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Basciu A, Athar M, Kurt H, Neville C, Malloci G, Muredda FC, Bosin A, Ruggerone P, Bonvin AMJJ, Vargiu AV. Predicting binding events in very flexible, allosteric, multi-domain proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.02.597018. [PMID: 38895346 PMCID: PMC11185556 DOI: 10.1101/2024.06.02.597018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Knowledge of the structures formed by proteins and small ligands is of fundamental importance for understanding molecular principles of chemotherapy and for designing new and more effective drugs. Due to the still high costs and to the several limitations of experimental techniques, it is most often desirable to predict these ligand-protein complexes in silico , particularly when screening for new putative drugs from databases of millions of compounds. While virtual screening based on molecular docking is widely used for this purpose, it generally fails in mimicking binding events associated with large conformational changes in the protein, particularly when the latter involve multiple domains. In this work, we describe a new methodology aimed at generating bound-like conformations of very flexible and allosteric proteins bearing multiple binding sites. Validation was performed on the enzyme adenylate kinase (ADK), a paradigmatic example of proteins that undergo very large conformational changes upon ligand binding. By only exploiting the unbound structure and the putative binding sites of the protein, we generated a significant fraction of bound-like structures, which employed in ensemble-docking calculations allowed to find native-like poses of substrates, inhibitors, and catalytically incompetent binders. Our protocol provides a general framework for the generation of bound-like conformations of flexible proteins that are suitable to host different ligands, demonstrating high sensitivity to the fine chemical details that regulate protein's activity. We foresee applications in virtual screening for difficult targets, prediction of the impact of amino acid mutations on structure and dynamics, and protein engineering.
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2
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Shuto Y, Walinda E, Morimoto D, Sugase K. Conformational Fluctuations and Induced Orientation of a Protein, Its Solvation Shell, and Bulk Water in Weak Non-Unfolding External Electric Fields. J Phys Chem B 2023; 127:7417-7430. [PMID: 37587419 DOI: 10.1021/acs.jpcb.3c01683] [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: 08/18/2023]
Abstract
Extreme external electric fields have been reported to disrupt the tertiary structure of stably folded proteins; however, the effects of weaker electric fields on many biomolecules, especially net-uncharged proteins, and on the surrounding aqueous environment have been rarely discussed. To explore these effects at the atomic level, here, we have used molecular dynamics simulations to estimate rotational motion and induced structural fluctuations in the model protein ubiquitin and its hydration layer due to applied non-unfolding electrostatic fields. When exposed to weak electric fields of up to 0.2 V nm-1, ubiquitin displayed competition between internal structure-maintaining molecular interactions and the external orienting force, which disrupted the local structure in certain regions of the protein. Moreover, relative to hydration water, bulk water showed a greater tendency to align with the electric field, indicating that the presence of protein caused hydration water to acquire rotational mobility different from that in a pure-water system. The differential influence of the applied electric field on the hydration and bulk water surrounding ubiquitin will be common to almost all (nonmembrane) biomacromolecules. Our findings highlight the importance of local dipoles and their electric polarizability even in net-uncharged biomolecules.
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Affiliation(s)
- Yusuke Shuto
- Graduate School of Agriculture, Kyoto University, N346 Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Erik Walinda
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Daichi Morimoto
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kenji Sugase
- Graduate School of Agriculture, Kyoto University, N346 Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
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3
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Razzokov J, Fazliev S, Makhkamov M, Marimuthu P, Baev A, Kurganov E. Effect of Electric Field on α-Synuclein Fibrils: Revealed by Molecular Dynamics Simulations. Int J Mol Sci 2023; 24:ijms24076312. [PMID: 37047286 PMCID: PMC10094641 DOI: 10.3390/ijms24076312] [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: 12/23/2022] [Revised: 02/24/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
The self-association of amylogenic proteins to the fibril form is considered a pivotal factor in the pathogenesis of neurodegenerative diseases, including Parkinson’s disease (PD). PD causes unintended or uncontrollable movements in its common symptoms. α-synuclein is the major cause of PD development and thus has been the main target of numerous studies to suppress and sequester its expression or effectively degrade it. Nonetheless, to date, there are no efficient and proven ways to prevent pathological protein aggregation. Recent investigations proposed applying an external electric field to interrupt the fibrils. This method is a non-invasive approach that has a certain benefit over others. We performed molecular dynamics (MD) simulations by applying an electric field on highly toxic fibrils of α-synuclein to gain a molecular-level insight into fibril disruption mechanisms. The results revealed that the applied external electric field induces substantial changes in the conformation of the α-synuclein fibrils. Furthermore, we show the threshold value for electric field strength required to completely disrupt the α-synuclein fibrils by opening the hydrophobic core of the fibril. Thus, our findings might serve as a valuable foundation to better understand molecular-level mechanisms of the α-synuclein fibrils disaggregation process under an applied external electric field.
