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Haque MA, Park IS. An expeditious and facile method of amyloid beta (1-42) purification. PLoS One 2024; 19:e0307213. [PMID: 38990960 PMCID: PMC11239053 DOI: 10.1371/journal.pone.0307213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 07/01/2024] [Indexed: 07/13/2024] Open
Abstract
For the study of amyloid beta (Aβ) associated toxicity which is supposed to be the main pathological agent in Alzheimer's disease (AD), it is important to secure Aβ peptide with appropriate biological activity. However, commercial and synthetic Aβ often have some pitfalls like less cell toxicity, prompt aggregation and excess price, using recombinant technology, these issues can be resolved though the method also suffered from some problems such as low yield, aggregation and prolong time to purify. Thus, we previously developed an easy, economic and convenient method for Aβ42 purification using highly expressed GroES-Ubiquitin-Aβ42 fusion protein. The method was efficient, but further development was performed to improve the procedure and increase the yield. Focus was on the isolation of the fusion protein (GroES-Ubiquitin) from Aβ42 peptide. After a series of systematic testing with several chemicals, we found that methanol could precipitate efficiently the fusion protein, while the Aβ peptide was recovered in the supernatant. By this method, Aβ peptide was easily purified without tedious chromatographic steps which are main obstacles to purify the peptide in the previous method. This method yielded ~20 mg highly pure Aβ42 peptide from 1-liter bacterial culture. Different biophysical characterizations and bioactivity assays indicate that the peptide purified using this method was competitive with others which have been previously reported whereas considering the simplicity, final yield and time of purification, this method is the optimal solution.
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Affiliation(s)
- Md. Aminul Haque
- Department of Biomedical Sciences, Chosun University, Dong-gu, Gwangju, Korea
- School of Pharmacy, BRAC University, Merul Badda, Dhaka, Bangladesh
- Research Lab, Rufaida BioMeds, Aftabnagar, Dhaka, Bangladesh
| | - Il Seon Park
- Department of Biomedical Sciences, Chosun University, Dong-gu, Gwangju, Korea
- Department of Cellular and Molecular Medicine, Chosun University, Dong-gu, Gwangju, Korea
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2
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Do TM, Horinek D, Matubayasi N. How ATP suppresses the fibrillation of amyloid peptides: analysis of the free-energy contributions. Phys Chem Chem Phys 2024; 26:11880-11892. [PMID: 38568008 DOI: 10.1039/d4cp00179f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2024]
Abstract
Recent experiments have revealed that adenosine triphosphate (ATP) suppresses the fibrillation of amyloid peptides - a process closely linked to neurodegenerative diseases such as Alzheimer's and Parkinson's. Apart from the adsorption of ATP onto amyloid peptides, the molecular understanding is still limited, leaving the underlying mechanism for the fibrillation suppression by ATP largely unclear, especially in regards to the molecular energetics. Here we provide an explanation at the molecular scale by quantifying the free energies using all-atom molecular dynamics simulations. We found that the changes of the free energies due to the addition of ATP lead to a significant equilibrium shift towards monomeric peptides in agreement with experiments. Despite ATP being a highly charged species, the decomposition of the free energies reveals that the van der Waals interactions with the peptide are decisive in determining the relative stabilization of the monomeric state. While the phosphate moiety exhibits strong electrostatic interactions, the compensation by the water solvent results in a minor, overall Coulomb contribution. Our quantitative analysis of the free energies identifies which intermolecular interactions are responsible for the suppression of the amyloid fibril formation by ATP and offers a promising method to analyze the roles of similarly complex cosolvents in aggregation processes.
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Affiliation(s)
- Tuan Minh Do
- Institute of Physical and Theoretical Chemistry, University of Regensburg, 93040 Regensburg, Germany
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, 560-8531 Toyonaka, Osaka, Japan.
| | - Dominik Horinek
- Institute of Physical and Theoretical Chemistry, University of Regensburg, 93040 Regensburg, Germany
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, 560-8531 Toyonaka, Osaka, Japan.
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3
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Saccuzzo EG, Mebrat MD, Scelsi HF, Kim M, Ma MT, Su X, Hill SE, Rheaume E, Li R, Torres MP, Gumbart JC, Van Horn WD, Lieberman RL. Competition between inside-out unfolding and pathogenic aggregation in an amyloid-forming β-propeller. Nat Commun 2024; 15:155. [PMID: 38168102 PMCID: PMC10762032 DOI: 10.1038/s41467-023-44479-2] [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: 02/14/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
Studies of folded-to-misfolded transitions using model protein systems reveal a range of unfolding needed for exposure of amyloid-prone regions for subsequent fibrillization. Here, we probe the relationship between unfolding and aggregation for glaucoma-associated myocilin. Mutations within the olfactomedin domain of myocilin (OLF) cause a gain-of-function, namely cytotoxic intracellular aggregation, which hastens disease progression. Aggregation by wild-type OLF (OLFWT) competes with its chemical unfolding, but only below the threshold where OLF loses tertiary structure. Representative moderate (OLFD380A) and severe (OLFI499F) disease variants aggregate differently, with rates comparable to OLFWT in initial stages of unfolding, and variants adopt distinct partially folded structures seen along the OLFWT urea-unfolding pathway. Whether initiated with mutation or chemical perturbation, unfolding propagates outward to the propeller surface. In sum, for this large protein prone to amyloid formation, the requirement for a conformational change to promote amyloid fibrillization leads to direct competition between unfolding and aggregation.
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Affiliation(s)
- Emily G Saccuzzo
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, USA
| | - Mubark D Mebrat
- Biodesign Center for Personalized Diagnostics, Arizona State University, Tempe, USA
- School of Molecular Sciences, Arizona State University, Tempe, USA
| | - Hailee F Scelsi
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, USA
| | - Minjoo Kim
- Biodesign Center for Personalized Diagnostics, Arizona State University, Tempe, USA
- School of Molecular Sciences, Arizona State University, Tempe, USA
| | - Minh Thu Ma
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, USA
| | - Xinya Su
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, USA
| | - Shannon E Hill
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, USA
| | - Elisa Rheaume
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, USA
| | - Renhao Li
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta and Department of Pediatrics, Emory University School of Medicine, Atlanta, USA
| | - Matthew P Torres
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, USA
| | - James C Gumbart
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, USA
- School of Physics, Georgia Institute of Technology, Atlanta, USA
| | - Wade D Van Horn
- Biodesign Center for Personalized Diagnostics, Arizona State University, Tempe, USA.
- School of Molecular Sciences, Arizona State University, Tempe, USA.
| | - Raquel L Lieberman
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, USA.
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4
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Moore KBE, Horgan NG, Lenters B, Fortin JS. Diabetes mellitus drug discovery: insights into targeting feline and human amylin with small molecules. Vet Q 2023; 43:1-12. [PMID: 37729105 PMCID: PMC10557562 DOI: 10.1080/01652176.2023.2260442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/13/2023] [Indexed: 09/22/2023] Open
Abstract
BACKGROUND Type 2 diabetes (T2D) is a health concern for both humans and cats, with cases rising over the past decade. Around 70% of patients from either species exhibit pancreatic aggregates of islet amyloid polypeptide (IAPP), a protein that proves toxic upon misfolding. These misfolded protein aggregates congregate in the islets of Langerhans of the pancreas, diminishing the capability of β-cells to produce insulin and further perpetuating disease. OBJECTIVE Our team's drug discovery program is investigating newly synthesized compounds that could diminish aggregates of both human and feline IAPP, potentially disrupting the progression of T2D. MATERIAL AND METHODS We prepared 24 compounds derived from diaryl urea, as ureas have previously demonstrated great potential at reducing accumulations of misfolded proteins. Biophysical methods were employed to analyze the anti-aggregation activity of these compounds at inhibiting and/or disrupting IAPP fibril formation in vitro. RESULTS The results demonstrate that compounds 12 and 24 were most effective at reducing the fibrillization and aggregation of both human and feline IAPP. When compared with the control for each experiment, samples treated with either compound 12 or 24 exhibited fewer accumulations of amyloid-like fibrils. CONCLUSION Urea-based compounds, such as compounds 12 and 24, may prove crucial in future pre-clinical studies in the search for therapeutics for T2D.
