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Author Cordeiro, R.M.; Yusupov, M.; Razzokov, J.; Bogaerts, A.
Title Parametrization and Molecular Dynamics Simulations of Nitrogen Oxyanions and Oxyacids for Applications in Atmospheric and Biomolecular Sciences Type A1 Journal article
Year 2020 Publication Journal Of Physical Chemistry B Abbreviated Journal J Phys Chem B
Volume 124 Issue 6 Pages 1082-1089
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract (up) Nitrogen oxyanions and oxyacids are important agents in atmospheric chemistry and medical biology. Although their chemical behavior in solution is relatively well understood, they may behave very differently at the water/air interface of atmospheric aerosols or at the membrane/water interface of cells. Here, we developed a fully classical model for molecular dynamics simulations of NO3−, NO2−, HNO3, and HNO2 in the framework of the GROMOS 53A6 and 54A7 force field versions. The model successfully accounted for the poorly structured solvation shell and ion pairing tendency of NO3−. Accurate pure-liquid properties and hydration free energies were obtained for the oxyacids. Simulations at the water/air interface showed a local enrichment of HNO3 and depletion of NO3−. The effect was discussed in light of earlier spectroscopic data and ab initio calculations, suggesting that HNO3 behaves as a weaker acid at the surface of water. Our model will hopefully allow for efficient and accurate simulations of nitrogen oxyanions and oxyacids in solution and at microheterogeneous interface environments.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000512222500015 Publication Date 2020-02-13
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1520-6106 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 3.3 Times cited Open Access
Notes We thank Universidade Federal do ABC for providing the computational resources needed for completion of this work. This study was financed in part by the Coordenaçaõ de Aperfeiçoamento de Pessoal de Nı ́vel Superior – Brasil (CAPES) – Finance Code 001. Approved Most recent IF: 3.3; 2020 IF: 3.177
Call Number PLASMANT @ plasmant @c:irua:166488 Serial 6340
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Author Lin, A.; Razzokov, J.; Verswyvel, H.; Privat-Maldonado, A.; De Backer, J.; Yusupov, M.; Cardenas De La Hoz, E.; Ponsaerts, P.; Smits, E.; Bogaerts, A.
Title Oxidation of Innate Immune Checkpoint CD47 on Cancer Cells with Non-Thermal Plasma Type A1 Journal article
Year 2021 Publication Cancers Abbreviated Journal Cancers
Volume 13 Issue 3 Pages 579
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Laboratory for Experimental Hematology (LEH); Center for Oncological Research (CORE)
Abstract (up) Non-thermal plasma (NTP) therapy has been emerging as a promising cancer treatment strategy, and recently, its ability to locally induce immunogenic cancer cell death is being unraveled. We hypothesized that the chemical species produced by NTP reduce immunosuppressive surface proteins and checkpoints that are overexpressed on cancerous cells. Here, 3D in vitro tumor models, an in vivo mouse model, and molecular dynamics simulations are used to investigate the effect of NTP on CD47, a key innate immune checkpoint. CD47 is immediately modulated after NTP treatment and simulations reveal the potential oxidized salt-bridges responsible for conformational changes. Umbrella sampling simulations of CD47 with its receptor, signal-regulatory protein alpha (SIRPα), demonstrate that the induced-conformational changes reduce its binding affinity. Taken together, this work provides new insight into fundamental, chemical NTP-cancer cell interaction mechanisms and a previously overlooked advantage of present NTP cancer therapy: reducing immunosuppressive signals on the surface of cancer cells.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000614960600001 Publication Date 2021-02-02
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 2072-6694 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor Times cited Open Access OpenAccess
Notes We thank Erik Fransen (University of Antwerp; Antwerp, Belgium) for his help and guidance on the statistical analysis. Approved Most recent IF: NA
Call Number PLASMANT @ plasmant @c:irua:176455 Serial 6709
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Author Yusupov, M.; Bogaerts, A.; Huygh, S.; Snoeckx, R.; van Duin, A.C.T.; Neyts, E.C.
Title Plasma-induced destruction of bacterial cell wall components : a reactive molecular dynamics simulation Type A1 Journal article
Year 2013 Publication The journal of physical chemistry: C : nanomaterials and interfaces Abbreviated Journal J Phys Chem C
Volume 117 Issue 11 Pages 5993-5998
Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract (up) Nonthermal atmospheric pressure plasmas are gaining increasing attention for biomedical applications. However, very little fundamental information on the interaction mechanisms between the plasma species and biological cells is currently available. We investigate the interaction of important plasma species, such as OH, H2O2, O, O3, as well as O2 and H2O, with bacterial peptidoglycan by means of reactive molecular dynamics simulations, aiming for a better understanding of plasma disinfection. Our results show that OH, O, O3, and H2O2 can break structurally important bonds of peptidoglycan (i.e., CO, CN, or CC bonds), which consequently leads to the destruction of the bacterial cell wall. The mechanisms behind these breakups are, however, dependent on the impinging plasma species, and this also determines the effectiveness of the cell wall destruction.
Address
Corporate Author Thesis
Publisher Place of Publication Washington, D.C. Editor
Language Wos 000316773000056 Publication Date 2013-02-23
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1932-7447;1932-7455; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 4.536 Times cited 59 Open Access
Notes Approved Most recent IF: 4.536; 2013 IF: 4.835
Call Number UA @ lucian @ c:irua:107154 Serial 2636
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Author Bogaerts, A.; Yusupov, M.; Razzokov, J.; Van der Paal, J.
Title Plasma for cancer treatment: How can RONS penetrate through the cell membrane? Answers from computer modeling Type A1 Journal article
Year 2019 Publication Frontiers of Chemical Science and Engineering Abbreviated Journal Front Chem Sci Eng
Volume Issue Pages
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract (up) Plasma is gaining increasing interest for cancer

treatment, but the underlying mechanisms are not yet fully

understood. Using computer simulations at the molecular

level, we try to gain better insight in how plasma-generated

reactive oxygen and nitrogen species (RONS) can

penetrate through the cell membrane. Specifically, we

compare the permeability of various (hydrophilic and

hydrophobic) RONS across both oxidized and nonoxidized cell membranes. We also study pore formation,

and how it is hampered by higher concentrations of

cholesterol in the cell membrane, and we illustrate the

much higher permeability of H2O2 through aquaporin

channels. Both mechanisms may explain the selective

cytotoxic effect of plasma towards cancer cells. Finally, we

also discuss the synergistic effect of plasma-induced

oxidation and electric fields towards pore formation.