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Affiliation(s)
- Jamoliddin Razzokov
- Institute of Fundamental and Applied Research, National Research University TIIAME, Kori Niyoziy 39, Tashkent 100000, Uzbekistan
- R&D Center, New Uzbekistan University, Mustaqillik Avenue 54, Tashkent 100007, Uzbekistan
- Institute of Material Sciences, Academy of Sciences, Chingiz Aytmatov 2b, Tashkent 100084, Uzbekistan
- Department of Physics, National University of Uzbekistan, Universitet 4, Tashkent 100174, Uzbekistan
- Correspondence: ; Tel.: +998-90-116-23-20
| | - Sunnatullo Fazliev
- Max Planck School Matter to Life, Jahnstrasse 29, 69120 Heidelberg, Germany
- Faculty of Engineering Sciences, Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Mukhriddin Makhkamov
- Laboratory of Experimental Biophysics, Centre for Advanced Technologies, Tashkent 100174, Uzbekistan
| | - Parthiban Marimuthu
- Pharmaceutical Science Laboratory (PSL–Pharmacy) and Structural Bioinformatics Laboratory (SBL–Biochemistry), Faculty of Science and Engineering, Åbo Akademi University, FI-20520 Turku, Finland
| | - Artyom Baev
- Laboratory of Experimental Biophysics, Centre for Advanced Technologies, Tashkent 100174, Uzbekistan
- Department of Biophysics, Biological Faculty, National University of Uzbekistan, Universitet 4, Tashkent 100174, Uzbekistan
| | - Erkin Kurganov
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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4
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Wu R, Ou X, Zhang L, Song X, Wang Z, Dong M, Liu L. Electric Field Effect on Inhibiting the Co-fibrillation of Amyloid Peptides by Modulating the Aggregation Pathway. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:12346-12355. [PMID: 36173231 DOI: 10.1021/acs.langmuir.2c02055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
With the revelation of the close link between Alzheimer's disease (AD) and type II diabetes (T2D) and the possible assembly of multiple amyloid peptides therein, it is critical to understand and regulate the co-fibrillation pathway between related amyloid peptides. Here, we show experimentally and theoretically that electric field (EF) inhibited hybrid amyloid fibrillation of β-amyloid peptide (Aβ) and human islet amyloid peptide (hIAPP) by modulating the hetero-aggregation pathway. Experimental results confirm that the β-sheet secondary structure of amyloid peptides would be disrupted under small static EF and accompanied by transforming fibril aggregates into amorphous particles in vitro. Molecular dynamics simulations further demonstrate that even with the transformation of the secondary structure from β-sheet to random coil, the strong interaction between Aβ and hIAPP peptides would remain largely unaffected under the small static EF, leading to the formation of amorphous nanoparticles observed in the experiments. This inhibitory effect of EF on the co-fibrillation of multiple amyloid peptides might contribute to reducing the mutual deterioration of different degenerative diseases and show great potential for the noninvasive treatment of amyloid-related diseases.