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Affiliation(s)
- Kendall B. E. Moore
- Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA
| | - Natalie G. Horgan
- Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA
| | - Brooke Lenters
- Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA
| | - Jessica S. Fortin
- Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN, USA
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5
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Nirmalraj PN, Rossell MD, Dachraoui W, Thompson D, Mayer M. In Situ Observation of Chemically Induced Protein Denaturation at Solvated Interfaces. ACS APPLIED MATERIALS & INTERFACES 2023; 15:48015-48026. [PMID: 37797325 PMCID: PMC10591235 DOI: 10.1021/acsami.3c10510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 09/22/2023] [Indexed: 10/07/2023]
Abstract
Proteins unfold in chaotropic salt solutions, a process that is difficult to observe at the single protein level. The work presented here demonstrates that a liquid-based atomic force microscope and graphene liquid-cell-based scanning transmission electron microscope make it possible to observe chemically induced protein unfolding. To illustrate this capability, ferritin proteins were deposited on a graphene surface, and the concentration-dependent urea- or guanidinium-induced changes of morphology were monitored for holo-ferritin with its ferrihydrite core as well as apo-ferritin without this core. Depending on the chaotropic agent the liquid-based imaging setup captured an unexpected transformation of natively folded holo-ferritin proteins into rings after urea treatment but not after guanidinium treatment. Urea treatment of apo-ferritin did not result in nanorings, confirming that nanorings are a specific signature of denaturation of holo-ferritins after exposture to sufficiently high urea concentrations. Mapping the in situ images with molecular dynamics simulations of ferritin subunits in urea solutions suggests that electrostatic destabilization triggers denaturation of ferritin as urea makes direct contact with the protein and also disrupts the water H-bonding network in the ferritin solvation shell. Our findings deepen the understanding of protein denaturation studied using label-free techniques operating at the solid-liquid interface.
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Affiliation(s)
- Peter Niraj Nirmalraj
- Transport
at Nanoscale Interfaces Laboratory, Swiss
Federal Laboratories for Materials Science and Technology, Überlandstrasse 129, 8600 Dübendorf, Switzerland
- Adolphe
Merkle Institute, University of Fribourg, Chemin des Verdiers 4, CH-1700 Fribourg, Switzerland
| | - Marta D. Rossell
- Electron
Microscopy Center, Swiss Federal Laboratories
for Materials Science and Technology, Überlandstrasse 129, 8600 Dübendorf, Switzerland
| | - Walid Dachraoui
- Electron
Microscopy Center, Swiss Federal Laboratories
for Materials Science and Technology, Überlandstrasse 129, 8600 Dübendorf, Switzerland
| | - Damien Thompson
- Department
of Physics, Bernal Institute, University
of Limerick, Limerick V94T9PX, Ireland
| | - Michael Mayer
- Adolphe
Merkle Institute, University of Fribourg, Chemin des Verdiers 4, CH-1700 Fribourg, Switzerland
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6
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Sedov I, Khaibrakhmanova D. Molecular Mechanisms of Inhibition of Protein Amyloid Fibril Formation: Evidence and Perspectives Based on Kinetic Models. Int J Mol Sci 2022; 23:ijms232113428. [PMID: 36362217 PMCID: PMC9657184 DOI: 10.3390/ijms232113428] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 10/29/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022] Open
Abstract
Inhibition of fibril formation is considered a possible treatment strategy for amyloid-related diseases. Understanding the molecular nature of inhibitor action is crucial for the design of drug candidates. In the present review, we describe the common kinetic models of fibril formation and classify known inhibitors by the mechanism of their interactions with the aggregating protein and its oligomers. This mechanism determines the step or steps of the aggregation process that become inhibited and the observed changes in kinetics and equilibrium of fibril formation. The results of numerous studies indicate that possible approaches to antiamyloid inhibitor discovery include the search for the strong binders of protein monomers, cappers blocking the ends of the growing fibril, or the species absorbing on the surface of oligomers preventing nucleation. Strongly binding inhibitors stabilizing the native state can be promising for the structured proteins while designing the drug candidates targeting disordered proteins is challenging.
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Affiliation(s)
- Igor Sedov
- Chemical Institute, Kazan Federal University, Kremlevskaya 18, 420008 Kazan, Russia
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, 420111 Kazan, Russia
- Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russia
- Correspondence: ; Tel.: +7-9600503916
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7
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Mafimoghaddam S, Xu Y, Sherman MB, Orlova EV, Karki P, Orman MA, Vekilov PG. Suppression of amyloid-β fibril growth by drug-engineered polymorph transformation. J Biol Chem 2022; 298:102662. [PMID: 36334629 PMCID: PMC9720346 DOI: 10.1016/j.jbc.2022.102662] [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: 03/23/2022] [Revised: 10/24/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
Fibrillization of the protein amyloid β is assumed to trigger Alzheimer's pathology. Approaches that target amyloid plaques, however, have garnered limited clinical success, and their failures may relate to the scarce understanding of the impact of potential drugs on the intertwined stages of fibrillization. Here, we demonstrate that bexarotene, a T-cell lymphoma medication with known antiamyloid activity both in vitro and in vivo, suppresses amyloid fibrillization by promoting an alternative fibril structure. We employ time-resolved in situ atomic force microscopy to quantify the kinetics of growth of individual fibrils and supplement it with structure characterization by cryo-EM. We show that fibrils with structure engineered by the drug nucleate and grow substantially slower than "normal" fibrils; remarkably, growth remains stunted even in drug-free solutions. We find that the suppression of fibril growth by bexarotene is not because of the drug binding to the fibril tips or to the peptides in the solution. Kinetic analyses attribute the slow growth of drug-enforced fibril polymorph to the distinctive dynamics of peptide chain association to their tips. As an additional benefit, the bexarotene fibrils kill primary rat hippocampal neurons less efficiently than normal fibrils. In conclusion, the suggested drug-driven polymorph transformation presents a mode of action to irreversibly suppress toxic aggregates not only in Alzheimer's but also potentially in myriad diverse pathologies that originate with protein condensation.
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Affiliation(s)
- Sima Mafimoghaddam
- William A. Brookshire Department of Chemical & Biomolecular Engineering, University of Houston, Houston, Texas, USA
| | - Yuechuan Xu
- William A. Brookshire Department of Chemical & Biomolecular Engineering, University of Houston, Houston, Texas, USA
| | - Michael B. Sherman
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Elena V. Orlova
- Department of Biological Sciences, Institute for Structural and Molecular Biology, Birkbeck University of London, London, UK
| | - Prashant Karki
- William A. Brookshire Department of Chemical & Biomolecular Engineering, University of Houston, Houston, Texas, USA
| | - Mehmet A. Orman
- William A. Brookshire Department of Chemical & Biomolecular Engineering, University of Houston, Houston, Texas, USA
| | - Peter G. Vekilov
- William A. Brookshire Department of Chemical & Biomolecular Engineering, University of Houston, Houston, Texas, USA,Department of Chemistry, University of Houston, Houston, Texas, USA,For correspondence: Peter G. Vekilov
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8
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Sokolov PA, Rolich VI, Vezo OS, Belousov MV, Bondarev SA, Zhouravleva GA, Kasyanenko NA. Amyloid fibril length distribution from dynamic light scattering data. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2022; 51:325-333. [PMID: 35546203 DOI: 10.1007/s00249-022-01600-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/19/2022] [Accepted: 04/24/2022] [Indexed: 06/15/2023]
Abstract
The study of the aggregation of amyloid proteins is challenging. A new approach to processing dynamic light scattering data was developed and tested using aggregates of the well-known model Sup35NM amyloid. After filtering and calculating the moving averages of autocorrelation functions to reduce impacts of noise, each averaged autocorrelation function is converted to the fibril length distribution via numerical modeling. The processing results were verified using atomic force and scanning electron microscopy data. Analysis of fibril length distribution changes over time gives valuable information about the aggregation process.
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Affiliation(s)
- Petr A Sokolov
- Department of Physics, St. Petersburg University, 7-9-11 Universitetskaya Emb, St. Petersburg, 199034, Russia.
| | - Valeriy I Rolich
- Department of Physics, St. Petersburg University, 7-9-11 Universitetskaya Emb, St. Petersburg, 199034, Russia
| | - Olga S Vezo
- Department of Physics, St. Petersburg University, 7-9-11 Universitetskaya Emb, St. Petersburg, 199034, Russia
| | - Mikhail V Belousov
- Department of Genetics and Biotechnology, St. Petersburg University, 7-9-11 Universitetskaya Emb, St. Petersburg, 199034, Russia
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, 3 Podbelsky chausse, St. Petersburg, 196608, Russia
| | - Stanislav A Bondarev
- Department of Genetics and Biotechnology, St. Petersburg University, 7-9-11 Universitetskaya Emb, St. Petersburg, 199034, Russia
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology, St. Petersburg University, 7-9-11 Universitetskaya Emb, St. Petersburg, 199034, Russia
| | - Nina A Kasyanenko
- Department of Physics, St. Petersburg University, 7-9-11 Universitetskaya Emb, St. Petersburg, 199034, Russia
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9
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Sønderby TV, Najarzadeh Z, Otzen DE. Functional Bacterial Amyloids: Understanding Fibrillation, Regulating Biofilm Fibril Formation and Organizing Surface Assemblies. Molecules 2022; 27:4080. [PMID: 35807329 PMCID: PMC9268375 DOI: 10.3390/molecules27134080] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 02/01/2023] Open
Abstract
Functional amyloid is produced by many organisms but is particularly well understood in bacteria, where proteins such as CsgA (E. coli) and FapC (Pseudomonas) are assembled as functional bacterial amyloid (FuBA) on the cell surface in a carefully optimized process. Besides a host of helper proteins, FuBA formation is aided by multiple imperfect repeats which stabilize amyloid and streamline the aggregation mechanism to a fast-track assembly dominated by primary nucleation. These repeats, which are found in variable numbers in Pseudomonas, are most likely the structural core of the fibrils, though we still lack experimental data to determine whether the repeats give rise to β-helix structures via stacked β-hairpins (highly likely for CsgA) or more complicated arrangements (possibly the case for FapC). The response of FuBA fibrillation to denaturants suggests that nucleation and elongation involve equal amounts of folding, but protein chaperones preferentially target nucleation for effective inhibition. Smart peptides can be designed based on these imperfect repeats and modified with various flanking sequences to divert aggregation to less stable structures, leading to a reduction in biofilm formation. Small molecules such as EGCG can also divert FuBA to less organized structures, such as partially-folded oligomeric species, with the same detrimental effect on biofilm. Finally, the strong tendency of FuBA to self-assemble can lead to the formation of very regular two-dimensional amyloid films on structured surfaces such as graphite, which strongly implies future use in biosensors or other nanobiomaterials. In summary, the properties of functional amyloid are a much-needed corrective to the unfortunate association of amyloid with neurodegenerative disease and a testimony to nature's ability to get the best out of a protein fold.
