1
|
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
|
2
|
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
|
3
|
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
|
4
|
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
|
5
|
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
|
6
|
Wu H, Ghaani MR, Nandi PK, English NJ. Investigation of Dipolar Response of the Hydrated Hen-Egg White Lysozyme Complex under Externally Applied Electric Fields: Insights from Non-equilibrium Molecular Dynamics. J Phys Chem B 2022; 126:858-868. [PMID: 35060735 PMCID: PMC8819654 DOI: 10.1021/acs.jpcb.1c07096] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- HaoLun Wu
- School of Chemical & Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| | - Mohammad Reza Ghaani
- School of Chemical & Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| | - Prithwish K. Nandi
- School of Chemical & Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
- Irish Centre for High-End Computing, Trinity Enterprise Centre, Pearse Street, Dublin 2, Ireland
| | - Niall J. English
- School of Chemical & Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| |
Collapse
|
7
|
Wu H, Ghaani MR, Futera Z, English NJ. Effects of Externally Applied Electric Fields on the Manipulation of Solvated-Chignolin Folding: Static- versus Alternating-Field Dichotomy at Play. J Phys Chem B 2022; 126:376-386. [PMID: 35001614 PMCID: PMC8785190 DOI: 10.1021/acs.jpcb.1c06857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 12/06/2021] [Indexed: 12/20/2022]
Abstract
The interaction between a protein and external electric field (EF) can alter its structure and dynamical behavior, which has a potential impact on the biological function of proteins and cause uncertain health consequences. Conversely, the application of EFs of judiciously selected intensity and frequency can help to treat disease, and optimization of this requires a greater understanding of EF-induced effects underpinning basic protein biophysics. In the present study, chignolin─an artificial protein sufficiently small to undergo fast-folding events and transitions─was selected as an ideal prototype to investigate how, and to what extent, externally applied electric fields may manipulate or influence protein-folding phenomena. Nonequilibrium molecular dynamics (NEMD) simulations have been performed of solvated chignolin to determine the distribution of folding states and their underlying transition dynamics, in the absence and presence of externally applied electric fields (both static and alternating); a key focus has been to ascertain how folding pathways are altered in an athermal sense by external fields. Compared to zero-field conditions, a dramatically different─indeed, bifurcated─behavior of chignolin-folding processes emerges between static- and alternating-field scenarios, especially vis-à-vis incipient stages of hydrophobic-core formation: in alternating fields, fold-state populations diversified, with an attendant acceleration of state-hopping folding kinetics, featuring the concomitant emergence of a new, quasi-stable structure compared to the native structure, in field-shifted energy landscapes.
Collapse
Affiliation(s)
- HaoLun Wu
- School
of Chemical & Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| | - Mohammad Reza Ghaani
- School
of Chemical & Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| | - Zdeněk Futera
- Faculty
of Science, University of South Bohemia, České Budějovice 370 05, Czech Republic
| | - Niall J. English
- School
of Chemical & Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| |
Collapse
|
8
|
Molina-Peña R, Haji Mansor M, Najberg M, Thomassin JM, Gueza B, Alvarez-Lorenzo C, Garcion E, Jérôme C, Boury F. Nanoparticle-containing electrospun nanofibrous scaffolds for sustained release of SDF-1α. Int J Pharm 2021; 610:121205. [PMID: 34670119 DOI: 10.1016/j.ijpharm.2021.121205] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 11/28/2022]
Abstract
Chemokines such as stromal cell-derived factor-1α (SDF-1α) regulate the migration of cancer cells that can spread from their primary tumor site by migrating up an SDF-1α concentration gradient, facilitating their local invasion and metastasis. Therefore, the implantation of SDF-1α-releasing scaffolds can be a useful strategy to trap cancer cells expressing the CXCR4 receptor. In this work, SDF-1α was encapsulated into poly(lactic-co-glycolic acid) (PLGA)-based nanoparticles and subsequently electrospun with chitosan to produce nanofibrous scaffolds of average fiber diameter of 261 ± 45 nm, intended for trapping glioblastoma (GBM) cells. The encapsulated SDF-1α maintained its biological activity after the electrospinning process as assessed by its capacity to induce the migration of cancer cells. The scaffolds could also provide sustained release of SDF-1α for at least 5 weeks. Using NIH3T3 mouse fibroblasts, human Thp-1 macrophages, and rat primary astrocytes we showed that the scaffolds possessed high cytocompatibility in vitro. Furthermore, a 7-day follow-up of Fischer rats bearing implanted scaffolds demonstrated the absence of adverse effects in vivo. In addition, the nanofibrous structure of the scaffolds provided excellent anchoring sites to support the adhesion of human GBM cells by extension of their pseudopodia. The scaffolds also demonstrated slow degradation kinetics, which may be useful in maximizing the time window for trapping GBM cells. As surgical resection does not permit a complete removal of GBM tumors, our results support the future implantation of these scaffolds into the walls of the resection cavity to evaluate their capacity to attract and trap the residual GBM cells in the brain.