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Affiliation(s)
- Rongrong Wu
- Institute for Advanced Materials, Jiangsu University, Zhenjiang 212013, China
| | - Xinwen Ou
- Zhejiang Province Key Laboratory of Quantum Technology and Device, School of Physics, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Liwei Zhang
- Institute for Advanced Materials, Jiangsu University, Zhenjiang 212013, China
| | - Xiaolu Song
- Institute for Advanced Materials, Jiangsu University, Zhenjiang 212013, China
| | - Zengkai Wang
- Institute for Advanced Materials, Jiangsu University, Zhenjiang 212013, China
| | - Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C DK-8000, Denmark
| | - Lei Liu
- Institute for Advanced Materials, Jiangsu University, Zhenjiang 212013, China
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5
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Kuang Z, Luginsland J, Thomas RJ, Dennis PB, Kelley-Loughnane N, Roach WP, Naik RR. Molecular dynamics simulations explore effects of electric field orientations on spike proteins of SARS-CoV-2 virions. Sci Rep 2022; 12:12986. [PMID: 35906467 PMCID: PMC9334739 DOI: 10.1038/s41598-022-17009-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 07/19/2022] [Indexed: 11/21/2022] Open
Abstract
Emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its current worldwide spread have caused a pandemic of acute respiratory disease COVID-19. The virus can result in mild to severe, and even to fatal respiratory illness in humans, threatening human health and public safety. The spike (S) protein on the surface of viral membrane is responsible for viral entry into host cells. The discovery of methods to inactivate the entry of SARS-CoV-2 through disruption of the S protein binding to its cognate receptor on the host cell is an active research area. To explore other prevention strategies against the quick spread of the virus and its mutants, non-equilibrium molecular dynamics simulations have been employed to explore the possibility of manipulating the structure–activity of the SARS-CoV-2 spike glycoprotein by applying electric fields (EFs) in both the protein axial directions and in the direction perpendicular to the protein axis. We have found out the application of EFs perpendicular to the protein axis is most effective in denaturing the HR2 domain which plays critical role in viral-host membrane fusion. This finding suggests that varying irradiation angles may be an important consideration in developing EF based non-invasive technologies to inactivate the virus.
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Affiliation(s)
- Zhifeng Kuang
- Materials and Manufacturing Directorate, Air Force Research Laboratory, WPAFB, Dayton, OH, 45433, USA.
| | - John Luginsland
- Work Performed With Confluent Sciences, LLC, Albuquerque, NM, 87111, USA
| | - Robert J Thomas
- 711th Human Performance Wing, Air Force Research Laboratory, JBSA Fort Sam Houston, San Antonio, TX, 78234, USA
| | - Patrick B Dennis
- Materials and Manufacturing Directorate, Air Force Research Laboratory, WPAFB, Dayton, OH, 45433, USA
| | - Nancy Kelley-Loughnane
- Materials and Manufacturing Directorate, Air Force Research Laboratory, WPAFB, Dayton, OH, 45433, USA
| | - William P Roach
- Air Force Office of Scientific Research, Arlington, VA, 22203, USA
| | - Rajesh R Naik
- 711Th Human Performance Wing, Air Force Research Laboratory, WPAFB, Dayton, OH, 45433, USA.
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6
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Noble BB, Todorova N, Yarovsky I. Electromagnetic bioeffects: a multiscale molecular simulation perspective. Phys Chem Chem Phys 2022; 24:6327-6348. [PMID: 35245928 DOI: 10.1039/d1cp05510k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Electromagnetic bioeffects remain an enigma from both the experimental and theoretical perspectives despite the ubiquitous presence of related technologies in contemporary life. Multiscale computational modelling can provide valuable insights into biochemical systems and predict how they will be perturbed by external stimuli. At a microscopic level, it can be used to determine what (sub)molecular scale reactions various stimuli might induce; at a macroscopic level, it can be used to examine how these changes affect dynamic behaviour of essential molecules within the crowded biomolecular milieu in living tissues. In this review, we summarise and evaluate recent computational studies that examined the impact of externally applied electric and electromagnetic fields on biologically relevant molecular systems. First, we briefly outline the various methodological approaches that have been employed to study static and oscillating field effects across different time and length scales. The practical value of such modelling is then illustrated through representative case-studies that showcase the diverse effects of electric and electromagnetic field on the main physiological solvent - water, and the essential biomolecules - DNA, proteins, lipids, as well as some novel biomedically relevant nanomaterials. The implications and relevance of the theoretical multiscale modelling to practical applications in therapeutic medicine are also discussed. Finally, we summarise ongoing challenges and potential opportunities for theoretical modelling to advance the current understanding of electromagnetic bioeffects for their modulation and/or beneficial exploitation in biomedicine and industry.