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Affiliation(s)
- Thorbjørn Vincent Sønderby
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark; (T.V.S.); (Z.N.)
- Sino-Danish Center (SDC), Eastern Yanqihu Campus, University of Chinese Academy of Sciences, 380 Huaibeizhuang, Huairou District, Beijing 101400, China
| | - Zahra Najarzadeh
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark; (T.V.S.); (Z.N.)
| | - Daniel Erik Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark; (T.V.S.); (Z.N.)
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10
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Galamba N. Aggregation of a Parkinson's Disease-Related Peptide: When Does Urea Weaken Hydrophobic Interactions? ACS Chem Neurosci 2022; 13:1769-1781. [PMID: 35616516 PMCID: PMC9775218 DOI: 10.1021/acschemneuro.2c00169] [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] [Indexed: 12/25/2022] Open
Abstract
While the exact cause of neurodegenerative diseases such as Alzheimer's disease and Parkinson's disease is not completely understood, compelling evidence implicates the aggregation of specific proteins and peptides. Co-solvents can provide molecular insight into protein aggregation mechanisms and the chemical nature of potential aggregation inhibitors. Here, we study, through molecular simulations, the hydration and binding free energies of an amphiphilic peptide from the nonamyloid-β component (NAC), a key aggregation-prone domain of α-synuclein, in water and an 8 M aqueous urea solution. Isoleucine, glycine, and serine peptides of the same length are also studied to unravel the role of urea in the hydration and aggregation of hydrophobic and hydrophilic domains. A strong impact of urea in hindering the aggregation of the NAC subdomain is observed. A slightly weaker aggregation inhibition is observed for the Gly and Ser peptides, whereas a much lower aggregation inhibitory activity is found for the Ile peptide, seemingly contrasting with urea's protein unfolding mechanism. This behavior is shown to derive from a lower profusion of urea next to the hydrophobic side chains and the backbone of the Ile's peptide in the dimeric form. As a consequence, β-sheets, formed upon aggregation, remain nearly intact. Hydrophilic neighbor groups in the amphiphilic NAC subdomain, however, are shown to anchor enough urea to weaken hydrophobic interactions and disrupt β-sheet structures. Our results indicate that urea's activity is potentiated in amphiphilic domains and that potential drugs could disrupt hydrophobic β-sheet-rich regions while not binding primarily to hydrophobic amino acids.
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11
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Devi S, Chaturvedi M, Fatima S, Priya S. Environmental factors modulating protein conformations and their role in protein aggregation diseases. Toxicology 2022; 465:153049. [PMID: 34818560 DOI: 10.1016/j.tox.2021.153049] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/12/2021] [Accepted: 11/20/2021] [Indexed: 12/13/2022]
Abstract
The adverse physiological conditions have been long known to impact protein synthesis, folding and functionality. Major physiological factors such as the effect of pH, temperature, salt and pressure are extensively studied for their impact on protein structure and homeostasis. However, in the current scenario, the environmental risk factors (pollutants) have gained impetus in research because of their increasing concentrations in the environment and strong epidemiologic link with protein aggregation disorders. Here, we review the physiological and environmental risk factors for their impact on protein conformational changes, misfolding, aggregation, and associated pathological conditions, especially environmental risk factors associated pathologies.
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Affiliation(s)
- Shweta Devi
- Systems Toxicology and Health Risk Assessment Group, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, CSIR-Indian Institute of Toxicology Research, Lucknow-226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Minal Chaturvedi
- Systems Toxicology and Health Risk Assessment Group, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, CSIR-Indian Institute of Toxicology Research, Lucknow-226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Siraj Fatima
- Systems Toxicology and Health Risk Assessment Group, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, CSIR-Indian Institute of Toxicology Research, Lucknow-226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Smriti Priya
- Systems Toxicology and Health Risk Assessment Group, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, CSIR-Indian Institute of Toxicology Research, Lucknow-226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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12
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Xavier P, Galamba N. Effect of urea on the hydration and aggregation of hydrophobic and amphiphilic solute models: Implications to protein aggregation. J Chem Phys 2021; 155:144501. [PMID: 34654309 DOI: 10.1063/5.0064707] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Despite the emergence of a molecular picture of urea's protein unfolding mechanism in the past few decades, less is known about its action mechanism on protein aggregation. This is especially relevant for understanding the aggregation of amyloid proteins and peptides, implicated in several neurodegenerative diseases. While urea is believed to weaken the hydrophobic effect, a picture consistent with the decrease in the excess chemical potential of sufficiently large alkanes, interactions with protein polar side chains and backbone atoms are also important. Here, we study, through molecular dynamics, the hydration and aggregation of several alkanes and amphiphilic "mutants" of n-dodecane, in an 8M aqueous urea solution, aiming at getting insight into urea's mode of action. A size-dependent crossover temperature is found, above which the hydration of the alkanes is favored in the aqueous urea solution. The hydration of the alkanes is enhanced via entropy, with the enthalpy opposing hydration, consistent with experiments. The reason is that although solute-solvent interactions are favorable, these are overwhelmed by urea-water and urea-urea interactions. In contrast, water-water interactions and entropy are favored by a water depletion around the solute and a reduced water depletion around methane explains its exceptional solubility decrease. Furthermore, we show that while urea favors the hydration of n-dodecane and the amphiphilic mutants, it slightly enhances and reduces, respectively, the aggregation of the alkanes and the amphiphilic mutants. Thus, opposite to the common view, our results show that urea does not necessarily weaken hydrophobic interactions despite solvation being favored.
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Affiliation(s)
- P Xavier
- Biosystems and Integrative Sciences Institute, Faculty of Sciences of the University of Lisbon, C8, Campo Grande, 1749-016 Lisbon, Portugal
| | - N Galamba
- Biosystems and Integrative Sciences Institute, Faculty of Sciences of the University of Lisbon, C8, Campo Grande, 1749-016 Lisbon, Portugal
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13
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Matubayasi N. Solvation energetics of proteins and their aggregates analyzed by all-atom molecular dynamics simulations and the energy-representation theory of solvation. Chem Commun (Camb) 2021; 57:9968-9978. [PMID: 34505117 DOI: 10.1039/d1cc03395f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Solvation is a controlling factor for the structure and function of proteins. This article addresses the effects of solvation from an energetic perspective for the fluctuations and cosolvent-induced changes in protein structures and the equilibrium of aggregate formation for a peptide. A theoretical framework to analyze the solvation effects with an explicit solvent is introduced by adopting the energy-representation theory of solvation, and the connection of the solvation free energy to the protein structure and the aggregation tendency is quantitatively described in combination with all-atom molecular dynamics simulations. The interaction components that govern the solvation effects on the structural variations of proteins are further identified through correlation analysis, and a computational scheme to assess the shift of an aggregation equilibrium due to the addition of a cosolvent is provided.
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Affiliation(s)
- Nobuyuki Matubayasi
- Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan.
