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Author |
Oliveira, M.C.; Yusupov, M.; Bogaerts, A.; Cordeiro, R.M. |
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Title |
Lipid Oxidation: Role of Membrane Phase-Separated Domains |
Type |
A1 Journal Article |
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Year |
2021 |
Publication |
Journal Of Chemical Information And Modeling |
Abbreviated Journal |
J Chem Inf Model |
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Volume |
61 |
Issue |
6 |
Pages |
2857-2868 |
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Keywords |
A1 Journal Article; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ; |
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Abstract |
Lipid oxidation is associated with several inflammatory and neurodegenerative diseases, but many questions to unravel its effects on biomembranes are still open due to the complexity of the topic. For instance, recent studies indicated that phase-separated domains can have a significant effect on membrane function. It is reported that domain interfaces are “hot spots” for pore formation, but the underlying mechanisms and the effect of oxidation-induced phase separation on membranes remain elusive. Thus, to evaluate the permeability of the membrane coexisting of liquid-ordered (Lo) and liquid-disordered (Ld) domains, we performed atomistic molecular dynamics simulations. Specifically, we studied the membrane permeability of nonoxidized or oxidized homogeneous membranes (single-phase) and at the Lo/Ld domain interfaces of heterogeneous membranes, where the Ld domain is composed of either oxidized or nonoxidized lipids. Our simulation results reveal that the addition of only 1.5% of lipid aldehyde molecules at the Lo/Ld domain interfaces of heterogeneous membranes increases the membrane permeability, whereas their addition at homogeneous membranes does not have any effect. This study is of interest for a better understanding of cancer treatment methods based on oxidative stress (causing among others lipid oxidation), such as plasma medicine and photodynamic therapy. |
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Wos |
000669541400034 |
Publication Date |
2021-06-28 |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
1549-9596 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
3.76 |
Times cited |
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Open Access |
OpenAccess |
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Notes |
Fonds Wetenschappelijk Onderzoek, 1200219N ; Coordenação de Aperfeiçoamento de Pessoal de NÃvel Superior; We thank Universidade Federal do ABC for providing the computational resources needed for completion of this work and CAPES for the scholarship granted. M.Y. acknowledges the Flanders Research Foundation (grant 1200219N) for financial support. |
Approved |
Most recent IF: 3.76 |
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Call Number |
PLASMANT @ plasmant @c:irua:179766 |
Serial |
6806 |
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Permanent link to this record |
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Author |
Attri, P.; Razzokov, J.; Yusupov, M.; Koga, K.; Shiratani, M.; Bogaerts, A. |
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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 |
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Year |
2020 |
Publication |
International Journal Of Biological Macromolecules |
Abbreviated Journal |
Int J Biol Macromol |
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Volume |
148 |
Issue |
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Pages |
657-665 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
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. |
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Wos |
000522094600066 |
Publication Date |
2020-01-20 |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0141-8130 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
8.2 |
Times cited |
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Open Access |
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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 |
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Call Number |
PLASMANT @ plasmant @c:irua:165585 |
Serial |
5444 |
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Permanent link to this record |
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Author |
Yusupov, M.; Neyts, E.C.; Verlackt, C.C.; Khalilov, U.; van Duin, A.C.T.; Bogaerts, A. |
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Title |
Inactivation of the endotoxic biomolecule lipid A by oxygen plasma species : a reactive molecular dynamics study |
Type |
A1 Journal article |
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Year |
2015 |
Publication |
Plasma processes and polymers |
Abbreviated Journal |
Plasma Process Polym |
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Volume |
12 |
Issue |
12 |
Pages |
162-171 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
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. |
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Place of Publication |
Weinheim |
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Wos |
000350275400005 |
Publication Date |
2014-09-17 |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
1612-8850; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.846 |
Times cited |
18 |
Open Access |
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Notes |
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Approved |
Most recent IF: 2.846; 2015 IF: 2.453 |
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Call Number |
c:irua:123540 |
Serial |
1589 |
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Permanent link to this record |
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Author |
Rezaei, M.; Ghasemitarei, M.; Razzokov, J.; Yusupov, M.; Ghorbanalilu, M.; Ejtehadi, M.R. |
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Title |
In silico study of the impact of oxidation on pyruvate transmission across the hVDAC1 protein channel |
Type |
A1 Journal article |
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Year |
2024 |
Publication |
Archives of biochemistry and biophysics |
