1
|
Paul S, Mondal S, Shenogina I, Cui Q. The molecular basis for the increased stability of the FUS-LC fibril at the anionic membrane- and air-water interfaces. Chem Sci 2024; 15:13788-13799. [PMID: 39211498 PMCID: PMC11352777 DOI: 10.1039/d4sc02295e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 07/22/2024] [Indexed: 09/04/2024] Open
Abstract
Self-organization of biomolecules can lead to the formation of liquid droplets, hydrogels, and irreversible aggregates that bear immense significance in biology and diseases. Despite the considerable number of studies conducted on biomolecular condensation in bulk solution, there is still a lack of understanding of how different surfaces regulate the condensation process. In this context, recent studies showed that, in contrast to zwitterionic lipid membranes, anionic membranes promoted the production of liquid droplets of FUsed in Sarcoma Low Complexity domain (FUS-LC) despite exhibiting no specific protein-lipid interactions. Moreover, the air-water interface led to a solid fibril-like aggregate of FUS-LC. The molecular mechanism of condensation/aggregation of proteins in response to surfaces of various charged states or levels of hydrophobicity remains to be better elucidated. Here, we provide initial insights into this question by investigating the stability of a small β fibril state of FUS-LC in bulk solution vs. membrane- and air-water interfaces. We perform multiple independent molecular dynamics simulations with distinct starting conformations for each system to demonstrate the statistical significance of our findings. Our study demonstrates the stability of the FUS-LC fibril in the presence of anionic membranes on the μs timescale while the fibril falls apart in bulk solution. We observe that a zwitterionic membrane does not enhance the stability of the fibril and 1,2-dioleoyl-sn-glycero-3-phospho-l-serine (DOPS) has a higher propensity to stabilize the fibril than dioleoylphosphatidylglycerol (DOPG), in qualitative agreement with experiments. We further show that the fibril becomes more stable at the air-water interface. We pinpoint interfacial solvation at the membrane- and air-water interfaces as a key factor that contributes to the stabilization of the peptide assembly.
Collapse
Affiliation(s)
- Sanjoy Paul
- Department of Chemistry, Boston University 590 Commonwealth Avenue Massachusetts-02215 USA
| | - Sayantan Mondal
- Department of Chemistry, Boston University 590 Commonwealth Avenue Massachusetts-02215 USA
| | - Irina Shenogina
- Department of Physics, University of Illinois Urbana-Champaign USA
| | - Qiang Cui
- Department of Chemistry, Boston University 590 Commonwealth Avenue Massachusetts-02215 USA
- Departments of Physics, and Biomedical Engineering, Boston University Massachusetts-02215 USA
| |
Collapse
|
2
|
Garika V, Babbar S, Samanta S, Harilal S, Eisenberg-Lerner A, Rotfogel Z, Pikhay E, Shehter I, Elkayam A, Bashouti MY, Akabayov B, Ron I, Hazan G, Roizin Y, Shalev G. Addressing the challenge of solution gating in biosensors based on field-effect transistors. Biosens Bioelectron 2024; 265:116689. [PMID: 39208511 DOI: 10.1016/j.bios.2024.116689] [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: 04/21/2024] [Revised: 08/16/2024] [Accepted: 08/18/2024] [Indexed: 09/04/2024]
Abstract
Transistor-based biosensing (BioFET) is a long-enduring vision for next generation medical diagnostics. The study addresses a challenge associated with the BioFET solution gating. The standard BioFET sensing measurement involves sweeping of the solution gate (Vsol) with a concurrent measurement of the source-drain current (IDS). This IDS-Vsol sweep poses a great challenge, as Vsol does not only determine IDS, but also determines the pH levels, ion concentrations, and electric fields at the sensing area double layer accommodating the biomolecules. Therefore, inevitably, an IDS-Vsol sweep implies that the sensing area double layer is not in an electrochemical equilibrium, but rather in a continuous transient state as electrochemical potential gradients induce transient ion currents continuously affecting double layer hosting the biomolecules and the biological interactions. This challenge calls for a BioFET design which permits IDS sweeping from an off-state to an on-state while keeping Vsol constant and the double layer sensing area in electrochemical equilibrium. The study explores a BioFET design addressing this challenge by decoupling the solution potential from IDS gating. Specific and label-free sensing of ferritin in 0.5 μL drops of 1:100 diluted plasma is pursued. We show an excellent sensing performance once the solution potential and IDS gating are decoupled, with a limit-of-detection of 10 fg/ml, a dynamic range of 10 orders of magnitude in ferritin concentration and excellent linearity and sensitivity. In contrast, a poor sensing performance is recorded for the conventional Vsol sweep performed in parallel to the above. Extensive control measurements quantifying the non-specific signals are reported.
Collapse
Affiliation(s)
- Vijay Garika
- School of Electrical Engineering, Ben-Gurion University of the Negev, Israel
| | - Shubham Babbar
- School of Electrical Engineering, Ben-Gurion University of the Negev, Israel
| | - Soumadri Samanta
- School of Electrical Engineering, Ben-Gurion University of the Negev, Israel
| | - Sherina Harilal
- Department of Solar Energy and Environmental Physics, Swiss Institute for Dryland Environmental and Energy Research, J. Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, 8499000, Israel
| | | | - Ziv Rotfogel
- Ophthalmology Research Laboratory, Kaplan Medical Center, Rehovot, Israel; Faculty of Medicine, Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Evgeny Pikhay
- Tower Semiconductor, PO Box 619, Migdal Haemek, Israel
| | - Inna Shehter
- Tower Semiconductor, PO Box 619, Migdal Haemek, Israel
| | - Ayala Elkayam
- Tower Semiconductor, PO Box 619, Migdal Haemek, Israel
| | - Muhammad Y Bashouti
- Department of Solar Energy and Environmental Physics, Swiss Institute for Dryland Environmental and Energy Research, J. Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, 8499000, Israel; The Ilse-Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, POB 653, Beer-Sheva, 8410501, Israel
| | - Barak Akabayov
- Department of Chemistry and Data Science Research Center, Ben-Gurion University of the Negev, 8410501, Beer-Sheva, Israel
| | - Izhar Ron
- School of Electrical Engineering, Ben-Gurion University of the Negev, Israel
| | - Guy Hazan
- School of Medicine, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel; Pediatric Department D, Soroka University, Medical Center, Beer-Sheva, Israel
| | - Yakov Roizin
- Tower Semiconductor, PO Box 619, Migdal Haemek, Israel
| | - Gil Shalev
- School of Electrical Engineering, Ben-Gurion University of the Negev, Israel; The Ilse-Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, POB 653, Beer-Sheva, 8410501, Israel.