Collapse
Affiliation(s)
- Rodolfo Molina-Peña
- Univ Angers, Université de Nantes, Inserm, CRCINA, SFR ICAT, F-49000 Angers, France
| | - Muhammad Haji Mansor
- Univ Angers, Université de Nantes, Inserm, CRCINA, SFR ICAT, F-49000 Angers, France; Center for Education and Research on Macromolecules (CERM), CESAM-UR, University of Liège, B-4000 Liège, Belgium
| | - Mathie Najberg
- Univ Angers, Université de Nantes, Inserm, CRCINA, SFR ICAT, F-49000 Angers, France; Departamento de Farmacología, Farmacia y Tecnología Farmacéutica, I+D Farma (GI-1645), Facultad de Farmacia, and Health Research Institute of Santiago de Compostela (IDIS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Jean-Michel Thomassin
- Center for Education and Research on Macromolecules (CERM), CESAM-UR, University of Liège, B-4000 Liège, Belgium
| | - Baya Gueza
- Univ Angers, Université de Nantes, Inserm, CRCINA, SFR ICAT, F-49000 Angers, France
| | - Carmen Alvarez-Lorenzo
- Departamento de Farmacología, Farmacia y Tecnología Farmacéutica, I+D Farma (GI-1645), Facultad de Farmacia, and Health Research Institute of Santiago de Compostela (IDIS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Emmanuel Garcion
- Univ Angers, Université de Nantes, Inserm, CRCINA, SFR ICAT, F-49000 Angers, France
| | - Christine Jérôme
- Center for Education and Research on Macromolecules (CERM), CESAM-UR, University of Liège, B-4000 Liège, Belgium
| | - Frank Boury
- Univ Angers, Université de Nantes, Inserm, CRCINA, SFR ICAT, F-49000 Angers, France.
| |
Collapse
|
9
|
Carlsen A, Tabard-Cossa V. Mapping shifts in nanopore signal to changes in protein and protein-DNA conformation. Proteomics 2021; 22:e2100068. [PMID: 34845853 DOI: 10.1002/pmic.202100068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/28/2021] [Accepted: 11/12/2021] [Indexed: 11/08/2022]
Abstract
Solid-state nanopores have been used extensively in biomolecular studies involving DNA and proteins. However, the interpretation of signals generated by the translocation of proteins or protein-DNA complexes remains challenging. Here, we investigate the behavior of monovalent streptavidin and the complex it forms with short biotinylated DNA over a range of nanopore sizes, salts, and voltages. We describe a simple geometric model that is broadly applicable and employ it to explain observed variations in conductance blockage and dwell time with experimental conditions. The general approach developed here underscores the value of nanopore-based protein analysis and represents progress toward the interpretation of complex translocation signals.