Keywords plasma medicine, cancer treatment, computer

modelling, cell membrane, reactive oxygen and nitrogen

species
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000468848400004 Publication Date 2019-03-22
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 2095-0179 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 1.712 Times cited 5 Open Access Not_Open_Access: Available from 23.05.2020
Notes We acknowledge financial support from the Research Foundation–Flanders (FWO; Grant Nos. 1200216N and 11U5416N). The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. We are also very thankful to R. Cordeiro for the very interesting discussions. Approved Most recent IF: 1.712
Call Number PLASMANT @ plasmant @UA @ admin @ c:irua:159977 Serial 5172
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Author Chai, Z.-N.; Wang, X.-C.; Yusupov, M.; Zhang, Y.-T.
Title Unveiling the interaction mechanisms of cold atmospheric plasma and amino acids by machine learning Type A1 Journal article
Year 2024 Publication Plasma processes and polymers Abbreviated Journal
Volume Issue Pages 1-26
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract (up) Plasma medicine has attracted tremendous interest in a variety of medical conditions, ranging from wound healing to antimicrobial applications, even in cancer treatment, through the interactions of cold atmospheric plasma (CAP) and various biological tissues directly or indirectly. The underlying mechanisms of CAP treatment are still poorly understood although the oxidative effects of CAP with amino acids, peptides, and proteins have been explored experimentally. In this study, machine learning (ML) technology is introduced to efficiently unveil the interaction mechanisms of amino acids and reactive oxygen species (ROS) in seconds based on the data obtained from the reactive molecular dynamics (MD) simulations, which are performed to probe the interaction of five types of amino acids with various ROS on the timescale of hundreds of picoseconds but with the huge computational load of several days. The oxidative reactions typically start with H-abstraction, and the details of the breaking and formation of chemical bonds are revealed; the modification types, such as nitrosylation, hydroxylation, and carbonylation, can be observed. The dose effects of ROS are also investigated by varying the number of ROS in the simulation box, indicating agreement with the experimental observation. To overcome the limits of timescales and the size of molecular systems in reactive MD simulations, a deep neural network (DNN) with five hidden layers is constructed according to the reaction data and employed to predict the type of oxidative modification and the probability of occurrence only in seconds as the dose of ROS varies. The well-trained DNN can effectively and accurately predict the oxidative processes and productions, which greatly improves the computational efficiency by almost ten orders of magnitude compared with the reactive MD simulation. This study shows the great potential of ML technology to efficiently unveil the underpinning mechanisms in plasma medicine based on the data from reactive MD simulations or experimental measurements. In this study, since reactive molecular dynamics simulation can currently only describe interactions between a few hundred atoms in a few hundred picoseconds, deep neural networks (DNN) are introduced to enhance the simulation results by predicting more data efficiently. image
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 001202061200001 Publication Date 2024-04-15
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1612-8850 ISBN Additional Links UA library record; WoS full record
Impact Factor 3.5 Times cited Open Access
Notes Approved Most recent IF: 3.5; 2024 IF: 2.846
Call Number UA @ admin @ c:irua:205512 Serial 9181
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Author Neyts, E.C.; Yusupov, M.; Verlackt, C.C.; Bogaerts, A.
Title Computer simulations of plasmabiomolecule and plasmatissue interactions for a better insight in plasma medicine Type A1 Journal article
Year 2014 Publication Journal of physics: D: applied physics Abbreviated Journal J Phys D Appl Phys
Volume 47 Issue 29 Pages 293001
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract (up) Plasma medicine is a rapidly evolving multidisciplinary field at the intersection of chemistry, biochemistry, physics, biology, medicine and bioengineering. It holds great potential in medical, health care, dentistry, surgical, food treatment and other applications. This multidisciplinary nature and variety of possible applications come along with an inherent and intrinsic complexity. Advancing plasma medicine to the stage that it becomes an everyday tool in its respective fields requires a fundamental understanding of the basic processes, which is lacking so far. However, some major advances have already been made through detailed experiments over the last 15 years. Complementary, computer simulations may provide insight that is difficultif not impossibleto obtain through experiments. In this review, we aim to provide an overview of the various simulations that have been carried out in the context of plasma medicine so far, or that are relevant for plasma medicine. We focus our attention mostly on atomistic simulations dealing with plasmabiomolecule interactions. We also provide a perspective and tentative list of opportunities for future modelling studies that are likely to further advance the field.
Address
Corporate Author Thesis
Publisher Place of Publication London Editor
Language Wos 000338860300001 Publication Date 2014-06-26
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0022-3727;1361-6463; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 2.588 Times cited 28 Open Access
Notes Approved Most recent IF: 2.588; 2014 IF: 2.721
Call Number UA @ lucian @ c:irua:117853 Serial 472
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Author Ghasemitarei, M.; Ghorbi, T.; Yusupov, M.; Zhang, Y.; Zhao, T.; Shali, P.; Bogaerts, A.
Title Effects of Nitro-Oxidative Stress on Biomolecules: Part 1—Non-Reactive Molecular Dynamics Simulations Type A1 Journal Article
Year 2023 Publication Biomolecules Abbreviated Journal Biomolecules
Volume 13 Issue 9 Pages 1371
Keywords A1 Journal Article; plasma medicine; reactive oxygen and; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ;
Abstract (up) Plasma medicine, or the biomedical application of cold atmospheric plasma (CAP), is an expanding field within plasma research. CAP has demonstrated remarkable versatility in diverse biological applications, including cancer treatment, wound healing, microorganism inactivation, and skin disease therapy. However, the precise mechanisms underlying the effects of CAP remain incompletely understood. The therapeutic effects of CAP are largely attributed to the generation of reactive oxygen and nitrogen species (RONS), which play a crucial role in the biological responses induced by CAP. Specifically, RONS produced during CAP treatment have the ability to chemically modify cell membranes and membrane proteins, causing nitro-oxidative stress, thereby leading to changes in membrane permeability and disruption of cellular processes. To gain atomic-level insights into these interactions, non-reactive molecular dynamics (MD) simulations have emerged as a valuable tool. These simulations facilitate the examination of larger-scale system dynamics, including protein-protein and protein-membrane interactions. In this comprehensive review, we focus on the applications of non-reactive MD simulations in studying the effects of CAP on cellular components and interactions at the atomic level, providing a detailed overview of the potential of CAP in medicine. We also review the results of other MD studies that are not related to plasma medicine but explore the effects of nitro-oxidative stress on cellular components and are therefore important for a broader understanding of the underlying processes.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 001071356400001 Publication Date 2023-09-11
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 2218-273X ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor Times cited Open Access Not_Open_Access
Notes This research received no external funding. Approved Most recent IF: NA
Call Number PLASMANT @ plasmant @c:irua:200380 Serial 8958
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Author Laroussi, M.; Bekeschus, S.; Keidar, M.; Bogaerts, A.; Fridman, A.; Lu, X.; Ostrikov, K.; Hori, M.; Stapelmann, K.; Miller, V.; Reuter, S.; Laux, C.; Mesbah, A.; Walsh, J.; Jiang, C.; Thagard, S.M.; Tanaka, H.; Liu, D.; Yan, D.; Yusupov, M.
Title Low-Temperature Plasma for Biology, Hygiene, and Medicine: Perspective and Roadmap Type A1 Journal article
Year 2022 Publication IEEE transactions on radiation and plasma medical sciences Abbreviated Journal IEEE Trans. Radiat. Plasma Med. Sci.
Volume 6 Issue 2 Pages 127-157
Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract (up) Plasma, the fourth and most pervasive state of matter in the visible universe, is a fascinating medium that is connected to the beginning of our universe itself. Man-made plasmas are at the core of many technological advances that include the fabrication of semiconductor devices, which enabled the modern computer and communication revolutions. The introduction of low temperature, atmospheric pressure plasmas to the biomedical field has ushered a new revolution in the healthcare arena that promises to introduce plasma-based therapies to combat some thorny and long-standing medical challenges. This article presents an overview of where research is at today and discusses innovative concepts and approaches to overcome present challenges and take the field to the next level. It is written by a team of experts who took an in-depth look at the various applications of plasma in hygiene, decontamination, and medicine, made critical analysis, and proposed ideas and concepts that should help the research community focus their efforts on clear and practical steps necessary to keep the field advancing for decades to come.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000750257400005 Publication Date 2021-12-14
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 2469-7311 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor Times cited Open Access OpenAccess
Notes Research Foundation—Flanders, 1200219N ; Approved Most recent IF: NA
Call Number PLASMANT @ plasmant @c:irua:185875 Serial 6907
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Author Attri, P.; Yusupov, M.; Park, J.H.; Lingamdinne, L.P.; Koduru, J.R.; Shiratani, M.; Choi, E.H.; Bogaerts, A.
Title Mechanism and comparison of needle-type non-thermal direct and indirect atmospheric pressure plasma jets on the degradation of dyes Type A1 Journal article
Year 2016 Publication Scientific reports Abbreviated Journal Sci Rep-Uk
Volume 6 Issue 6 Pages 34419
Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract (up) Purified water supply for human use, agriculture and industry is the major global priority nowadays. The advanced oxidation process based on atmospheric pressure non-thermal plasma (NTP) has been used for purification of wastewater, although the underlying mechanisms of degradation of organic pollutants are still unknown. In this study we employ two needle-type atmospheric pressure non-thermal plasma jets, i.e., indirect (ID-APPJ) and direct (D-APPJ) jets operating at Ar feed gas, for the treatment of methylene blue, methyl orange and congo red dyes, for two different times (i.e., 20 min and 30 min). Specifically, we study the decolorization/degradation of all three dyes using the above mentioned plasma sources, by means of UV-Vis spectroscopy, HPLC and a density meter. We also employ mass spectroscopy to verify whether only decolorization or also degradation takes place after treatment of the dyes by the NTP jets. Additionally, we analyze the interaction of OH radicals with all three dyes using reactive molecular dynamics simulations, based on the density functional-tight binding method. This investigation represents the first report on the degradation of these three different dyes by two types of NTP setups, analyzed by various methods, and based on both experimental and computational studies.
Address Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
Corporate Author Thesis
Publisher Place of Publication Editor
Language English Wos 000385172300001 Publication Date 2016-10-06
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 2045-2322 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 4.259 Times cited 23 Open Access
Notes We gratefully acknowledge the grant received from the SRC program of the National Research Foundation of Korea (NRF), funded by the Korean Government (MEST) (No. 20100029418). PA is thankful to FY 2015 Japan Society for the Promotion of Science (JSPS) invitation fellowship. This work was partly supported by MEXT KAKENHI Grant Number 24108009 and JSPS KAKENHI Grant Number JP16H03895. M. Y. gratefully acknowledges financial support from the Research Foundation – Flanders (FWO), grant number 1200216N. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. Approved Most recent IF: 4.259
Call Number PLASMANT @ plasmant @ c:irua:135847 Serial 4283
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Author Yusupov, M.; Neyts, E.C.; Verlackt, C.C.; Khalilov, U.; van Duin, A.C.T.; Bogaerts, A.
Title Inactivation of the endotoxic biomolecule lipid A by oxygen plasma species : a reactive molecular dynamics study Type A1 Journal article
Year 2015 Publication Plasma processes and polymers Abbreviated Journal Plasma Process Polym
Volume 12 Issue 12 Pages 162-171
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract (up) Reactive molecular dynamics simulations are performed to study the interaction of reactive oxygen species, such as OH, HO2 and H2O2, with the endotoxic biomolecule lipid A of the gram-negative bacterium Escherichia coli. It is found that the aforementioned plasma species can destroy the lipid A, which consequently results in reducing its toxic activity. All bond dissociation events are initiated by hydrogen-abstraction reactions. However, the mechanisms behind these dissociations are dependent on the impinging plasma species, i.e. a clear difference is observed in the mechanisms upon impact of HO2 radicals and H2O2 molecules on one hand and OH radicals on the other hand. Our simulation results are in good agreement with experimental observations.
Address
Corporate Author Thesis
Publisher Place of Publication Weinheim Editor
Language Wos 000350275400005 Publication Date 2014-09-17
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1612-8850; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 2.846 Times cited 18 Open Access
Notes Approved Most recent IF: 2.846; 2015 IF: 2.453
Call Number c:irua:123540 Serial 1589
Permanent link to this record
 
