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Chen X, Wang J, Mo Z, Han L, Cheng K, Xie C, Liu G, Jiang L, Wang K, Pan J. Development of Ru-polypyridyl complexes for real-time monitoring of Aβ oligomers and inhibition of Aβ fibril formation. Biomater Sci 2024; 12:1449-1453. [PMID: 38390765 DOI: 10.1039/d3bm01929b] [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: 02/24/2024]
Abstract
The aggregation of amyloid-β (Aβ) is one of the important pathological markers of Alzheimer's disease. Ruthenium(II) complexes have good stability, low cytotoxicity, a high fluorescence quantum yield, and a good Stokes shift as fluorescent probes. Based on this, we constructed a fluorescent probe for in vivo real-time imaging and inhibition of Aβ-fibril formation using a complex of Ru polypyridine with organic fluorophores (N,N-dimethylaniline) and hydrophobic peptides (KLVFF). DLS and TEM studies have shown that Ru-YH has an inhibitory effect on the fibrotic aggregation of Aβ. Both in vivo and in vitro studies have shown that Ru-WJ and Ru-YH can quickly cross the blood-brain barrier and successfully detect Aβ in early (2.5-month old) transgenic mouse models. In summary, we have explored the potential of Ru complex based biological probes for early diagnosis and inhibition of AD.
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Affiliation(s)
- Xian Chen
- College of Health Science and Engineering, Hubei University, Wuhan 430062, P. R. China.
| | - Jiaoyang Wang
- College of Health Science and Engineering, Hubei University, Wuhan 430062, P. R. China.
| | - Zhenzhuo Mo
- College of Health Science and Engineering, Hubei University, Wuhan 430062, P. R. China.
| | - Lu Han
- College of Health Science and Engineering, Hubei University, Wuhan 430062, P. R. China.
| | - Kaiqing Cheng
- College of Health Science and Engineering, Hubei University, Wuhan 430062, P. R. China.
| | - Cheng Xie
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, PR China
| | - Genyan Liu
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, 430205, PR China
| | - Lijun Jiang
- College of Life Sciences, Central China Normal University, Wuhan 430062, P. R. China
| | - Kai Wang
- College of Health Science and Engineering, Hubei University, Wuhan 430062, P. R. China.
| | - Jie Pan
- College of Health Science and Engineering, Hubei University, Wuhan 430062, P. R. China.
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2
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Galzitskaya OV, Grishin SY, Glyakina AV, Dovidchenko NV, Konstantinova AV, Kravchenko SV, Surin AK. The Strategies of Development of New Non-Toxic Inhibitors of Amyloid Formation. Int J Mol Sci 2023; 24:3781. [PMID: 36835194 PMCID: PMC9964835 DOI: 10.3390/ijms24043781] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 02/16/2023] Open
Abstract
In recent years, due to the aging of the population and the development of diagnostic medicine, the number of identified diseases associated with the accumulation of amyloid proteins has increased. Some of these proteins are known to cause a number of degenerative diseases in humans, such as amyloid-beta (Aβ) in Alzheimer's disease (AD), α-synuclein in Parkinson's disease (PD), and insulin and its analogues in insulin-derived amyloidosis. In this regard, it is important to develop strategies for the search and development of effective inhibitors of amyloid formation. Many studies have been carried out aimed at elucidating the mechanisms of amyloid aggregation of proteins and peptides. This review focuses on three amyloidogenic peptides and proteins-Aβ, α-synuclein, and insulin-for which we will consider amyloid fibril formation mechanisms and analyze existing and prospective strategies for the development of effective and non-toxic inhibitors of amyloid formation. The development of non-toxic inhibitors of amyloid will allow them to be used more effectively for the treatment of diseases associated with amyloid.
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Affiliation(s)
- Oxana V. Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Sergei Y. Grishin
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia
| | - Anna V. Glyakina
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
- Institute of Mathematical Problems of Biology RAS, The Branch of Keldysh Institute of Applied Mathematics, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Nikita V. Dovidchenko
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Anastasiia V. Konstantinova
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
- Faculty of Biotechnology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Sergey V. Kravchenko
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia
| | - Alexey K. Surin
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
- The Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Russia
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3
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Jaklin M, Hritz J, Hribar-Lee B. A new fibrillization mechanism of β-lactoglobulin in glycine solutions. Int J Biol Macromol 2022; 216:414-425. [PMID: 35803407 PMCID: PMC10039397 DOI: 10.1016/j.ijbiomac.2022.06.182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/15/2022] [Accepted: 06/27/2022] [Indexed: 11/26/2022]
Abstract
Even though amyloid aggregates were discovered many years ago the mechanism of their formation is still a mystery. Because of their connection to many of untreatable neurodegenerative diseases the motivation for finding a common aggregation path is high. We report a new high heat induced fibrillization path of a model protein β-lactoglobulin (BLG) when incubated in glycine instead of water at pH 2. By combining atomic force microscopy (AFM), transmission emission microscopy (TEM), dynamic light scattering (DLS) and circular dichroism (CD) we predict that the basic building blocks of fibrils made in glycine are not peptides, but rather spheroid oligomers of different height that form by stacking of ring-like structures. Spheroid oligomers linearly align to form fibrils by opening up and combining. We suspect that glycine acts as an hydrolysation inhibitor which consequently promotes a different fibrillization path. By combining the known data on fibrillization in water with our experimental conclusions we come up with a new fibrillization scheme for BLG. We show that by changing the fibrillization conditions just by small changes in buffer composition can dramatically change the aggregation pathway and the effect of buffer shouldn't be neglected. Fibrils seen in our study are also gaining more and more attention because of their pore-like structure and a possible cytotoxic mechanism by forming pernicious ion-channels. By preparing them in a simple model system as BLG we opened a new way to study their formation.
