Numerical simulation of physicochemical interactions between oxygen atom and phosphatidylcholine due to direct irradiation of atmospheric pressure nonequilibrium plasma to biological membrane with quantum mechanical molecular dynamics

Uchida, Satoshi; Yoshida, Taketo; Tochikubo, Fumiyoshi

doi:10.1088/1361-6463/aa84ee

Cited by 5 publications

(3 citation statements)

References 35 publications

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“…In general, the interaction of ROS with the above mentioned model systems always leads to the breaking and formation of some bonds, eventually resulting in the modification of these systems, as revealed by the simulations. In, quantum mechanical MD simulations were applied to investigate the interaction of oxygen atoms with phosphatidylcholine, that is, a single cell membrane lipid. Furthermore, combined DFTB and non‐reactive MD simulations were used to study the ROS oxidation of the head groups and lipid tails in the cell membrane .…”

Section: Introductionmentioning

confidence: 99%

Impact of plasma oxidation on structural features of human epidermal growth factor

Yusupov

Lackmann

Razzokov

et al. 2018

Plasma Processes & Polymers

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We perform computer simulations supported by experiments to investigate the oxidation of an important signaling protein, that is, human epidermal growth factor (hEGF), caused by cold atmospheric plasma (CAP) treatment. Specifically, we study the conformational changes of hEGF with different degrees of oxidation, to mimic short and long CAP treatment times. Our results indicate that the oxidized structures become more flexible, due to their conformational changes and breakage of the disulfide bonds, especially at higher oxidation degrees. MM/GBSA calculations reveal that an increasing oxidation level leads to a lower binding free energy of hEGF with its receptor. These results help to understand the fundamentals of the use of CAP for wound healing versus cancer treatment at short and longer treatment times.

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Section: Introductionmentioning

confidence: 99%

Impact of plasma oxidation on structural features of human epidermal growth factor

Yusupov

Lackmann

Razzokov

et al. 2018

Plasma Processes & Polymers

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“…The mechanisms of physicochemical interactions between the O-atoms and the solid surface were also elaborated by Uchida et al [27]. Unlike Longo et al [24], Uchida took into account also the various kinetic energies of impinging O-atoms.…”

Section: Introductionmentioning

confidence: 99%

Generation of Neutral Chemically Reactive Species in Low-Pressure Plasma

Primc

2022

Front. Phys.

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The surface finish of organic and inorganic materials treated by gaseous plasma usually depends on the fluxes and fluencies of chemically reactive species such as molecular radicals. In low-pressure plasmas, the dissociation of molecules to parent atoms depends on the production rate in the gas phase and on the loss rate on surfaces. The processing will be efficient if the loss rate is minimized. The methods for minimizing the loss rate and thus increasing the processing efficiency are presented and discussed. The dissociation fraction of simple molecules exceeds 10% providing the plasma-facing materials are smooth with a low coefficient for heterogeneous surface recombination. The density of atoms in a plasma reactor increases with increasing pressure reaching a maximum and decreases with further pressure increase, which is explained by two competing processes. The energy efficiency also exhibits a maximum, which may be as high as 30% if plasma is sustained by electrodeless high-frequency discharges. Optimization of energy efficiency is not only beneficial for the costs of material processing but also for the prevention of excessive heating of treated materials. The latter is particularly important for organic materials because the surface functional groups are not stable but decay with increasing surface temperature.

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“…To understand the precise cell functions underlying such effects, systematic biological-reaction models suitable for CAP studies are necessary. To date, various numerical models have been developed to study CAP-induced RONS agents and their multiphase interactions 19 in the gas phase 20–23 , in the liquid phase 24,25 , at the gas–liquid interface 26,27 and with biological targets from macroscopic 28–30 and microscopic viewpoints 31,32 . Despite great progress being made in modelling studies, they have not been applied to intracellular biochemical processes.…”

Section: Introductionmentioning

confidence: 99%

Numerical modelling of the effects of cold atmospheric plasma on mitochondrial redox homeostasis and energy metabolism

Murakami

2019

Sci Rep

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A biochemical reaction model clarifies for the first time how cold atmospheric plasmas (CAPs) affect mitochondrial redox homeostasis and energy metabolism. Fundamental mitochondrial functions in pyruvic acid oxidation, the tricarboxylic acid (TCA) cycle and oxidative phosphorylation involving the respiratory chain (RC), adenosine triphosphate/adenosine diphosphate (ATP/ADP) synthesis machinery and reactive oxygen species/reactive nitrogen species (ROS/RNS)-mediated mechanisms are numerically simulated. The effects of CAP irradiation are modelled as 1) the influx of hydrogen peroxide (HO) to an ROS regulation system and 2) the change in mitochondrial transmembrane potential induced by RNS on membrane permeability. The CAP-induced stress modifies the dynamics of intramitochondrial HO and superoxide anions, i.e., the rhythm and shape of ROS oscillation are disturbed by HO infusion. Furthermore, CAPs control the ROS oscillatory behaviour, nicotinamide adenine dinucleotide redox state and ATP/ADP conversion through the reaction mixture over the RC, the TCA cycle and ROS regulation system. CAPs even induce a homeostatic or irreversible state transition in cell metabolism. The present computational model demonstrates that CAPs crucially affect essential mitochondrial functions, which in turn affect redox signalling, metabolic cooporation and cell fate decision of survival or death.

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Numerical simulation of physicochemical interactions between oxygen atom and phosphatidylcholine due to direct irradiation of atmospheric pressure nonequilibrium plasma to biological membrane with quantum mechanical molecular dynamics

Cited by 5 publications

References 35 publications

Impact of plasma oxidation on structural features of human epidermal growth factor

Impact of plasma oxidation on structural features of human epidermal growth factor

Generation of Neutral Chemically Reactive Species in Low-Pressure Plasma

Numerical modelling of the effects of cold atmospheric plasma on mitochondrial redox homeostasis and energy metabolism

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