarizability plays in amyloid misfolding and the role of heterogeneous microenvironments that arise as conformational change takes place.
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Affiliation(s)
- Darcy S Davidson
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Joshua A Kraus
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Julia M Montgomery
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Justin A Lemkul
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
- Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, United States
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7
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Adzhubei AA, Tolstova AP, Strelkova MA, Mitkevich VA, Petrushanko IY, Makarov AA. Interaction Interface of Aβ 42 with Human Na,K-ATPase Studied by MD and ITC and Inhibitor Screening by MD. Biomedicines 2022; 10:biomedicines10071663. [PMID: 35884966 PMCID: PMC9313104 DOI: 10.3390/biomedicines10071663] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/05/2022] [Accepted: 07/05/2022] [Indexed: 12/14/2022] Open
Abstract
Alzheimer’s disease (AD) is a neurodegenerative disease accompanied by progressive cognitive and memory dysfunction due to disruption of normal electrotonic properties of neurons and neuronal loss. The Na,K-ATPase interaction with beta amyloid (Aβ) plays an important role in AD pathogenesis. It has been shown that Na,K-ATPase activity in the AD brain was significantly lower than those in age-matched control brain. The interaction of Aβ42 with Na,K-ATPase and subsequent oligomerization leads to inhibition of the enzyme activity. In this study interaction interfaces between three common Aβ42 isoforms, and different conformations of human Na,K-ATPase (α1β1) have been obtained using molecular modeling, including docking and molecular dynamics (MD). Interaction sites of Na,K-ATPase with Aβ42 are localized between extracellular parts of α- and β- subunits and are practically identical for Na,K-ATPase at different conformations. Thermodynamic parameters for the formation of Na,K-ATPase:Aβ42 complex at different conformations acquired by isothermal titration calorimetry (ITC) are similar, which is in line with the data of molecular modeling. Similarity of Na,K-ATPase interaction interfaces with Aβ in all conformations allowed us to cross-screen potential inhibitors for this interaction and find pharmaceutical compounds that could block it.
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Affiliation(s)
| | - Anna P. Tolstova
- Correspondence: (A.P.T.); (A.A.M.); Tel.: +7-499-135-4095 (A.A.M.)
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8
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Kistwal T, Mukhopadhyay A, Dasgupta S, Sharma KP, Datta A. Ultraslow Biological Water-Like Dynamics in Waterless Liquid Protein. J Phys Chem Lett 2022; 13:4389-4393. [PMID: 35548934 DOI: 10.1021/acs.jpclett.2c00702] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Fluorescence correlation spectroscopy and time-dependent fluorescence Stokes shift have been employed to elucidate dynamics in different time scales, ranging from picoseconds to nanoseconds, for human serum albumin, in its native and cationized forms as well as in the self-assembled complex of the cationized protein with the polymer surfactant (PS) glycolic acid ethoxylate lauryl ether. The effect of crowding in this complex, especially in the waterless condition, is of prime importance in this context. Excellent correlation of the dynamics with the structures, obtained by circular dichroism and Fourier transform infrared spectroscopy, has been observed. Slow solvation, associated classically with biological water, has been observed in these systems, even in the waterless condition. This apparently intriguing observation has been rationalized by the relaxation of segments of the protein and the PS in the microenvironment of the fluorescent probe.