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Affiliation(s)
- Matej Jaklin
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Večna pot 113, Ljubljana SI-1000, Slovenia
| | - Jozef Hritz
- CEITEC Masaryk University Kamenice 5, Brno 625 00, Czech Republic; Department of Chemistry, Faculty of Science, Masaryk University Kamenice 5, Brno 625 00, Czech Republic
| | - Barbara Hribar-Lee
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Večna pot 113, Ljubljana SI-1000, Slovenia.
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4
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Glyakina AV, Balabaev NK, Galzitskaya OV. Determination of the Most Stable Packing of Peptides from Ribosomal S1 Protein, Protein Bgl2p, and Aβ peptide in β-layers During Molecular Dynamics Simulations. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2340:221-233. [PMID: 35167077 DOI: 10.1007/978-1-0716-1546-1_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Our task was to determine the most stable packing of peptides in β-layers to construct an oligomer structure for fibril growth. The β-layers consisting of eight short peptides with the amino acid sequences IVRGVVVAID, VDSWNVLVAG (VESWNVLVAG), KLVFFAEDVG, and IIGLMVGGVV were built. These sequences correspond to the amyloidogenic regions of ribosomal S1 protein from E. coli, protein glucantransferase Bgl2p from the yeast cell wall, and Aβ peptide. First, the amyloidogenic regions were predicted theoretically, and then were confirmed experimentally. Four β-layers with different orientation of the peptides in the layers and the layers relative to each other were constructed. To determine the most stable packing of β-strands, the molecular dynamic (MD) simulations in explicit water were carried out. Two charge states (pH3 and pH5) for each β-layer were considered. The fraction of the secondary structure was a measure of stability for β-layers. β-Layers, in which β-strands are antiparallel relative to each other, were the most stable. Using this packing for β-strands, we constructed the oligomer structures and also checked their stability by using MD simulations.
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Affiliation(s)
- Anna V Glyakina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.,Institute of Mathematical Problems of Biology RAS, Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Pushchino, Russia
| | - Nikolai K Balabaev
- Institute of Mathematical Problems of Biology RAS, Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Pushchino, Russia
| | - Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia. .,Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.
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5
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Jaragh-Alhadad LA, Falahati M. Tin oxide nanoparticles trigger the formation of amyloid β oligomers/protofibrils and underlying neurotoxicity as a marker of Alzheimer's diseases. Int J Biol Macromol 2022; 204:154-160. [PMID: 35124024 DOI: 10.1016/j.ijbiomac.2022.01.190] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/11/2022] [Accepted: 01/29/2022] [Indexed: 02/07/2023]
Abstract
Alzheimer's disease (AD) is known as one of the most common forms of dementia, and oligomerization of amyloid β (Aβ42) peptides can result in the onset of AD. Tin oxide nanoparticles (SnO2 NPs) showed several applications in biomedical fields can trigger unwanted interaction with proteins and inducing protein aggregation. Herein, we synthesized SnO2 NPs via the hydrothermal method and characterized by UV-visible, XRD, FTIR, TEM, and DLS techniques. Afterward, the formation of Aβ42 amyloid oligomers/protofibrils treated alone and with SnO2 NPs was explored by ThT and Nile red fluorescence and CD spectroscopic methods along with TEM imaging. The neurotoxicity of different spices of Aβ42 samples against PC-12 cells was then explored by MTT and caspase-3 activity assays. The characterization of SnO2 NPs confirmed the successful synthesis of crystalline NPs (20-30 nm). Different biophysical and cellular analyses indicated that SnO2 NPs accelerated Aβ42 fibrillogenesis and promoted amyloid oligomers/protofibrils cytotoxicity. As compared to the Aβ42 samples grown alone, the ThT and ANS fluorescence intensity along with ellipticity results indicated the promotory effect of SnO2 NPs on the formation of oligomers/protofibrils. Also, the cellular results showed that the treated Aβ42 samples with SnO2 NPs further reduced cell viability through activation of caspase-3. In conclusion, SnO2 NPs greatly accelerate the fibrillation of Aβ42 peptides and lead to the formation of more toxic species. The present data may offer further warrants into nano-based systems for biomedical applications in the central nervous system.
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Affiliation(s)
- Laila Abdulmohsen Jaragh-Alhadad
- Department of Chemistry, College of Science, Kuwait University, Safat 13060, Kuwait; Cardiovascular and Metabolic Sciences Department, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio 44195, USA.
| | - Mojtaba Falahati
- Laboratory Experimental Oncology and Nanomedicine Innovation Center Erasmus (NICE), Department of Pathology, Erasmus Medical Center, Rotterdam, the Netherlands; Department of Nanotechnology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
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6
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Galzitskaya O, Selivanova O, Dzhus U, Marchenkov V, Suvorina MY, Surin A. Influence of Chaperones on Amyloid Formation of Аβ Peptide. Curr Protein Pept Sci 2022; 23:44-51. [DOI: 10.2174/1389203723666220127152545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 12/15/2021] [Accepted: 12/20/2021] [Indexed: 11/22/2022]
Abstract
Background:
An extensive study of the folding and stability of proteins and their complexes
has revealed a number of problems and questions that need to be answered. One of them is the
effect of chaperones on the process of fibrillation of various proteins and peptides.