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14
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Frustrated peptide chains at the fibril tip control the kinetics of growth of amyloid-β fibrils. Proc Natl Acad Sci U S A 2021; 118:2110995118. [PMID: 34518234 DOI: 10.1073/pnas.2110995118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2021] [Indexed: 11/18/2022] Open
Abstract
Amyloid fibrillization is an exceedingly complex process in which incoming peptide chains bind to the fibril while concertedly folding. The coupling between folding and binding is not fully understood. We explore the molecular pathways of association of Aβ40 monomers to fibril tips by combining time-resolved in situ scanning probe microscopy with molecular modeling. The comparison between experimental and simulation results shows that a complex supported by nonnative contacts is present in the equilibrium structure of the fibril tip and impedes fibril growth in a supersaturated solution. The unraveling of this frustrated state determines the rate of fibril growth. The kinetics of growth of freshly cut fibrils, in which the bulk fibril structure persists at the tip, complemented by molecular simulations, indicate that this frustrated complex comprises three or four monomers in nonnative conformations and likely is contained on the top of a single stack of peptide chains in the fibril structure. This pathway of fibril growth strongly deviates from the common view that the conformational transformation of each captured peptide chain is templated by the previously arrived peptide. The insights into the ensemble structure of the frustrated complex may guide the search for suppressors of Aβ fibrillization. The uncovered dynamics of coupled structuring and assembly during fibril growth are more complex than during the folding of most globular proteins, as they involve the collective motions of several peptide chains that are not guided by a funneled energy landscape.
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15
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Gandolfi D, Boiani GM, Bigiani A, Mapelli J. Modeling Neurotransmission: Computational Tools to Investigate Neurological Disorders. Int J Mol Sci 2021; 22:4565. [PMID: 33925434 PMCID: PMC8123833 DOI: 10.3390/ijms22094565] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/22/2021] [Accepted: 04/25/2021] [Indexed: 02/06/2023] Open
Abstract
The investigation of synaptic functions remains one of the most fascinating challenges in the field of neuroscience and a large number of experimental methods have been tuned to dissect the mechanisms taking part in the neurotransmission process. Furthermore, the understanding of the insights of neurological disorders originating from alterations in neurotransmission often requires the development of (i) animal models of pathologies, (ii) invasive tools and (iii) targeted pharmacological approaches. In the last decades, additional tools to explore neurological diseases have been provided to the scientific community. A wide range of computational models in fact have been developed to explore the alterations of the mechanisms involved in neurotransmission following the emergence of neurological pathologies. Here, we review some of the advancements in the development of computational methods employed to investigate neuronal circuits with a particular focus on the application to the most diffuse neurological disorders.
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Affiliation(s)
- Daniela Gandolfi
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Via Campi 287, 41125 Modena, Italy; (D.G.); (G.M.B.); (A.B.)
| | - Giulia Maria Boiani
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Via Campi 287, 41125 Modena, Italy; (D.G.); (G.M.B.); (A.B.)
| | - Albertino Bigiani
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Via Campi 287, 41125 Modena, Italy; (D.G.); (G.M.B.); (A.B.)
- Center for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, Via Campi 287, 41125 Modena, Italy
| | - Jonathan Mapelli
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Via Campi 287, 41125 Modena, Italy; (D.G.); (G.M.B.); (A.B.)
- Center for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, Via Campi 287, 41125 Modena, Italy
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16
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Noor A, Zafar S, Zerr I. Neurodegenerative Proteinopathies in the Proteoform Spectrum-Tools and Challenges. Int J Mol Sci 2021; 22:1085. [PMID: 33499319 PMCID: PMC7865347 DOI: 10.3390/ijms22031085] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 12/11/2022] Open
Abstract
Proteinopathy refers to a group of disorders defined by depositions of amyloids within living tissue. Neurodegenerative proteinopathies, including Alzheimer's disease, Parkinson's disease, Creutzfeldt-Jakob disease, and others, constitute a large fraction of these disorders. Amyloids are highly insoluble, ordered, stable, beta-sheet rich proteins. The emerging theory about the pathophysiology of neurodegenerative proteinopathies suggests that the primary amyloid-forming proteins, also known as the prion-like proteins, may exist as multiple proteoforms that contribute differentially towards the disease prognosis. It is therefore necessary to resolve these disorders on the level of proteoforms rather than the proteome. The transient and hydrophobic nature of amyloid-forming proteins and the minor post-translational alterations that lead to the formation of proteoforms require the use of highly sensitive and specialized techniques. Several conventional techniques, like gel electrophoresis and conventional mass spectrometry, have been modified to accommodate the proteoform theory and prion-like proteins. Several new ones, like imaging mass spectrometry, have also emerged. This review aims to discuss the proteoform theory of neurodegenerative disorders along with the utility of these proteomic techniques for the study of highly insoluble proteins and their associated proteoforms.
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Affiliation(s)
- Aneeqa Noor
- Department of Neurology, University Medical Center Göttingen, 37075 Göttingen, Germany; (A.N.); (I.Z.)
- German Center for Neurodegenerative Diseases (DZNE), 37075 Göttingen, Germany
| | - Saima Zafar
- Department of Neurology, University Medical Center Göttingen, 37075 Göttingen, Germany; (A.N.); (I.Z.)
- German Center for Neurodegenerative Diseases (DZNE), 37075 Göttingen, Germany
- Biomedical Engineering and Sciences Department, School of Mechanical and Manufacturing Engineering (SMME), National University of Sciences and Technology (NUST), Bolan Road, H-12, 44000 Islamabad, Pakistan
| | - Inga Zerr
- Department of Neurology, University Medical Center Göttingen, 37075 Göttingen, Germany; (A.N.); (I.Z.)
- German Center for Neurodegenerative Diseases (DZNE), 37075 Göttingen, Germany
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17
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Chen N, Zhao Z, Wang Y, Dimova R. Resolving the Mechanisms of Soy Glycinin Self-Coacervation and Hollow-Condensate Formation. ACS Macro Lett 2020; 9:1844-1852. [PMID: 35653686 DOI: 10.1021/acsmacrolett.0c00709] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Self-coacervation of animal-derived proteins has been extensively investigated while that of plant proteins remains largely unexplored. Here, we study the process of soy glycinin self-coacervation and transformation into hollow condensates. The protein hexameric structure composed of hydrophilic and hydrophobic polypeptides is crucial for coacervation. The process is driven by charge screening of the intrinsically disordered region of acidic polypeptides, allowing for weak hydrophobic interactions between exposed hydrophobic polypeptides. We find that the coacervate surface exhibits order, which stabilizes the coacervate shape during hollow-condensate formation. The latter process occurs via nucleation and growth of protein-poor phase in the coacervate interior, during which another ordered layer at the inner surface is formed. Aging enhances the stability of both coacervates and hollow condensates. Understanding plant protein coacervation holds promises for fabricating novel functional materials.
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Affiliation(s)
- Nannan Chen
- Guangdong Saskatchewan Oilseed Joint Laboratory, Department of Food Science and Engineering, Jinan University, 510632 Guangzhou, China
- Max Planck Institute of Colloids and Interfaces, Department of Theory and Bio-Systems, Science Park Golm, 14424 Potsdam, Germany
| | - Ziliang Zhao
- Max Planck Institute of Colloids and Interfaces, Department of Theory and Bio-Systems, Science Park Golm, 14424 Potsdam, Germany
| | - Yong Wang
- Guangdong Saskatchewan Oilseed Joint Laboratory, Department of Food Science and Engineering, Jinan University, 510632 Guangzhou, China
| | - Rumiana Dimova
- Max Planck Institute of Colloids and Interfaces, Department of Theory and Bio-Systems, Science Park Golm, 14424 Potsdam, Germany
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18
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Cosolvent effects on the growth of amyloid fibrils. Curr Opin Struct Biol 2020; 60:101-109. [DOI: 10.1016/j.sbi.2019.12.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 12/08/2019] [Accepted: 12/16/2019] [Indexed: 02/05/2023]
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19
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Masutani K, Yamamori Y, Kim K, Matubayasi N. Free-energy analysis of the hydration and cosolvent effects on the β-sheet aggregation through all-atom molecular dynamics simulation. J Chem Phys 2019; 150:145101. [DOI: 10.1063/1.5088395] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Keiichi Masutani
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Yu Yamamori
- Artificial Intelligence Research Center and Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Koto, Tokyo 135-0064, Japan
| | - Kang Kim
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
- Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto 615-8520, Japan
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20
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Lin Y, Penna M, Thomas MR, Wojciechowski JP, Leonardo V, Wang Y, Pashuck ET, Yarovsky I, Stevens MM. Residue-Specific Solvation-Directed Thermodynamic and Kinetic Control over Peptide Self-Assembly with 1D/2D Structure Selection. ACS NANO 2019; 13:1900-1909. [PMID: 30673202 PMCID: PMC6396410 DOI: 10.1021/acsnano.8b08117] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 01/16/2019] [Indexed: 05/18/2023]
Abstract
Understanding the self-organization and structural transformations of molecular ensembles is important to explore the complexity of biological systems. Here, we illustrate the crucial role of cosolvents and solvation effects in thermodynamic and kinetic control over peptide association into ultrathin Janus nanosheets, elongated nanobelts, and amyloid-like fibrils. We gained further insight into the solvation-directed self-assembly (SDSA) by investigating residue-specific peptide solvation using molecular dynamics modeling. We proposed the preferential solvation of the aromatic and alkyl domains on the peptide backbone and protofibril surface, which results in volume exclusion effects and restricts the peptide association between hydrophobic walls. We explored the SDSA phenomenon in a library of cosolvents (protic and aprotic), where less polar cosolvents were found to exert a stronger influence on the energetic balance at play during peptide propagation. By tailoring cosolvent polarity, we were able to achieve precise control of the peptide nanostructures with 1D/2D shape selection. We also illustrated the complexity of the SDSA system with pathway-dependent peptide aggregation, where two self-assembly states ( i.e., thermodynamic equilibrium state and kinetically trapped state) from different sample preparation methods were obtained.