Collapse
Affiliation(s)
- Autumn Carlsen
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada
| | | |
Collapse
|
10
|
Zhu Y, Wang J, Vanga SK, Raghavan V. Visualizing structural changes of egg avidin to thermal and electric field stresses by molecular dynamics simulation. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.112139] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
11
|
Zamponi M, Petrella R, Mollica PA. Picosecond Pulsed Electric Fields and Promise in Neurodegeneration Research. Bioelectricity 2021. [DOI: 10.1089/bioe.2021.0005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Martina Zamponi
- School of Medical Diagnostic and Translational Sciences, Old Dominion University, Norfolk, Virginia, USA
- Biomedical Engineering Institute, Old Dominion University, Norfolk, Virginia, USA
| | - Ross Petrella
- Joint Department of Biomedical Engineering at the University of North Carolina and North Carolina State University, Raleigh, North Carolina, USA
| | - Peter A. Mollica
- School of Medical Diagnostic and Translational Sciences, Old Dominion University, Norfolk, Virginia, USA
- Molecular Diagnostics Laboratory, Sentara Norfolk General Hospital, Norfolk, Virginia, USA
| |
Collapse
|
12
|
Rodella C, Cespón J, Repetto C, Pellicciari MC. Customized Application of tDCS for Clinical Rehabilitation in Alzheimer's Disease. Front Hum Neurosci 2021; 15:687968. [PMID: 34393740 PMCID: PMC8358653 DOI: 10.3389/fnhum.2021.687968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/30/2021] [Indexed: 11/16/2022] Open
Affiliation(s)
- Claudia Rodella
- Department of Psychology, Catholic University of Sacred Heart, Milan, Italy
| | - Jesús Cespón
- Basque Center on Cognition, Brain and Language, San Sebastian, Spain
| | - Claudia Repetto
- Department of Psychology, Catholic University of Sacred Heart, Milan, Italy
| | | |
Collapse
|
13
|
Brouzet C, Mittal N, Rosén T, Takeda Y, Söderberg LD, Lundell F, Takana H. Effect of Electric Field on the Hydrodynamic Assembly of Polydisperse and Entangled Fibrillar Suspensions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:8339-8347. [PMID: 34176263 DOI: 10.1021/acs.langmuir.1c01196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Dynamics of colloidal particles can be controlled by the application of electric fields at micrometer-nanometer length scales. Here, an electric field-coupled microfluidic flow-focusing device is designed for investigating the effect of an externally applied alternating current (AC) electric field on the hydrodynamic assembly of cellulose nanofibrils (CNFs). We first discuss how the nanofibrils align parallel to the direction of the applied field without flow. Then, we apply an electric field during hydrodynamic assembly in the microfluidic channel and observe the effects on the mechanical properties of the assembled nanostructures. We further discuss the nanoscale orientational dynamics of the polydisperse and entangled fibrillar suspension of CNFs in the channel. It is shown that electric fields induced with the electrodes locally increase the degree of orientation. However, hydrodynamic alignment is demonstrated to be much more efficient than the electric field for aligning CNFs. The results are useful for understanding the development of the nanostructure when designing high-performance materials with microfluidics in the presence of external stimuli.
Collapse
Affiliation(s)
- Christophe Brouzet
- Wallenberg Wood Science Center and Linné FLOW Centre, KTH Royal Institute of Technology, Stockholm SE-100 44, Sweden
| | - Nitesh Mittal
- Wallenberg Wood Science Center and Linné FLOW Centre, KTH Royal Institute of Technology, Stockholm SE-100 44, Sweden
| | - Tomas Rosén
- Wallenberg Wood Science Center and Linné FLOW Centre, KTH Royal Institute of Technology, Stockholm SE-100 44, Sweden
| | - Yusuke Takeda
- Institute of Fluid Science, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - L Daniel Söderberg
- Wallenberg Wood Science Center and Linné FLOW Centre, KTH Royal Institute of Technology, Stockholm SE-100 44, Sweden
| | - Fredrik Lundell
- Wallenberg Wood Science Center and Linné FLOW Centre, KTH Royal Institute of Technology, Stockholm SE-100 44, Sweden
| | - Hidemasa Takana
- Institute of Fluid Science, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| |
Collapse
|
14
|
Průša J, Ayoub AT, Chafai DE, Havelka D, Cifra M. Electro-opening of a microtubule lattice in silico. Comput Struct Biotechnol J 2021; 19:1488-1496. [PMID: 33815687 PMCID: PMC7985272 DOI: 10.1016/j.csbj.2021.02.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/10/2021] [Accepted: 02/12/2021] [Indexed: 11/28/2022] Open
Abstract
Modulation of the structure and function of biomaterials is essential for advancing bio-nanotechnology and biomedicine. Microtubules (MTs) are self-assembled protein polymers that are essential for fundamental cellular processes and key model compounds for the design of active bio-nanomaterials. In this in silico study, a 0.5 μs-long all-atom molecular dynamics simulation of a complete MT with approximately 1.2 million atoms in the system indicated that a nanosecond-scale intense electric field can induce the longitudinal opening of the cylindrical shell of the MT lattice, modifying the structure of the MT. This effect is field-strength- and temperature-dependent and occurs on the cathode side. A model was formulated to explain the opening on the cathode side, which resulted from an electric-field-induced imbalance between electric torque on tubulin dipoles and cohesive forces between tubulin heterodimers. Our results open new avenues for electromagnetic modulation of biological and artificial materials through action on noncovalent molecular interactions.
