Cellular Processes Involved in Jurkat Cells Exposed to Nanosecond Pulsed Electric Field

Recently, nanosecond pulsed electric field (nsPEF) has been considered as a new tool for tumor therapy, but its molecular mechanism of function remains to be fully elucidated. Here, we explored the cellular processes of Jurkat cells exposed to nanosecond pulsed electric field. Differentially expressed genes (DEGs) were acquired from the GEO2R, followed by analysis with a series of bioinformatics tools. Subsequently, 3D protein models of hub genes were modeled by Modeller 9.21 and Rosetta 3.9. Then, a 100 ns molecular dynamics simulation for each hub protein was performed with GROMACS 2018.2. Finally, three kinds of nsPEF voltages (0.01, 0.05, and 0.5 mV/mm) were used to simulate the molecular dynamics of hub proteins for 100 ns. A total of 1769 DEGs and eight hub genes were obtained. Molecular dynamic analysis, including root mean square deviation (RMSD), root mean square fluctuation (RMSF), and the Rg, demonstrated that the 3D structure of hub proteins was built, and the structural characteristics of hub proteins under different nsPEFs were acquired. In conclusion, we explored the effect of nsPEF on Jurkat cell signaling pathway from the perspective of molecular informatics, which will be helpful in understanding the complex effects of nsPEF on acute T-cell leukemia Jurkat cells.

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Molecular dynamics simulation of the nanosecond pulsed electric field effect on kinesin nanomotor

Scientific Reports ◽

10.1038/s41598-019-56052-3 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 2

Author(s):

Jiří Průša ◽

Michal Cifra

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Electric Field ◽

Molecular Motors ◽

Pulsed Electric Field ◽

Motor Domain ◽

Dynamics Simulation ◽

Electric Field Effect ◽

Kinesin Motor ◽

Nanosecond Pulsed Electric Field

AbstractKinesin 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.

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Effects of an Electric Field on the Conformational Transition of the Protein: Pulsed and Oscillating Electric Fields with Different Frequencies

Polymers ◽

10.3390/polym14010123 ◽

2021 ◽

Vol 14 (1) ◽

pp. 123

Author(s):

Qun Zhang ◽

Dongqing Shao ◽

Peng Xu ◽

Zhouting Jiang

Keyword(s):

Dipole Moment ◽

Secondary Structure ◽

Electric Field ◽

Root Mean Square ◽

Structure Analysis ◽

Electric Fields ◽

Conformational Changes ◽

Pulsed Electric Field ◽

Mean Square ◽

Secondary Structure Analysis

The effect of pulsed and oscillating electric fields with different frequencies on the conformational properties of all-α proteins was investigated by molecular dynamics simulations. The root mean square deviation, the root mean square fluctuation, the dipole moment distribution, and the secondary structure analysis were used to assess the protein samples’ structural characteristics. In the simulation, we found that the higher frequency of the electric field influences the rapid response to the secondary structural transitions. However, the conformational changes measured by RMSD are diminished by applying the electrical field with a higher frequency. During the dipole moment analysis, we found that the magnitude and frequency of the dipole moment was directly related to the strength and frequency of the external electric field. In terms of the type of electric fields, we found that the average values of RMSD and RMSF of whole molecular protein are larger when the protein is exposed in the pulsed electric field. Concerning the typical sample 1BBL, the secondary structure analysis showed that two alpha-helix segments both transit to turns or random coils almost simultaneously when it is exposed in a pulsed electric field. Meanwhile, two segments present the different characteristic times when the transition occurs in the condition of an oscillating electric field. This study also demonstrated that the protein with fewer charged residues or more residues in forming α-helical structures display the higher conformational stability. These conclusions, achieved using MD simulations, provide a theoretical understanding of the effect of the frequency and expression form of external electric fields on the conformational changes of the all-α proteins with charged residues and the guidance for anticipative applications.