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Affiliation(s)
- Yiyang Lin
- Department
of Materials, Department of Bioengineering, and Institute for Biomedical
Engineering, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Matthew Penna
- School
of Engineering, RMIT University, Melbourne, Victoria 3001, Australia
| | - Michael R. Thomas
- Department
of Materials, Department of Bioengineering, and Institute for Biomedical
Engineering, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Jonathan P. Wojciechowski
- Department
of Materials, Department of Bioengineering, and Institute for Biomedical
Engineering, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Vincent Leonardo
- Department
of Materials, Department of Bioengineering, and Institute for Biomedical
Engineering, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Ye Wang
- Department
of Materials, Department of Bioengineering, and Institute for Biomedical
Engineering, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - E. Thomas Pashuck
- Department
of Materials, Department of Bioengineering, and Institute for Biomedical
Engineering, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Irene Yarovsky
- School
of Engineering, RMIT University, Melbourne, Victoria 3001, Australia
- E-mail:
| | - Molly M. Stevens
- School
of Engineering, RMIT University, Melbourne, Victoria 3001, Australia
- E-mail:
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21
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Mondal B, Reddy G. Cosolvent Effects on the Growth of Protein Aggregates Formed by a Single Domain Globular Protein and an Intrinsically Disordered Protein. J Phys Chem B 2019; 123:1950-1960. [DOI: 10.1021/acs.jpcb.8b11128] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Balaka Mondal
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, Karnataka, India
| | - Govardhan Reddy
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012, Karnataka, India
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22
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Paranjapye N, Daggett V. De Novo Designed α-Sheet Peptides Inhibit Functional Amyloid Formation of Streptococcus mutans Biofilms. J Mol Biol 2018; 430:3764-3773. [PMID: 30006266 PMCID: PMC6168415 DOI: 10.1016/j.jmb.2018.07.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 06/29/2018] [Accepted: 07/02/2018] [Indexed: 12/11/2022]
Abstract
Streptococcus mutans is a bacterial species that predominates in the oral microbiome. S. mutans binds to the tooth surface, metabolizes sugars and produces acid, leading to cavity formation. S. mutans can also cause infectious endocarditis. Recent evidence suggests that S. mutans biofilms contain amyloid fibrils. Amyloids are insoluble fibrillar protein aggregates, and bacteria use functional amyloids to improve robustness of their biofilms. While the functional amyloids in bacteria such as Escherichia coli and Staphylococcus aureus have been heavily investigated, little is known about the mechanism of S. mutans amyloid formation. Previous results from our laboratory with the amyloidogenic proteins and peptides from the aforementioned bacteria and other mammalian amyloid systems suggest that amyloid formation progresses via an intermediate that adopts a unique secondary structure-α-sheet. De novo designed peptides with alternating l- and d-amino acid also adopt an α-sheet secondary structure and inhibit amyloid formation by binding to soluble oligomeric species during amyloidogenesis. Inhibition of fibrillization by α-sheet peptides suggests the presence of α-sheet during amyloid formation. To investigate the mechanism of functional amyloid formation in S. mutans, α-sheet peptides were compared to epigallocatechin gallate for their ability to inhibit fibril formation in S. mutans. Inhibition was demonstrated in a biofilm plate assay and on hydroxyapatite surfaces both in S. mutans alone and in bacteria from human saliva. The observed inhibition suggests that an α-sheet mediated mechanism may be operative during functional amyloid formation.
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Affiliation(s)
- Natasha Paranjapye
- Department of Bioengineering, University of Washington, Box 355013, Seattle, WA 98195-5013, USA
| | - Valerie Daggett
- Department of Bioengineering, University of Washington, Box 355013, Seattle, WA 98195-5013, USA.
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23
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Hassan M, Abbas Q, Seo SY, Shahzadi S, Ashwal HA, Zaki N, Iqbal Z, Moustafa AA. Computational modeling and biomarker studies of pharmacological treatment of Alzheimer's disease (Review). Mol Med Rep 2018; 18:639-655. [PMID: 29845262 PMCID: PMC6059694 DOI: 10.3892/mmr.2018.9044] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 07/05/2017] [Indexed: 12/31/2022] Open
Abstract
Alzheimer's disease (AD) is a complex and multifactorial disease. In order to understand the genetic influence in the progression of AD, and to identify novel pharmaceutical agents and their associated targets, the present study discusses computational modeling and biomarker evaluation approaches. Based on mechanistic signaling pathway approaches, various computational models, including biochemical and morphological models, are discussed to explore the strategies that may be used to target AD treatment. Different biomarkers are interpreted on the basis of morphological and functional features of amyloid β plaques and unstable microtubule‑associated tau protein, which is involved in neurodegeneration. Furthermore, imaging and cerebrospinal fluids are also considered to be key methods in the identification of novel markers for AD. In conclusion, the present study reviews various biochemical and morphological computational models and biomarkers to interpret novel targets and agonists for the treatment of AD. This review also highlights several therapeutic targets and their associated signaling pathways in AD, which may have potential to be used in the development of novel pharmacological agents for the treatment of patients with AD. Computational modeling approaches may aid the quest for the development of AD treatments with enhanced therapeutic efficacy and reduced toxicity.
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Affiliation(s)
- Mubashir Hassan
- Department of Biology, College of Natural Sciences, Kongju National University, Gongju, Chungcheongnam 32588, Republic of Korea
- Institute of Molecular Science and Bioinformatics, Dyal Singh Trust Library, Lahore 54000, Pakistan
| | - Qamar Abbas
- Department of Physiology, University of Sindh, Jamshoro 76080, Pakistan
| | - Sung-Yum Seo
- Department of Biology, College of Natural Sciences, Kongju National University, Gongju, Chungcheongnam 32588, Republic of Korea
| | - Saba Shahzadi
- Institute of Molecular Science and Bioinformatics, Dyal Singh Trust Library, Lahore 54000, Pakistan
- Department of Bioinformatics, Virtual University Davis Road Campus, Lahore 54000, Pakistan
| | - Hany Al Ashwal
- College of Information Technology, United Arab Emirates University, Al-Ain 15551, United Arab Emirates
| | - Nazar Zaki
- College of Information Technology, United Arab Emirates University, Al-Ain 15551, United Arab Emirates
| | - Zeeshan Iqbal
- Institute of Molecular Science and Bioinformatics, Dyal Singh Trust Library, Lahore 54000, Pakistan
| | - Ahmed A. Moustafa
- School of Social Sciences and Psychology, Western Sydney University, Sydney, NSW 2751, Australia
- MARCS Institute for Brain, Behavior and Development, Western Sydney University, Sydney, NSW 2751, Australia
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24
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Li HR, Chen TC, Hsiao CL, Shi L, Chou CY, Huang JR. The physical forces mediating self-association and phase-separation in the C-terminal domain of TDP-43. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1866:214-223. [PMID: 28988034 DOI: 10.1016/j.bbapap.2017.10.001] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 09/22/2017] [Accepted: 10/02/2017] [Indexed: 12/14/2022]
Abstract
The TAR DNA-binding protein of 43kDa (TDP-43) has been identified as the main component of amyotrophic lateral sclerosis (ALS) cytoplasmic inclusions. The link between this proteinopathy and TDP-43's intrinsically disordered C-terminal domain is well known, but recently also, this domain has been shown to be involved in the formation of the membraneless organelles that mediate TDP-43's functions. The mechanisms that underpin the liquid-liquid phase separation (LLPS) of these membraneless organelles undergo remain elusive. Crucially though, these factors may be the key to understanding the delicate balance between TDP-43's physiological and pathological functions. In this study, we used nuclear magnetic resonance spectroscopy and optical methods to demonstrate that an α-helical component in the centre (residues 320-340) of the C-terminal domain is related to the protein's self-association and LLPS. Systematically analysing ALS-related TDP-43 mutants (G298S, M337V, and Q331K) in different buffer conditions at different temperatures, we prove that this phase separation is driven by hydrophobic interactions but is inhibited by electrostatic repulsion. Based on these findings, we rationally introduced a mutant, W334G, and demonstrate that this mutant disrupts LLPS without disturbing this α-helical propensity. This tryptophan may serve as a key residue in this protein's LLPS.