 
Author Oliveira, M.C.; Yusupov, M.; Cordeiro, R.M.; Bogaerts, A.
Title Unraveling the permeation of reactive species across nitrated membranes by computer simulations Type A1 Journal Article;Reactive oxygen and nitrogen species
Year 2021 Publication Computers In Biology And Medicine Abbreviated Journal Comput Biol Med
Volume 136 Issue Pages 104768
Keywords A1 Journal Article;Reactive oxygen and nitrogen species; Nitro-oxidative stress; Molecular dynamics simulations; Nitrated membranes; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ;
Abstract (up) Reactive oxygen and nitrogen species (RONS) are involved in many biochemical processes, including nitrooxidative stress that causes cancer cell death, observed in cancer therapies such as photodynamic therapy and cold atmospheric plasma. However, their mechanisms of action and selectivity still remain elusive due to the complexity of biological cells. For example, it is not well known how RONS generated by cancer therapies permeate the cell membrane to cause nitro-oxidative damage. There are many studies dedicated to the perme­ation of RONS across native and oxidized membranes, but not across nitrated membranes, another lipid product also generated during nitro-oxidative stress. Herein, we performed molecular dynamics (MD) simulations to calculate the free energy barrier of RONS permeation across nitrated membranes. Our results show that hy­drophilic RONS, such as hydroperoxyl radical (HO2) and peroxynitrous acid (ONOOH), have relatively low barriers compared to hydrogen peroxide (H2O2) and hydroxyl radical (HO), and are more prone to permeate the membrane than for the native or peroxidized membranes, and similar to aldehyde-oxidized membranes. Hy­drophobic RONS like molecular oxygen (O2), nitrogen dioxide (NO2) and nitric oxide (NO) even have insignif­icant barriers for permeation. Compared to native and peroxidized membranes, nitrated membranes are more permeable, suggesting that we must not only consider oxidized membranes during nitro-oxidative stress, but also nitrated membranes, and their role in cancer therapies.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000696938800003 Publication Date 2021-08-17
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0010-4825 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 1.836 Times cited Open Access OpenAccess
Notes We thank University of Antwerp and Coordination of Superior Level Staff Improvement (CAPES, Brazil) for the scholarship granted and for providing the computational resources needed for completion of this work. M. Yusupov acknowledges the Flanders Research Foundation (grant 1200219N) for financial support. Approved Most recent IF: 1.836
Call Number PLASMANT @ plasmant @c:irua:181082 Serial 6807
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Author Tit, N.; Al Ezzi, M.M.; Abdullah, H.M.; Yusupov, M.; Kouser, S.; Bahlouli, H.; Yamani, Z.H.
Title Detection of CO2 using CNT-based sensors: Role of Fe catalyst on sensitivity and selectivity Type A1 Journal article
Year 2017 Publication Materials chemistry and physics Abbreviated Journal Mater Chem Phys
Volume 186 Issue 186 Pages 353-364
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract (up) The adsorption of CO2 on surfaces of graphene and carbon nanotubes (CNTs), decorated with Fe atoms, are investigated using the self-consistent-charge density-functional tight-binding (SCC-DFTB) method, neglecting the heat effects. Fe ad-atoms are more stable when they are dispersed on hollow sites. They introduce a large density of states at the Fermi level (N-F); where keeping such density low would help in gas sensing. Furthermore, the Fe ad-atom can weaken the C=O double bonds of the chemisorbed CO2 molecule, paving the way for oxygen atoms to drain more charges from Fe. Consequently, chemisorption of CO2 molecules reduces both N-F and the conductance while it enhances the sensitivity with the increasing gas dose. Conducting armchair CNTs (ac-CNTs) have higher sensitivity than graphene and semiconducting zigzag CNTs (zz-CNT5). Comparative study of sensitivity of ac-CNT-Fe composite towards various gases (e.g., O-2, N-2, H-2, H2O, CO and CO2) has shown high sensitivity and selectivity towards CO, CO2 and H2O gases. (C) 2016 Elsevier B.V. All rights reserved.
Address
Corporate Author Thesis
Publisher Place of Publication Lausanne Editor
Language Wos 000390621200044 Publication Date 2016-11-04
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0254-0584 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 2.084 Times cited 17 Open Access Not_Open_Access
Notes Approved Most recent IF: 2.084
Call Number UA @ lucian @ c:irua:140333 Serial 4465
Permanent link to this record
 