| |
Collapse
|
3
|
Chen C, Yan ZS, Ma YQ, Ding HM. Effect of Terahertz Waves on the Structure of the Aβ42 Monomer, Dimer, and Protofibril: Insights from Molecular Dynamics Simulations. ACS Chem Neurosci 2023; 14:4128-4138. [PMID: 37983764 DOI: 10.1021/acschemneuro.3c00485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023] Open
Abstract
Amyloid-β (Aβ) and its assemblies play important roles in the pathogenesis of Alzheimer's disease (AD). Recent studies conducted by experimental and computational researchers have extensively explored the structure, assembly, and influence of biomolecules and cell membranes on Aβ. However, the impact of terahertz waves on the structures of Aβ monomers and aggregates remains largely unexplored. In this study, we systematically investigate the molecular mechanisms by which terahertz waves affect the structure of the Aβ42 monomer, dimer, and tetramer through all-atom molecular dynamics (MD) simulations. Our findings indicate that terahertz waves at a specific frequency (42.55 THz) can enhance intramolecular and intermolecular interactions in the Aβ42 monomer and dimer, respectively, by resonating with the symmetric stretching mode of the -COO- groups and the symmetric bending/stretching mode of -CH3 groups. Consequently, the β-structure content of the Aβ42 monomer is greatly increased, and the binding energy between the monomers in the Aβ42 dimer is significantly enhanced. Additionally, our observations suggest that terahertz waves can mildly stabilize the structure of tetrameric protofibrils by enhancing the interactions among peripheral peptides. Furthermore, we also investigated the effect of the frequency of terahertz waves on the structure of Aβ42. The present study contributes to a better understanding of the impact of external fields on the biobehavior of Aβ42 peptides and may shed some light on the potential risks associated with electromagnetic field radiation.
Collapse
Affiliation(s)
- Chen Chen
- National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Zeng-Shuai Yan
- National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Yu-Qiang Ma
- National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Hong-Ming Ding
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Severi M, Zerbetto F. Polaritonic Chemistry: Hindering and Easing Ground State Polyenic Isomerization via Breakdown of σ-π Separation. J Phys Chem Lett 2023; 14:9145-9149. [PMID: 37796008 PMCID: PMC10577679 DOI: 10.1021/acs.jpclett.3c02081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 09/06/2023] [Indexed: 10/06/2023]
Abstract
The ground state conformational isomerization in polyenes is a symmetry allowed process. Its low energy barrier is governed by electron density transfer from the formal single bond that is rotated to the nearby formal double bonds. Along the reaction pathway, the transition state is therefore destabilized. The rules of polaritonic chemistry, i.e., chemistry in a nanocavity with reflecting windows, are barely beginning to be laid out. The standing electric field of the nanocavity couples strongly with the molecular wave function and modifies the potential energy curve in unexpected ways. A quantum electrodynamics approach, applied to the torsional degree of freedom of the central bond of butadiene, shows that formation of the polariton mixes the σ-π frameworks thereby stabilizing/destabilizing the planar, reactant-like conformations. The values of the fundamental mode of the cavity field used in the absence of the cavity do not trigger this mechanism.
Collapse
Affiliation(s)
- Marco Severi
- Department
of Chemistry G. Ciamician, University of
Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Francesco Zerbetto
- Department
of Chemistry G. Ciamician, University of
Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Salimi A, Chatterjee S, Lee JY. Exposure to the electric field: A potential way to block the aggregation of histidine tautomeric isomers of β-amyloid. Int J Biol Macromol 2023; 232:123385. [PMID: 36693605 DOI: 10.1016/j.ijbiomac.2023.123385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023]
Abstract
Controlling protein misfolding and accumulation in neurodegeneration is a challenge in chemical neuroscience. The application of appropriate electric fields (EFs) can be a potential noninvasive therapy to treat neuro disorders. The effect of EFs of varying intensities and directions on the conformational dynamics of β-Amyloid40 (Aβ40) under histidine tautomerism has been investigated for the first time. Our findings suggest that peptides tend to align their dipole moments with the orientation of EF. Irrespective of the EF direction, the dipole moment magnitude is affected by the EF strength. With the conformational changes, the EF strength equal to 0.5 V/nm destroyed the β-sheet content of the δδδ isomer as a potentially toxic agent. The content of the alpha-helical structure which can be transformed into the β-sheet is reduced. The strength of the EF showed a significant influence on the reduction of the number of intra-protein hydrogen bonds especially when EF is equal to 0.5 V/nm which could facilitate destabilization of the structure of the peptides. Current findings provide quantitative insights into the tautomerization-mediated Aβ40 dynamic and conformational changes induced by the external EFs in aqueous solutions, which may provide beneficial information for use as a therapeutic technique.