Abbreviated Journal |
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Volume |
751 |
Issue |
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Pages |
109835-109837 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
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. |
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Wos |
001127850500001 |
Publication Date |
2023-11-23 |
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Abbreviated Series Title |
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Series Issue |
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Edition |
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ISSN |
0003-9861; 1096-0384 |
ISBN |
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Additional Links |
UA library record; WoS full record |
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Impact Factor |
3.9 |
Times cited |
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Open Access |
Not_Open_Access |
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Notes |
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Approved |
Most recent IF: 3.9; 2024 IF: 3.165 |
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Call Number |
UA @ admin @ c:irua:202185 |
Serial |
9046 |
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Permanent link to this record |
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Author |
Yusupov, M.; Lackmann, J.-W.; Razzokov, J.; Kumar, S.; Stapelmann, K.; Bogaerts, A. |
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Title |
Impact of plasma oxidation on structural features of human epidermal growth factor |
Type |
A1 Journal article |
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Year |
2018 |
Publication |
Plasma processes and polymers |
Abbreviated Journal |
Plasma Process Polym |
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Volume |
15 |
Issue |
8 |
Pages |
1800022 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
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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Wos |
000441895700004 |
Publication Date |
2018-05-07 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
1612-8850 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.846 |
Times cited |
7 |
Open Access |
Not_Open_Access |
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Notes |
Fonds Wetenschappelijk Onderzoek, 1200216N ; Bundesministerium für Bildung und Forschung, 03Z22DN12 ; |
Approved |
Most recent IF: 2.846 |
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Call Number |
PLASMANT @ plasmant @c:irua:152815 |
Serial |
5008 |
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Permanent link to this record |
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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. |
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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 |
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Year |
2019 |
Publication |
Physical chemistry, chemical physics |
Abbreviated Journal |
Phys Chem Chem Phys |
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Volume |
21 |
Issue |
35 |
Pages |
19327-19341 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
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. |
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Wos |
000486175400045 |
Publication Date |
2019-08-21 |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
1463-9076; 1463-9084 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
4.123 |
Times cited |
1 |
Open Access |
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Notes |
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Approved |
Most recent IF: 4.123 |
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Call Number |
UA @ admin @ c:irua:162782 |
Serial |
6303 |
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Permanent link to this record |
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Author |
Khosravian, N.; Bogaerts, A.; Huygh, S.; Yusupov, M.; Neyts, E.C. |
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Title |
How do plasma-generated OH radicals react with biofilm components? Insights from atomic scale simulations |
Type |
A1 Journal article |
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Year |
2015 |
Publication |
Biointerphases |
Abbreviated Journal |
Biointerphases |
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Volume |
10 |
Issue |
10 |
Pages |
029501 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
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. |
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Wos |
000357195600019 |
Publication Date |
2014-12-17 |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
1934-8630;1559-4106; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.603 |
Times cited |
10 |
Open Access |
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Notes |
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Approved |
Most recent IF: 2.603; 2015 IF: 3.374 |
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Call Number |
c:irua:121371 |
Serial |
1492 |
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Permanent link to this record |
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Author |
Oliveira, M.C.; Yusupov, M.; Bogaerts, A.; Cordeiro, R.M. |
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Title |
How do nitrated lipids affect the properties of phospholipid membranes? |
Type |
A1 Journal article |
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Year |
2020 |
Publication |
Archives Of Biochemistry And Biophysics |
Abbreviated Journal |
Arch Biochem Biophys |
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Volume |
695 |
Issue |
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Pages |
108548 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