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Affiliation(s)
- Tanuja Kistwal
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Anasua Mukhopadhyay
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Souradip Dasgupta
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Kamendra P Sharma
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Anindya Datta
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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9
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Ngoc TD, Le TN, Nguyen TVA, Mechler A, Hoa NT, Nam NL, Vo QV. Mechanistic and Kinetic Studies of the Radical Scavenging Activity of 5- O-Methylnorbergenin: Theoretical and Experimental Insights. J Phys Chem B 2022; 126:702-707. [PMID: 35029995 DOI: 10.1021/acs.jpcb.1c09196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
5-O-Methylnorbergenin (5-OMB), a natural compound isolated from Rourea harmandiana, is a compound with potential antioxidant activity based on its chemical structure; however, this activity has not been investigated thus far. In this study, the antioxidant activity of 5-OMB was evaluated by experimental and computational methods. 5-OMB exhibited high activity in DPPH (IC50 = 7.25 ± 0.94 μM) and ABTS•+ (IC50 = 4.23 ± 0.12 μM) assays, higher than the reference compound Trolox. The computational results consistently show that 5-OMB is an excellent HOO• radical scavenger (koverall = 8.14 × 108 M-1 s-1) in water at physiological pH, however it only exerts weak activity in lipid medium (koverall = 3.02 × 102 M-1 s-1). The reaction follows the formal hydrogen transfer mechanism in nonpolar solvents, whereas both the sequential proton loss electron transfer and the formal hydrogen transfer pathways contribute to the activity in aqueous solution. There is a good agreement between experimental and computational data, suggesting that 5-OMB is a promising natural radical scavenger in aqueous physiological environment.
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Affiliation(s)
- Thuc Dinh Ngoc
- Department of Science and Technology Management, Hong Duc University, Thanh Hoa 40000, Vietnam
| | - Thanh Nguyen Le
- Institute of Marine Biochemistry (IMBC), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Caugiay, Hanoi 100000, Vietnam.,Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Caugiay, Hanoi 100000, Vietnam
| | - Thi Van Anh Nguyen
- University of Science and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Caugiay, Hanoi 100000, Vietnam
| | - Adam Mechler
- Department of Chemistry and Physics, La Trobe University, La Trobe, Victoria 3086, Australia
| | - Nguyen Thi Hoa
- The University of Danang - University of Technology and Education, Danang 550000, Vietnam
| | - Nguyen Linh Nam
- The University of Danang - University of Technology and Education, Danang 550000, Vietnam
| | - Quan V Vo
- The University of Danang - University of Technology and Education, Danang 550000, Vietnam
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10
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Dey A, Maiti S. Determining the Stoichiometry of Amyloid Oligomers by Single-Molecule Photobleaching. Methods Mol Biol 2022; 2538:55-74. [PMID: 35951293 DOI: 10.1007/978-1-0716-2529-3_5] [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] [Indexed: 06/15/2023]
Abstract
Small oligomers are the initial intermediates in the pathway to amyloid fibril formation. They have a distinct identity from the monomers as well as from the protofibrils and the fibrils, both in their structure and in their properties. In many cases, they play a crucial biological role. However, due to their transient nature, they are difficult to characterize. "Oligomer" is a diffuse definition, encompassing aggregates of many different sizes, and this lack of precise definition causes much confusion and disagreement between different research groups. Here, we define the small oligomers as "n"-mers with n < 10, which is the size range in which the amyloid proteins typically exist at the initial phase of the aggregation process. Since the oligomers dynamically interconvert into each other, a solution of aggregating amyloid proteins will contain a distribution of sizes. A precise characterization of an oligomeric solution will, therefore, require quantification of the relative population of each size. Size-based separation methods, such as size-exclusion chromatography, are typically used to characterize this distribution. However, if the interconversion between oligomers of different sizes is fast, this would not yield reliable results. Single-molecule photobleaching (smPB) is a direct method to evaluate this size distribution in a heterogeneous solution without separation. In addition, understanding the mechanism of action of amyloid oligomers requires knowing the affinity of each oligomer type to different cellular components, such as the cell membrane. These measurements are also amenable to smPB. Here we show how to perform smPB, both for oligomers in solution and for oligomers attached to the membrane.
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Affiliation(s)
- Arpan Dey
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Sudipta Maiti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India.