Collapse
Affiliation(s)
- Abbas Salimi
- Department of Chemistry, Sungkyunkwan University, Suwon 16419, Republic of Korea.
| | - Sompriya Chatterjee
- Department of Chemistry, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jin Yong Lee
- Department of Chemistry, Sungkyunkwan University, Suwon 16419, Republic of Korea.
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Samaranayake CP, Sastry SK. Molecular dynamics evidence for nonthermal effects of electric fields on pectin methylesterase activity. Phys Chem Chem Phys 2021; 23:14422-14432. [PMID: 34180917 DOI: 10.1039/d0cp05950a] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Experimental studies relevant to the nonthermal effects of electric fields on biological systems are emerging. However, these effects are poorly understood at the molecular level. The present study investigates pectin methylesterase, a cell wall modifying enzyme in plants, exposed to various electric field strengths. Molecular dynamics (MD) of the enzyme were studied with and without (thermal-only) electric field applications. The measurements were interpreted on the basis of equivalent energy input to gain insights into the effect of electric field treatment time at a constant temperature (50 °C). Results reveal that electric fields exert nonthermal effects on both local and global protein structure. In 1 μs simulations, the results show significant (P ≤ 0.05) shrinkage of the catalytic domain and shortening of enzyme-water hydrogen bond lifetime by a 50 V cm-1 electric field. Unwinding of the helical segments, altered intra- and intermolecular hydrogen bond patterns, and increased hydration are also caused by the 50 V cm-1 electric field. This study serves to understand the electric field influence on the functional role of proteins.
Collapse
Affiliation(s)
- Chaminda P Samaranayake
- Department of Food, Agricultural and Biological Engineering, The Ohio State University, 590 Woody Hayes Drive, Columbus, Ohio 43210, USA.
| | - Sudhir K Sastry
- Department of Food, Agricultural and Biological Engineering, The Ohio State University, 590 Woody Hayes Drive, Columbus, Ohio 43210, USA.
| |
Collapse
|
12
|
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: 6] [Impact Index Per Article: 2.0] [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.
Collapse
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
| |
Collapse
|
13
|
De D, Pawar N, Gupta AN. Electric field-driven conformational changes in the elastin protein. Phys Chem Chem Phys 2021; 23:4195-4204. [PMID: 33586747 DOI: 10.1039/d0cp04813e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The formation of aggregates and amyloids, a hallmark of many protein misfolding diseases, depends on many intrinsic and extrinsic factors. Many approaches (in vitro, in vivo, and in silico) have been attempted to inhibit the aggregation process so that the progression of these diseases can be controlled. We investigate the effect of a static electric field (EF; 120 V cm-1 and 200 V cm-1) on the conformational change of elastin protein using light scattering, spectroscopy, and microscopy techniques. Laser light scattering and photoluminescence spectroscopy show the formation of fibrils of unexposed elastin with aging, whereas disruption of fibril formation with EF exposed elastin. The size of EF exposed elastin first increases and exhibits an apex, and subsequently decreases with an increasing time of exposure. We observed that a decrease in the size of EF exposed elastin depends on the strength of the EF, faster decrement at higher EF. FTIR data show that EF modifies elastin protein's secondary structures; it facilitates the interconversion of β-sheets and turns into α-helix structures. The SEM images of unexposed and EF exposed elastin confirms the observation through light scattering and PL techniques. The effect of an EF on protein conformation and amyloids is promising to treat Parkinson's disease, a protein misfolding disease.
Collapse
Affiliation(s)
- Debajyoti De
- Department of Physics, Indian Institute of Technology Kharagpur, WB 721302, India.
| | - Nisha Pawar
- Department of Physics, Indian Institute of Technology Kharagpur, WB 721302, India.
| | - Amar Nath Gupta
- Department of Physics, Indian Institute of Technology Kharagpur, WB 721302, India.
| |
Collapse
|
14
|
Cingolani M, Mummolo L, Lugli F, Zaffagnini M, Genovese D. Protein aggregation detection with fluorescent macromolecular and nanostructured probes: challenges and opportunities. NEW J CHEM 2021. [DOI: 10.1039/d1nj01606g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nanoprobes based on various nanomaterials, polymers or AIEgens are overcoming previous limitations for diagnosis and therapy of early-stage protein aggregation.
Collapse
Affiliation(s)
- Matteo Cingolani
- Dipartimento di Chimica “Giacomo Ciamician”
- Università di Bologna
- 40126 Bologna
- Italy
| | - Liviana Mummolo
- Dipartimento di Chimica “Giacomo Ciamician”
- Università di Bologna
- 40126 Bologna
- Italy
| | - Francesca Lugli
- Dipartimento di Chimica “Giacomo Ciamician”
- Università di Bologna
- 40126 Bologna
- Italy
| | - Mirko Zaffagnini
- Dipartimento di Farmacia e Biotecnologia
- Università di Bologna
- 40126 Bologna
- Italy
| | - Damiano Genovese
- Dipartimento di Chimica “Giacomo Ciamician”
- Università di Bologna
- 40126 Bologna
- Italy
| |
Collapse
|
15
|
Kwon J, Choi JS, Lee J, Na J, Sung J, Lee HJ, Lee HS, Lim YB, Choi HJ. Disaggregation of Amyloid-β Plaques by a Local Electric Field Generated by a Vertical Nanowire Electrode Array. ACS APPLIED MATERIALS & INTERFACES 2020; 12:55596-55604. [PMID: 33269924 DOI: 10.1021/acsami.0c16000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The aggregation and accumulation of amyloid-β (Aβ) peptides is a characteristic pathology for Alzheimer's disease (AD). Although noninvasive therapies involving stimulation by electric field (EF) have been reported, the efficiency of Aβ disaggregation needs to be further improved for this strategy to be used in clinical settings. In this study, we show that an electrode based on a vertical nanowire electrode array (VNEA) is far more superior to a typical flat-type electrode in disaggregating Aβ plaques. The enhanced disaggregation efficiency of VNEA is due to the formation of high-strength local EF between the nanowires, as verified by in silico and empirical evidence. Compared with those of the flat electrode, the simulation data revealed that 19.8-fold and 8.8-fold higher EFs are generated above and between the nanowires, respectively. Moreover, empirical cyclic voltammetry data demonstrated that VNEA had a 2.7-fold higher charge capacity than the flat electrode; this is associated with the higher surface area of VNEA. The conformational transition of Aβ peptides between the β-sheet and α-helix could be sensitively monitored in real time by the newly designed in situ circular dichroism instrument. This highly efficient EF-configuration of VNEA will lower the stimulation power for disaggregating the Aβ plaques, compared to that of other existing field-mediated modulation systems. Considering the complementary metal-oxide-semiconductor-compatibility and biocompatible strength of the EF for perturbing the Aβ aggregation, our study could pave the way for the potential use of electric stimulation devices for in vivo therapeutic application as well as scientific studies for AD.