Biological membranes are under constant attack of free radicals, which may lead to lipid nitro-oxidation, pro ducing a complex mixture of nitro-oxidized lipids that are responsible for structural and dynamic changes on the membrane. Despite the latter, nitro-oxidized lipids are also associated with several inflammatory and neuro degenerative diseases, the underlying mechanisms of which remain elusive. We perform atomistic molecular dynamics simulations using several isomers of nitro-oxidized lipids to study their effect on the structure and permeability of the membrane, as well as the interaction between the mixture of these products in the phospholipid membrane environment. Our results show that the stereo- and positional isomers have a stronger effect on the properties of the membrane composed of oxidized lipids compared to that containing nitrated lipids. Nevertheless, nitrated lipids lead to three-fold increase in water permeability compared to oxidized lipids. In addition, we show that in a membrane consisting of combined nitro-oxidized lipid products, the presence of oxidized lipids protects the membrane from transient pores. Is well stablished that plasma application and photodynamic therapy produces a number of oxidative species used to kill cancer cells, through membrane damage induced by nitro-oxidative stress. This study is important to elucidate the mechanisms and the molecular level properties involving the reactive species produced during that cancer therapies. |
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Wos |
000594173400010 |
Publication Date |
0000-00-00 |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0003-9861 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
3.9 |
Times cited |
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Open Access |
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Notes |
CAPES; Flanders Research Foundation, 1200219N ; We thank Universidade Federal do ABC for providing the computational resources needed for completion of this work and CAPES for scholarship granted. M.Y. acknowledges the Flanders Research Foundation (grant 1200219N) for financial support. |
Approved |
Most recent IF: 3.9; 2020 IF: 3.165 |
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Call Number |
PLASMANT @ plasmant @c:irua:173861 |
Serial |
6440 |
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Permanent link to this record |
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Author |
Kumar, N.; Shaw, P.; Razzokov, J.; Yusupov, M.; Attri, P.; Uhm, H.S.; Choi, E.H.; Bogaerts, A. |
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Title |
Enhancement of cellular glucose uptake by reactive species: a promising approach for diabetes therapy |
Type |
A1 Journal article |
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Year |
2018 |
Publication |
RSC advances |
Abbreviated Journal |
Rsc Adv |
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Volume |
8 |
Issue |
18 |
Pages |
9887-9894 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
It is generally known that antidiabetic activity is associated with an increased level of glucose uptake in adipocytes and skeletal muscle cells. However, the role of exogenous reactive oxygen and nitrogen species (RONS) in muscle development and more importantly in glucose uptake is largely unknown. We investigate the effect of RONS generated by cold atmospheric plasma (CAP) in glucose uptake. We show that the glucose uptake is significantly enhanced in differentiated L6 skeletal muscle cells after CAP treatment. We also observe a significant increase of the intracellular Ca++ and ROS level, without causing toxicity. One of the possible reasons for an elevated level of glucose uptake as well as intracellular ROS and Ca++ ions is probably the increased oxidative stress leading to glucose transport. |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Language |
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Wos |
000430451800036 |
Publication Date |
2018-03-08 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
2046-2069 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
3.108 |
Times cited |
1 |
Open Access |
OpenAccess |
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Notes |
We gratefully acknowledge nancial support from the Research Foundation – Flanders (FWO), grant numbers 12J5617N, 1200216N and from the European Marie Skłodowska-Curie Individual Fellowship “Anticancer-PAM” within Horizon2020 (grant number 743546). We are also thankful to the Plasma Bioscience Research Center at Kwangwoon University for providing the core facilities for the experimental work as well as nancial support by the Leading Foreign Research Institute Recruitment program (Grant # NRF-2016K1A4A3914113) through the Basic Science Research Program of the National Research Founda |
Approved |
Most recent IF: 3.108 |
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Call Number |
PLASMANT @ plasmant @c:irua:149564 |
Serial |
4909 |
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Permanent link to this record |
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Author |
Yusupov, M.; Bultinck, E.; Depla, D.; Bogaerts, A. |
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Title |
Elucidating the asymmetric behavior of the discharge in a dual magnetron sputter deposition system |
Type |
A1 Journal article |
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Year |
2011 |
Publication |
Applied physics letters |
Abbreviated Journal |
Appl Phys Lett |
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Volume |
98 |
Issue |
13 |
Pages |
131502-131502,3 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
A magnetron discharge is characterized by drifts of the charged particles guiding center, caused by the magnetic field, in contrast to unmagnetized discharges. Because of these drifts, a pronounced asymmetry of the discharge can be observed in a dual magnetron setup. In this work, it is found that the shape of the discharge in a dual magnetron configuration depends on the magnetic field configuration. In a closed configuration, strong drifts were observed in one preferential direction, whereas in a mirror configuration the deflection of the discharge was not so pronounced. Our calculations confirm experimental observations. |
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Publisher |
American Institute of Physics |
Place of Publication |
New York, N.Y. |
Editor |
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Language |
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Wos |
000289153600017 |
Publication Date |
2011-04-01 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0003-6951; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
