1
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Aguilar MI, Yarovsky I. Quest for New Generation Biocompatible Materials: Tailoring β-Peptide Structure and Interactions via Synergy of Experiments and Modelling. J Mol Biol 2024:168646. [PMID: 38848868 DOI: 10.1016/j.jmb.2024.168646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/03/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024]
Abstract
Peptide-based self-assembly has been used to produce a wide range of nanostructures. While most of these systems involve self-assembly of α-peptides, more recently β-peptides have also been shown to undergo supramolecular self-assembly, and have been used to produce materials for applications in tissue engineering, cell culture and drug delivery. In order to engineer new materials with specific structure and function, theoretical molecular modelling can provide significant insights into the collective balance of non-covalent interactions that drive the self-assembly and determine the structure of the resultant supramolecular materials under different conditions. However, this approach has only recently become feasible for peptide-based self-assembled nanomaterials, particularly those that incorporate non α-amino acids. This perspective provides an overview of the challenges associated with computational modelling of the self-assembly of β-peptides and the recent success using a combination of experimental and computational techniques to provide insights into the self-assembly mechanisms and fully atomistic models of these new biocompatible materials.
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Affiliation(s)
- Marie-Isabel Aguilar
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.
| | - Irene Yarovsky
- School of Engineering, RMIT University, Melbourne, Victoria 3001, Australia.
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2
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Joeres E, Drusch S, Töpfl S, Juadjur A, Psathaki OE, Heinz V, Terjung N. Formation of amyloid fibrils from ovalbumin under Ohmic heating. Heliyon 2023; 9:e22061. [PMID: 38027889 PMCID: PMC10658388 DOI: 10.1016/j.heliyon.2023.e22061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 11/01/2023] [Accepted: 11/03/2023] [Indexed: 12/01/2023] Open
Abstract
Ohmic heating (OH) is an alternative sustainable heating technology that has demonstrated its potential to modify protein structures and aggregates. Furthermore, certain protein aggregates, namely amyloid fibrils (AF), are associated with an enhanced protein functionality, such as gelation. This study evaluates how Ohmic heating (OH) influences the formation of AF structures from ovalbumin source under two electric field strength levels, 8.5 to 10.5 and 24.0-31.0 V/cm, respectively. Hence, AF aggregate formation was assessed over holding times ranging from 30 to 1200 sunder various environmental conditions (3.45 and 67.95 mM NaCl, 80, 85 and 90 °C, pH = 7). AF were formed under all conditions. SDS-PAGE revealed that OH had a higher tendency to preserve native ovalbumin molecules. Furthermore, Congo Red and Thioflavin T stainings indicated that OH reduces the amount of AF structures. This finding was supported by FTIR measurements, which showed OH samples to contain lower amounts of beta-sheets. Field flow fractioning revealed smaller-sized aggregates or aggregate clusters occurred after OH treatment. In contrast, prolonged holding time or higher treatment temperatures increased ThT fluorescence, beta-sheet structures and aggregate as well as cluster sizes. Ionic strength was found to dominate the effects of electric field strength under different environmental conditions.
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Affiliation(s)
- Eike Joeres
- DIL – German Institute of Food Technologies (DIL e.V.), Professor-von-Klitzing-Str. 7, 49160, Quakenbrück, Germany
- Technical University of Berlin, Institute of Food Technology and Food Chemistry, Department of Food Technology and Food Material Science, Königin-Luise-Str. 22, 14195, Berlin, Germany
| | - Stephan Drusch
- Technical University of Berlin, Institute of Food Technology and Food Chemistry, Department of Food Technology and Food Material Science, Königin-Luise-Str. 22, 14195, Berlin, Germany
| | - Stefan Töpfl
- University of Applied Science Osnabrück, Department of Agricultural Science and Landscape Architecture, Oldenburger Landstr. 62, 49090, Osnabrück, Germany
| | - Andreas Juadjur
- DIL – German Institute of Food Technologies (DIL e.V.), Professor-von-Klitzing-Str. 7, 49160, Quakenbrück, Germany
| | | | - Volker Heinz
- DIL – German Institute of Food Technologies (DIL e.V.), Professor-von-Klitzing-Str. 7, 49160, Quakenbrück, Germany
| | - Nino Terjung
- DIL – German Institute of Food Technologies (DIL e.V.), Professor-von-Klitzing-Str. 7, 49160, Quakenbrück, Germany
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3
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Vacek J, Zatloukalová M, Dorčák V, Cifra M, Futera Z, Ostatná V. Electrochemistry in sensing of molecular interactions of proteins and their behavior in an electric field. Mikrochim Acta 2023; 190:442. [PMID: 37847341 PMCID: PMC10582152 DOI: 10.1007/s00604-023-05999-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 09/12/2023] [Indexed: 10/18/2023]
Abstract
Electrochemical methods can be used not only for the sensitive analysis of proteins but also for deeper research into their structure, transport functions (transfer of electrons and protons), and sensing their interactions with soft and solid surfaces. Last but not least, electrochemical tools are useful for investigating the effect of an electric field on protein structure, the direct application of electrochemical methods for controlling protein function, or the micromanipulation of supramolecular protein structures. There are many experimental arrangements (modalities), from the classic configuration that works with an electrochemical cell to miniaturized electrochemical sensors and microchip platforms. The support of computational chemistry methods which appropriately complement the interpretation framework of experimental results is also important. This text describes recent directions in electrochemical methods for the determination of proteins and briefly summarizes available methodologies for the selective labeling of proteins using redox-active probes. Attention is also paid to the theoretical aspects of electron transport and the effect of an external electric field on the structure of selected proteins. Instead of providing a comprehensive overview, we aim to highlight areas of interest that have not been summarized recently, but, at the same time, represent current trends in the field.