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Excitation of murine cardiac myocytes by nanosecond pulsed electric field

Journal of Cardiovascular Electrophysiology ◽

10.1111/jce.13834 ◽

2019 ◽

Vol 30 (3) ◽

pp. 392-401 ◽

Cited By ~ 5

Author(s):

Jan E. Azarov ◽

Iurii Semenov ◽

Maura Casciola ◽

Andrei G. Pakhomov

Keyword(s):

Electric Field ◽

Cardiac Myocytes ◽

Pulsed Electric Field ◽

Nanosecond Pulsed Electric Field

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Effects of the Temperature and the pH on the Main Protease of SARS-CoV-2: A Molecular Dynamics Simulation Study

Biointerface Research in Applied Chemistry ◽

10.33263/briac126.72397248 ◽

2021 ◽

Vol 12 (6) ◽

pp. 7239-7248

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Root Mean Square ◽

Dynamics Simulation ◽

Effect Of Temperature ◽

Water Molecules ◽

Mean Square ◽

Main Protease ◽

Decreasing Ph ◽

Increasing Temperature

The novel coronavirus, recognized as COVID-19, is the cause of an infection outbreak in December 2019. The effect of temperature and pH changes on the main protease of SARS-CoV-2 were investigated using all-atom molecular dynamics simulation. The obtained results from the root mean square deviation (RMSD) and root mean square fluctuations (RMSF) analyses showed that at a constant temperature of 25℃ and pH=5, the conformational change of the main protease is more significant than that of pH=6 and 7. Also, by increasing temperature from 25℃ to 55℃ at constant pH=7, a remarkable change in protein structure was observed. The radial probability of water molecules around the main protease was decreased by increasing temperature and decreasing pH. The weakening of the binding energy between the main protease and water molecules due to the increasing temperature and decreasing pH has reduced the number of hydrogen bonds between the main protease and water molecules. Finding conditions that alter the conformation of the main protease could be fundamental because this change could affect the virus’s functionality and its ability to impose illness.

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Safety and Efficacy of Nanosecond Pulsed Electric Field Treatment of Sebaceous Gland Hyperplasia

Dermatologic Surgery ◽

10.1097/dss.0000000000002154 ◽

2020 ◽

Vol 46 (6) ◽

pp. 803-809 ◽

Cited By ~ 5

Author(s):

Girish S. Munavalli ◽

Brian D. Zelickson ◽

Mona M. Selim ◽

Suzanne L. Kilmer ◽

Thomas E. Rohrer ◽

...

Keyword(s):

Electric Field ◽

Sebaceous Gland ◽

Pulsed Electric Field ◽

Safety And Efficacy ◽

Nanosecond Pulsed Electric Field ◽

Pulsed Electric Field Treatment ◽

Electric Field Treatment

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Nanosecond Pulsed Electric Field Lab‐on‐Chip Integrated in Super‐Resolution Microscope for Cytoskeleton Imaging

Advanced Materials Technologies ◽

10.1002/admt.201900669 ◽

2019 ◽

Vol 5 (3) ◽

pp. 1900669 ◽

Cited By ~ 2

Author(s):

Daniel Havelka ◽

Djamel Eddine Chafai ◽

Ondrej Krivosudský ◽

Anastasiya Klebanovych ◽

František Vostárek ◽

...

Keyword(s):

Electric Field ◽

Super Resolution ◽

Pulsed Electric Field ◽

Lab On Chip ◽

Nanosecond Pulsed Electric Field ◽

On Chip

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Concepts and Capabilities of In-House Built Nanosecond Pulsed Electric Field (nsPEF) Generators for Electroporation: State of Art

Applied Sciences ◽

10.3390/app10124244 ◽

2020 ◽

Vol 10 (12) ◽

pp. 4244

Author(s):

Paulius Butkus ◽

Arūnas Murauskas ◽

Sonata Tolvaišienė ◽

Vitalij Novickij

Keyword(s):

Electric Field ◽

High Frequency ◽

Pulsed Electric Field ◽

Cell Permeabilization ◽

Pulse Generators ◽

Nanosecond Pulsed Electric Field ◽

Forming Characteristics ◽

State Of Art ◽

Frequency Pulse

Electroporation is a pulsed electric field triggered phenomenon of cell permeabilization, which is extensively used in biomedical and biotechnological context. There is a growing scientific demand for high-voltage and/or high-frequency pulse generators for electropermeabilization of cells (electroporators). In the scope of this article we have reviewed the basic topologies of nanosecond pulsed electric field (nsPEF) generators for electroporation and the parametric capabilities of various in-house built devices, which were introduced in the last two decades. Classification of more than 60 various nsPEF generators was performed and pulse forming characteristics (pulse shape, voltage, duration and repetition frequency) were listed and compared. Lastly, the trends in the development of the electroporation technology were discussed.

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