3.411 |
Times cited |
4 |
Open Access |
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Notes |
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Approved |
Most recent IF: 3.411; 2011 IF: 3.844 |
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Call Number |
UA @ lucian @ c:irua:87867 |
Serial |
1026 |
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Permanent link to this record |
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Author |
Ghasemitarei, M.; Ghorbi, T.; Yusupov, M.; Zhang, Y.; Zhao, T.; Shali, P.; Bogaerts, A. |
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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 |
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Keywords |
A1 Journal Article; plasma medicine; reactive oxygen and; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ; |
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Abstract |
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. |
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Place of Publication |
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Language |
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Wos |
001071356400001 |
Publication Date |
2023-09-11 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
2218-273X |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
|
Times cited |
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Open Access |
Not_Open_Access |
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Notes |
This research received no external funding. |
Approved |
Most recent IF: NA |
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Call Number |
PLASMANT @ plasmant @c:irua:200380 |
Serial |
8958 |
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Permanent link to this record |
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Author |
Ghasemitarei, M.; Yusupov, M.; Razzokov, J.; Shokri, B.; Bogaerts, A. |
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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 |
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Volume |
674 |
Issue |
|
Pages |
108114 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
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. |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Wos |
000525439700011 |
Publication Date |
2019-09-23 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0003-9861 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
3.165 |
Times cited |
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Open Access |
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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 |
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Call Number |
PLASMANT @ plasmant @c:irua:163474 |
Serial |
5372 |
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Permanent link to this record |
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Author |
Kovács, A.; Yusupov, M.; Cornet, I.; Billen, P.; Neyts, E.C. |
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Title |
Effect of natural deep eutectic solvents of non-eutectic compositions on enzyme stability |
Type |
A1 Journal article |
|
Year |
2022 |
Publication |
Journal Of Molecular Liquids |
Abbreviated Journal |
J Mol Liq |
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Volume |
366 |
Issue |
|
Pages |
120180-17 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Biochemical Wastewater Valorization & Engineering (BioWaVE); Intelligence in PRocesses, Advanced Catalysts and Solvents (iPRACS) |
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Abstract |
Natural deep eutectic solvents (NADES) represent a green alternative to common organic solvents in the biochemical industry due to their benign behavior and tailorable properties, in particular as media for enzymatic reactions. However, to fully exploit their potential in enzymatic reactions, there is a need for a more fundamental understanding of how these neoteric solvents influence the course of these reac-tions. Thus, the aim of this study is to investigate the influence of NADES with various molar composi-tions on the stability and structure of enzymes, applying molecular dynamics simulations. This can help to better understand the effect of individual compounds of NADES, in addition to eutectic mixtures. More specifically, we simulate the behavior of Candida antarctica lipase B (CALB) enzyme in NADES com-posed of choline chloride with either urea, ethylene glycol or glycerol. Hereto, we monitor the NADES microstructure, the general stability of the enzyme and changes in the structure of its active sites and sur-face residues. Our simulations show that none of the studied NADES systems significantly disrupt the microstructure of the solvent or the stability of the CALB enzyme within the time scales of the simula-tions. The enzyme preserves its initial structure, size and intra-chain hydrogen bonds in all investigated compositions and, for the first time reported, also in NADES with increased hydrogen bond donating com-pound ratios. As the main novelty, our results indicate that, in addition to the composition, the molar ratio can be an additional variable to fine-tune the physicochemical properties of NADES without altering the enzyme characteristics. These findings could facilitate the development and application of task -tailored NADES media for biocatalytic processes. (c) 2022 Elsevier B.V. All rights reserved. |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Language |
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Wos |
000865431800010 |
Publication Date |
2022-08-25 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0167-7322 |
ISBN |
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Additional Links |
UA library record; WoS full record |
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Impact Factor |
6 |
Times cited |
|
Open Access |
Not_Open_Access |
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Notes |
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Approved |
Most recent IF: 6 |
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Call Number |
UA @ admin @ c:irua:191538 |
Serial |
7265 |
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Permanent link to this record |
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Author |