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Affiliation(s)
- Jan Vacek
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, 77515, Olomouc, Czech Republic.
| | - Martina Zatloukalová
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, 77515, Olomouc, Czech Republic
| | - Vlastimil Dorčák
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, 77515, Olomouc, Czech Republic
| | - Michal Cifra
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberska 1014/57, 18200, Prague, Czech Republic
| | - Zdeněk Futera
- Faculty of Science, University of South Bohemia, Branisovska 1760, 37005, Ceske Budejovice, Czech Republic
| | - Veronika Ostatná
- Institute of Biophysics, The Czech Academy of Sciences, v.v.i., Kralovopolska 135, 61200, Brno, Czech Republic
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4
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Vargas-Rosales P, D’Addio A, Zhang Y, Caflisch A. Disrupting Dimeric β-Amyloid by Electric Fields. ACS PHYSICAL CHEMISTRY AU 2023; 3:456-466. [PMID: 37780539 PMCID: PMC10540290 DOI: 10.1021/acsphyschemau.3c00021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/26/2023] [Accepted: 06/26/2023] [Indexed: 10/03/2023]
Abstract
The early oligomers of the amyloid Aβ peptide are implicated in Alzheimer's disease, but their transient nature complicates the characterization of their structure and toxicity. Here, we investigate the stability of the minimal toxic species, i.e., β-amyloid dimers, in the presence of an oscillating electric field. We first use deep learning (AlphaFold-multimer) for generating initial models of Aβ42 dimers. The flexibility and secondary structure content of the models are then analyzed by multiple runs of molecular dynamics (MD). Structurally stable models are similar to ensemble representatives from microsecond-long MD sampling. Finally, we employ the validated model as the starting structure of MD simulations in the presence of an external oscillating electric field and observe a fast decay of β-sheet content at high field strengths. Control simulations using the helical dimer of the 42-residue leucine zipper peptide show higher structural stability than the Aβ42 dimer. The simulation results provide evidence that an external electric field (oscillating at 1 GHz) can disrupt amyloid oligomers which should be further investigated by experiments with brain organoids in vitro and eventually in vivo.
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Affiliation(s)
| | - Alessio D’Addio
- Department of Biochemistry, University of Zurich, CH-8057 Zürich, Switzerland
| | - Yang Zhang
- Department of Biochemistry, University of Zurich, CH-8057 Zürich, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, CH-8057 Zürich, Switzerland
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5
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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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6
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Salehi N, Lohrasebi A, Bordbar AK. Preventing the amyloid-beta peptides accumulation on the cell membrane by applying GHz electric fields: A molecular dynamic simulation. J Mol Graph Model 2023; 123:108516. [PMID: 37216829 DOI: 10.1016/j.jmgm.2023.108516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 05/03/2023] [Accepted: 05/07/2023] [Indexed: 05/24/2023]
Abstract
Alzheimer's disease is associated with accumulating different amyloid peptides on the nerve cell membranes. The non-thermal effects of the GHz electric fields in this topic have yet to be well recognized. Hence, in this study, the impacts of 1 and 5 GHz electric fields on the amyloid peptide proteins accumulation on the cell membrane have been investigated, utilizing molecular dynamics (MD) simulation. The obtained results indicated that this range of electric fields did not significantly affect the peptide structure. Moreover, it was found that the peptide penetration into the membrane was increased as the field frequency was increased when the system was exposed to a 20 mv/nm oscillating electric field. In addition, it was observed that the protein-membrane interaction is reduced significantly in the presence of the 70 mv/nm electric field. The molecular level results reported in this study could be helpful in better understanding Alzheimer's disease.
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Affiliation(s)
- N Salehi
- Department of Chemistry, University of Isfahan, Isfahan, 81746-73441, Iran
| | - A Lohrasebi
- Department of Physics, University of Isfahan, Isfahan, 81746-73441, Iran.
| | - A K Bordbar
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, CA, USA.