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
|
15
|
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
|
16
|
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: 377] [Impact Index Per Article: 125.7] [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.
Collapse
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
| |
Collapse
|
17
|
Song X, Bu Y. Electric field controlled uphill electron migration along α-helical oligopeptides. Phys Chem Chem Phys 2021; 23:1464-1474. [PMID: 33399139 DOI: 10.1039/d0cp05085g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A systematic study on applied electric field effects (Eapp) on electron transfer along the peptides is very important for the regulation of electron transfer behaviors so as to realize the functions of proteins. In this work, we computationally investigated the uphill migration behaviors of excess electrons along the peptide chains under Eapp using the density functional theory method. We examined the electronic property changes of the model α-helical oligopeptides, the dynamics behavior of an excess electron along the peptide chains under Eapp opposite to the internal dipole field of peptides. We found that Eapp of different intensities can effectively modulate the electron-binding abilities, Frontier molecular orbital (FMO) energies and distributions, dipole moments and other corresponding properties with different degrees. The electron-binding abilities of α-helical oligopeptides revealed by vertical electron affinity and FMO energies decrease in weak Eapp and then increase greatly in high Eapp, while the dipole moments change mildly in weak Eapp and increase significantly until a threshold and then become gentle in high Eapp. Analysis of FMO and electron distributions indicates that an excess electron can migrate uphill from the N-terminus to the C-terminus of the α-helical peptides in an irregular jump mode as Eapp linearly increases. Another interesting finding is that α-helical peptides with diverse chain lengths have different sensitivities to Eapp. The longer the peptide is, the more obvious the effects of Eapp are. Additionally, compared to the Eapp effect on linear oligopeptides, we summarized the systematic rule about the Eapp effect on excess electron migration uphill along the peptide chains. Clearly, this work not only enriches the information of the Eapp effect on electronic properties and electron transfers in the helical peptides, but also provides a new perspective for modulating electron migration behaviors in protein electronics engineering.
Collapse
Affiliation(s)
- Xiufang Song
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China.
| | - Yuxiang Bu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China.
| |
Collapse
|
18
|
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
|
19
|
Rodrigues RM, Avelar Z, Machado L, Pereira RN, Vicente AA. Electric field effects on proteins - Novel perspectives on food and potential health implications. Food Res Int 2020; 137:109709. [PMID: 33233283 DOI: 10.1016/j.foodres.2020.109709] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/22/2020] [Accepted: 09/06/2020] [Indexed: 12/29/2022]
Abstract
Electric fields (EF) technologies have been establishing a solid position in emergent food processing and have seen as serious alternatives to traditional thermal processing. During the last decades, research has been devoted to elucidation of technological and safety issues but also fundamental aspects related with interaction of electric fields (EF) with important macromolecules, such as proteins. Proteins are building blocks for the development of functional networks that can encompass health benefits (i.e. nutritional and bioactive properties) but may be also linked with adverse effects such as neurodegenerative diseases (amyloid fibrils) and immunological responses. The biological function of a protein depends on its tridimensional structure/conformation, and latest research evidences that EF can promote disturbances on protein conformation, change their unfolding mechanisms, aggregation and interaction patterns. This review aims at bringing together these recent findings as well as providing novel perspectives about how EF can shape the behavior of proteins towards the development of innovative foods, aiming at consumers' health and wellbeing.
Collapse
Affiliation(s)
- Rui M Rodrigues
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Zita Avelar
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Luís Machado
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Ricardo N Pereira
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.