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11
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Zinc Induced Aβ 16 Aggregation Modeled by Molecular Dynamics. Int J Mol Sci 2021; 22:ijms222212161. [PMID: 34830056 PMCID: PMC8622866 DOI: 10.3390/ijms222212161] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/29/2021] [Accepted: 11/07/2021] [Indexed: 11/17/2022] Open
Abstract
It is widely accepted that the addition of zinc leads to the formation of neurotoxic nonfibrillar aggregates of beta-amyloid peptides Aβ40 and Aβ42 and at the same time destabilizes amyloid fibrils. However, the mechanism of the effect of zinc on beta-amyloid is not fully understood. In this study, a fast zinc-induced aggregation of Aβ16 (as compared to a system without zinc) via the formation of Aβ16 dimers with one zinc ion coordinated in the metal-binding site 11EVHH14, followed by their polymerization, has been studied by molecular dynamics. The best aggregation was shown by the system composed of Aβ16 dimers bound by one zinc ion, with no additional zinc in solution. The presence of Aβ16 dimers was a major condition, sufficient for fast aggregation into larger complexes. It has been shown that the addition of zinc to a system with already formed dimers does not substantially affect the characteristics and rate of aggregation. At the same time, an excessive concentration of zinc at the early stages of the formation of conglomerates can negatively affect aggregation, since in systems where zinc ions occupied the 11EVHH14 coordination center and the His6 residue of every Aβ16 monomer, the aggregation proceeded more slowly and the resulting complexes were not as large as in the zinc-free Aβ system. Thus, this study has shown that the formation of Aβ16 dimers bound through zinc ions at the 11EVHH14 sites of the peptides plays an important role in the formation of neurotoxic non-fibrillar aggregates of beta-amyloid peptide Aβ16. The best energetically favorable structure has been obtained for the complex of two Aβ16 dimers with two zinc ions.
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12
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Guo X, Bao X, Wang X, Liu D, Liu P, Chi T, Ji X, Zheng Z, Chen G, Zou L. OAB-14 Effectively Ameliorates the Dysfunction of the Endosomal-Autophagic-Lysosomal Pathway in APP/PS1 Transgenic Mice. ACS Chem Neurosci 2021; 12:3985-3993. [PMID: 34652916 DOI: 10.1021/acschemneuro.1c00209] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In Alzheimer's disease (AD), damaged Aβ clearance contributes to elevated levels of Aβ that cause a series of cytotoxic cascade reactions. Thus, targeting Aβ clearance has now been considered a valid therapeutic approach for AD. Cellular uptake and degradation are important mechanisms for Aβ clearance, which are mainly performed by the endosomal-autophagic-lysosomal (EAL) pathway. Our previous study showed that OAB-14, a novel small molecule designed with bexarotene as the lead compound, treatment for 3 months significantly alleviated cognitive disorders and remarkably reduced the deposition of Aβ without affecting its production in APP/PS1 transgenic mice. Here, we further revealed that enhancement of the EAL activity is one of the mechanisms that increases Aβ clearance after OAB-14 administration for 3 months. OAB-14 facilitates receptor-mediated endocytosis and restores autophagy flux via the AMPK/mTOR pathway. Meanwhile, OAB-14 enhances the lysosomal activity, and reduced Aβ accumulation in lysosomes was observed in OAB-14-treated AD mice. These results suggest that OAB-14 may promote Aβ clearance in lysosomes by alleviating the EAL dysfunction in AD mice.