 
Author Razzokov, J.; Yusupov, M.; Bogaerts, A.
Title Oxidation destabilizes toxic amyloid beta peptide aggregation Type A1 Journal article
Year 2019 Publication Scientific reports Abbreviated Journal Sci Rep-Uk
Volume 9 Issue 1 Pages 5476
Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract (up) The aggregation of insoluble amyloid beta (Aβ) peptides in the brain is known to trigger the onset of neurodegenerative diseases, such as Alzheimer’s disease. In spite of the massive number of investigations, the underlying mechanisms to destabilize the Aβ aggregates are still poorly understood. Some studies indicate the importance of oxidation to destabilize the Aβ aggregates. In particular, oxidation induced by cold atmospheric plasma (CAP) has demonstrated promising results in eliminating these toxic aggregates. In this paper, we investigate the effect of oxidation on the stability of an Aβ pentamer. By means of molecular dynamics simulations and umbrella sampling, we elucidate the conformational changes of Aβ pentamer in the presence of oxidized residues, and we estimate the dissociation free energy of the terminal peptide out of the pentamer form. The calculated dissociation free energy of the terminal peptide is also found to decrease with increasing oxidation. This indicates that Aβ pentamer aggregation becomes less favorable upon oxidation. Our study contributes to a better insight in one of the potential mechanisms for inhibition of toxic Aβ peptide aggregation, which is considered to be the main culprit to Alzheimer’s disease.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000462990000018 Publication Date 2019-04-02
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 2045-2322 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 4.259 Times cited 5 Open Access OpenAccess
Notes M.Y. gratefully acknowledges financial support from the Research Foundation – Flanders (FWO), grant 1200216N and 1200219N. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. Approved Most recent IF: 4.259
Call Number PLASMANT @ plasmant @UA @ admin @ c:irua:159367 Serial 5182
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Author Yusupov, M.; Neyts, E.C.; Simon, P.; Berdiyorov, G.; Snoeckx, R.; van Duin, A.C.T.; Bogaerts, A.
Title Reactive molecular dynamics simulations of oxygen species in a liquid water layer of interest for plasma medicine Type A1 Journal article
Year 2014 Publication Journal of physics: D: applied physics Abbreviated Journal J Phys D Appl Phys
Volume 47 Issue 2 Pages 025205-25209
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract (up) The application of atmospheric pressure plasmas in medicine is increasingly gaining attention in recent years, although very little is currently known about the plasma-induced processes occurring on the surface of living organisms. It is known that most bio-organisms, including bacteria, are coated by a liquid film surrounding them, and there might be many interactions between plasma species and the liquid layer before the plasma species reach the surface of the bio-organisms. Therefore, it is essential to study the behaviour of the reactive species in a liquid film, in order to determine whether these species can travel through this layer and reach the biomolecules, or whether new species are formed along the way. In this work, we investigate the interaction of reactive oxygen species (i.e. O, OH, HO2 and H2O2) with water, which is assumed as a simple model system for the liquid layer surrounding biomolecules. Our computational investigations show that OH, HO2 and H2O2 can travel deep into the liquid layer and are hence in principle able to reach the bio-organism. Furthermore, O, OH and HO2 radicals react with water molecules through hydrogen-abstraction reactions, whereas no H-abstraction reaction takes place in the case of H2O2. This study is important to gain insight into the fundamental operating mechanisms in plasma medicine, in general, and the interaction mechanisms of plasma species with a liquid film, in particular.
Address
Corporate Author Thesis
Publisher Place of Publication London Editor
Language Wos 000329108000013 Publication Date 2013-12-13
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0022-3727;1361-6463; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 2.588 Times cited 51 Open Access
Notes Approved Most recent IF: 2.588; 2014 IF: 2.721
Call Number UA @ lucian @ c:irua:112286 Serial 2823
Permanent link to this record
 