| | - António A Vicente
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| |
Collapse
|
20
|
Singh A, Khatun S, Nath Gupta A. Simultaneous Detection of Tyrosine and Structure‐Specific Intrinsic Fluorescence in the Fibrillation of Alzheimer's Associated Peptides. Chemphyschem 2020; 21:2585-2598. [DOI: 10.1002/cphc.202000587] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/17/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Anurag Singh
- Biophysics and Soft Matter Laboratory Department of Physics Indian Institute of Technology Kharagpur 721302 India
| | - Suparna Khatun
- Biophysics and Soft Matter Laboratory Department of Physics Indian Institute of Technology Kharagpur 721302 India
| | - Amar Nath Gupta
- Biophysics and Soft Matter Laboratory Department of Physics Indian Institute of Technology Kharagpur 721302 India
| |
Collapse
|
21
|
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
|
22
|
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
|
23
|
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: 11] [Impact Index Per Article: 2.2] [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
|
24
|
Zhang J, Tang T, Jiang Z, Liu Y, Jiang A. The modification of ovalbumin surface properties treated by pulsed electric field combined with divalent metal ions. Food Chem 2019; 293:455-462. [DOI: 10.1016/j.foodchem.2019.05.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 04/15/2019] [Accepted: 05/02/2019] [Indexed: 11/25/2022]
|
25
|
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
|
26
|
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
|
27
|
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
|
28
|
Pandey G, Morla S, Nemade HB, Kumar S, Ramakrishnan V. Modulation of aggregation with an electric field; scientific roadmap for a potential non-invasive therapy against tauopathies. RSC Adv 2019; 9:4744-4750. [PMID: 35514655 PMCID: PMC9060620 DOI: 10.1039/c8ra09993f] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 01/22/2019] [Indexed: 11/21/2022] Open
Abstract
Toxic aggregation of tau protein to neurofibrillary tangles (NFTS) is a central pathological event involved in tauopathies. Inhibition of tau protein aggregation can serve as a straightforward therapeutic strategy. However, tau-based therapeutic solutions are not very common. Phenothiazine methylene blue (tau protein inhibitor) is currently the only drug under phase III clinical trials. In this work, a non-invasive strategy is presented for modulating the aggregation of core peptide segments of tau protein (VQIVYK and VQIINK) by using electric fields of varying strengths. We use thioflavin T staining, tyrosine fluorescence assay, electron microscopy, IR, dynamic and static light scattering, and neuronal toxicity estimation, for verifying the effect of electric field on the aggregation kinetics, morphology, conformational state and cellular toxicity of peptide systems. Our observations suggest that electric field arrests the self-assembly of VQIVYK and VQIINK fibrils thereby reducing the neurotoxicity instigated by them. Based on our observations, we propose a prospective scheme for a futuristic non-invasive therapeutic device.
Collapse
Affiliation(s)
- Gaurav Pandey
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati Guwahati-781039 India +91 361 258 2249 +91 361 258 2227
| | - Sudhir Morla
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati Guwahati-781039 India +91 361 258 2249 +91 361 258 2227
| | - Harshal B Nemade
- Department of Electronics and Electrical Engineering, Indian Institute of Technology Guwahati Guwahati-781039 India
| | - Sachin Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati Guwahati-781039 India +91 361 258 2249 +91 361 258 2227
| | - Vibin Ramakrishnan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati Guwahati-781039 India +91 361 258 2249 +91 361 258 2227
| |
Collapse
|
29
|
Prozorov T, Almeida TP, Kovács A, Dunin-Borkowski RE. Off-axis electron holography of bacterial cells and magnetic nanoparticles in liquid. J R Soc Interface 2018; 14:rsif.2017.0464. [PMID: 29021160 DOI: 10.1098/rsif.2017.0464] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 09/18/2017] [Indexed: 12/19/2022] Open
Abstract
The mapping of electrostatic potentials and magnetic fields in liquids using electron holography has been considered to be unrealistic. Here, we show that hydrated cells of Magnetospirillum magneticum strain AMB-1 and assemblies of magnetic nanoparticles can be studied using off-axis electron holography in a fluid cell specimen holder within the transmission electron microscope. Considering that the holographic object and reference wave both pass through liquid, the recorded electron holograms show sufficient interference fringe contrast to permit reconstruction of the phase shift of the electron wave and mapping of the magnetic induction from bacterial magnetite nanocrystals. We assess the challenges of performing in situ magnetization reversal experiments using a fluid cell specimen holder, discuss approaches for improving spatial resolution and specimen stability, and outline future perspectives for studying scientific phenomena, ranging from interparticle interactions in liquids and electrical double layers at solid-liquid interfaces to biomineralization and the mapping of electrostatic potentials associated with protein aggregation and folding.
Collapse
Affiliation(s)
- Tanya Prozorov
- Division of Materials Sciences and Engineering, Ames Laboratory, Ames, IA 50011, USA
| | - Trevor P Almeida
- Department of Earth Science and Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - András Kovács
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Grünberg Institute, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Rafal E Dunin-Borkowski
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons and Peter Grünberg Institute, Forschungszentrum Jülich, 52425 Jülich, Germany
| |
Collapse
|
30
|
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
|
31
|
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]
|
32
|
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
|
33
|
Marracino P, Liberti M, Vernier PT, Apollonio F. A statistical analytical model for hydrophilic electropore characterization: a comparison study. RSC Adv 2017. [DOI: 10.1039/c7ra03812g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A new procedure for lipid pore characterization, which extracts the pore geometry from a statistical analysis of the tridimensional surface of the pore, is compared with other methods in the literature.