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Affiliation(s)
- Xiaoli Guo
- Department of Pharmacology, Life Science and Biopharmaceutics School, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, Liaoning 110016, P. R. China
| | - Xuefei Bao
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, Liaoning 110016, P. R. China
| | - Xiaojuan Wang
- Department of Pharmacology, Life Science and Biopharmaceutics School, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, Liaoning 110016, P. R. China
| | - Danyang Liu
- Department of Pharmacology, Life Science and Biopharmaceutics School, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, Liaoning 110016, P. R. China
| | - Peng Liu
- Department of Pharmacology, Life Science and Biopharmaceutics School, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, Liaoning 110016, P. R. China
| | - Tianyan Chi
- Department of Pharmacology, Life Science and Biopharmaceutics School, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, Liaoning 110016, P. R. China
| | - Xuefei Ji
- Department of Pharmacology, Life Science and Biopharmaceutics School, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, Liaoning 110016, P. R. China
| | - Zhonghui Zheng
- Shandong Xinhua Pharmaceutical Co., Ltd., Zibo, Shandong 255086, P. R. China
| | - Guoliang Chen
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, Liaoning 110016, P. R. China
| | - Libo Zou
- Department of Pharmacology, Life Science and Biopharmaceutics School, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, Liaoning 110016, P. R. China
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13
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Hivare P, Panda C, Gupta S, Bhatia D. Programmable DNA Nanodevices for Applications in Neuroscience. ACS Chem Neurosci 2021; 12:363-377. [PMID: 33433192 DOI: 10.1021/acschemneuro.0c00723] [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] [Indexed: 12/13/2022] Open
Abstract
The broad area of neuroscience has witnessed an increasing exploitation of a variety of synthetic biomaterials with controlled nanosized features. Different bionanomaterials offer very peculiar physicochemical and biochemcial properties contributing to the development of novel imaging devices toward imaging the brain, or as smartly functionalized scaffolds, or diverse tools contributing toward a better understanding of nervous tissue and its functions. DNA nanotechnology-based devices and scaffolds have emerged as ideal materials for cellular and tissue engineering due to their very biocompatible properties, robust adaptation with diverse biological systems, and biosafety in terms of reduced immune response triggering. Here we present technologies with respect to DNA nanodevices that are designed to better interact with nervous systems like neural cells, advanced molecular imaging technologies for imaging brain, biomaterials in neural regeneration, neuroprotection, and targeted delivery of drugs and small molecules across the blood-brain barrier. Along with comments regarding the progress of DNA nanotechnology in neuroscience, we also present a perspective on challenges and opportunities for applying DNA nanotechnology in applications pertaining to neurosciences.
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Affiliation(s)
- Pravin Hivare
- Biological Engineering discipline, Indian Institute of Technology Gandhinagar, Palaj 382355, Gandhinagar, India
| | - Chinmaya Panda
- Biological Engineering discipline, Indian Institute of Technology Gandhinagar, Palaj 382355, Gandhinagar, India
| | - Sharad Gupta
- Biological Engineering discipline, Indian Institute of Technology Gandhinagar, Palaj 382355, Gandhinagar, India
- Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, Palaj 382355, Gandhinagar, India
| | - Dhiraj Bhatia
- Biological Engineering discipline, Indian Institute of Technology Gandhinagar, Palaj 382355, Gandhinagar, India
- Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, Palaj 382355, Gandhinagar, India
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14
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Scheidt HA, Das A, Korn A, Krueger M, Maiti S, Huster D. Structural characteristics of oligomers formed by pyroglutamate-modified amyloid β peptides studied by solid-state NMR. Phys Chem Chem Phys 2020; 22:16887-16895. [PMID: 32666970 DOI: 10.1039/d0cp02307h] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Neuronal plaques of amyloid β (Aβ) peptides of varying length carrying different posttranslational modifications represent a molecular hallmark of Alzheimer's disease. It is believed that transient oligomeric Aβ assemblies associating in early fibrillation events represent particularly cytotoxic peptide aggregates. Also, N-terminally truncated (in position 3 or 11) and pyroglutamate modified peptides exhibited an increased toxicity compared to the wildtype. In the current study, the molecular structure of oligomeric species of pGlu3-Aβ(3-40) and pGlu11-Aβ(11-40) was investigated using solid-state NMR spectroscopy. On the secondary structure level, for both modified peptides a large similarity between oligomers and mature fibrils of the modified peptides was found mainly based on 13C NMR chemical shift data. Some smaller structural differences were detected in the vicinity of the respective modification site. Also, the crucial early folding molecular contact between residues Phe19 and Leu34 could be observed for the oligomers of both modified peptide species. Therefore, it has to be concluded that the major secondary structure elements of Aβ are already present in oligomers of pGlu3-Aβ(3-40) and pGlu11-Aβ(11-40). These posttranslationally modified peptides arrange in a similar fashion as observed for wild type Aβ(1-40).