 
Author Khosravian, N.; Bogaerts, A.; Huygh, S.; Yusupov, M.; Neyts, E.C.
Title How do plasma-generated OH radicals react with biofilm components? Insights from atomic scale simulations Type A1 Journal article
Year 2015 Publication Biointerphases Abbreviated Journal Biointerphases
Volume 10 Issue 10 Pages 029501
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract (up) The application of nonthermal atmospheric pressure plasma is emerging as an alternative and efficient technique for the inactivation of bacterial biofilms. In this study, reactive molecular dynamics simulations were used to examine the reaction mechanisms of hydroxyl radicals, as key reactive oxygen plasma species in biological systems, with several organic molecules (i.e., alkane, alcohol, carboxylic acid, and amine), as prototypical components of biomolecules in the biofilm. Our results demonstrate that organic molecules containing hydroxyl and carboxyl groups may act as trapping agents for the OH radicals. Moreover, the impact of OH radicals on N-acetyl-glucosamine, as constituent component of staphylococcus epidermidis biofilms, was investigated. The results show how impacts of OH radicals lead to hydrogen abstraction and subsequent molecular damage. This study thus provides new data on the reaction mechanisms of plasma species, and particularly the OH radicals, with fundamental components of bacterial biofilms.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000357195600019 Publication Date 2014-12-17
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1934-8630;1559-4106; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 2.603 Times cited 10 Open Access
Notes Approved Most recent IF: 2.603; 2015 IF: 3.374
Call Number c:irua:121371 Serial 1492
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Author Van der Paal, J.; Hong, S.-H.; Yusupov, M.; Gaur, N.; Oh, J.-S.; Short, R.D.; Szili, E.J.; Bogaerts, A.
Title How membrane lipids influence plasma delivery of reactive oxygen species into cells and subsequent DNA damage : an experimental and computational study Type A1 Journal article
Year 2019 Publication Physical chemistry, chemical physics Abbreviated Journal Phys Chem Chem Phys
Volume 21 Issue 35 Pages 19327-19341
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract (up) The mechanisms of plasma in medicine are broadly attributed to plasma-derived reactive oxygen and nitrogen species (RONS). In order to exert any intracellular effects, these plasma-derived RONS must first traverse a major barrier in the cell membrane. The cell membrane lipid composition, and thereby the magnitude of this barrier, is highly variable between cells depending on type and state (e.g. it is widely accepted that healthy and cancerous cells have different membrane lipid compositions). In this study, we investigate how plasma-derived RONS interactions with lipid membrane components can potentially be exploited in the future for treatment of diseases. We couple phospholipid vesicle experiments, used as simple cell models, with molecular dynamics (MD) simulations of the lipid membrane to provide new insights into how the interplay between phospholipids and cholesterol may influence the response of healthy and diseased cell membranes to plasma-derived RONS. We focus on the (i) lipid tail saturation degree, (ii) lipid head group type, and (iii) membrane cholesterol fraction. Using encapsulated molecular probes, we study the influence of the above membrane components on the ingress of RONS into the vesicles, and subsequent DNA damage. Our results indicate that all of the above membrane components can enhance or suppress RONS uptake, depending on their relative concentration within the membrane. Further, we show that higher RONS uptake into the vesicles does not always correlate with increased DNA damage, which is attributed to ROS reactivity and lifetime. The MD simulations indicate the multifactorial chemical and physical processes at play, including (i) lipid oxidation, (ii) lipid packing, and (iii) lipid rafts formation. The methods and findings presented here provide a platform of knowledge that could be leveraged in the development of therapies relying on the action of plasma, in which the cell membrane and oxidative stress response in cells is targeted.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000486175400045 Publication Date 2019-08-21
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1463-9076; 1463-9084 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 4.123 Times cited 1 Open Access
Notes Approved Most recent IF: 4.123
Call Number UA @ admin @ c:irua:162782 Serial 6303
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Author Rezaei, M.; Ghasemitarei, M.; Razzokov, J.; Yusupov, M.; Ghorbanalilu, M.; Ejtehadi, M.R.
Title In silico study of the impact of oxidation on pyruvate transmission across the hVDAC1 protein channel Type A1 Journal article
Year 2024 Publication Archives of biochemistry and biophysics Abbreviated Journal
Volume 751 Issue Pages 109835-109837
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract (up) The overexpression of voltage dependent anion channels (VDACs), particularly VDAC1, in cancer cells compared to normal cells, plays a crucial role in cancer cell metabolism, apoptosis regulation, and energy homeostasis. In this study, we used molecular dynamics (MD) simulations to investigate the effect of a low level of VDAC1 oxidation (induced e.g., by cold atmospheric plasma (CAP)) on the pyruvate (Pyr) uptake by VDAC1. Inhibiting Pyr uptake through VDAC1 can suppress cancer cell proliferation. Our primary target was to study the translocation of Pyr across the native and oxidized forms of hVDAC1, the human VDAC1. Specifically, we employed MD simulations to analyze the hVDAC1 structure by modifying certain cysteine residues to cysteic acids and methionine residues to methionine sulfoxides, which allowed us to investigate the effect of oxidation. Our results showed that the free energy barrier for Pyr translocation through the native and oxidized channel was approximately 4.3 +/- 0.7 kJ mol-1 and 10.8 +/- 1.8 kJ mol-1, respectively. An increase in barrier results in a decrease in rate of Pyr permeation through the oxidized channel. Thus, our results indicate that low levels of CAP oxidation reduce Pyr translocation, resulting in decreased cancer cell proliferation. Therefore, low levels of oxidation are likely sufficient to treat cancer cells given the inhibition of Pyr uptake.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 001127850500001 Publication Date 2023-11-23
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0003-9861; 1096-0384 ISBN Additional Links UA library record; WoS full record
Impact Factor 3.9 Times cited Open Access Not_Open_Access
Notes Approved Most recent IF: 3.9; 2024 IF: 3.165
Call Number UA @ admin @ c:irua:202185 Serial 9046
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Author Elmonov, A.A.; Yusupov, M.S.; Dzhurakhalov, A.A.; Bogaerts, A.
Title Sputtering of Si(001) and SiC(001) by grazing ion bombardment Type P1 Proceeding
Year 2008 Publication Abbreviated Journal
Volume Issue Pages 209-213
Keywords P1 Proceeding; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract (up) The peculiarities of sputtering processes at 0.5-5 keV Ne grazing ion bombardment of Si(001) and SiC(001) surfaces and their possible application for the surface modification have been studied by computer simulation. Sputtering yields in the primary knock-on recoil atoms regime versus the initial energy of incident ions (E(0) = 0.5-5 keV) and angle of incidence (psi = 0-30 degrees) counted from a target surface have been calculated. Comparative studies of layer-by-layer sputtering for Si(001) and SiC(001) surfaces versus the initial energy of incident ions as well as an effective sputtering and sputtering threshold are discussed.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos Publication Date 0000-00-00
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue 84 Edition
ISSN 978-86-80019-27-7 ISBN Additional Links UA library record; WoS full record;