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7
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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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8
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Chakraborty A, Venkatramani R. Capturing the Polarization Response of Solvated Proteins under Constant Electric Fields in Molecular Dynamics Simulations. Chemphyschem 2023; 24:e202200646. [PMID: 36395205 DOI: 10.1002/cphc.202200646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 11/10/2022] [Indexed: 11/19/2022]
Abstract
We capture and compare the polarization response of a solvated globular protein ubiquitin to static electric (E-fields) using atomistic molecular dynamics simulations. We collectively follow E-field induced changes, electrical and structural, occurring across multiple trajectories using the magnitude of the protein dipole vector (Pp ). E-fields antiparallel to Pp induce faster structural changes and more facile protein unfolding relative to parallel fields of the same strength. While weak E-fields (0.1-0.5 V/nm) do not unfold ubiquitin and produce a reversible polarization, strong E-fields (1-2 V/nm) unfold the protein through a pathway wherein the helix:β-strand interactions rupture before those for the β1-β5 clamp. Independent of E-field direction, high E-field induced structural changes are also reversible if the field is switched off before Pp exceeds 2 times its equilibrium value. We critically examine the dependence of water properties, protein rotational diffusion and E-field induced protein unfolding pathways on the thermostat/barostat parameters used in our simulations.
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Affiliation(s)
- Anustup Chakraborty
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai 400005, Maharashtra, India
| | - Ravindra Venkatramani
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai 400005, Maharashtra, India
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9
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Gou D, Huang K, Liu Y, Shi H, Wu Z. Molecular Dynamics Research of Spatial Orientation and Kinetic Energy of Active Site Collision of Carnosine under Weak Microwave Irradiation. J Phys Chem B 2022; 126:7686-7700. [PMID: 36134752 DOI: 10.1021/acs.jpcb.2c03930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The molecular mechanism of the microwave nonthermal effect is still not clear. This work investigated the spatial orientation and kinetic energy of active site collision of carnosine, a natural bioactive dipeptide, under the weak microwave irradiation using the molecular dynamics simulation. Our results showed the influences of the temperature, microwave intensity, microwave frequency, and microwave polarization mode (linear polarization and circular polarization) on the spatial orientation and kinetic energy of active site collision of carnosine. First, under the constant intensity and frequency of linear polarization microwave irradiation, the increment of the collision probability between the 6N atom of carnosine and the 28H atom of the other carnosine at effective space angle decreases from 85.0% to 3.5% with increasing temperature. Second, with the increase of microwave intensity, the change of spatial orientation and kinetic energy becomes more and more significant. However, the change of circular polarization microwaves on the spatial orientation and kinetic energy of collision is weaker than that of linear polarization. Third, under the constant intensity of linear polarization microwave irradiation, the collision probability between the 6N atom and the 28H atom at effective space angle decreases from 70.2% to 14.7% with increasing frequency. Finally, under the microwave polarization, the spatial orientation and kinetic energy of molecular collision are changed, which is summarized as the microwave postpolarization effect (MWPPE). The dependence of MWPPE on temperature, microwave intensity, microwave frequency, and polarization mode is very complicated. In the end, this effect can provide a new insight into the molecular mechanism of the microwave nonthermal effect.
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Affiliation(s)
- Dezhi Gou
- College of Electronics and Information Engineering, Sichuan University, Chengdu 610065, China
| | - Kama Huang
- College of Electronics and Information Engineering, Sichuan University, Chengdu 610065, China
| | - Ying Liu
- College of Electronics and Information Engineering, Sichuan University, Chengdu 610065, China
| | - Hongxiao Shi
- College of Electronics and Information Engineering, Sichuan University, Chengdu 610065, China
| | - Zhiyan Wu
- College of Electronic and Electrical Engineering, Henan Normal University, Xinxiang, Henan 453007, China
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10
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Response to "Non-thermal microwave effects: Conceptual and methodological problems". Food Chem 2022; 390:133216. [PMID: 35594767 DOI: 10.1016/j.foodchem.2022.133216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 04/12/2022] [Accepted: 05/11/2022] [Indexed: 11/20/2022]
Abstract
The objective of this response letter is to expose the reader of Food Chemistry to the most recent advances and discussions about non-thermal effects of microwaves on microorganisms and enzymes. Although these effects showed to be too subtle for any practical use in food processing, experimental and molecular dynamics studies bring evidences that electric fields at low frequencies or with high intensity can have non-thermal effects, such as activity changes in enzymes during ohmic processing or electroporation of cells in pulsed electric field processing. This brief review broadens the scope of this controversial topic to show that innovative experiments and simulations are collaborating with the advance of emerging electro technologies in food processing. .