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Affiliation(s)
- Holger A Scheidt
- Institute for Medical Physics and Biophysics, Leipzig University Härtelstr. 16-18, D-04107 Leipzig, Germany.
| | - Anirban Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005, India
| | - Alexander Korn
- Institute for Medical Physics and Biophysics, Leipzig University Härtelstr. 16-18, D-04107 Leipzig, Germany.
| | - Martin Krueger
- Institute of Anatomy, Leipzig University, Liebigstraße 13, 04103 Leipzig, Germany
| | - Sudipta Maiti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005, India
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, Leipzig University Härtelstr. 16-18, D-04107 Leipzig, Germany. and Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005, India
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15
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Lermyte F. Roles, Characteristics, and Analysis of Intrinsically Disordered Proteins: A Minireview. Life (Basel) 2020; 10:E320. [PMID: 33266184 PMCID: PMC7761095 DOI: 10.3390/life10120320] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/24/2020] [Accepted: 11/26/2020] [Indexed: 12/11/2022] Open
Abstract
In recent years, there has been a growing understanding that a significant fraction of the eukaryotic proteome is intrinsically disordered, and that these conformationally dynamic proteins play a myriad of vital biological roles in both normal and pathological states. In this review, selected examples of intrinsically disordered proteins are highlighted, with particular attention for a few which are relevant in neurological disorders and in viral infection. Next, the underlying causes for the intrinsic disorder are discussed, along with computational methods used to predict whether a given amino acid sequence is likely to adopt a folded or unfolded state in the solution. Finally, biophysical methods for the analysis of intrinsically disordered proteins will be discussed, as well as the unique challenges they pose in this context due to their highly dynamic nature.
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Affiliation(s)
- Frederik Lermyte
- Department of Chemistry, Technical University of Darmstadt, Alarich-Weiss-Straße 4, 64287 Darmstadt, Germany
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16
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Caneus J, Akanda N, Rumsey JW, Guo X, Jackson M, Long CJ, Sommerhage F, Georgieva S, Kanaan NM, Morgan D, Hickman JJ. A human induced pluripotent stem cell-derived cortical neuron human-on-a chip system to study Aβ 42 and tau-induced pathophysiological effects on long-term potentiation. ALZHEIMER'S & DEMENTIA (NEW YORK, N. Y.) 2020; 6:e12029. [PMID: 32490141 PMCID: PMC7253154 DOI: 10.1002/trc2.12029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 03/26/2020] [Accepted: 04/26/2020] [Indexed: 12/28/2022]
Abstract
INTRODUCTION The quest to identify an effective therapeutic strategy for neurodegenerative diseases, such as mild congitive impairment (MCI) and Alzheimer's disease (AD), suffers from the lack of good human-based models. Animals represent the most common models used in basic research and drug discovery studies. However, safe and effective compounds identified in animal studies often translate poorly to humans, yielding unsuccessful clinical trials. METHODS A functional in vitro assay based on long-term potentiation (LTP) was used to demonstrate that exposure to amyloid beta (Aβ42) and tau oligomers, or brain extracts from AD transgenic mice led to prominent changes in human induced pluripotent stem cells (hiPSC)-derived cortical neurons, notably, without cell death. RESULTS Impaired information processing was demonstrated by treatment of neuron-MEA (microelectrode array) systems with the oligomers and brain extracts by reducing the effects of LTP induction. These data confirm the neurotoxicity of molecules linked to AD pathology and indicate the utility of this human-based system to model aspects of AD in vitro and study LTP deficits without loss of viability; a phenotype that more closely models the preclinical or early stage of AD. DISCUSSION In this study, by combining multiple relevant and important molecular and technical aspects of neuroscience research, we generated a new, fully human in vitro system to model and study AD at the preclinical stage. This system can serve as a novel drug discovery platform to identify compounds that rescue or alleviate the initial neuronal deficits caused by Aβ42 and/or tau oligomers, a main focus of clinical trials.