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Affiliation(s)
- Benjamin B Noble
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, Australia. .,Australian Centre for Electromagnetic Bioeffects Research, Australia
| | - Nevena Todorova
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, Australia. .,Australian Centre for Electromagnetic Bioeffects Research, Australia
| | - Irene Yarovsky
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, Australia. .,Australian Centre for Electromagnetic Bioeffects Research, Australia
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7
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Heo L, Sugita Y, Feig M. Protein assembly and crowding simulations. Curr Opin Struct Biol 2022; 73:102340. [PMID: 35219215 PMCID: PMC8957576 DOI: 10.1016/j.sbi.2022.102340] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/07/2022] [Accepted: 01/18/2022] [Indexed: 11/17/2022]
Abstract
Proteins encounter frequent molecular interactions in biological environments. Computer simulations have become an increasingly important tool in providing mechanistic insights into how such interactions in vivo relate to their biological function. The review here focuses on simulations describing protein assembly and molecular crowding effects as two important aspects that are distinguished mainly by how specific and long-lived protein contacts are. On the topic of crowding, recent simulations have provided new insights into how crowding affects protein folding and stability, modulates enzyme activity, and affects diffusive properties. Recent studies of assembly processes focus on assembly pathways, especially for virus capsids, amyloid aggregation pathways, and the role of multivalent interactions leading to phase separation. Also, discussed are technical challenges in achieving increasingly realistic simulations of interactions in cellular environments.
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Affiliation(s)
- Lim Heo
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA. https://twitter.com/huhlim
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Computational Biophysics Research Team, RIKEN Center for Computational Science, 6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.
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8
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Havelka D, Zhernov I, Teplan M, Lánský Z, Chafai DE, Cifra M. Lab-on-chip microscope platform for electro-manipulation of a dense microtubules network. Sci Rep 2022; 12:2462. [PMID: 35165315 PMCID: PMC8844285 DOI: 10.1038/s41598-022-06255-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 01/18/2022] [Indexed: 12/20/2022] Open
Abstract
Pulsed electric field (PEF) technology is promising for the manipulation of biomolecular components and has potential applications in biomedicine and bionanotechnology. Microtubules, nanoscopic tubular structures self-assembled from protein tubulin, serve as important components in basic cellular processes as well as in engineered biomolecular nanosystems. Recent studies in cell-based models have demonstrated that PEF affects the cytoskeleton, including microtubules. However, the direct effects of PEF on microtubules are not clear. In this work, we developed a lab-on-a-chip platform integrated with a total internal reflection fluorescence microscope system to elucidate the PEF effects on a microtubules network mimicking the cell-like density of microtubules. The designed platform enables the delivery of short (microsecond-scale), high-field-strength (\documentclass[12pt]{minimal}
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\begin{document}$$\le$$\end{document}≤ 25 kV/cm) electric pulses far from the electrode/electrolyte interface. We showed that microsecond PEF is capable of overcoming the non-covalent microtubule bonding force to the substrate and translocating the microtubules. This microsecond PEF effect combined with macromolecular crowding led to aggregation of microtubules. Our results expand the toolbox of bioelectronics technologies and electromagnetic tools for the manipulation of biomolecular nanoscopic systems and contribute to the understanding of microsecond PEF effects on a microtubule cytoskeleton.
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9
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Průša J, Ayoub AT, Chafai DE, Havelka D, Cifra M. Electro-opening of a microtubule lattice in silico. Comput Struct Biotechnol J 2021; 19:1488-1496. [PMID: 33815687 PMCID: PMC7985272 DOI: 10.1016/j.csbj.2021.02.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/10/2021] [Accepted: 02/12/2021] [Indexed: 11/28/2022] Open
Abstract
Modulation of the structure and function of biomaterials is essential for advancing bio-nanotechnology and biomedicine. Microtubules (MTs) are self-assembled protein polymers that are essential for fundamental cellular processes and key model compounds for the design of active bio-nanomaterials. In this in silico study, a 0.5 μs-long all-atom molecular dynamics simulation of a complete MT with approximately 1.2 million atoms in the system indicated that a nanosecond-scale intense electric field can induce the longitudinal opening of the cylindrical shell of the MT lattice, modifying the structure of the MT. This effect is field-strength- and temperature-dependent and occurs on the cathode side. A model was formulated to explain the opening on the cathode side, which resulted from an electric-field-induced imbalance between electric torque on tubulin dipoles and cohesive forces between tubulin heterodimers. Our results open new avenues for electromagnetic modulation of biological and artificial materials through action on noncovalent molecular interactions.