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Affiliation(s)
- Hao-Ru Li
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, No. 155 Section 2, Li-nong Street, Taipei, Taiwan
| | - Tsai-Chen Chen
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, No. 155 Section 2, Li-nong Street, Taipei, Taiwan
| | - Chih-Lun Hsiao
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, No. 155 Section 2, Li-nong Street, Taipei, Taiwan
| | - Lin Shi
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, No. 155 Section 2, Li-nong Street, Taipei, Taiwan
| | - Chi-Yuan Chou
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, No. 155 Section 2, Li-nong Street, Taipei, Taiwan
| | - Jie-Rong Huang
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, No. 155 Section 2, Li-nong Street, Taipei, Taiwan; Institute of Biomedical Informatics, National Yang-Ming University, No. 155 Section 2, Li-nong Street, Taipei, Taiwan.
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25
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Siddaramaiah M, Satyamoorthy K, Rao BSS, Roy S, Chandra S, Mahato KK. Identification of protein secondary structures by laser induced autofluorescence: A study of urea and GnHCl induced protein denaturation. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 174:44-53. [PMID: 27875744 DOI: 10.1016/j.saa.2016.11.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 11/11/2016] [Accepted: 11/12/2016] [Indexed: 06/06/2023]
Abstract
In the present study an attempt has been made to interrogate the bulk secondary structures of some selected proteins (BSA, HSA, lysozyme, trypsin and ribonuclease A) under urea and GnHCl denaturation using laser induced autofluorescence. The proteins were treated with different concentrations of urea (3M, 6M, 9M) and GnHCl (2M, 4M, 6M) and the corresponding steady state autofluorescence spectra were recorded at 281nm pulsed laser excitations. The recorded fluorescence spectra of proteins were then interpreted based on the existing PDB structures of the proteins and the Trp solvent accessibility (calculated using "Scratch protein predictor" at 30% threshold). Further, the influence of rigidity and conformation of the indole ring (caused by protein secondary structures) on the intrinsic fluorescence properties of proteins were also evaluated using fluorescence of ANS-HSA complexes, CD spectroscopy as well as with trypsin digestion experiments. The outcomes obtained clearly demonstrated GnHCl preferably disrupt helix as compared to the beta β-sheets whereas, urea found was more effective in disrupting β-sheets as compared to the helices. The other way round the proteins which have shown detectable change in the intrinsic fluorescence at lower concentrations of GnHCl were rich in helices whereas, the proteins which showed detectable change in the intrinsic fluorescence at lower concentrations of urea were rich in β-sheets. Since high salt concentrations like GnHCl and urea interfere in the secondary structure analysis by circular dichroism Spectrometry, the present method of analyzing secondary structures using laser induced autofluorescence will be highly advantageous over existing tools for the same.
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Affiliation(s)
- Manjunath Siddaramaiah
- Department of Biophysics, School of Life Sciences, Manipal University, Manipal, Karnataka 576104, India
| | | | - Bola Sadashiva Satish Rao
- Department of Radiation Biology and Toxicology, School of Life Sciences, Manipal University, Manipal, Karnataka 576104, India
| | - Suparna Roy
- School of Life Sciences, Manipal University, Manipal, Karnataka 576104, India
| | - Subhash Chandra
- Department of Biophysics, School of Life Sciences, Manipal University, Manipal, Karnataka 576104, India
| | - Krishna Kishore Mahato
- Department of Biophysics, School of Life Sciences, Manipal University, Manipal, Karnataka 576104, India.
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26
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Siposova K, Kozar T, Musatov A. Interaction of nonionic detergents with the specific sites of lysozyme amyloidogenic region - inhibition of amyloid fibrillization. Colloids Surf B Biointerfaces 2016; 150:445-455. [PMID: 27842932 DOI: 10.1016/j.colsurfb.2016.11.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 11/02/2016] [Accepted: 11/05/2016] [Indexed: 11/15/2022]
Abstract
Two nonionic detergents, Triton X-100 (TX-100) and n-dodecyl-β-d-maltoside (DDM) were tested for their ability to affect lysozyme amyloid aggregation. We have demonstrated that fibrillization of lysozyme is completely inhibited by low sub-micellar concentrations of both of these detergents. The apparent IC50 values were calculated to be 22μM and 26μM for TX-100 and DDM, respectively. The detergent/protein ratio is not the only parameter controlling inhibition. The precise timing of the detergent addition was found to be also crucial. It appears that the primary inhibitory activity of detergents resulted from inhibition of nuclei formation, in addition to inhibition of fibril polymerization at the early stage of protofibrils growth. The docking study revealed that Asn-59, Trp-63 and Ala-107, all present within the lysozyme amyloidogenic region, were involved in the interaction with both detergents. In addition, TX-100 also interacted with Gln-57 and Asp-103 within lysozyme. Moreover, based on our computational results, TX-100 bridges the Gln-57 and Ala-107 amino acids of the amyloidogenic segment of lysozyme and therefore inhibits more effectively the amyloid fibril formation. Along these lines, the knowledge gained from our study indicates that the detergents or their derivatives may be applicable as a promising strategy for the modulation of lysozyme protein aggregation.
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Affiliation(s)
- Katarina Siposova
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Kosice, Slovakia.
| | - Tibor Kozar
- Center for multimodal imaging, Institute of Physics, Faculty of Science, P.J. Safarik University, Srobarova 2, 041 54 Kosice, Slovakia
| | - Andrey Musatov
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Kosice, Slovakia
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27
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Peptides Composed of Alternating L- and D-Amino Acids Inhibit Amyloidogenesis in Three Distinct Amyloid Systems Independent of Sequence. J Mol Biol 2016; 428:2317-2328. [PMID: 27012425 DOI: 10.1016/j.jmb.2016.03.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 03/07/2016] [Accepted: 03/12/2016] [Indexed: 11/23/2022]
Abstract
There is now substantial evidence that soluble oligomers are primary toxic agents in amyloid diseases. The development of an antibody recognizing the toxic soluble oligomeric forms of different and unrelated amyloid species suggests a common conformational intermediate during amyloidogenesis. We previously observed a common occurrence of a novel secondary structure element, which we call α-sheet, in molecular dynamics (MD) simulations of various amyloidogenic proteins, and we hypothesized that the toxic conformer is composed of α-sheet structure. As such, α-sheet may represent a conformational signature of the misfolded intermediates of amyloidogenesis and a potential unique binding target for peptide inhibitors. Recently, we reported the design and characterization of a novel hairpin peptide (α1 or AP90) that adopts stable α-sheet structure and inhibits the aggregation of the β-Amyloid Peptide Aβ42 and transthyretin. AP90 is a 23-residue hairpin peptide featuring alternating D- and L-amino acids with favorable conformational propensities for α-sheet formation, and a designed turn. For this study, we reverse engineered AP90 to identify which of its design features is most responsible for conferring α-sheet stability and inhibitory activity. We present experimental characterization (CD and FTIR) of seven peptides designed to accomplish this. In addition, we measured their ability to inhibit aggregation in three unrelated amyloid species: Aβ42, transthyretin, and human islet amylin polypeptide. We found that a hairpin peptide featuring alternating L- and D-amino acids, independent of sequence, is sufficient for conferring α-sheet structure and inhibition of aggregation. Additionally, we show a correlation between α-sheet structural stability and inhibitory activity.
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Watt AD, Crespi GAN, Down RA, Ascher DB, Gunn A, Perez KA, McLean CA, Villemagne VL, Parker MW, Barnham KJ, Miles LA. Anti-Aβ antibody target engagement: a response to Siemers et al. Acta Neuropathol 2014; 128:611-4. [PMID: 25120193 DOI: 10.1007/s00401-014-1333-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 08/07/2014] [Indexed: 10/24/2022]
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Proctor CJ, Boche D, Gray DA, Nicoll JAR. Investigating interventions in Alzheimer's disease with computer simulation models. PLoS One 2013; 8:e73631. [PMID: 24098635 PMCID: PMC3782376 DOI: 10.1371/journal.pone.0073631] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 07/25/2013] [Indexed: 12/26/2022] Open
Abstract
Progress in the development of therapeutic interventions to treat or slow the progression of Alzheimer's disease has been hampered by lack of efficacy and unforeseen side effects in human clinical trials. This setback highlights the need for new approaches for pre-clinical testing of possible interventions. Systems modelling is becoming increasingly recognised as a valuable tool for investigating molecular and cellular mechanisms involved in ageing and age-related diseases. However, there is still a lack of awareness of modelling approaches in many areas of biomedical research. We previously developed a stochastic computer model to examine some of the key pathways involved in the aggregation of amyloid-beta (Aβ) and the micro-tubular binding protein tau. Here we show how we extended this model to include the main processes involved in passive and active immunisation against Aβ and then demonstrate the effects of this intervention on soluble Aβ, plaques, phosphorylated tau and tangles. The model predicts that immunisation leads to clearance of plaques but only results in small reductions in levels of soluble Aβ, phosphorylated tau and tangles. The behaviour of this model is supported by neuropathological observations in Alzheimer patients immunised against Aβ. Since, soluble Aβ, phosphorylated tau and tangles more closely correlate with cognitive decline than plaques, our model suggests that immunotherapy against Aβ may not be effective unless it is performed very early in the disease process or combined with other therapies.