Yusupov, M.; Wende, K.; Kupsch, S.; Neyts, E.C.; Reuter, S.; Bogaerts, A. |
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Title |
Effect of head group and lipid tail oxidation in the cell membrane revealed through integrated simulations and experiments |
Type |
A1 Journal article |
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Year |
2017 |
Publication |
Scientific reports |
Abbreviated Journal |
Sci Rep-Uk |
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Volume |
7 |
Issue |
7 |
Pages |
5761 |
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Keywords |
A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
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. |
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Thesis |
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Language |
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Wos |
000405746500072 |
Publication Date |
2017-07-12 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
2045-2322 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
4.259 |
Times cited |
27 |
Open Access |
OpenAccess |
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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 |
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Call Number |
PLASMANT @ plasmant @ c:irua:144627 |
Serial |
4630 |
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Permanent link to this record |
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Author |
Matnazarova, S.; Khalilov, U.; Yusupov, M. |
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Title |
Effect of endohedral nickel atoms on the hydrophilicity of carbon nanotubes |
Type |
A1 Journal article |
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Year |
2023 |
Publication |
Molecular simulation |
Abbreviated Journal |
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Volume |
49 |
Issue |
17 |
Pages |
1575-1581 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
Carbon nanotubes (CNTs) have been successfully used in biomedicine, including cancer therapy, due to their unique physico-chemical properties. Because pristine CNTs exhibit hydrophobic behaviour, they can have a cytotoxic effect on cells, which limits their practical use in biomedicine. The toxicity of CNTs can be reduced by adding water-soluble functional radicals to their surface, i.e. by increasing their hydrophilicity. Another possibility for increasing the hydrophilicity of CNTs is probably filling them with endohedral metal atoms, which has not yet been studied. Thus, in this study, we use computer simulations to investigate the combined effect of endohedral nickel atoms and functional groups on the hydrophilicity of CNTs. Our simulation results show that the introduction of endohedral nickel atoms into CNTs increases their binding energy with functional groups. We also find that the addition of functional groups to the surface of CNT, along with filling it with endohedral nickel atoms, leads to an increase in the dipole moment of the CNT as well as its interaction energy with water, thereby increasing the hydrophilicity of the CNT and, consequently, its solubility in water. This, in turn, can lead to a decrease in CNT toxicity. |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Editor |
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Language |
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Wos |
001059544800001 |
Publication Date |
2023-09-06 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0892-7022 |
ISBN |
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Additional Links |
UA library record; WoS full record |
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Impact Factor |
2.1 |
Times cited |
|
Open Access |
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Notes |
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Approved |
Most recent IF: 2.1; 2023 IF: 1.254 |
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Call Number |
UA @ admin @ c:irua:199261 |
Serial |
9027 |
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Permanent link to this record |
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Author |
Ghasemitarei, M.; Privat-Maldonado, A.; Yusupov, M.; Rahnama, S.; Bogaerts, A.; Ejtehadi, M.R. |
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Title |
Effect of Cysteine Oxidation in SARS-CoV-2 Receptor-Binding Domain on Its Interaction with Two Cell Receptors: Insights from Atomistic Simulations |
Type |
A1 Journal article |
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Year |
2022 |
Publication |
Journal Of Chemical Information And Modeling |
Abbreviated Journal |
J Chem Inf Model |
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Volume |
62 |
Issue |
1 |
Pages |
129-141 |
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Keywords |
A1 Journal article; Pharmacology. Therapy; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
Binding of the SARS-CoV-2 S-glycoprotein to cell receptors is vital for the entry of the virus into cells and subsequent infection. ACE2 is the main cell receptor for SARS-CoV-2, which can attach to the C-terminal receptor-binding domain (RBD) of the SARS-CoV-2 S-glycoprotein. The GRP78 receptor plays an anchoring role, which attaches to the RBD and increases the chance of other RBDs binding to ACE2. Although high levels of reactive oxygen and nitrogen species (RONS) are produced during viral infections, it is not clear how they affect the RBD structure and its binding to ACE2 and GRP78. In this research, we apply molecular dynamics simulations to study the effect of oxidation of the highly reactive cysteine (Cys) amino acids of the RBD on its binding to ACE2 and GRP78. The interaction energy of both ACE2 and GRP78 with the whole RBD, as well as with the RBD main regions, is compared in both the native and oxidized RBDs. Our results show that the interaction energy between the oxidized RBD and ACE2 is strengthened by 155 kJ/mol, increasing the binding of the RBD to ACE2 after oxidation. In addition, the interaction energy between the RBD and GRP78 is slightly increased by 8 kJ/mol after oxidation, but this difference is not significant. Overall, these findings highlight the role of RONS in the binding of the SARS-CoV-2 S-glycoprotein to host cell receptors and suggest an alternative mechanism by which RONS could modulate the entrance of viral particles into the cells. |