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Affiliation(s)
- Jiří Průša
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Prague 18251, Czech Republic
| | - Ahmed Taha Ayoub
- Biomolecular Simulation Center, Department of Chemistry, Faculty of Pharmacy, Heliopolis University, Cairo 11777, Egypt
| | - Djamel Eddine Chafai
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Prague 18251, Czech Republic
| | - Daniel Havelka
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Prague 18251, Czech Republic
| | - Michal Cifra
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Prague 18251, Czech Republic
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10
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Tharushi Perera PG, Todorova N, Vilagosh Z, Bazaka O, Nguyen THP, Bazaka K, Crawford RJ, Croft RJ, Yarovsky I, Ivanova EP. Translocation of silica nanospheres through giant unilamellar vesicles (GUVs) induced by a high frequency electromagnetic field. RSC Adv 2021; 11:31408-31420. [PMID: 35496859 PMCID: PMC9041541 DOI: 10.1039/d1ra05459g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/14/2021] [Indexed: 01/20/2023] Open
Abstract
Membrane model systems capable of mimicking live cell membranes were used for the first time in studying the effects arising from electromagnetic fields (EMFs) of 18 GHz where membrane permeability was observed following exposure.
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Affiliation(s)
- Palalle G. Tharushi Perera
- School of Science, RMIT University, PO Box 2476, Melbourne, VIC 3001, Australia
- Faculty Science, Engineering and Technology, Swinburne University of Technology, PO Box 218, Hawthorn, VIC 3122, Australia
| | - Nevena Todorova
- School of Engineering, RMIT University, PO Box 2476, Melbourne, VIC 3001, Australia
| | - Zoltan Vilagosh
- Faculty Science, Engineering and Technology, Swinburne University of Technology, PO Box 218, Hawthorn, VIC 3122, Australia
| | - Olha Bazaka
- School of Science, RMIT University, PO Box 2476, Melbourne, VIC 3001, Australia
| | | | - Kateryna Bazaka
- School of Engineering, College of Engineering and Computer Science, The Australian National University, Canberra, ACT 2600, Australia
| | - Russell J. Crawford
- School of Science, RMIT University, PO Box 2476, Melbourne, VIC 3001, Australia
| | - Rodney J. Croft
- School of Psychology, Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Irene Yarovsky
- School of Engineering, RMIT University, PO Box 2476, Melbourne, VIC 3001, Australia
| | - Elena P. Ivanova
- School of Science, RMIT University, PO Box 2476, Melbourne, VIC 3001, Australia
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11
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Pagano K, Tomaselli S, Molinari H, Ragona L. Natural Compounds as Inhibitors of Aβ Peptide Aggregation: Chemical Requirements and Molecular Mechanisms. Front Neurosci 2020; 14:619667. [PMID: 33414705 PMCID: PMC7783407 DOI: 10.3389/fnins.2020.619667] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/04/2020] [Indexed: 12/29/2022] Open
Abstract
Alzheimer’s disease (AD) is one of the most common neurodegenerative disorders, with no cure and preventive therapy. Misfolding and extracellular aggregation of Amyloid-β (Aβ) peptides are recognized as the main cause of AD progression, leading to the formation of toxic Aβ oligomers and to the deposition of β-amyloid plaques in the brain, representing the hallmarks of AD. Given the urgent need to provide alternative therapies, natural products serve as vital resources for novel drugs. In recent years, several natural compounds with different chemical structures, such as polyphenols, alkaloids, terpenes, flavonoids, tannins, saponins and vitamins from plants have received attention for their role against the neurodegenerative pathological processes. However, only for a small subset of them experimental evidences are provided on their mechanism of action. This review focuses on those natural compounds shown to interfere with Aβ aggregation by direct interaction with Aβ peptide and whose inhibitory mechanism has been investigated by means of biophysical and structural biology experimental approaches. In few cases, the combination of approaches offering a macroscopic characterization of the oligomers, such as TEM, AFM, fluorescence, together with high-resolution methods could