Collapse
Affiliation(s)
- Juyoung Kwon
- Department of Materials Science and Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Jun Shik Choi
- Department of Materials Science and Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Jaejun Lee
- Department of Materials Science and Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Jukwan Na
- Department of Materials Science and Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Jaesuk Sung
- Department of Materials Science and Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Hyo-Jung Lee
- Department of Materials Science and Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Hye-Soo Lee
- Department of Materials Science and Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Yong-Beom Lim
- Department of Materials Science and Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Heon-Jin Choi
- Department of Materials Science and Engineering, Yonsei University, Seoul 03722, Republic of Korea
| |
Collapse
|
16
|
Pandey G, Ramakrishnan V. Invasive and non-invasive therapies for Alzheimer's disease and other amyloidosis. Biophys Rev 2020; 12:1175-1186. [PMID: 32930962 PMCID: PMC7575678 DOI: 10.1007/s12551-020-00752-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/31/2020] [Indexed: 12/12/2022] Open
Abstract
Advancements in medical science have facilitated in extending human lives. The increased life expectancy, though, has come at a cost. The cases of an aging population suffering from degenerative diseases like Alzheimer's disease (AD) are presently at its all-time high. Amyloidosis disorders such as AD are triggered by an abnormal transition of soluble proteins into their highly ordered aggregated forms. The landscape of amyloidosis treatment remains unchanged, and there is no cure for such disorders. However, an increased understanding of the mechanism of amyloid self-assembly has given hope for a possible therapeutic solution. In this review, we will discuss the current state of molecular and non-molecular options for therapeutic intervention of amyloidosis. We highlight the efficacy of non-invasive physical therapies as possible alternatives to their molecular counterparts. Graphical abstract.
Collapse
Affiliation(s)
- Gaurav Pandey
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, India
| | - Vibin Ramakrishnan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, India.
| |
Collapse
|
17
|
Song Y, Wu R, Wang Y, Liu L, Dong M. Structural conversion of human islet amyloid polypeptide aggregates under an electric field. Chem Commun (Camb) 2020; 56:11497-11500. [PMID: 32852504 DOI: 10.1039/d0cc04466k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Electric fields (EFs) in biological systems are well known, and their presence implies the activity of protein ion channels and pumps in various cells. The aggregation of islet amyloid polypeptides (IAPP) was recently found in human brain tissue, and this was related to the electrical activity of neurons and caused neuronal loss. However, the association between amyloid formation and the electric field is still unknown. Herein a direct method to stimulate the formation of the hIAPP peptide under an EF is reported.
Collapse
Affiliation(s)
- Yongxiu Song
- Institute for Advanced Materials, Jiangsu University, China.
| | | | | | | | | |
Collapse
|
18
|
Miceli M, Muscat S, Morbiducci U, Cavaglià M, Deriu MA. Ultrasonic waves effect on S-shaped β-amyloids conformational dynamics by non-equilibrium molecular dynamics. J Mol Graph Model 2020; 96:107518. [DOI: 10.1016/j.jmgm.2019.107518] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 12/16/2019] [Accepted: 12/20/2019] [Indexed: 12/15/2022]
|
19
|
Todorova N, Bentvelzen A, Yarovsky I. Electromagnetic field modulates aggregation propensity of amyloid peptides. J Chem Phys 2020; 152:035104. [DOI: 10.1063/1.5126367] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- N. Todorova
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, Australia
- Australian Centre for Electromagnetic Bioeffects Research, Australia
| | - A. Bentvelzen
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, Australia
- Australian Centre for Electromagnetic Bioeffects Research, Australia
| | - I. Yarovsky
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, Australia
- Australian Centre for Electromagnetic Bioeffects Research, Australia
| |
Collapse
|
20
|
Elucidating the Effect of Static Electric Field on Amyloid Beta 1-42 Supramolecular Assembly. J Mol Graph Model 2020; 96:107535. [PMID: 31978828 DOI: 10.1016/j.jmgm.2020.107535] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 12/06/2019] [Accepted: 01/09/2020] [Indexed: 02/07/2023]
Abstract
Amyloid-β (Aβ) aggregation is recognized to be a key toxic factor in the pathogenesis of Alzheimer disease, which is the most common progressive neurodegenerative disorder. In vitro experiments have elucidated that Aβ aggregation depends on several factors, such as pH, temperature and peptide concentration. Despite the research effort in this field, the fundamental mechanism responsible for the disease progression is still unclear. Recent research has proposed the application of electric fields as a non-invasive therapeutic option leading to the disruption of amyloid fibrils. In this regard, a molecular level understanding of the interactions governing the destabilization mechanism represents an important research advancement. Understanding the electric field effects on proteins, provides a more in-depth comprehension of the relationship between protein conformation and electrostatic dipole moment. The present study focuses on investigating the effect of static Electric Field (EF) on the conformational dynamics of Aβ fibrils by all-atom Molecular Dynamics (MD) simulations. The outcome of this work provides novel insight into this research field, demonstrating how the Aβ assembly may be destabilized by the applied EF.