Impact Factor Times cited Open Access
Notes Approved Most recent IF: NA
Call Number UA @ lucian @ c:irua:95704 Serial 3112
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Author Duan, J.; Ma, M.; Yusupov, M.; Cordeiro, R.M.; Lu, X.; Bogaerts, A.
Title The penetration of reactive oxygen and nitrogen species across the stratum corneum Type A1 Journal article
Year 2020 Publication Plasma Processes And Polymers Abbreviated Journal Plasma Process Polym
Volume Issue Pages
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract (up) The penetration of reactive oxygen and nitrogen species (RONS) across the stratum corneum (SC) is a necessary and crucial process in many skin‐related plasma medical applications. To gain more insights into this penetration behavior, we combined experimental measurements of the permeability of dry and moist SC layers with computer simulations of model lipid membranes. We measured the permeation of relatively stable molecules, which are typically generated by plasma, namely H2O2, NO3−, and NO2−. Furthermore, we calculated the permeation free energy profiles of the major plasma‐generated RONS and their derivatives (i.e., H2O2, OH, HO2, O2, O3, NO, NO2, N2O4, HNO2, HNO3, NO2−, and NO3−) across native and oxidized SC lipid bilayers, to understand the mechanisms of RONS permeation across the SC. Our results indicate that hydrophobic RONS (i.e., NO, NO2, O2, O3, and N2O4) can translocate more easily across the SC lipid bilayer than hydrophilic RONS (i.e., H2O2, OH, HO2, HNO2, and HNO3) and ions (i.e., NO2− and NO3−) that experience much higher permeation barriers. The permeability of RONS through the SC skin lipids is enhanced when the skin is moist and the lipids are oxidized. These findings may help to understand the underlying mechanisms of plasma interaction with a biomaterial and to optimize the environmental parameters in practice in plasma medical applications.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000536892900001 Publication Date 2020-06-02
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1612-8850 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 3.5 Times cited Open Access
Notes National Natural Science Foundation of China, 51625701 51977096 ; Fonds Wetenschappelijk Onderzoek, 1200219N ; China Scholarship Council, 201806160128 ; M. Y. acknowledges the Research Foundation Flanders (FWO) for financial support (Grant No. 1200219N). This study was partially supported by the National Natural Science Foundation of China (Grant No: 51625701 and 51977096) and the China Scholarship Council (Grant No: 201806160128). All computational work was performed using the Turing HPC infrastructure at the CalcUA Core Facility of the University of Antwerp (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI), and the UA. Approved Most recent IF: 3.5; 2020 IF: 2.846
Call Number PLASMANT @ plasmant @c:irua:169709 Serial 6372
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Author Abduvokhidov, D.; Yusupov, M.; Shahzad, A.; Attri, P.; Shiratani, M.; Oliveira, M.C.; Razzokov, J.
Title Unraveling the Transport Properties of RONS across Nitro-Oxidized Membranes Type A1 Journal Article
Year 2023 Publication Biomolecules Abbreviated Journal Biomolecules
Volume 13 Issue 7 Pages 1043
Keywords A1 Journal Article; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ;
Abstract (up) The potential of cold atmospheric plasma (CAP) in biomedical applications has received significant interest, due to its ability to generate reactive oxygen and nitrogen species (RONS). Upon exposure to living cells, CAP triggers alterations in various cellular components, such as the cell membrane. However, the permeation of RONS across nitrated and oxidized membranes remains understudied. To address this gap, we conducted molecular dynamics simulations, to investigate the permeation capabilities of RONS across modified cell membranes. This computational study investigated the translocation processes of less hydrophilic and hydrophilic RONS across the phospholipid bilayer (PLB), with various degrees of oxidation and nitration, and elucidated the impact of RONS on PLB permeability. The simulation results showed that less hydrophilic species, i.e., NO, NO2, N2O4, and O3, have a higher penetration ability through nitro-oxidized PLB compared to hydrophilic RONS, i.e., HNO3, s-cis-HONO, s-trans-HONO, H2O2, HO2, and OH. In particular, nitro-oxidation of PLB, induced by, e.g., cold atmospheric plasma, has minimal impact on the penetration of free energy barriers of less hydrophilic species, while it lowers these barriers for hydrophilic RONS, thereby enhancing their translocation across nitro-oxidized PLB. This research contributes to a better understanding of the translocation abilities of RONS in the field of plasma biomedical applications and highlights the need for further analysis of their role in intracellular signaling pathways.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 001035160000001 Publication Date 2023-06-27
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 2218-273X ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor Times cited Open Access Not_Open_Access
Notes This research was funded by the Innovative Development Agency of the Republic of Uzbekistan, grant number FZ-2020092817. Approved Most recent IF: NA
Call Number PLASMANT @ plasmant @c:irua:198154 Serial 8803
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Author Khalilov, U.; Uljayev, U.; Mehmonov, K.; Nematollahi, P.; Yusupov, M.; Neyts, E.C.; Neyts, E.C.
Title Can endohedral transition metals enhance hydrogen storage in carbon nanotubes? Type A1 Journal article
Year 2024 Publication International journal of hydrogen energy Abbreviated Journal
Volume 55 Issue Pages 640-610
Keywords A1 Journal article; Engineering sciences. Technology; Modelling and Simulation in Chemistry (MOSAIC); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract (up) The safe and efficient use of hydrogen energy, which is in high demand worldwide today, requires efficient hydrogen storage. Despite significant advances in hydrogen storage using carbon-based nanomaterials, including carbon nanotubes (CNTs), efforts to substantially increase the storage capacity remain less effective. In this work, we demonstrate the effect of endohedral transition metal atoms on the hydrogen storage capacity of CNTs using reactive molecular dynamics simulations. We find that an increase in the volume fraction of endohedral nickel atoms leads to an increase in the concentration of physisorbed hydrogen molecules around single-walled CNTs (SWNTs) by approximately 1.6 times compared to pure SWNTs. The obtained results provide insight into the underlying mechanisms of how endohedral transition metal atoms enhance the hydrogen storage ability of SWNTs under nearly ambient conditions.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 001142427400001 Publication Date 2023-11-24
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0360-3199 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 7.2 Times cited Open Access Not_Open_Access
Notes Approved Most recent IF: 7.2; 2024 IF: 3.582
Call Number UA @ admin @ c:irua:202315 Serial 9006
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Author Mehmonov, K.; Ergasheva, A.; Yusupov, M.; Khalilov, U.
Title The role of carbon monoxide in the catalytic synthesis of endohedral carbyne Type A1 Journal article
Year 2023 Publication Journal of applied physics Abbreviated Journal
Volume 134 Issue 14 Pages 144303-144307