Methods:
We studied the effect of molecular chaperones, such as GroEL and α-crystallin, on the fibrillogenesis
of the Aβ(1-42) peptide using electron microscopy and surface plasmon resonance.
Results:
Recombinant GroEL and Aβ(1-42) were isolated and purified. It was shown that the assembly
of GroEL occurs without the addition of magnesium and potassium ions, as is commonly believed.
According to the electron microscopy results, GroEL insignificantly affects the fibrillogenesis of the
Aβ(1-42) peptide, while α-crystallin prevents the elongation of the Aβ(1-42) peptide fibrils. We have
demonstrated that GroEL interacts nonspecifically with Aβ(1-42), while α-crystallin does not interact
with Aβ(1-42) at all using surface plasmon resonance.
Conclusion:
The data obtained will help us understand the process of amyloid formation and the effect
of various components on it.
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Affiliation(s)
- O.V. Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, 4 Institutskaya str., Pushchino, Moscow Region, 142290,
Russia
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino Moscow
Region, Russia
| | - O.M. Selivanova
- Institute of Protein Research, Russian Academy of Sciences, 4 Institutskaya str., Pushchino, Moscow Region, 142290,
Russia
| | - U.F. Dzhus
- Institute of Protein Research, Russian Academy of Sciences, 4 Institutskaya str., Pushchino, Moscow Region, 142290,
Russia
| | - V.V. Marchenkov
- Institute of Protein Research, Russian Academy of Sciences, 4 Institutskaya str., Pushchino, Moscow Region, 142290,
Russia
| | - M. Yu. Suvorina
- Institute of Protein Research, Russian Academy of Sciences, 4 Institutskaya str., Pushchino, Moscow Region, 142290,
Russia
| | - A.K. Surin
- Institute of Protein Research, Russian Academy of Sciences, 4 Institutskaya str., Pushchino, Moscow Region, 142290,
Russia
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk Moscow Region, Russia
- The Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino
Moscow Region, Russia
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7
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Galzitskaya OV, Selivanova OM, Gorbunova EY, Mustaeva LG, Azev VN, Surin AK. Mechanism of Amyloid Gel Formation by Several Short Amyloidogenic Peptides. NANOMATERIALS 2021; 11:nano11113129. [PMID: 34835893 PMCID: PMC8621528 DOI: 10.3390/nano11113129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 11/16/2022]
Abstract
Under certain conditions, many proteins/peptides are capable of self-assembly into various supramolecular formations: fibrils, films, amyloid gels. Such formations can be associated with pathological phenomena, for example, with various neurodegenerative diseases in humans (Alzheimer’s, Parkinson’s and others), or perform various functions in the body, both in humans and in representatives of other domains of life. Recently, more and more data have appeared confirming the ability of many known and, probably, not yet studied proteins/peptides, to self-assemble into quaternary structures. Fibrils, biofilms and amyloid gels are promising objects for the developing field of research of nanobiotechnology. To develop methods for obtaining nanobiomaterials with desired properties, it is necessary to study the mechanism of such structure formation, as well as the influence of various factors on this process. In this work, we present the results of a study of the structure of biogels formed by four 10-membered amyloidogenic peptides: the VDSWNVLVAG peptide (AspNB) and its analogue VESWNVLVAG (GluNB), which are amyloidogenic fragments of the glucantransferase Bgl2p protein from a yeast cell wall, and amyloidogenic peptides Aβ(31–40), Aβ(33–42) from the Aβ(1–42) peptide. Based on the analysis of the data, we propose a possible mechanism for the formation of amyloid gels with these peptides.
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Affiliation(s)
- Oxana V. Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (O.M.S.); (A.K.S.)
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia
- Correspondence: ; Tel.: +7-903-675-0156
| | - Olga M. Selivanova
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (O.M.S.); (A.K.S.)
| | - Elena Y. Gorbunova
- The Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia; (E.Y.G.); (L.G.M.); (V.N.A.)
| | - Leila G. Mustaeva
- The Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia; (E.Y.G.); (L.G.M.); (V.N.A.)
| | - Viacheslav N. Azev
- The Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia; (E.Y.G.); (L.G.M.); (V.N.A.)
| | - Alexey K. Surin
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (O.M.S.); (A.K.S.)
- The Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia; (E.Y.G.); (L.G.M.); (V.N.A.)
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Russia
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8
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Andrade S, Loureiro JA, Pereira MC. Caffeic acid for the prevention and treatment of Alzheimer's disease: The effect of lipid membranes on the inhibition of aggregation and disruption of Aβ fibrils. Int J Biol Macromol 2021; 190:853-861. [PMID: 34480909 DOI: 10.1016/j.ijbiomac.2021.08.198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 08/09/2021] [Accepted: 08/26/2021] [Indexed: 10/20/2022]
Abstract
The onset of Alzheimer's disease (AD) is triggered by the aggregation of amyloid β (Aβ) peptides which leads to the formation of fibrils. Molecules that are able to inhibit fibrillation and/or disrupt fibrils have aroused interest for AD therapy. Fibrillation is a complex process highly dependent on the surrounding environment. One of the most relevant factors affecting Aβ aggregation is the presence of cellular membranes. Here, the ability of caffeic acid (CA) in preventing the Aβ1-42 aggregation and disaggregating mature fibrils was evaluated in a membrane-like environment and in a bulk solution for comparison. To this end, liposomes were used as in vitro models of neuronal membranes. CA exhibited strong activity in inhibiting the fibrillation of Aβ1-42 in the aqueous medium, which remained in the presence of liposomes. Furthermore, CA disrupted instantly preformed fibrils in the aqueous medium. However, the CA's disaggregating activity was disturbed by the presence of lipid membranes. Instead of being immediate, the CA's disaggregating activity increased over time. The moderate affinity of CA for the lipid bilayer may explain the distinct fibrils disaggregation profiles. These findings emphasize the therapeutic potential of CA in preventing and treating AD, thus justifying further investigations in animal models.