Collapse
Affiliation(s)
- P. Marracino
- Department of Information Engineering, Electronics, and Telecommunications
- Sapienza University of Rome
- Rome
- Italy
| | - M. Liberti
- Department of Information Engineering, Electronics, and Telecommunications
- Sapienza University of Rome
- Rome
- Italy
| | - P. T. Vernier
- Frank Reidy Research Center for Bioelectrics
- Old Dominion University
- Norfolk
- USA
| | - F. Apollonio
- Department of Information Engineering, Electronics, and Telecommunications
- Sapienza University of Rome
- Rome
- Italy
| |
Collapse
|
34
|
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
|
35
|
Evidence-based guidelines on the therapeutic use of transcranial direct current stimulation (tDCS). Clin Neurophysiol 2016; 128:56-92. [PMID: 27866120 DOI: 10.1016/j.clinph.2016.10.087] [Citation(s) in RCA: 1009] [Impact Index Per Article: 126.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 10/18/2016] [Accepted: 10/20/2016] [Indexed: 12/19/2022]
Abstract
A group of European experts was commissioned by the European Chapter of the International Federation of Clinical Neurophysiology to gather knowledge about the state of the art of the therapeutic use of transcranial direct current stimulation (tDCS) from studies published up until September 2016, regarding pain, Parkinson's disease, other movement disorders, motor stroke, poststroke aphasia, multiple sclerosis, epilepsy, consciousness disorders, Alzheimer's disease, tinnitus, depression, schizophrenia, and craving/addiction. The evidence-based analysis included only studies based on repeated tDCS sessions with sham tDCS control procedure; 25 patients or more having received active treatment was required for Class I, while a lower number of 10-24 patients was accepted for Class II studies. Current evidence does not allow making any recommendation of Level A (definite efficacy) for any indication. Level B recommendation (probable efficacy) is proposed for: (i) anodal tDCS of the left primary motor cortex (M1) (with right orbitofrontal cathode) in fibromyalgia; (ii) anodal tDCS of the left dorsolateral prefrontal cortex (DLPFC) (with right orbitofrontal cathode) in major depressive episode without drug resistance; (iii) anodal tDCS of the right DLPFC (with left DLPFC cathode) in addiction/craving. Level C recommendation (possible efficacy) is proposed for anodal tDCS of the left M1 (or contralateral to pain side, with right orbitofrontal cathode) in chronic lower limb neuropathic pain secondary to spinal cord lesion. Conversely, Level B recommendation (probable inefficacy) is conferred on the absence of clinical effects of: (i) anodal tDCS of the left temporal cortex (with right orbitofrontal cathode) in tinnitus; (ii) anodal tDCS of the left DLPFC (with right orbitofrontal cathode) in drug-resistant major depressive episode. It remains to be clarified whether the probable or possible therapeutic effects of tDCS are clinically meaningful and how to optimally perform tDCS in a therapeutic setting. In addition, the easy management and low cost of tDCS devices allow at home use by the patient, but this might raise ethical and legal concerns with regard to potential misuse or overuse. We must be careful to avoid inappropriate applications of this technique by ensuring rigorous training of the professionals and education of the patients.