shed light on the complex mechanism of inhibition. In particular, solution NMR spectroscopy, through peptide-based and ligand-based observation, was successfully employed to investigate the interactions of the natural compounds with both soluble NMR-visible (monomer and low molecular weight oligomers) and NMR-invisible (high molecular weight oligomers and protofibrils) species. The molecular determinants of the interaction of promising natural compounds are here compared to infer the chemical requirements of the inhibitors and the common mechanisms of inhibition. Most of the data converge to indicate that the Aβ regions relevant to perturb the aggregation cascade and regulate the toxicity of the stabilized oligomers, are the N-term and β1 region. The ability of the natural aggregation inhibitors to cross the brain blood barrier, together with the tactics to improve their low bioavailability are discussed. The analysis of the data ensemble can provide a rationale for the selection of natural compounds as molecular scaffolds for the design of new therapeutic strategies against the progression of early and late stages of AD.
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Affiliation(s)
- Katiuscia Pagano
- NMR Laboratory, Istituto di Scienze e Tecnologie Chimiche (SCITEC), Consiglio Nazionale delle Ricerche - CNR, Milan, Italy
| | - Simona Tomaselli
- NMR Laboratory, Istituto di Scienze e Tecnologie Chimiche (SCITEC), Consiglio Nazionale delle Ricerche - CNR, Milan, Italy
| | - Henriette Molinari
- NMR Laboratory, Istituto di Scienze e Tecnologie Chimiche (SCITEC), Consiglio Nazionale delle Ricerche - CNR, Milan, Italy
| | - Laura Ragona
- NMR Laboratory, Istituto di Scienze e Tecnologie Chimiche (SCITEC), Consiglio Nazionale delle Ricerche - CNR, Milan, Italy
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12
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Wang M, Falke S, Schubert R, Lorenzen K, Cheng QD, Exner C, Brognaro H, Mudogo CN, Betzel C. Pulsed electric fields induce modulation of protein liquid-liquid phase separation. SOFT MATTER 2020; 16:8547-8553. [PMID: 32909579 DOI: 10.1039/d0sm01478h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The time-resolved dynamic assembly and the structures of protein liquid dense clusters (LDCs) were analyzed under pulsed electric fields (EFs) applying complementary polarized and depolarized dynamic light scattering (DLS/DDLS), optical microscopy, and transmission electron microscopy (TEM). We discovered that pulsed EFs substantially affected overall morphologies and spatial distributions of protein LDCs and microcrystals, and affected the phase diagrams of LDC formation, including enabling protein solutions to overcome the diffusive flux energy barrier to phase separate. Data obtained from DLS/DDLS and TEM showed that LDCs appeared as precursors of protein crystal nuclei, followed by the formation of ordered structures within LDCs applying a pulsed EF. Experimental results of circular dichroism spectroscopy provided evidence that the protein secondary structure content is changing under EFs, which may consequently modulate protein-protein interactions, and the morphology, dimensions, and internal structure of LDCs. Data and results obtained unveil options to modulate the phase diagram of crystallization, and physical morphologies of protein LDCs and microcrystals by irradiating sample suspensions with pulsed EFs.
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Affiliation(s)
- Mengying Wang
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Build. 22a, Notkestr. 85, 22607, Hamburg, Germany.
| | - Sven Falke
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Build. 22a, Notkestr. 85, 22607, Hamburg, Germany.
| | - Robin Schubert
- European XFEL GmbH, Holzkoppel 4, 22869 Schenefeld, Germany
| | | | - Qing-di Cheng
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Build. 22a, Notkestr. 85, 22607, Hamburg, Germany.
| | - Christian Exner
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Build. 22a, Notkestr. 85, 22607, Hamburg, Germany.
| | - Hévila Brognaro
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Build. 22a, Notkestr. 85, 22607, Hamburg, Germany.
| | - Célestin Nzanzu Mudogo
- Department of Basic Sciences, School of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Build. 22a, Notkestr. 85, 22607, Hamburg, Germany.