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Affiliation(s)
- Stéphanie Andrade
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Joana Angélica Loureiro
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal.
| | - Maria Carmo Pereira
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal.
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Abstract
A rapid-acting insulin lispro and long-acting insulin glargine are commonly used for the treatment of diabetes. Clinical cases have described the formation of injectable amyloidosis with these insulin analogues, but their amyloid core regions of fibrils were unknown. To reveal these regions, we have analysed the hydrolyzates of insulin fibrils and its analogues using high-performance liquid chromatography and mass spectrometry methods and found that insulin and its analogues have almost identical amyloid core regions that intersect with the predicted amyloidogenic regions. The obtained results can be used to create new insulin analogues with a low ability to form fibrils. Abbreviations a.a., amino acid residues; HPLC-MS, high-performance liquid chromatography/mass spectrometry; m/z, mass-to-charge ratio; TEM, transmission electron microscopy.
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Affiliation(s)
- Alexey K Surin
- Institute of Protein Research, Russian Academy of Sciences , Pushchino, Russian Federation.,State Research Center for Applied Microbiology and Biotechnology , Obolensk, Russian Federation.,The Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences , Pushchino, Russian Federation
| | - Sergei Yu Grishin
- Institute of Protein Research, Russian Academy of Sciences , Pushchino, Russian Federation
| | - Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences , Pushchino, Russian Federation.,Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences , Pushchino, Russian Federation
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10
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Raghavan SS, Iqbal S, Ayyadurai N, Gunasekaran K. Insights in the structural understanding of amyloidogenicity and mutation-led conformational dynamics of amyloid beta (Aβ) through molecular dynamics simulations and principal component analysis. J Biomol Struct Dyn 2021; 40:5577-5587. [PMID: 33438527 DOI: 10.1080/07391102.2021.1871955] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Abnormal protein aggregation in the nervous tissue leads to several neurodegenerative disorders like Alzheimer's disease (AD). In AD, accumulation of the amyloid beta (Aβ) peptide is proposed to be an early important event in pathogenesis. Significant research efforts are devoted so as to understand the Aβ misfolding and aggregation. Molecular dynamics (MD) simulations complement experiments and provide structural information at the atomic level with dynamics without facing the same experimental limitations. Artificial missense mutations are employed experimentally and computationally for providing insights into the structure-function relationships of amyloid-β in relation to the pathologies of AD. Present work describes the MD simulations for 100 ns so as to probe the structural and conformational dynamics of Aβ1-42 assemblies and its mutants. Essential dynamics analysis with respect to conformational deviation of Cα was evaluated to identify the largest residual fluctuation of Cα. Conformational stability of all Aβ mutants was analyzed by computing RMSD, deciphering the convergence is reached in the last 20 ns in all replicas. To highlight the low frequency mode of motion corresponding to the highest amplitude, atomic displacements seen in trajectory, distance pair principal component analysis (dpPCA) was performed, which adumbrated mutations strongly affect the conformational dynamics of investigated model when compared with wild type. Dynamic cross correlation matrix (DCCM) also suggests the conserved interactions of wild Aβ and imply mutations in β3-β4 loop region induce deformity and residual fluctuations as observed from simulation. Present study indicate the mutational energy landscape which induces deformation leading to fibrillation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sriram Srinivasa Raghavan
- Department of Crystallography and Biophysics, University of Madras, Chennai, India.,Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.,Division of Biotechnology, Council of Scientific and Industrial Research-Central Leather Research Institute (CSIR-CLRI), Chennai, India
| | - Saleem Iqbal
- Department of Crystallography and Biophysics, University of Madras, Chennai, India.,Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, India
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11
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Peng Z, Peralta MDR, Cox DL, Toney MD. Bottom-up synthesis of protein-based nanomaterials from engineered β-solenoid proteins. PLoS One 2020; 15:e0229319. [PMID: 32084222 PMCID: PMC7034853 DOI: 10.1371/journal.pone.0229319] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 01/02/2020] [Indexed: 02/04/2023] Open
Abstract
Biomolecular self-assembly is an emerging bottom-up approach for the synthesis of novel nanomaterials. DNA and viruses have both been used to create scaffolds but the former lacks chemical diversity and the latter lack spatial control. To date, the use of protein scaffolds to template materials on the nanoscale has focused on amyloidogenic proteins that are known to form fibrils or two-protein systems where a second protein acts as a cross-linker. We previously developed a unique approach for self-assembly of nanomaterials based on engineering β-solenoid proteins (BSPs) to polymerize into micrometer-length fibrils. BSPs have highly regular geometries, tunable lengths, and flat surfaces that are amenable to engineering and functionalization. Here, we present a newly engineered BSP based on the antifreeze protein of the beetle Rhagium inquisitor (RiAFP-m9), which polymerizes into stable fibrils under benign conditions. Gold nanoparticles were used to functionalize the RiAFP-m9 fibrils as well as those assembled from the previously described SBAFP-m1 protein. Cysteines incorporated into the sequences provide site-specific gold attachment. Additionally, silver was deposited on the gold-labelled fibrils by electroless plating to create nanowires. These results bolster prospects for programable self-assembly of BSPs to create scaffolds for functional nanomaterials.