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Affiliation(s)
- Julbert Caneus
- NanoScience Technology CenterUniversity of Central FloridaOrlandoFloridaUSA
| | - Nesar Akanda
- NanoScience Technology CenterUniversity of Central FloridaOrlandoFloridaUSA
| | | | - Xiufang Guo
- NanoScience Technology CenterUniversity of Central FloridaOrlandoFloridaUSA
| | | | | | - Frank Sommerhage
- NanoScience Technology CenterUniversity of Central FloridaOrlandoFloridaUSA
| | - Sanya Georgieva
- NanoScience Technology CenterUniversity of Central FloridaOrlandoFloridaUSA
| | - Nicholas M. Kanaan
- Department of Translational NeuroscienceMichigan State UniversityCollege of Human Medicine, Grand Rapids Research CenterGrand RapidsMichiganUSA
| | - David Morgan
- Department of Translational NeuroscienceMichigan State UniversityCollege of Human Medicine, Grand Rapids Research CenterGrand RapidsMichiganUSA
| | - James J. Hickman
- NanoScience Technology CenterUniversity of Central FloridaOrlandoFloridaUSA
- Hesperos Inc.OrlandoFloridaUSA
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17
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Saranya V, Mary PV, Vijayakumar S, Shankar R. The hazardous effects of the environmental toxic gases on amyloid beta-peptide aggregation: A theoretical perspective. Biophys Chem 2020; 263:106394. [PMID: 32480019 DOI: 10.1016/j.bpc.2020.106394] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/12/2020] [Accepted: 05/12/2020] [Indexed: 12/13/2022]
Abstract
Alzheimer's disease (AD) is one of the leading causes of dementia in elderly people. It has been well documented that the exposure to environmental toxins such as CO, CO2, SO2 and NO2 that are present in the air is considered as a hallmark for the progression of Alzheimer's disease. However, their actual mechanism by which environmental toxin triggers the aggregation of Aβ42 peptide at the molecular and atomic levels remain unknown. In this study, molecular dynamics simulation was carried out to study the aggregation mechanism of the Aβ42 peptide due to its interaction of toxic gas (CO, CO2, SO2 and NO2). During the 400 ns simulation, all the Aβ42 interacted toxic gas (CO, CO2, SO2, and NO2) complexes have smaller Root Mean Square Deviation values when compared to the Aβ42 peptide, which shows that the interaction of toxic gases (CO, CO2, SO2, and NO2) would increase the Aβ42 peptide structural stability. The radius of gyration analysis also supports that Aβ42 interacted CO2 and SO2 complexes have the minimum value in the range of 0.95 nm and 1.5 nm. It is accounted that the Aβ42 interacted CO2 and SO2 complexes have a greater compact structure in comparison to Aβ42 interacted CO and NO2 complexes. Furthermore, all the Aβ42 interacted toxic gas (CO, CO2, SO2, and NO2) complexes exhibited an enhanced secondary structural probability for coil and turn regions with a reduced α-helix probability, which indicates that the interaction of toxic gases may enhance the toxicity and aggregation of Aβ42.
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Affiliation(s)
- Vasudevan Saranya
- Molecular Simulation Laboratory, Department of Physics, Bharathiar University, Coimbatore 641 046, India
| | - Pitchumani Violet Mary
- Department of Physics, Sri Shakthi Institute of Engineering and Technology, Coimbatore 641 062, India
| | | | - Ramasamy Shankar
- Molecular Simulation Laboratory, Department of Physics, Bharathiar University, Coimbatore 641 046, India.
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A spectroscopic and computational intervention of interaction of lysozyme with 6-mercaptopurine. Anal Bioanal Chem 2020; 412:2565-2577. [DOI: 10.1007/s00216-020-02483-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/09/2020] [Accepted: 02/03/2020] [Indexed: 12/26/2022]
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