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13
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Highlighting the effect of amyloid beta assemblies on the mechanical properties and conformational stability of cell membrane. J Mol Graph Model 2020; 100:107670. [PMID: 32711259 DOI: 10.1016/j.jmgm.2020.107670] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 01/05/2023]
Abstract
Alzheimer disease (AD) is the most common cause of dementia, characterized by a progressive decline in cognitive function due to the abnormal aggregation and deposition of Amyloid beta (Aβ) fibrils in the brain of patients. In this context, the molecular mechanisms of protein misfolding and aggregation that are known to induce significant biophysical alterations in cells, including destabilization of plasma membranes, remain partially unclear. Physical interaction between the Aβ assemblies and the membrane leads to the disruption of the cell membrane in multiple ways including, surface carpeting, generation of transmembrane channels and detergent-like membrane dissolution. Understanding the impact of amyloidogenic protein in different stages of aggregation with the plasma membrane, plays a crucial role to fully elucidate the pathological mechanisms of AD. Within this framework, computer simulations represent a powerful tool able to shed lights on the interactions governing the structural influence of Aβ proteins on biological membrane. In this study, molecular dynamics (MD) simulations have been performed in order to characterize how POPC bilayer conformational and mechanical properties are affected by the interaction with Aβ11-42 peptide, oligomer and fibril.
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Muscat S, Pallante L, Stojceski F, Danani A, Grasso G, Deriu MA. The Impact of Natural Compounds on S-Shaped Aβ42 Fibril: From Molecular Docking to Biophysical Characterization. Int J Mol Sci 2020; 21:ijms21062017. [PMID: 32188076 PMCID: PMC7139307 DOI: 10.3390/ijms21062017] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/06/2020] [Accepted: 03/13/2020] [Indexed: 12/18/2022] Open
Abstract
The pursuit for effective strategies inhibiting the amyloidogenic process in neurodegenerative disorders, such as Alzheimer’s disease (AD), remains one of the main unsolved issues, and only a few drugs have demonstrated to delay the degeneration of the cognitive system. Moreover, most therapies induce severe side effects and are not effective at all stages of the illness. The need to find novel and reliable drugs appears therefore of primary importance. In this context, natural compounds have shown interesting beneficial effects on the onset and progression of neurodegenerative diseases, exhibiting a great inhibitory activity on the formation of amyloid aggregates and proving to be effective in many preclinical and clinical studies. However, their inhibitory mechanism is still unclear. In this work, ensemble docking and molecular dynamics simulations on S-shaped Aβ42 fibrils have been carried out to evaluate the influence of several natural compounds on amyloid conformational behaviour. A deep understanding of the interaction mechanisms between natural compounds and Aβ aggregates may play a key role to pave the way for design, discovery and optimization strategies toward an efficient destabilization of toxic amyloid assemblies.
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Affiliation(s)
- Stefano Muscat
- Dalle Molle Institute for Artificial Intelligence (IDSIA), University of Italian Switzerland (USI), University of Applied Science and Art of Southern Switzerland (SUPSI), CH-6928 Manno, Switzerland
| | - Lorenzo Pallante
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, IT-10128 Torino, Italy
| | - Filip Stojceski
- Dalle Molle Institute for Artificial Intelligence (IDSIA), University of Italian Switzerland (USI), University of Applied Science and Art of Southern Switzerland (SUPSI), CH-6928 Manno, Switzerland
| | - Andrea Danani
- Dalle Molle Institute for Artificial Intelligence (IDSIA), University of Italian Switzerland (USI), University of Applied Science and Art of Southern Switzerland (SUPSI), CH-6928 Manno, Switzerland
| | - Gianvito Grasso
- Dalle Molle Institute for Artificial Intelligence (IDSIA), University of Italian Switzerland (USI), University of Applied Science and Art of Southern Switzerland (SUPSI), CH-6928 Manno, Switzerland
| | - Marco Agostino Deriu
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, IT-10128 Torino, Italy
- Correspondence:
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