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Affiliation(s)
- Zeyu Peng
- Department of Chemistry, University of California Davis, Davis, California, United States of America
- * E-mail:
| | - Maria D. R. Peralta
- Department of Chemistry, University of California Davis, Davis, California, United States of America
| | - Daniel L. Cox
- Department of Physics, University of California Davis, Davis, California, United States of America
| | - Michael D. Toney
- Department of Chemistry, University of California Davis, Davis, California, United States of America
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12
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Galzitskaya OV. Oligomers Are Promising Targets for Drug Development in the Treatment of Proteinopathies. Front Mol Neurosci 2020; 12:319. [PMID: 32076398 PMCID: PMC7006448 DOI: 10.3389/fnmol.2019.00319] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 12/16/2019] [Indexed: 12/31/2022] Open
Abstract
Currently, there is no effective treatment of proteinopathies, as well as their diagnosis in the early stages of the disease until the first clinical symptoms appear. The proposed model of fibrillation of the Aβ peptide and its fragments not only describes molecular rearrangements, but also offers models of processes that occur during the formation of amyloid aggregates. Since this model is also characteristic of other proteins and peptides, a new potential target for drug development in the treatment of Alzheimer’s disease (AD) and other proteinopathies is proposed on the basis of this model. In our opinion, it is oligomers that are promising targets for innovative developments in the treatment of these diseases.
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Affiliation(s)
- Oxana V Galzitskaya
- Laboratory of Bioinformatics and Proteomics, Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia.,Laboratory of the Structure and Function of Muscle Proteins, Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Russia
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13
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Lee M, Yoon J, Shin S. Computational Study on Structure and Aggregation Pathway of Aβ42 Amyloid Protofibril. J Phys Chem B 2019; 123:7859-7868. [DOI: 10.1021/acs.jpcb.9b07195] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- MinJun Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Jeseong Yoon
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Seokmin Shin
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
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14
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Galzitskaya O. New Mechanism of Amyloid Fibril Formation. Curr Protein Pept Sci 2019; 20:630-640. [PMID: 30686252 DOI: 10.2174/1389203720666190125160937] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 01/15/2019] [Accepted: 01/18/2019] [Indexed: 12/18/2022]
Abstract
Polymorphism is a specific feature of the amyloid structures. We have studied the amyloid structures and the process of their formation using the synthetic and recombinant preparations of Aβ peptides and their three fragments. The fibrils of different morphology were obtained for these peptides. We suppose that fibril formation by Aβ peptides and their fragments proceeds according to the simplified scheme: destabilized monomer → ring-like oligomer → mature fibril that consists of ringlike oligomers. We are the first who did 2D reconstruction of amyloid fibrils provided that just a ringlike oligomer is the main building block in fibril of any morphology, like a cell in an organism. Taking this into account it is easy to explain the polymorphism of fibrils as well as the splitting of mature fibrils under different external actions, the branching and inhomogeneity of fibril diameters. Identification of regions in the protein chains that form the backbone of amyloid fibril is a direction in the investigation of amyloid formation. It has been demonstrated for Aβ(1-42) peptide and its fragments that their complete structure is inaccessible for the action of proteases, which is an evidence of different ways of association of ring-like oligomers with the formation of fibrils. Based on the electron microscopy and mass spectrometry data, we have proposed a molecular model of the fibril formed by both Aβ peptide and its fragments. In connection with this, the unified way of formation of fibrils by oligomers, which we have discovered, could facilitate the development of relevant fields of medicine of common action.
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Affiliation(s)
- Oxana Galzitskaya
- Group of Bioinformatics, Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russian Federation
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15
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Penke B, Bogár F, Paragi G, Gera J, Fülöp L. Key Peptides and Proteins in Alzheimer's Disease. Curr Protein Pept Sci 2019; 20:577-599. [PMID: 30605056 DOI: 10.2174/1389203720666190103123434] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/03/2018] [Accepted: 12/27/2018] [Indexed: 02/02/2023]
Abstract
Alzheimer's Disease (AD) is a form of progressive dementia involving cognitive impairment, loss of learning and memory. Different proteins (such as amyloid precursor protein (APP), β- amyloid (Aβ) and tau protein) play a key role in the initiation and progression of AD. We review the role of the most important proteins and peptides in AD pathogenesis. The structure, biosynthesis and physiological role of APP are shortly summarized. The details of trafficking and processing of APP to Aβ, the cytosolic intracellular Aβ domain (AICD) and small soluble proteins are shown, together with other amyloid-forming proteins such as tau and α-synuclein (α-syn). Hypothetic physiological functions of Aβ are summarized. The mechanism of conformational change, the formation and the role of neurotoxic amyloid oligomeric (oAβ) are shown. The fibril formation process and the co-existence of different steric structures (U-shaped and S-shaped) of Aβ monomers in mature fibrils are demonstrated. We summarize the known pathogenic and non-pathogenic mutations and show the toxic interactions of Aβ species after binding to cellular receptors. Tau phosphorylation, fibrillation, the molecular structure of tau filaments and their toxic effect on microtubules are shown. Development of Aβ and tau imaging in AD brain and CSF as well as blood biomarkers is shortly summarized. The most probable pathomechanisms of AD including the toxic effects of oAβ and tau; the three (biochemical, cellular and clinical) phases of AD are shown. Finally, the last section summarizes the present state of Aβ- and tau-directed therapies and future directions of AD research and drug development.