Collapse
|
21
|
Průša J, Cifra M. Molecular dynamics simulation of the nanosecond pulsed electric field effect on kinesin nanomotor. Sci Rep 2019; 9:19721. [PMID: 31873109 PMCID: PMC6928163 DOI: 10.1038/s41598-019-56052-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 11/18/2019] [Indexed: 12/23/2022] Open
Abstract
Kinesin is a biological molecular nanomotor which converts chemical energy into mechanical work. To fulfill various nanotechnological tasks in engineered environments, the function of biological molecular motors can be altered by artificial chemical modifications. The drawback of this approach is the necessity of designing and creating a new motor construct for every new task. We propose that intense nanosecond-scale pulsed electric field could modify the function of nanomotors. To explore this hypothesis, we performed molecular dynamics simulation of a kinesin motor domain docked on a subunit of its microtubule track - a single tubulin heterodimer. In the simulation, we exposed the kinesin motor domain to intense (100 MV/m) electric field up to 30 ns. We found that both the magnitude and angle of the kinesin dipole moment are affected. Furthermore, we found that the electric field affects contact surface area between kinesin and tubulin, the structure and dynamics of the functionally important kinesin segments, including microtubule binding motifs as well as nucleotide hydrolysis site which power the nanomotor. These findings indicate that external intense nanosecond-scale electric field could alter kinesin behavior. Our results contribute to developing novel electromagnetic methods for modulating the function of biomolecular matter at the nanoscale.
Collapse
Affiliation(s)
- Jiří Průša
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberska 1014/57, Prague, 18251, Czech Republic.,Faculty of Chemical Engineering, University of Chemistry and Technology Prague, Technicka 5, Prague, 16628, Czech Republic
| | - Michal Cifra
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberska 1014/57, Prague, 18251, Czech Republic.
| |
Collapse
|
22
|
della Valle E, Marracino P, Pakhomova O, Liberti M, Apollonio F. Nanosecond pulsed electric signals can affect electrostatic environment of proteins below the threshold of conformational effects: The case study of SOD1 with a molecular simulation study. PLoS One 2019; 14:e0221685. [PMID: 31454403 PMCID: PMC6711501 DOI: 10.1371/journal.pone.0221685] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 08/13/2019] [Indexed: 12/19/2022] Open
Abstract
Electric fields can be a powerful tool to interact with enzymes or proteins, with an intriguing perspective to allow protein manipulation. Recently, researchers have focused the interest on intracellular enzyme modifications triggered by the application of nanosecond pulsed electric fields. These findings were also supported by theoretical predictions from molecular dynamics simulations focussing on significant variations in protein secondary structures. In this work, a theoretical study utilizing molecular dynamics simulations is proposed to explore effects of electric fields of high intensity and very short nanosecond duration applied to the superoxide dismutase (Cu/Zn-SOD or SOD-1), an important enzyme involved in the cellular antioxidant defence mechanism. The effects of 100-nanosecond pulsed electric fields, with intensities ranging from 108 to 7x108 V/m, on a single SOD1 enzyme are presented. We demonstrated that the lowest intensity of 108 V/m, although not inducing structural changes, can produce electrostatic modifications on the reaction centre of the enzyme, as apparent from the dipolar response and the electric field distribution of the protein active site. Electric pulses above 5x108 V/m produced a fast transition between the folded and a partially denatured state, as inferred by the secondary structures analysis. Finally, for the highest field intensity used (7x108 V/m), a not reversible transition toward an unfolded state was observed.
Collapse
Affiliation(s)
- Elena della Valle
- BioElectronic Vision Lab, University of Michigan, Ann Arbor, Michigan, United States of America
| | | | - Olga Pakhomova
- Frank Reidy Research Center for Bioelectrics, Old Dominion University, Norfolk, Virginia, United States of America
| | - Micaela Liberti
- Department of Information Engineering, Electronics and Telecommunications, Sapienza University of Rome, Rome, Italy
| | - Francesca Apollonio
- Department of Information Engineering, Electronics and Telecommunications, Sapienza University of Rome, Rome, Italy
| |
Collapse
|
23
|
Tubulin response to intense nanosecond-scale electric field in molecular dynamics simulation. Sci Rep 2019; 9:10477. [PMID: 31324834 PMCID: PMC6642143 DOI: 10.1038/s41598-019-46636-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 06/18/2019] [Indexed: 12/12/2022] Open
Abstract
Intense pulsed electric fields are known to act at the cell membrane level and are already being exploited in biomedical and biotechnological applications. However, it is not clear if electric pulses within biomedically-attainable parameters could directly influence intra-cellular components such as cytoskeletal proteins. If so, a molecular mechanism of action could be uncovered for therapeutic applications of such electric fields. To help clarify this question, we first identified that a tubulin heterodimer is a natural biological target for intense electric fields due to its exceptional electric properties and crucial roles played in cell division. Using molecular dynamics simulations, we then demonstrated that an intense - yet experimentally attainable - electric field of nanosecond duration can affect the bβ-tubulin’s C-terminus conformations and also influence local electrostatic properties at the GTPase as well as the binding sites of major tubulin drugs site. Our results suggest that intense nanosecond electric pulses could be used for physical modulation of microtubule dynamics. Since a nanosecond pulsed electric field can penetrate the tissues and cellular membranes due to its broadband spectrum, our results are also potentially significant for the development of new therapeutic protocols.