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract (up) The unique physical properties of carbyne, a novel carbon nanostructure, have attracted considerable interest in modern nanotechnology. While carbyne synthesis has been accomplished successfully using diverse techniques, the underlying mechanisms governing the carbon monoxide-dependent catalytic synthesis of endohedral carbyne remain poorly understood. In this simulation-based study, we investigate the synthesis of endohedral carbyne from carbon and carbon monoxide radicals in the presence of a nickel catalyst inside double-walled carbon nanotubes with a (5,5)@(10,10) structure. The outcome of our investigation demonstrates that the incorporation of the carbon atom within the Ni-n@(5,5)@(10,10) model system initiates the formation of an elongated carbon chain. In contrast, upon the introduction of carbon monoxide radicals, the growth of the carbyne chain is inhibited as a result of the oxidation of endohedral nickel clusters by oxygen atoms after the initial steps of nucleation. Our findings align with prior theoretical, simulation, and experimental investigations, reinforcing their consistency and providing valuable insights into the synthesis of carbyne-based nanodevices that hold promising potential for future advancements in nanotechnology.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 001083993400003 Publication Date 2023-10-10
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0021-8979; 1089-7550 ISBN Additional Links UA library record; WoS full record
Impact Factor 3.2 Times cited Open Access
Notes Approved Most recent IF: 3.2; 2023 IF: 2.068
Call Number UA @ admin @ c:irua:201233 Serial 9106
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Author Han, I.; Song, I.S.; Choi, S.A.; Lee, T.; Yusupov, M.; Shaw, P.; Bogaerts, A.; Choi, E.H.; Ryu, J.J.
Title Bioactive Nonthermal Biocompatible Plasma Enhances Migration on Human Gingival Fibroblasts Type A1 Journal article
Year 2023 Publication Advanced healthcare materials Abbreviated Journal
Volume 12 Issue 4 Pages 2200527
Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract (up) This study hypothesizes that the application of low-dose nonthermal biocompatible dielectric barrier discharge plasma (DBD-NBP) to human gingival fibroblasts (HGFs) will inhibit colony formation but not cell death and induce matrix metalloproteinase (MMP) expression, extracellular matrix (ECM) degradation, and subsequent cell migration, which can result in enhanced wound healing. HGFs treated with plasma for 3 min migrate to each other across the gap faster than those in the control and 5-min treatment groups on days 1 and 3. The plasma-treated HGFs show significantly high expression levels of the cell cycle arrest-related p21 gene and enhanced MMP activity. Focal adhesion kinase (FAK) mediated attenuation of wound healing or actin cytoskeleton rearrangement, and plasma-mediated reversal of this attenuation support the migratory effect of DBD-NBP. Further, this work performs computer simulations to investigate the effect of oxidation on the stability and conformation of the catalytic kinase domain (KD) of FAK. It is found that the oxidation of highly reactive amino acids (AAs) Cys427, Met442, Cys559, Met571, Met617, and Met643 changes the conformation and increases the structural flexibility of the FAK protein and thus modulates its function and activity. Low-dose DBD-NBP-induces host cell cycle arrest, ECM breakdown, and subsequent migration, thus contributing to the enhanced wound healing process.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000897762100001 Publication Date 2022-11-14
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 2192-2640 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 10 Times cited Open Access OpenAccess
Notes National Research Foundation of Korea; Kementerian Pendidikan, 2020R1I1A1A01073071 2021R1A6A1A03038785 ; Approved Most recent IF: 10; 2023 IF: 5.11
Call Number PLASMANT @ plasmant @c:irua:192804 Serial 7242
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Author Attri, P.; Razzokov, J.; Yusupov, M.; Koga, K.; Shiratani, M.; Bogaerts, A.
Title Influence of osmolytes and ionic liquids on the Bacteriorhodopsin structure in the absence and presence of oxidative stress: A combined experimental and computational study Type A1 Journal article
Year 2020 Publication International Journal Of Biological Macromolecules Abbreviated Journal Int J Biol Macromol
Volume 148 Issue Pages 657-665
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract (up) Understanding the folding and stability of membrane proteins is of great importance in protein science. Recently, osmolytes and ionic liquids (ILs) are increasingly being used as drug delivery systems in the biopharmaceutical industry. However, the stability of membrane proteins in the presence of osmolytes and ILs is not yet fully understood. Besides, the effect of oxidative stress on membrane proteins with osmolytes or ILs has not been investigated. Therefore, we studied the influence of osmolytes and ILs as co-solvents on the stability of a model membrane protein (i.e., Bacteriorhodopsin in purple membrane of Halobacterium salinarum), using UV–Vis spectroscopy and molecular dynamics (MD) simulations. The MD simulations allowed us to determine the flexibility and solvent accessible surface area (SASA) of Bacteriorhodopsin protein in the presence and/or absence of cosolvents, as well as to carry out principal component analysis (PCA) to identify the most important movements in this protein. In addition, by means of UV–Vis spectroscopy we studied the effect of oxidative stress generated by cold atmospheric plasma on the stability of Bacteriorhodopsin in the presence and/or absence of co-solvents. This study is important for a better understanding of the stability of proteins in the presence of oxidative stress.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000522094600066 Publication Date 2020-01-20
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0141-8130 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 8.2 Times cited Open Access
Notes Horizon2020, 743546 ; JSPS, 19H05462 16H03895 ; Nagoya University; We gratefully acknowledge the European Marie Skłodowska-Curie Individual Fellowship “Anticancer-PAM” within Horizon2020 (grant number 743546). This work was also supported by JSPS-KAKENHI 19H05462 and 16H03895, the joint usage/research program of Center for Low-temperature Plasma Science, Nagoya University and also supported by JSPS and RCL under the Japan-Lithuania Research Cooperative Program. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. Approved Most recent IF: 8.2; 2020 IF: 3.671
Call Number PLASMANT @ plasmant @c:irua:165585 Serial 5444
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Author Yusupov, M.; Lackmann, J.-W.; Razzokov, J.; Kumar, S.; Stapelmann, K.; Bogaerts, A.
Title Impact of plasma oxidation on structural features of human epidermal growth factor Type A1 Journal article
Year 2018 Publication Plasma processes and polymers Abbreviated Journal Plasma Process Polym
Volume 15 Issue 8 Pages 1800022
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract (up) 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.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000441895700004 Publication Date 2018-05-07
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1612-8850 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 2.846 Times cited 7 Open Access Not_Open_Access
Notes Fonds Wetenschappelijk Onderzoek, 1200216N ; Bundesministerium für Bildung und Forschung, 03Z22DN12 ; Approved Most recent IF: 2.846
Call Number PLASMANT @ plasmant @c:irua:152815 Serial 5008
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Author Razzokov, J.; Yusupov, M.; Vanuytsel, S.; Neyts, E.C.; Bogaerts, A.
Title Phosphatidylserine flip-flop induced by oxidation of the plasma membrane: a better insight by atomic scale modeling Type A1 Journal article
Year 2017 Publication Plasma processes and polymers Abbreviated Journal Plasma Process Polym
Volume 14 Issue 10 Pages 1700013
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract (up) We perform molecular dynamics simulations to study the flip-flop motion of phosphatidylserine (PS) across the plasma membrane upon increasing oxidation degree of the membrane. Our computational results show that an increase of the oxidation degree in the lipids leads to a decrease of the free energy barrier for translocation of PS through the membrane. In other words, oxidation of the lipids facilitates PS flip-flop motion across the membrane, because in native phospholipid bilayers this is only a “rare event” due to the high energy barriers for the translocation of PS. The present study provides an atomic-scale insight into the mechanisms of the PS flip-flop upon oxidation of lipids, as produced for example by cold atmospheric plasma, in living cells.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000413045800010 Publication Date 2017-04-05