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Affiliation(s)
- Botond Penke
- Department of Medical Chemistry, Interdisciplinary Excellence Centre, University of Szeged, Dom square 8, Szeged, H-6720, Hungary
| | - Ferenc Bogár
- Department of Medical Chemistry, Interdisciplinary Excellence Centre, University of Szeged, Dom square 8, Szeged, H-6720, Hungary.,MTA-SZTE Biomimetic Systems Research Group, University of Szeged, H-6720 Szeged, Dom square 8, Hungary
| | - Gábor Paragi
- MTA-SZTE Biomimetic Systems Research Group, University of Szeged, H-6720 Szeged, Dom square 8, Hungary.,Institute of Physics, University of Pécs, H-7624 Pecs, Ifjusag utja 6, Hungary
| | - János Gera
- Department of Medical Chemistry, Interdisciplinary Excellence Centre, University of Szeged, Dom square 8, Szeged, H-6720, Hungary
| | - Lívia Fülöp
- Department of Medical Chemistry, Interdisciplinary Excellence Centre, University of Szeged, Dom square 8, Szeged, H-6720, Hungary
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16
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Xue C, Tran J, Wang H, Park G, Hsu F, Guo Z. Aβ42 fibril formation from predominantly oligomeric samples suggests a link between oligomer heterogeneity and fibril polymorphism. ROYAL SOCIETY OPEN SCIENCE 2019; 6:190179. [PMID: 31417723 PMCID: PMC6689619 DOI: 10.1098/rsos.190179] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 06/10/2019] [Indexed: 05/27/2023]
Abstract
Amyloid-β (Aβ) oligomers play a central role in the pathogenesis of Alzheimer's disease. Oligomers of different sizes, morphology and structures have been reported in both in vivo and in vitro studies, but there is a general lack of understanding about where to place these oligomers in the overall process of Aβ aggregation and fibrillization. Here, we show that Aβ42 spontaneously forms oligomers with a wide range of sizes in the same sample. These Aβ42 samples contain predominantly oligomers, and they quickly form fibrils upon incubation at 37°C. When fractionated using ultrafiltration filters, the samples enriched with smaller oligomers form fibrils at a faster rate than the samples enriched with larger oligomers, with both a shorter lag time and faster fibril growth rate. This observation is independent of Aβ42 batches and hexafluoroisopropanol treatment. Furthermore, the fibrils formed by the samples enriched with larger oligomers are more readily solubilized by epigallocatechin gallate, a main catechin component of green tea. These results suggest that the fibrils formed by larger oligomers may adopt a different structure from fibrils formed by smaller oligomers, pointing to a link between oligomer heterogeneity and fibril polymorphism.
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Affiliation(s)
| | | | | | | | | | - Zhefeng Guo
- Department of Neurology, Brain Research Institute, Molecular Biology Institute, University of California, 710 Westwood Plaza, Los Angeles, CA 90095, USA
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17
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Surin AK, Grishin SY, Galzitskaya OV. Identification of Amyloidogenic Regions in the Spine of Insulin Fibrils. BIOCHEMISTRY (MOSCOW) 2019; 84:47-55. [PMID: 30927525 DOI: 10.1134/s0006297919010061] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
To reveal conformational changes resulting in the formation of insulin fibrils, it is necessary to identify amyloidogenic regions in the structure of protein monomers. Different models of insulin fibrillogenesis have been proposed previously. However, precise regions responsible for the formation of amyloid fibrils have not been identified. Using bioinformatics programs for predicting amyloidogenic regions, we have determined some common amyloidogenic sequences in the structure of insulin monomers. The use of limited proteolysis and mass spectrometry analysis of the obtained protein fragments resistant to the action of proteases allowed us to identify amino acid sequences in the insulin structure that can form the spine of the insulin fibrils. The obtained results are in agreement with the earlier proposed model of fibril formation from the ring-like oligomers and can be used for designing insulin analogs resistant to amyloidogenesis.
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Affiliation(s)
- A K Surin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia. .,State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow Region, 142279, Russia.,Gamaleya Research Center of Epidemiology and Microbiology, Moscow, 123098, Russia
| | - S Yu Grishin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia. .,Lomonosov Moscow State University, Moscow, 119991, Russia
| | - O V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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18
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Xi W, Dean DN, Stockmal KA, Morgan SE, Hansmann UHE, Rangachari V. Large fatty acid-derived Aβ42 oligomers form ring-like assemblies. J Chem Phys 2019; 150:075101. [PMID: 30795679 DOI: 10.1063/1.5082659] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
As the primary toxic species in the etiology of Alzheimer disease (AD) are low molecular weight oligomers of Aβ, it is crucial to understand the structure of Aβ oligomers for gaining molecular insights into AD pathology. We have earlier demonstrated that in the presence of fatty acids, Aβ42 peptides assemble as 12-24mer oligomers. These Large Fatty Acid-derived Oligomers (LFAOs) exist predominantly as 12mers at low and as 24mers at high concentrations. The 12mers are more neurotoxic than the 24mers and undergo self-replication, while the latter propagate to morphologically distinct fibrils with succinct pathological consequences. In order to glean into their functional differences and similarities, we have determined their structures in greater detail by combining molecular dynamic simulations with biophysical measurements. We conjecture that the LFAO are made of Aβ units in an S-shaped conformation, with the 12mers forming a double-layered hexamer ring (6 × 2) while the structure of 24mers is a double-layered dodecamer ring (12 × 2). A closer inspection of the (6 × 2) and (12 × 2) structures reveals a concentration and pH dependent molecular reorganization in the assembly of 12 to 24mers, which seems to be the underlying mechanism for the observed biophysical and cellular properties of LFAOs.