Collapse
|
36
|
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
|
37
|
Calabrò E, Magazù S. Parallel β-sheet vibration band increases with proteins dipole moment under exposure to 1765 MHz microwaves. Bioelectromagnetics 2016; 37:99-107. [DOI: 10.1002/bem.21956] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Accepted: 01/13/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Emanuele Calabrò
- Department of Physics and Earth Sciences; University of Messina; Messina Italy
| | - Salvatore Magazù
- Department of Physics and Earth Sciences; University of Messina; Messina Italy
| |
Collapse
|
38
|
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: 142] [Impact Index Per Article: 17.8] [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
|
39
|
Lugli F, Toschi F, Biscarini F, Zerbetto F. Electric Field Effects on Short Fibrils of Aβ Amyloid Peptides. J Chem Theory Comput 2015; 6:3516-26. [PMID: 26617101 DOI: 10.1021/ct1001335] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amyloid fibrils are highly ordered protein aggregates, which are associated with many neurodegenerative diseases. The assembling dynamics of monomeric beta-amyloid peptides, Aβ, into small aggregates (and then into long fibrils) is still debated and has become a hot topic. In this study, we conducted molecular dynamics simulations in explicit water of small Aβ protofibrils (from monomer to pentamer) under the perturbation of an externally applied electric field with the aim of investigating the fundamental molecular interactions involved in the aggregation mechanism. Dynamics of small adducts of Aβ(16-42) in the presence of an electric field, which was shown before to accelerate the conformational change of a single molecule, indicate that the structural resilience increases with the number of molecules in the aggregate. In particular, for 50 ns, the pentamer shows an enhanced stability in secondary structure, number of hydrogen bonds, and number of salt bridges, even in the presence of the field perturbation. The resilience to the field perturbation is linked to the variation of the induced dipole moment of the aggregates that tends to level off very rapidly with the growing number of molecules, thereby reducing the energy available per molecule to produce structural changes. The results also show that in the presence of the field the stability of the hydrophobic second β-sheet (β2, residues 31-42) is higher than that of the first one (β1, residues 18-26). In particular, we identify Gly33, Gly37, and Met35 as the most important residues that stabilize the intermolecular packing and may act as nucleation sites for fibrillization. Furthermore, dynamics of the full-length Aβ(1-42) pentameric aggregate, which include the highly charged random coil residues 1-15, confirmed the key role of the second hydrophobic core in the protofibril structure.
Collapse
Affiliation(s)
- Francesca Lugli
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via F. Selmi 2, 40126 Bologna, Italy and ISMN CNR, V. Gobetti, Bologna, Italy
| | - Francesca Toschi
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via F. Selmi 2, 40126 Bologna, Italy and ISMN CNR, V. Gobetti, Bologna, Italy
| | - Fabio Biscarini
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via F. Selmi 2, 40126 Bologna, Italy and ISMN CNR, V. Gobetti, Bologna, Italy
| | - Francesco Zerbetto
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, via F. Selmi 2, 40126 Bologna, Italy and ISMN CNR, V. Gobetti, Bologna, Italy
| |
Collapse
|
40
|
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
|
41
|
Abstract
Folding and aggregation lie on competing reaction pathways in proteins. Altering the occupancy of one pathway is automatically relayed to the other pathway, leading to a shift in the balance between the two processes. In particular, it is known that the stabilization of the native state through mutations or solvent alterations is able to halt aggregation. In this work, we explore the feasibility of using external electric field as an agent preventing aggregation through the promotion of folding. We use an atomically accurate protein model and computer simulations to investigate folding and aggregation of alanine polypeptides in electric field of varying strength. The studied peptides are mostly unstructured in the absence of the field but experience a transition into α-helical states when the field is applied. The transition is accompanied by the disassembly of preseeded stacked β-sheets, which are used as a model of amyloid fibrils, suggesting that electric field can be employed to control aggregation propensity of intrinsically disordered peptides. According to our calculations, the strength of the field required for the disaggregation could be suitable for both controlled in vitro experiments as well as for experiments on live cells. Additionally, our estimates suggest that endogenous electric fields may have a significant effect on in vivo amyloid formation.
Collapse
Affiliation(s)
- Andrij Baumketner
- Institute for Condensed Matter Physics, National Academy of Sciences of Ukraine , 1 Svientsistsky Str, Lviv 79011, Ukraine
| |
Collapse
|
42
|
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
|
43
|
Wang H, Schütte C, Ciccotti G, Delle Site L. Exploring the Conformational Dynamics of Alanine Dipeptide in Solution Subjected to an External Electric Field: A Nonequilibrium Molecular Dynamics Simulation. J Chem Theory Comput 2014; 10:1376-86. [DOI: 10.1021/ct400993e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Han Wang
- Institute
for Mathematics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Christof Schütte
- Institute
for Mathematics, Freie Universität Berlin, 14195 Berlin, Germany
- Zuse Institute Berlin, 14195 Berlin, Germany
| | - Giovanni Ciccotti
- School
of Physics, University College Dublin, Belfield, Dublin 4, Ireland
- Dipartimento
di Fisica, Università “La Sapienza” and CNISM, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Luigi Delle Site
- Institute
for Mathematics, Freie Universität Berlin, 14195 Berlin, Germany
| |
Collapse
|
44
|
Artsruni GG, Sahakyan GV, Poghosyan GA. The in vitro influence of the external electrostatic field on the physical parameters of erythrocyte membranes. Biophysics (Nagoya-shi) 2014. [DOI: 10.1134/s0006350913060031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
45
|
Bekard I, Dunstan DE. Electric field induced changes in protein conformation. SOFT MATTER 2014; 10:431-7. [PMID: 24652412 DOI: 10.1039/c3sm52653d] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The effect of a low strength oscillating electric field on the conformation of Bovine Serum Albumin (BSA) and Lysozyme in solution has been measured. A purpose built cell has been used to measure the real time autofluorescence and Circular Dichroism of the protein solutions exposed to electric fields of differing strength and frequency. Exposure to the electric fields results in protein unfolding for both Lysozyme and BSA. The applied field strengths are extremely small compared to the protein inter-chain intra-molecular forces. We propose a model whereby the electrophoretic motion of the proteins leads to a frictional force that results in protein unfolding. For BSA and Lysozyme in the electric fields used in this study, the shear rates at the protein surface under electrophoretic motion are of order 10(3) and 10(4) s(-1) respectively. Prolonged electric field exposure results in significant frictional energy dissipation in the proteins. The energy dissipated in the proteins results in protein unfolding, which is a critical initial step for protein aggregation and potentially amyloid fibril formation.