Collapse
|
24
|
Saikia J, Pandey G, Sasidharan S, Antony F, Nemade HB, Kumar S, Chaudhary N, Ramakrishnan V. Electric Field Disruption of Amyloid Aggregation: Potential Noninvasive Therapy for Alzheimer's Disease. ACS Chem Neurosci 2019; 10:2250-2262. [PMID: 30707008 DOI: 10.1021/acschemneuro.8b00490] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The aggregation of β-amyloid peptides is a key event in the formative stages of Alzheimer's disease. Promoting folding and inhibiting aggregation was reported as an effective strategy in reducing Aβ-elicited toxicity. This study experimentally investigates the influence of the external electric field (EF) and magnetic field (MF) of varying strengths on the in vitro fibrillogenesis of hydrophobic core sequence, Aβ16-22, and its parent peptide, Aβ1-42. Biophysical methods such as ThT fluorescence, static light scattering, circular dichroism, and infrared spectroscopy suggest that EF has a stabilizing effect on the secondary structure, initiating a conformational switch of Aβ16-22 and Aβ1-42 from β to non-β conformation. This observation was further corroborated by dynamic light scattering and transmission electron microscopic studies. To mimic in vivo conditions, we repeated ThT fluorescence assay with Aβ1-42 in human cerebrospinal fluid to verify EF-mediated modulation. The self-seeding of Aβ1-42 and cross-seeding with Aβ1-40 to verify that the autocatalytic amplification of self-assembly as a result of secondary nucleation also yields comparable results in EF-exposed and unexposed samples. Aβ-elicited toxicity of EF-treated samples in two neuroblastoma cell lines (SH-SY5Y and IMR-32) and human embryonic kidney cell line (HEK293) were found to be 15-38% less toxic than the EF untreated ones under identical conditions. Experiments with fluorescent labeled Aβ1-42 to correlate reduced cytotoxicity and cell internalization suggest a comparatively smaller uptake of the EF-treated peptides. Our results provide a scientific roadmap for future noninvasive, therapeutic solutions for the treatment of Alzheimer's disease.
Collapse
|
25
|
Ilieva S, Cheshmedzhieva D, Dudev T. Electric field influence on the helical structure of peptides: insights from DFT/PCM computations. Phys Chem Chem Phys 2019; 21:16198-16206. [DOI: 10.1039/c9cp01542f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The switching of the electric field with a particular directionality could be used for the healing of misfolded proteins.
Collapse
Affiliation(s)
- Sonia Ilieva
- Faculty of Chemistry and Pharmacy
- Sofia University
- Sofia 1164
- Bulgaria
| | | | - Todor Dudev
- Faculty of Chemistry and Pharmacy
- Sofia University
- Sofia 1164
- Bulgaria
| |
Collapse
|
26
|
Lu Y, Shi XF, Salsbury FR, Derreumaux P. Influence of electric field on the amyloid-β(29-42) peptides embedded in a membrane bilayer. J Chem Phys 2018; 148:045105. [DOI: 10.1063/1.5018459] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yan Lu
- School of Physics and Optoelectronic Engineering, Xidian University, Xi’an 710071, China
| | - Xiao-Feng Shi
- School of Physics and Optoelectronic Engineering, Xidian University, Xi’an 710071, China
| | - Freddie R. Salsbury
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina 27106, USA
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| |
Collapse
|
27
|
Sen S, Chakraborty M, Goley S, Dasgupta S, DasGupta S. Fibrillar disruption by AC electric field induced oscillation: A case study with human serum albumin. Biophys Chem 2017; 226:23-33. [DOI: 10.1016/j.bpc.2017.04.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 04/07/2017] [Accepted: 04/12/2017] [Indexed: 11/25/2022]
|
28
|
Modulation of Peptide Based Nano-Assemblies with Electric and Magnetic Fields. Sci Rep 2017; 7:2726. [PMID: 28578415 PMCID: PMC5457452 DOI: 10.1038/s41598-017-02609-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/12/2017] [Indexed: 12/30/2022] Open
Abstract
Peptide based nano-assemblies with their self-organizing ability has shown lot of promise due to their high degree of thermal and chemical stability, for biomaterial fabrication. Developing an effective way to control the organization of these structures is important for fabricating application-oriented materials at the molecular level. The present study reports the impact of electric and magnetic field-mediated perturbation of the self-assembly phenomenon, upon the chemical and structural properties of diphenylalanine assembly. Our studies show that, electric field effectively arrests aggregation and self-assembly formation, while the molecule is allowed to anneal in the presence of applied electric fields of varying magnitudes, both AC and DC. The electric field exposure also modulated the morphology of the self-assembled structures without affecting the overall chemical constitution of the material. Our results on the modulatory effect of the electric field are in good agreement with theoretical studies based on molecular dynamics reported earlier on amyloid forming molecular systems. Furthermore, we demonstrate that the self-assemblies formed post electric-field exposure, showed difference in their crystal habit. Modulation of nano-level architecture of peptide based model systems with external stimulus, points to a potentially rewarding strategy to re-work proven nano-materials to expand their application spectrum.