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Affiliation(s)
- Wenhui Xi
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Dexter N Dean
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406, USA
| | - Kelli A Stockmal
- School of Polymer Science and Engineering, University of Southern Mississippi, Hattiesburg, Mississippi 39406, USA
| | - Sarah E Morgan
- School of Polymer Science and Engineering, University of Southern Mississippi, Hattiesburg, Mississippi 39406, USA
| | - Ulrich H E Hansmann
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Vijayaraghavan Rangachari
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406, USA
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19
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Exploring the aggregation-prone regions from structural domains of human TDP-43. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1867:286-296. [PMID: 30315897 DOI: 10.1016/j.bbapap.2018.10.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 09/15/2018] [Accepted: 10/09/2018] [Indexed: 12/15/2022]
Abstract
TDP-43 (transactive- response DNA binding protein) amazes structural biologist as its aberrant ubiquitinated cytosolic inclusions is largely involved in neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). An important question in TDP-43 research is to identify the structural region mediating the formation of cytoplasmic pathological aggregates. In this study, we attempted to delineate the aggregation-prone sequences of the structural domain of TDP-43. Here, we investigated the self-assembly of peptides of TDP-43 using aggregation prediction algorithms, Zipper DB and AMYLPRED2. The three aggregation-prone peptides identified were from N-terminal domain (24GTVLLSTV31), and RNA recognition motifs, RRM1 (128GEVLMVQV135) and RRM2 (247DLIIKGIS254). Furthermore, the amyloid fibril forming propensities of these peptides were analyzed through different biophysical techniques and molecular dynamics simulation. Our study shows the different aggregation ability of conserved stretches in structural domain of TDP-43 that will possibly induce full-length aggregation of TDP-43 in vivo. The peptide form RRM2 demonstrates the higher intrinsic amyloid forming propensity and suggests that RRM2 might form the structural core of TDP-43 aggregation seen in vivo. The results of this study would help in designing peptide based inhibitors of TDP-43 aggregation.
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20
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Nakka PP, Li K, Forciniti D. Effect of Differences in the Primary Structure of the A-Chain on the Aggregation of Insulin Fragments. ACS OMEGA 2018; 3:9636-9647. [PMID: 31459094 PMCID: PMC6645046 DOI: 10.1021/acsomega.8b00500] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 08/08/2018] [Indexed: 06/10/2023]
Abstract
Bovine and human insulin have similar primary structures. In this article, the region of the insulin A-chain of bovine and human insulin where the amino acid composition is different was studied. Bovine insulin fragment (BIF) and human insulin fragment (HIF) were synthesized in solid-phase peptide synthesis. The effects of pH, temperature, urea, ionic strength, and stirring on the formation of fibrils were studied using a fractional factorial resolution III experimental design. Fibrillation was monitored by fluorescence and infrared spectroscopy and optical microscopy. Both fragments formed fibrils at pH 1.6 and a temperature of 60 °C. The lag time and apparent aggregation growth rate constant were determined using a two-parameter kinetic model. It was found that the bovine insulin fragment has a shorter lag time than the human insulin one, whereas the exponential phase rate was faster for HIF than for BIF. An increase in β-sheets content with time was observed in both fragments. The increase in β-sheets was preceded by an initial decrease in α-helices followed by an intermediate increase during the transition from the lag phase to elongation phase. Temperature and ionic strength are among the most important experimental factors during the lag phase, whereas ionic strength is replaced by pH during the elongation phase for both the fragments. Congo red binding confirmed the presence of ringlike oligomer structures rich in antiparallel β-sheets, which tend to form fibrils rich in parallel β-sheets.
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Affiliation(s)
- Paul P. Nakka
- Kielhorn Research Laboratory, Chemical
and Biochemical Engineering Department, Missouri University of Science and Technology, Rolla, Missouri 65409, United States
| | - Ke Li
- Kielhorn Research Laboratory, Chemical
and Biochemical Engineering Department, Missouri University of Science and Technology, Rolla, Missouri 65409, United States
| | - Daniel Forciniti
- Kielhorn Research Laboratory, Chemical
and Biochemical Engineering Department, Missouri University of Science and Technology, Rolla, Missouri 65409, United States
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21
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Townsend D, Hughes E, Akien G, Stewart KL, Radford SE, Rochester D, Middleton DA. Epigallocatechin-3-gallate remodels apolipoprotein A-I amyloid fibrils into soluble oligomers in the presence of heparin. J Biol Chem 2018; 293:12877-12893. [PMID: 29853648 PMCID: PMC6102129 DOI: 10.1074/jbc.ra118.002038] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 05/25/2018] [Indexed: 11/06/2022] Open
Abstract
Amyloid deposits of WT apolipoprotein A-I (apoA-I), the main protein component of high-density lipoprotein, accumulate in atherosclerotic plaques where they may contribute to coronary artery disease by increasing plaque burden and instability. Using CD analysis, solid-state NMR spectroscopy, and transmission EM, we report here a surprising cooperative effect of heparin and the green tea polyphenol (-)-epigallocatechin-3-gallate (EGCG), a known inhibitor and modulator of amyloid formation, on apoA-I fibrils. We found that heparin, a proxy for glycosaminoglycan (GAG) polysaccharides that co-localize ubiquitously with amyloid in vivo, accelerates the rate of apoA-I formation from monomeric protein and associates with insoluble fibrils. Mature, insoluble apoA-I fibrils bound EGCG (KD = 30 ± 3 μm; Bmax = 40 ± 3 μm), but EGCG did not alter the kinetics of apoA-I amyloid assembly from monomer in the presence or absence of heparin. EGCG selectively increased the mobility of specific backbone and side-chain sites of apoA-I fibrils formed in the absence of heparin, but the fibrils largely retained their original morphology and remained insoluble. By contrast, fibrils formed in the presence of heparin were mobilized extensively by the addition of equimolar EGCG, and the fibrils were remodeled into soluble 20-nm-diameter oligomers with a largely α-helical structure that were nontoxic to human umbilical artery endothelial cells. These results argue for a protective effect of EGCG on apoA-I amyloid associated with atherosclerosis and suggest that EGCG-induced remodeling of amyloid may be tightly regulated by GAGs and other amyloid co-factors in vivo, depending on EGCG bioavailability.