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 1612-8850 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 2.846 Times cited 9 Open Access Not_Open_Access
Notes Fonds Wetenschappelijk Onderzoek, 1200216N ; Approved Most recent IF: 2.846
Call Number PLASMANT @ plasmant @c:irua:149567 Serial 4910
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Author Ghasemitarei, M.; Yusupov, M.; Razzokov, J.; Shokri, B.; Bogaerts, A.
Title Effect of oxidative stress on cystine transportation by xC‾ antiporter Type A1 Journal article
Year 2019 Publication Archives of biochemistry and biophysics Abbreviated Journal Arch Biochem Biophys
Volume 674 Issue Pages 108114
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract (up) We performed computer simulations to investigate the effect of oxidation on the extracellular cystine (CYC) uptake by the xC− antiporter. The latter is important for killing of cancer cells. Specifically, applying molecular dynamics (MD) simulations we studied the transport of CYC across xCT, i.e., the light subunit of the xC− antiporter, in charge of bidirectional transport of CYC and glutamate. We considered the outward facing (OF) configuration of xCT, and to study the effect of oxidation, we modified the Cys327 residue, located in the vicinity of the extracellular milieu, to cysteic acid (CYO327). Our computational results showed that oxidation of Cys327 results in a free energy barrier for CYC translocation, thereby blocking the access of CYC to the substrate binding site of the OF system. The formation of the energy barrier was found to be due to the conformational changes in the channel. Analysis of the MD trajectories revealed that the reorganization of the side chains of the Tyr244 and CYO327 residues play a critical role in the OF channel blocking. Indeed, the calculated distance between Tyr244 and either Cys327 or CYO327 showed a narrowing of the channel after oxidation. The obtained free energy barrier for CYC translocation was found to be 33.9kJmol−1, indicating that oxidation of Cys327, by e.g., cold atmospheric plasma, is more effective in inhibiting the xC− antiporter than in the mutation of this amino acid to Ala (yielding a barrier of 32.4kJmol−1). The inhibition of the xC− antiporter may lead to Cys starvation in some cancer cells, eventually resulting in cancer cell death.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000525439700011 Publication Date 2019-09-23
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0003-9861 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 3.165 Times cited Open Access
Notes Ministry of Science, Research and Technology of Iran; University of Antwerp; Research Foundation − Flanders, 1200219N ; Universiteit Antwerpen; Hercules Foundation; Flemish Government; UA; M. G. acknowledges funding from the Ministry of Science, Research and Technology of Iran and from the University of Antwerp in Belgium. M. Y. gratefully acknowledges financial support from the Research Foundation − Flanders (FWO), grant number 1200219N. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. Finally, we thank A. S. Mashayekh Esfehan and A. Mohseni for their important comments on the manuscript. Approved Most recent IF: 3.165
Call Number PLASMANT @ plasmant @c:irua:163474 Serial 5372
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Author Yusupov, M.; Wende, K.; Kupsch, S.; Neyts, E.C.; Reuter, S.; Bogaerts, A.
Title Effect of head group and lipid tail oxidation in the cell membrane revealed through integrated simulations and experiments Type A1 Journal article
Year 2017 Publication Scientific reports Abbreviated Journal Sci Rep-Uk
Volume 7 Issue 7 Pages 5761
Keywords A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract (up) We report on multi-level atomistic simulations for the interaction of reactive oxygen species (ROS) with the head groups of the phospholipid bilayer, and the subsequent effect of head group and lipid tail oxidation on the structural and dynamic properties of the cell membrane. Our simulations are validated by experiments using a cold atmospheric plasma as external ROS source. We found that plasma treatment leads to a slight initial rise in membrane rigidity, followed by a strong and persistent increase in fluidity, indicating a drop in lipid order. The latter is also revealed by our simulations. This study is important for cancer treatment by therapies producing (extracellular) ROS, such as plasma treatment. These ROS will interact with the cell membrane, first oxidizing the head groups, followed by the lipid tails. A drop in lipid order might allow them to penetrate into the cell interior (e.g., through pores created due to oxidation of the lipid tails) and cause intracellular oxidative damage, eventually leading to cell death. This work in general elucidates the underlying mechanisms of ROS interaction with the cell membrane at the atomic level.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000405746500072 Publication Date 2017-07-12
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 2045-2322 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 4.259 Times cited 27 Open Access OpenAccess
Notes M.Y. gratefully acknowledges financial support from the Research Foundation – Flanders (FWO), grant number 1200216 N. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. S.R. and S.K. acknowledge funding by the BMBF (FKZ: 03Z2DN12). S.R. acknowledges funding by the Ministry of Education, Science and Culture of the State of Mecklenburg-Vorpommern (AU 15001). The authors thank M. Hammer for the support and discussion in the biophysical studies and J. Van der Paal for the interesting discussions. Approved Most recent IF: 4.259
Call Number PLASMANT @ plasmant @ c:irua:144627 Serial 4630
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Author Van der Paal, J.; Verlackt, C.C.; Yusupov, M.; Neyts, E.C.; Bogaerts, A.
Title Structural modification of the skin barrier by OH radicals : a reactive molecular dynamics study for plasma medicine Type A1 Journal article
Year 2015 Publication Journal of physics: D: applied physics Abbreviated Journal J Phys D Appl Phys
Volume 48 Issue 48 Pages 155202
Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT)
Abstract (up) While plasma treatment of skin diseases and wound healing has been proven highly effective, the underlying mechanisms, and more generally the effect of plasma radicals on skin tissue, are not yet completely understood. In this paper, we perform ReaxFF-based reactive molecular dynamics simulations to investigate the interaction of plasma generated OH radicals with a model system composed of free fatty acids, ceramides, and cholesterol molecules. This model system is an approximation of the upper layer of the skin (stratum corneum). All interaction mechanisms observed in our simulations are initiated by H-abstraction from one of the ceramides. This reaction, in turn, often starts a cascade of other reactions, which eventually lead to the formation of aldehydes, the dissociation of ceramides or the elimination of formaldehyde, and thus eventually to the degradation of the skin barrier function.
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Corporate Author Thesis
Publisher Place of Publication London Editor
Language Wos 000351856600007 Publication Date 2015-03-25
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0022-3727;1361-6463; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 2.588 Times cited 20 Open Access
Notes Approved Most recent IF: 2.588; 2015 IF: 2.721
Call Number c:irua:124230 Serial 3242
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