Collapse
Affiliation(s)
- Innocent Bekard
- CSL Behring, 189-209 Camp Road, Broadmeadows, Victoria, 3047, Australia
| | | |
Collapse
|
46
|
Benavidez TE, Garcia CD. Potential-assisted adsorption of bovine serum albumin onto optically transparent carbon electrodes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:14154-14162. [PMID: 24156567 PMCID: PMC3867293 DOI: 10.1021/la4029657] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
This article describes the effect of the applied potential on the adsorption of bovine serum albumin (BSA) to optically transparent carbon electrodes (OTCE). To decouple the effect of the applied potential from the high affinity of the protein for the bare surface, the surface of the OTCE was initially saturated with a layer of BSA. Experiments described in the article show that potential values higher than +500 mV induced a secondary adsorption process (not observed at open-circuit potential), yielding significant changes in the thickness (and adsorbed amount) of the BSA layer obtained. Although the process showed a significant dependence on the experimental conditions selected, the application of higher potentials, selection of pH values around the isoelectric point (IEP) of the protein, high concentrations of protein, and low ionic strengths yielded faster kinetics and the accumulation of larger amounts of protein on the substrate. These experiments, obtained around the IEP of the protein, contrast with the traditional hypothesis that enhanced electrostatic interactions between the polarized substrate and the (oppositely charged) protein are solely responsible for the enhanced adsorption. These results suggest that the potential applied to the electrode is able to polarize the adsorbed layer and induce dipole-dipole interactions between the adsorbed and the incoming protein. This mechanism could be responsible for the potential-dependent oversaturation of the surface and could bolster to the development of surfaces with enhanced catalytic activity and implants with improved biocompatibility.
Collapse
Affiliation(s)
| | - Carlos D. Garcia
- To whom correspondence should be addressed. One UTSA Circle, San Antonio, TX 78249, USA. Ph: (210) 458-5774, Fax: (210) 458-7428,
| |
Collapse
|
47
|
Effects of external electric fields on lysozyme adsorption by molecular dynamics simulations. Biophys Chem 2013; 179:26-34. [DOI: 10.1016/j.bpc.2013.05.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 04/28/2013] [Accepted: 05/01/2013] [Indexed: 11/23/2022]
|
48
|
|
49
|
Abstract
A possible therapeutic strategy for amyloid diseases involves the use of small molecule compounds to inhibit protein assembly into insoluble aggregates. According to the recently proposed Crystallization-Like Model, the kinetics of amyloid fibrillization can be retarded by decreasing the frequency of new fibril formation or by decreasing the elongation rate of existing fibrils. To the compounds that affect the nucleation and/or the growth steps we call true inhibitors. An apparent inhibition mechanism may however result from the alteration of thermodynamic properties such as the solubility of the amyloidogenic protein. Apparent inhibitors markedly influence protein aggregation kinetics measured in vitro, yet they are likely to lead to disappointing results when tested in vivo. This is because cells and tissues media are in general much more buffered against small variations in composition than the solutions prepared in lab. Here we show how to discriminate between true and apparent inhibition mechanisms from experimental data on protein aggregation kinetics. The goal is to be able to identify false positives much earlier during the drug development process.
Collapse
Affiliation(s)
- Pedro M Martins
- ICBAS, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal.
| |
Collapse
|
50
|
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
|