Collapse
|
29
|
Lu Y, Shi XF, Salsbury FR, Derreumaux P. Small static electric field strength promotes aggregation-prone structures in amyloid-β(29-42). J Chem Phys 2017; 146:145101. [DOI: 10.1063/1.4979866] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yan Lu
- School of Physics and Optoelectronic Engineering, Xidian University, Xi’an 710071, China
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina 27106, USA
| | - Xiao-Feng Shi
- School of Physics and Optoelectronic Engineering, Xidian University, Xi’an 710071, China
| | - Freddie R. Salsbury
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina 27106, USA
| | - Philippe Derreumaux
- Laboratoire de Biochimie Theorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Universite Paris Diderot, Sorbonne Paris Cite, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| |
Collapse
|
30
|
Todorova N, Bentvelzen A, English NJ, Yarovsky I. Electromagnetic-field effects on structure and dynamics of amyloidogenic peptides. J Chem Phys 2016; 144:085101. [PMID: 26931725 DOI: 10.1063/1.4941108] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Electromagnetic fields (EMFs) are ever-present, and so is the need to better understand their influence on human health and biological matter in general. The interaction between a molecular system and external EMF can alter the structure, and dynamical behaviour, and, hence, biological function of proteins with uncertain health consequences. This urges a detailed investigation of EMF-induced effects on basic protein biophysics. Here, we used all-atom non-equilibrium molecular dynamics simulations to understand and quantify the response mechanisms of the amyloidogenic apoC-II(60-70) peptides to non-ionising radiation by modelling their behaviour under external electromagnetic and electric fields of different strengths. Our simulations show high strength fields (>0.04 V/nm) cause structural changes in apoC-II(60-70) due to the peptide dipole alignment along the applied field direction, which disrupts the inherent β-hairpin conformation known to be the intermediate state for fibril formation. The intermediate field-strength range (0.04-0.004 V/nm) causes a significant acceleration in peptide dynamics, which leads to the increased population of structures with fibril-inhibiting characteristics, such as the separated N- and C-termini and colocation of the aromatic residues at the same peptide face. In contrast, lower field strengths (<0.004 V/nm) promote the formation of the amyloid-prone hairpin structures relative to the ambient conditions. These findings suggest that intermediate-strength electromagnetic fields could be considered for designing alternative treatments of amyloid diseases, while the very high and low field strengths could be employed for engineering well-ordered fibrillar aggregates for non-medicinal applications.
Collapse
Affiliation(s)
- Nevena Todorova
- School of Engineering, RMIT University, G.P.O. Box 2476, Melbourne, Australia
| | - Alan Bentvelzen
- School of Engineering, RMIT University, G.P.O. Box 2476, Melbourne, Australia
| | - Niall J English
- School of Chemical & Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| | - Irene Yarovsky
- School of Engineering, RMIT University, G.P.O. Box 2476, Melbourne, Australia
| |
Collapse
|
31
|
Yang PK. Effect of external electrostatic field on the stability of β sheet structures. Biopolymers 2016; 101:861-70. [PMID: 24459117 DOI: 10.1002/bip.22464] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 01/19/2014] [Accepted: 01/21/2014] [Indexed: 11/10/2022]
Abstract
To explore the effect of an external electrostatic field (EEF) on the stability of protein conformations, the molecular dynamic modeling approach was applied to evaluate the effect of an EEF along the x or y direction on a water cluster containing a parallel or antiparallel β sheet structure. The β sheet structure contained two strands with a (Gly)3 sequence separated by a distance d along the x direction. The mean forces between the two strands along the x direction were computed from the trajectories of molecular dynamics simulations. In the absence of the EEF, the forces between the two strands in vacuum were repulsive and attractive in the parallel and antiparallel β sheet structures, respectively. In contrast, the mean forces between the two strands in water were attractive in both the parallel and antiparallel β sheet structures. This is because the electric interactions between the two strands were shielded by water, and the hydrophobic effect dominated the interaction between the two strands. When an EEF >50 MV/cm was applied to the water cluster, the attractive force between the two strands in the parallel and antiparallel β sheet structures decreased and increased, respectively. Further, the binding affinity between the two strands in the parallel and antiparallel β sheet structures also decreased and increased, respectively. This is because the large EEF leads to dielectric saturation, and consequently reduces the effects of the dielectric shielding and hydrophobic interactions.
Collapse
Affiliation(s)
- Pei-Kun Yang
- Department of Biomedical Engineering, I-SHOU University, Kaohsiung 840, Taiwan, Republic of China
| |
Collapse
|
32
|
English NJ, Waldron CJ. Perspectives on external electric fields in molecular simulation: progress, prospects and challenges. Phys Chem Chem Phys 2016; 17:12407-40. [PMID: 25903011 DOI: 10.1039/c5cp00629e] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In this review, the application of a wide variety of external electric fields in molecular simulation shall be discussed, including time-varying and electromagnetic, as well as the utility and potential impact and prospects for exploitation of such simulations for real-world and industrial end use. In particular, non-equilibrium molecular dynamics will be discussed, as well as challenges in addressing adequate thermostatting and scaling field amplitudes to more experimentally relevant levels. Attention shall be devoted to recent progress and advances in external fields in ab initio molecular simulation and dynamics, as well as elusive challenges thereof (and, to some extent, for molecular dynamics from empirical potentials), such as timescales required to observe low-frequency and intensity field effects. The challenge of deterministic molecular dynamics in external fields in sampling phase space shall be discussed, along with prospects for application of fields in enhanced-sampling simulations. Finally, the application of external electric fields to a wide variety of aqueous, nanoscale and biological systems will be discussed, often motivated by the possibility of exploitation in real-world applications, which serve to underpin our molecular-level understanding of field effects in terms of microscopic mechanisms, and possibly with a view to control thereof.