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Affiliation(s)
- Carole J. Proctor
- Institute for Ageing and Health, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Delphine Boche
- Clinical Neurosciences, Clinical and Experimental Sciences, University of Southampton, Southampton, United Kingdom
| | - Douglas A. Gray
- Ottawa Hospital Research Institute, Ottawa, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada
| | - James A. R. Nicoll
- Clinical Neurosciences, Clinical and Experimental Sciences, University of Southampton, Southampton, United Kingdom
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Hu Y, Su B, Kim CS, Hernandez M, Rostagno A, Ghiso J, Kim JR. A strategy for designing a peptide probe for detection of β-amyloid oligomers. Chembiochem 2011; 11:2409-18. [PMID: 21031399 DOI: 10.1002/cbic.201000435] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Aggregation of β-amyloid (Aβ) is implicated in the pathology of Alzheimer's disease. Development of a robust strategy to detect Aβ oligomeric intermediates, which have been identified as significant toxic agents, would be highly beneficial in the screening of drug candidates as well as enhancing our understanding of Aβ oligomerization. Rapid, specific and quantitative detection, currently unavailable, would be highly preferred for accurate and reliable probing of transient Aβ oligomers. Here, we report the development of a novel peptide probe, PG46, based on the nature of Aβ self-assembly and the conformation-sensitive fluorescence of the biarsenical dye, FlAsH. PG46 was found to bind to Aβ oligomers and displayed an increase in FlAsH fluorescence upon binding. No such event was observed when PG46 was co-incubated with Aβ low-molecular-weight species or Aβ fibrils. Aβ oligomer detection was fast, and occurred within one hour without any additional sample incubation or preparation. We anticipate that the development of a strategy for detection of amyloid oligomers described in this study will be directly relevant to a host of other amyloidogenic proteins.
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Affiliation(s)
- Yang Hu
- Othmer-Jacobs Department of Chemical and Biological Engineering, Polytechnic Institute of New York University, 6 MetroTech Center, Brooklyn, NY 11201, USA
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31
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Schmit JD, Ghosh K, Dill K. What drives amyloid molecules to assemble into oligomers and fibrils? Biophys J 2011; 100:450-8. [PMID: 21244841 PMCID: PMC3021675 DOI: 10.1016/j.bpj.2010.11.041] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Revised: 11/06/2010] [Accepted: 11/09/2010] [Indexed: 11/22/2022] Open
Abstract
We develop a theory for three states of equilibrium of amyloid peptides: the monomer, oligomer, and fibril. We assume that the oligomeric state is a disordered micellelike collection of a few peptide chains held together loosely by hydrophobic interactions into a spherical hydrophobic core. We assume that fibrillar amyloid chains are aligned and further stabilized by steric zipper interactions-hydrogen bonding, steric packing, and specific hydrophobic side-chain contacts. The model makes a broad set of predictions that are consistent with experimental results: 1), Similar to surfactant micellization, amyloid oligomerization should increase with peptide concentration in solution. 2), The onset of fibrillization limits the concentration of oligomers in the solution. 3), The extent of Aβ fibrillization increases with peptide concentration. 4), The predicted average fibril length versus monomer concentration agrees with data on α-synuclein. 5), Full fibril length distributions agree with data on α-synuclein. 6), Denaturants should melt out fibrils. And finally, 7), added salt should stabilize fibrils by reducing repulsions between amyloid peptide chains. It is of interest that small changes in solvent conditions can tip the equilibrium balance between oligomer and fibril and cause large changes in rates through effects on the transition-state barrier. This model may provide useful insights into the physical processes underlying amyloid diseases.
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Affiliation(s)
- Jeremy D Schmit
- Department of Pharmaceutical Chemistry, University of California, San Francisco, USA.
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32
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Straub JE, Thirumalai D. Toward a molecular theory of early and late events in monomer to amyloid fibril formation. Annu Rev Phys Chem 2011; 62:437-63. [PMID: 21219143 PMCID: PMC11237996 DOI: 10.1146/annurev-physchem-032210-103526] [Citation(s) in RCA: 209] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Quantitative understanding of the kinetics of fibril formation and the molecular mechanism of transition from monomers to fibrils is needed to obtain insights into the growth of amyloid fibrils and more generally self-assembly multisubunit protein complexes. Significant advances using computations of protein aggregation in a number of systems have established generic and sequence-specific aspects of the early steps in oligomer formation. Theoretical considerations, which view oligomer and fibril growth as diffusion in a complex energy landscape, and computational studies, involving minimal lattice and coarse-grained models, have revealed general principles governing the transition from monomeric protein to ordered fibrillar aggregates. Detailed atomistic calculations have explored the early stages of the protein aggregation pathway for a number of amyloidogenic proteins, most notably amyloid β- (Aβ-) protein and fragments from proteins linked to various diseases. These computational studies have provided insights into the role of sequence, role of water, and specific interatomic interactions underlying the thermodynamics and dynamics of elementary kinetic steps in the aggregation pathway. Novel methods are beginning to illustrate the structural basis for the production of Aβ-peptides through interactions with secretases in the presence of membranes. We show that a variety of theoretical approaches, ranging from scaling arguments to minimal models to atomistic simulations, are needed as a complement to experimental studies probing the principles governing protein aggregation.
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Affiliation(s)
- John E Straub
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA.
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Gozal YM, Duong DM, Gearing M, Cheng D, Hanfelt JJ, Funderburk C, Peng J, Lah JJ, Levey AI. Proteomics analysis reveals novel components in the detergent-insoluble subproteome in Alzheimer's disease. J Proteome Res 2010; 8:5069-79. [PMID: 19746990 DOI: 10.1021/pr900474t] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Neurodegenerative diseases are often defined pathologically by the presence of protein aggregates. These aggregates, including amyloid plaques in Alzheimer's disease (AD), result from the abnormal accumulation and processing of proteins, and may ultimately lead to neuronal dysfunction and cell death. To date, conventional biochemical studies have revealed abundant core components in protein aggregates. However, rapidly improving proteomics technologies offer opportunities to revisit pathologic aggregate composition, and to identify less abundant but potentially important functional molecules that participate in neurodegeneration. The purpose of this study was to establish a proteomic strategy for the profiling of neurodegenerative disease tissues for disease-specific changes in protein abundance. Using high resolution liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS), we analyzed detergent-insoluble frontal cortex samples from AD and unaffected control cases. In addition, we analyzed samples from frontotemporal lobar degeneration (FTLD) cases to identify AD-specific changes not present in other neurodegenerative diseases. We used a labeling-free quantification technique to compare the abundance of identified peptides in the samples based on extracted ion current (XIC) of their corresponding ions. Of the 512 identified proteins, quantitation demonstrated significant changes in 81 AD-specific proteins. Following additional manual filtering, 11 proteins were accepted with high confidence as increased in AD compared to control and FTLD brains, including beta-amyloid, tau and apolipoprotein E, all well-established AD-linked proteins. In addition, we identified and validated the presence of serine protease 15, ankyrin B, and 14-3-3 eta in the detergent-insoluble fraction. Our results provide further evidence for the capacity of proteomics applications to identify conserved sets of disease-specific proteins in AD, to enhance our understanding of disease pathogenesis, and to deliver new candidates for the development of effective therapies for this, and other, devastating neurodegenerative disorders.
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Affiliation(s)
- Yair M Gozal
- Department of Neurology, Emory University, Atlanta, Georgia 30322, USA
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Mackintosh SH, Meade SJ, Healy JP, Sutton KH, Larsen NG, Squires AM, Gerrard JA. Wheat glutenin proteins assemble into a nanostructure with unusual structural features. J Cereal Sci 2009. [DOI: 10.1016/j.jcs.2008.08.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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35
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Armstrong RA, Lantos PL, Cairns NJ. What determines the molecular composition of abnormal protein aggregates in neurodegenerative disease? Neuropathology 2008; 28:351-65. [PMID: 18433435 DOI: 10.1111/j.1440-1789.2008.00916.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Abnormal protein aggregates, in the form of either extracellular plaques or intracellular inclusions, are an important pathological feature of the majority of neurodegenerative disorders. The major molecular constituents of these lesions, viz., beta-amyloid (Abeta), tau, and alpha-synuclein, have played a defining role in the diagnosis and classification of disease and in studies of pathogenesis. The molecular composition of a protein aggregate, however, is often complex and could be the direct or indirect consequence of a pathogenic gene mutation, be the result of cell degeneration, or reflect the acquisition of new substances by diffusion and molecular binding to existing proteins. This review examines the molecular composition of the major protein aggregates found in the neurodegenerative diseases including the Abeta and prion protein (PrP) plaques found in Alzheimer's disease (AD) and prion disease, respectively, and the cellular inclusions found in the tauopathies and synucleinopathies. The data suggest that the molecular constituents of a protein aggregate do not directly cause cell death but are largely the consequence of cell degeneration or are acquired during the disease process. These findings are discussed in relation to diagnosis and to studies of to disease pathogenesis.