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11
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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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12
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Müller WA, Sarkis JR, Marczak LDF, Muniz AR. Molecular dynamics study of the effects of static and oscillating electric fields in ovalbumin. INNOV FOOD SCI EMERG 2022. [DOI: 10.1016/j.ifset.2021.102911] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Noriega R. Measuring the Multiscale Dynamics, Structure, and Function of Biomolecules at Interfaces. J Phys Chem B 2021; 125:5667-5675. [PMID: 34042455 DOI: 10.1021/acs.jpcb.1c01546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The individual and collective structure and properties of biomolecules can change dramatically when they are localized at an interface. However, the small spatial extent of interfacial regions poses challenges to the detailed characterization of multiscale processes that dictate the structure and function of large biological units such as peptides, proteins, or nucleic acids. This Perspective surveys a broad set of tools that provide new opportunities to probe complex, dynamic interfaces across the vast range of temporal regimes that connect molecular-scale events to macroscopic observables. An emphasis is placed on the integration over multiple time scales, the use of complementary techniques, and the incorporation of external stimuli to control interfacial properties with spatial, temporal, and chemical specificity.
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Affiliation(s)
- Rodrigo Noriega
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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14
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Nguyen PH, Ramamoorthy A, Sahoo BR, Zheng J, Faller P, Straub JE, Dominguez L, Shea JE, Dokholyan NV, De Simone A, Ma B, Nussinov R, Najafi S, Ngo ST, Loquet A, Chiricotto M, Ganguly P, McCarty J, Li MS, Hall C, Wang Y, Miller Y, Melchionna S, Habenstein B, Timr S, Chen J, Hnath B, Strodel B, Kayed R, Lesné S, Wei G, Sterpone F, Doig AJ, Derreumaux P. Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis. Chem Rev 2021; 121:2545-2647. [PMID: 33543942 PMCID: PMC8836097 DOI: 10.1021/acs.chemrev.0c01122] [Citation(s) in RCA: 378] [Impact Index Per Article: 126.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein misfolding and aggregation is observed in many amyloidogenic diseases affecting either the central nervous system or a variety of peripheral tissues. Structural and dynamic characterization of all species along the pathways from monomers to fibrils is challenging by experimental and computational means because they involve intrinsically disordered proteins in most diseases. Yet understanding how amyloid species become toxic is the challenge in developing a treatment for these diseases. Here we review what computer, in vitro, in vivo, and pharmacological experiments tell us about the accumulation and deposition of the oligomers of the (Aβ, tau), α-synuclein, IAPP, and superoxide dismutase 1 proteins, which have been the mainstream concept underlying Alzheimer's disease (AD), Parkinson's disease (PD), type II diabetes (T2D), and amyotrophic lateral sclerosis (ALS) research, respectively, for many years.
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Affiliation(s)
- Phuong H Nguyen
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Bikash R Sahoo
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jie Zheng
- Department of Chemical & Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Peter Faller
- Institut de Chimie, UMR 7177, CNRS-Université de Strasbourg, 4 rue Blaise Pascal, 67000 Strasbourg, France
| | - John E Straub
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Laura Dominguez
- Facultad de Química, Departamento de Fisicoquímica, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - Nikolay V Dokholyan
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
- Department of Chemistry, and Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, London SW7 2AZ, U.K
- Molecular Biology, University of Naples Federico II, Naples 80138, Italy
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Saeed Najafi
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics & Faculty of Applied Sciences, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
| | - Antoine Loquet
- Institute of Chemistry & Biology of Membranes & Nanoobjects, (UMR5248 CBMN), CNRS, Université Bordeaux, Institut Européen de Chimie et Biologie, 33600 Pessac, France
| | - Mara Chiricotto
- Department of Chemical Engineering and Analytical Science, University of Manchester, Manchester M13 9PL, U.K
| | - Pritam Ganguly
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - James McCarty
- Chemistry Department, Western Washington University, Bellingham, Washington 98225, United States
| | - Mai Suan Li
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 700000, Vietnam
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Carol Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Yiming Wang
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Yifat Miller
- Department of Chemistry and The Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | | | - Birgit Habenstein
- Institute of Chemistry & Biology of Membranes & Nanoobjects, (UMR5248 CBMN), CNRS, Université Bordeaux, Institut Européen de Chimie et Biologie, 33600 Pessac, France
| | - Stepan Timr
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Jiaxing Chen
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Brianna Hnath
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Rakez Kayed
- Mitchell Center for Neurodegenerative Diseases, and Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Sylvain Lesné
- Department of Neuroscience, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Science, Multiscale Research Institute of Complex Systems, Fudan University, Shanghai 200438, China
| | - Fabio Sterpone
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Andrew J Doig
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, U.K
| | - Philippe Derreumaux
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
- Laboratory of Theoretical Chemistry, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
- Faculty of Pharmacy, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
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15
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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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