Collapse
Affiliation(s)
- Niall J English
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland.
| | | |
Collapse
|
33
|
Kuo SM, Yang PK. Factors altering the affinity of protein-ligand binding in an external electrostatic field. Bioelectrochemistry 2015; 104:17-25. [PMID: 25681551 DOI: 10.1016/j.bioelechem.2015.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Revised: 01/18/2015] [Accepted: 02/08/2015] [Indexed: 11/17/2022]
Abstract
The effects of an external electric field on the binding affinity for protein-ligand complexes was determined by applying electric field E(ext) to a water cluster containing two electric dipoles separated by a certain distance. The mean forces on these two dipoles were computed from the trajectories of molecular dynamics simulations. The results showed that the mean attractive force and the binding affinity between these two dipoles decreased with increasing E(ext). Two factors governing the effects of E(ext) on the binding affinity of protein-ligand interactions were proposed. (1) When E(ext) is applied to a water cluster containing protein-ligand complexes, the water molecules neighboring ligand will be repelled from the ligand; the mean van der Waals repulsive force exerted on the ligand by these water molecules would decrease, leading to a decrease in the binding affinity between the protein and the ligand. (2) The mean electrostatic force exerted on the ligand by the water molecules polarized by E(ext) is thought to result from the dielectric polarization (P(protein)) in the region occupied by the protein, where P(protein) is proportional to -E(ext).
Collapse
Affiliation(s)
- Shyh-Ming Kuo
- Department of Biomedical Engineering, College of Medicine, I-SHOU University, Kaohsiung 82445, Taiwan, ROC
| | - Pei-Kun Yang
- Department of Biomedical Engineering, College of Medicine, I-SHOU University, Kaohsiung 82445, Taiwan, ROC.
| |
Collapse
|
34
|
Wang X, Li Y, He X, Chen S, Zhang JZH. Effect of strong electric field on the conformational integrity of insulin. J Phys Chem A 2014; 118:8942-52. [PMID: 24796962 DOI: 10.1021/jp501051r] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A series of molecular dynamics (MD) simulations up to 1 μs for bovine insulin monomer in different external electric fields were carried out to study the effect of external electric field on conformational integrity of insulin. Our results show that the secondary structure of insulin is kept intact under the external electric field strength below 0.15 V/nm, but disruption of secondary structure is observed at 0.25 V/nm or higher electric field strength. Although the starting time of secondary structure disruption of insulin is not clearly correlated with the strength of the external electric field ranging between 0.15 and 0.60 V/nm, long time MD simulations demonstrate that the cumulative effect of exposure time under the electric field is a major cause for the damage of insulin's secondary structure. In addition, the strength of the external electric field has a significant impact on the lifetime of hydrogen bonds when it is higher than 0.60 V/nm. The fast evolution of some hydrogen bonds of bovine insulin in the presence of the 1.0 V/nm electric field shows that different microwaves could either speed up protein folding or destroy the secondary structure of globular proteins deponding on the intensity of the external electric field.
Collapse
Affiliation(s)
- Xianwei Wang
- State Key Laboratory of Precision Spectroscopy, Department of Physics, Institute of Theoretical and Computational Science, East China Normal University , Shanghai 200062, China
| | | | | | | | | |
Collapse
|
35
|
Damm M, Nusshold C, Cantillo D, Rechberger GN, Gruber K, Sattler W, Kappe CO. Can electromagnetic fields influence the structure and enzymatic digest of proteins? A critical evaluation of microwave-assisted proteomics protocols. J Proteomics 2012; 75:5533-43. [PMID: 22889711 PMCID: PMC3484400 DOI: 10.1016/j.jprot.2012.07.043] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 07/27/2012] [Accepted: 07/27/2012] [Indexed: 10/31/2022]
Abstract
This study reevaluates the putative advantages of microwave-assisted tryptic digests compared to conventionally heated protocols performed at the same temperature. An initial investigation of enzyme stability in a temperature range of 37-80 °C demonstrated that trypsin activity declines sharply at temperatures above 60 °C, regardless if microwave dielectric heating or conventional heating is employed. Tryptic digests of three proteins of different size (bovine serum albumin, cytochrome c and β-casein) were thus performed at 37 °C and 50 °C using both microwave and conventional heating applying accurate internal fiber-optic probe reaction temperature measurements. The impact of the heating method on protein degradation and peptide fragment generation was analyzed by SDS-PAGE and MALDI-TOF-MS. Time-dependent tryptic digestion of the three proteins and subsequent analysis of the corresponding cleavage products by MALDI-TOF provided virtually identical results for both microwave and conventional heating. In addition, the impact of electromagnetic field strength on the tertiary structure of trypsin and BSA was evaluated by molecular mechanics calculations. These simulations revealed that the applied field in a typical laboratory microwave reactor is 3-4 orders of magnitude too low to induce conformational changes in proteins or enzymes.
Collapse
Affiliation(s)
- Markus Damm
- Christian Doppler Laboratory for Microwave Chemistry (CDLMC) and Institute of Chemistry, Karl-Franzens-University Graz, Heinrichstrasse 28/I, A-8010 Graz, Austria
| | | | | | | | | | | | | |
Collapse
|
36
|
Andujar SA, Lugli F, Höfinger S, Enriz RD, Zerbetto F. Amyloid-β fibril disruption by C60—molecular guidance for rational drug design. Phys Chem Chem Phys 2012; 14:8599-607. [DOI: 10.1039/c2cp40680b] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
37
|
Spill YG, Pasquali S, Derreumaux P. Impact of Thermostats on Folding and Aggregation Properties of Peptides Using the Optimized Potential for Efficient Structure Prediction Coarse-Grained Model. J Chem Theory Comput 2011; 7:1502-10. [DOI: 10.1021/ct100619p] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yannick G. Spill
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS et Université Paris Diderot (Paris 7), Institut de Biologie Physico Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Samuela Pasquali
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS et Université Paris Diderot (Paris 7), Institut de Biologie Physico Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS et Université Paris Diderot (Paris 7), Institut de Biologie Physico Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| |
Collapse
|