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Pallarés I, Berenguer C, Avilés FX, Vendrell J, Ventura S. Self-assembly of human latexin into amyloid-like oligomers. BMC STRUCTURAL BIOLOGY 2007; 7:75. [PMID: 17996039 PMCID: PMC2212644 DOI: 10.1186/1472-6807-7-75] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2007] [Accepted: 11/08/2007] [Indexed: 11/28/2022]
Abstract
Background In conformational disorders, it is not evident which amyloid aggregates affect specific molecular mechanisms or cellular pathways, which cause disease because of their quantity and mechanical features and which states in aggregate formation are pathogenic. Due to the increasing consensus that prefibrillar oligomers play a major role in conformational diseases, there is a growing interest in understanding the characteristics of metastable polypeptide associations. Results Here, we show that human latexin, a protein that shares the same fold with cystatin C, assembles into stable spherical amyloid-like oligomers that bind thioflavin-T and congo red similarly to common amyloid structures but do not evolve into fibrils. Latexin self-assembly correlates with the formation of a mostly denaturated state rather than with the population of partially structured intermediates during the unfolding process. The results suggest that unfolding of α-helix 3 might be involved in the transition of latexin toward amyloidotic species, supporting the notion of the protective role of the native protein structure against polymerization. Conclusion Overall the data herein indicate that latexin could be a good model for the study of the structural and sequential determinants of oligomeric assemblies in protein aggregation processes.
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Affiliation(s)
- Irantzu Pallarés
- Departament de Bioquímica i Biologia Molecular, Facultat de Ciències, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain.
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37
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Shahnawaz M, Thapa A, Park IS. Stable activity of a deubiquitylating enzyme (Usp2-cc) in the presence of high concentrations of urea and its application to purify aggregation-prone peptides. Biochem Biophys Res Commun 2007; 359:801-5. [PMID: 17560941 DOI: 10.1016/j.bbrc.2007.05.186] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2007] [Accepted: 05/30/2007] [Indexed: 11/24/2022]
Abstract
Chemical synthesis of long or aggregation-prone peptide has been problematic. Its biological production has an advantage in that point, but it often forms inclusion body which creates difficulties in recovery of targets. As a deubiquitylating enzyme (Usp2-cc) was shown in this study to maintain its activity even in the presence of up to 4M urea, target peptide was purified by a single step of chromatography after overexpression as inclusion body, solubilization in urea and cleavage by the enzyme from the fusion protein consisting of GroES (used for high expression and easy to handle), ubiquitin (as a cleavage site) and target peptide. This system is a convenient tool for production of peptides that are difficult to be chemically synthesized and biologically purified.
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Affiliation(s)
- Mohammad Shahnawaz
- Research Center for Proteineous Materials, Department of Bio-materials Engineering, Chosun University, Gwanju 501-759, Republic of Korea
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38
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Lee S, Fernandez EJ, Good TA. Role of aggregation conditions in structure, stability, and toxicity of intermediates in the Abeta fibril formation pathway. Protein Sci 2007; 16:723-32. [PMID: 17327396 PMCID: PMC2203338 DOI: 10.1110/ps.062514807] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
beta-amyloid peptide (Abeta) is one of the main protein components of senile plaques associated with Alzheimer's disease (AD). Abeta readily aggregates to forms fibrils and other aggregated species that have been shown to be toxic in a number of studies. In particular, soluble oligomeric forms are closely related to neurotoxicity. However, the relationship between neurotoxicity and the size of Abeta aggregates or oligomers is still under investigation. In this article, we show that different Abeta incubation conditions in vitro can affect the rate of Abeta fibril formation, the conformation and stability of intermediates in the aggregation pathway, and toxicity of aggregated species formed. When gently agitated, Abeta aggregates faster than Abeta prepared under quiescent conditions, forming fibrils. The morphology of fibrils formed at the end of aggregation with or without agitation, as observed in electron micrographs, is somewhat different. Interestingly, intermediates or oligomers formed during Abeta aggregation differ greatly under agitated and quiescent conditions. Unfolding studies in guanidine hydrochloride indicate that fibrils formed under quiescent conditions are more stable to unfolding in detergent than aggregation associated oligomers or Abeta fibrils formed with agitation. In addition, Abeta fibrils formed under quiescent conditions were less toxic to differentiated SH-SY5Y cells than the Abeta aggregation associated oligomers or fibrils formed with agitation. These results highlight differences between Abeta aggregation intermediates formed under different conditions and provide insight into the structure and stability of toxic Abeta oligomers.
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Affiliation(s)
- Sungmun Lee
- Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, USA
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Vitrenko YA, Gracheva EO, Richmond JE, Liebman SW. Visualization of aggregation of the Rnq1 prion domain and cross-seeding interactions with Sup35NM. J Biol Chem 2006; 282:1779-87. [PMID: 17121829 DOI: 10.1074/jbc.m609269200] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Factors triggering the de novo appearance of prions are still poorly understood. In yeast, the appearance of one prion, [PSI(+)], is enhanced by the presence of another prion, [PIN(+)]. The [PSI(+)] and [PIN(+)] prion-forming proteins are, respectively, the translational termination factor Sup35 and the yet poorly characterized Rnq1 protein that is rich in glutamines and asparagines. The prion domain of Rnq1 (RnqPD) polymerizes more readily in vitro than the full-length protein. As is typical for amyloidogenic proteins, the reaction begins with a lag phase, followed by exponential growth. Seeding with pre-formed aggregates significantly shortens the lag. A generic antibody against pre-amyloid oligomer inhibits the unseeded but not the self-seeded reaction. As revealed by electron microscopy, RnqPD polymerizes predominantly into spherical species that eventually agglomerate. We observed infrequent fiber-like structures in samples taken at 4 h of polymerization, but in overnight samples SDS treatment was required to reveal fibers among agglomerates. Polymerization reactions in which RnqPD and the prion domain of Sup35 (Sup35NM) cross-seed each other proceeded with a shortened lag that only depends weakly on the protein concentration. Cross-seeded Sup35NM fibers appear to sprout from globular RnqPD aggregates as seen by electron microscopy. RnqPD spherical aggregates appear to associate with and, later occlude, Sup35NM seed fibers. Our kinetic and morphological analyses suggest that, upon cross-seeding, the aggregate provides the surface on which oligomers of the heterologous protein nucleate their subsequent amyloid formation.
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Affiliation(s)
- Yakov A Vitrenko
- Department of Biological Sciences, the University of Illinois, Chicago, Illinois 60607, USA
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Chen YR, Glabe CG. Distinct Early Folding and Aggregation Properties of Alzheimer Amyloid-β Peptides Aβ40 and Aβ42. J Biol Chem 2006; 281:24414-22. [PMID: 16809342 DOI: 10.1074/jbc.m602363200] [Citation(s) in RCA: 173] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The amyloid beta peptide (Abeta), composed of 40 or 42 amino acids, is a critical component in the etiology of the neurodegenerative Alzheimer disease. Abeta is prone to aggregate and forms amyloid fibrils progressively both in vitro and in vivo. To understand the process of amyloidogenesis, it is pivotal to examine the initial stages of the folding process. We examined the equilibrium folding properties, assembly states, and stabilities of the early folding stages of Abeta40 and Abeta42 prior to fibril formation. We found that Abeta40 and Abeta42 have different conformations and assembly states upon refolding from their unfolded ensembles. Abeta40 is predominantly an unstable and collapsed monomeric species, whereas Abeta42 populates a stable structured trimeric or tetrameric species at concentrations above approximately 12.5 microm. Thermodynamic analysis showed that the free energies of Abeta40 monomer and Abeta42 trimer/tetramer are approximately 1.1 and approximately 15/ approximately 22 kcal/mol, respectively. The early aggregation stages of Abeta40 and Abeta42 contain different solvent-exposed hydrophobic surfaces that are located at the sequences flanking its protease-resistant segment. The amyloidogenic folded structure of Abeta is important for the formation of spherical beta oligomeric species. However, beta oligomers are not an obligatory intermediate in the process of fibril formation because oligomerization is inhibited at concentrations of urea that have no effect on fibril formation. The distinct initial folding properties of Abeta40 and Abeta42 may play an important role in the higher aggregation potential and pathological significance of Abeta42.
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Affiliation(s)
- Yun-Ru Chen
- Department of Molecular Biology and Biochemistry, The University of California, Irvine, California 92697, USA
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