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Affiliation(s)
- David Townsend
- Department of Chemistry, Lancaster University, Lancaster LA1 4YB
| | - Eleri Hughes
- Department of Chemistry, Lancaster University, Lancaster LA1 4YB
| | - Geoffrey Akien
- Department of Chemistry, Lancaster University, Lancaster LA1 4YB
| | - Katie L Stewart
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - David Rochester
- Department of Chemistry, Lancaster University, Lancaster LA1 4YB
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22
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Galzitskaya OV, Galushko EI, Selivanova OM. Studies of the Process of Amyloid Formation by Aβ Peptide. BIOCHEMISTRY (MOSCOW) 2018; 83:S62-S80. [PMID: 29544432 DOI: 10.1134/s0006297918140079] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Studies of the process of amyloid formation by Aβ peptide have been topical due to the critical role of this peptide in the pathogenesis of Alzheimer's disease. Many articles devoted to this process are available in the literature; however, none of them gives a detailed description of the mechanism of the process of generation of amyloids. Moreover, there are no reliable data on the influence of modified forms of Aβ peptide on its amyloid formation. To appreciate the role of Aβ aggregation in the pathogenesis of Alzheimer's disease and to develop a strategy for its treatment, it is necessary to have a well-defined description of the molecular mechanism underlying the formation of amyloids as well as the contribution of each intermediate to this process. We are convinced that a combined analysis of theoretical and experimental methods is a way for understanding molecular mechanisms of numerous diseases. Based on our experimental data and molecular modeling, we have constructed a general model of the process of amyloid formation by Aβ peptide. Using the data described in our previous publications, we propose a model of amyloid formation by this peptide that differs from the generally accepted model. Our model can be applied to other proteins and peptides as well. According to this model, the main building unit for the formation of amyloid fibrils is a ring-like oligomer. Upon interaction with each other, ring-like oligomers form long fibrils of different morphology. This mechanism of generation of amyloid fibrils may be common for other proteins and peptides.
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Affiliation(s)
- O V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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23
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Selivanova OM, Surin AK, Ryzhykau YL, Glyakina AV, Suvorina MY, Kuklin AI, Rogachevsky VV, Galzitskaya OV. To Be Fibrils or To Be Nanofilms? Oligomers Are Building Blocks for Fibril and Nanofilm Formation of Fragments of Aβ Peptide. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:2332-2343. [PMID: 29338255 DOI: 10.1021/acs.langmuir.7b03393] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
To identify the key stages in the amyloid fibril formation we studied the aggregation of amyloidogenic fragments of Aβ peptide, Aβ(16-25), Aβ(31-40), and Aβ(33-42), using the methods of electron microscopy, X-ray analysis, mass spectrometry, and structural modeling. We have found that fragments Aβ(31-40) and Aβ(33-42) form amyloid fibrils in the shape of bundles and ribbons, while fragment Aβ(16-25) forms only nanofilms. We are the first who performed 2D reconstruction of amyloid fibrils by the Markham rotation technique on electron micrographs of negatively stained fragments of Aβ peptide. Combined analysis of the data allows us to speculate that both the fibrils and the films are formed via association of ring-shaped oligomers with the external diameter of about 6 to 7 nm, the internal diameter of 2 to 3 nm, and the height of ∼3 nm. We conclude that such oligomers are the main building blocks in fibrils of any morphology. The interaction of ring oligomers with each other in different ways makes it possible to explain their polymorphism. The new mechanism of polymerization of amyloidogenic proteins and peptides, described here, could stimulate new approaches in the development of future therapeutics for the treatment of amyloid-related diseases.
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Affiliation(s)
- Olga M Selivanova
- Institute of Protein Research, Russian Academy of Sciences , Pushchino 142290, Russia
| | - Alexey K Surin
- Institute of Protein Research, Russian Academy of Sciences , Pushchino 142290, Russia
- State Research Center for Applied Microbiology & Biotechnology , Obolensk 142279, Russia
| | - Yury L Ryzhykau
- Moscow Institute of Physics and Technology , Dolgoprudny 141701, Russian Federation
| | - Anna V Glyakina
- Institute of Protein Research, Russian Academy of Sciences , Pushchino 142290, Russia
- Institute of Mathematical Problems of Biology RAS, Keldysh Institute of Applied Mathematics of Russian Academy of Sciences , Pushchino 142290, Russia
| | - Mariya Yu Suvorina
- Institute of Protein Research, Russian Academy of Sciences , Pushchino 142290, Russia
| | - Alexander I Kuklin
- Moscow Institute of Physics and Technology , Dolgoprudny 141701, Russian Federation
- Joint Institute for Nuclear Research , Dubna 141980, Russian Federation
| | - Vadim V Rogachevsky
- Institute of Cell Biophysics, Russian Academy of Sciences , Pushchino 142290, Russia
| | - Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences , Pushchino 142290, Russia
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