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Publisher |
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Place of Publication |
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Language |
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Wos |
000740019000001 |
Publication Date |
2022-01-10 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
1549-9596 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
5.6 |
Times cited |
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Open Access |
Not_Open_Access |
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Notes |
Fonds Wetenschappelijk Onderzoek, 1200219N ; Binding of the SARS-CoV-2 S-glycoprotein to cell receptors is vital for the entry of the virus into cells and subsequent infection. ACE2 is the main cell receptor for SARS-CoV-2, which can attach to the C-terminal receptor-binding domain (RBD) of the SARS-CoV-2 S-glycoprotein. The GRP78 receptor plays an anchoring role, which attaches to the RBD and increases the chance of other RBDs binding to ACE2. Although high levels of reactive oxygen and nitrogen species (RONS) are produced during viral infections, it is not clear how they affect the RBD structure and its binding to ACE2 and GRP78. In this research, we apply molecular dynamics simulations to study the effect of oxidation of the highly reactive cysteine (Cys) amino acids of the RBD on its binding to ACE2 and GRP78. The interaction energy of both ACE2 and GRP78 with the whole RBD, as well as with the RBD main regions, is compared in both the native and oxidized RBDs. Our results show that the interaction energy between the oxidized RBD and ACE2 is strengthened by 155 kJ/mol, increasing the binding of the RBD to ACE2 after oxidation. In addition, the interaction energy between the RBD and GRP78 is slightly increased by 8 kJ/mol after oxidation, but this difference is not significant. Overall, these findings highlight the role of RONS in the binding of the SARS-CoV-2 S-glycoprotein to host cell receptors and suggest an alternative mechanism by which RONS could modulate the entrance of viral particles into the cells. |
Approved |
Most recent IF: 5.6 |
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Call Number |
PLASMANT @ plasmant @c:irua:185485 |
Serial |
7050 |
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Permanent link to this record |
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Author |
Tampieri, F.; Espona-Noguera, A.; Labay, C.; Ginebra, M.-P.; Yusupov, M.; Bogaerts, A.; Canal, C. |
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Title |
Does non-thermal plasma modify biopolymers in solution? A chemical and mechanistic study for alginate |
Type |
A1 Journal Article |
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Year |
2023 |
Publication |
Biomaterials Science |
Abbreviated Journal |
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Volume |
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Issue |
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Pages |
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Keywords |
A1 Journal Article; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ; |
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Abstract |
In the last decades, non-thermal plasma has been extensively investigated as a relevant tool for various biomedical applications, ranging from tissue decontamination to regeneration and from skin treatment to tumor therapies. This high versatility is due to the different kinds and amount of reactive oxygen and nitrogen species that can be generated during a plasma treatment and put in contact with the biological target. Some recent studies report that solutions of biopolymers with the ability to generate hydrogels, when treated with plasma, can enhance the generation of reactive species and influence their stability, resulting thus in the ideal media for indirect treatments of biological targets. The direct effects of the plasma treatment on the structure of biopolymers in water solution, as well as the chemical mechanisms responsible for the enhanced generation of RONS, are not yet fully understood. In this study, we aim at filling this gap by investigating, on the one hand, the nature and extent of the modifications induced by plasma treatment in alginate solutions, and, on the other hand, at using this information to explain the mechanisms responsible for the enhanced generation of reactive species as a consequence of the treatment. The approach we use is twofold: (i) investigating the effects of plasma treatment on alginate solutions, by size exclusion chromatography, rheology and scanning electron microscopy and (ii) study of a molecular model (glucuronate) sharing its chemical structure, by chromatography coupled with mass spectrometry and by molecular dynamics simulations. Our results point out the active role of the biopolymer chemistry during direct plasma treatment. Short-lived reactive species, such as OH radicals and O atoms, can modify the polymer structure, affecting its functional groups and causing partial fragmentation. Some of these chemical modifications, like the generation of organic peroxide, are likely responsible for the secondary generation of long-lived reactive species such as hydrogen peroxide and nitrite ions. This is relevant in view of using biocompatible hydrogels as vehicles for storage and delivery reactive species for targeted therapies. |
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Place of Publication |
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Language |
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Wos |
000973699000001 |
Publication Date |
2023-04-11 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
2047-4830 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
6.6 |
Times cited |
|
Open Access |
Not_Open_Access |
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Notes |
Agència de Gestió d’Ajuts Universitaris i de Recerca, SGR2022-1368 ; H2020 European Research Council, 714793 ; European Cooperation in Science and Technology, CA19110 CA20114 ; Secretaría de Estado de Investigación, Desarrollo e Innovación, PID2019-103892RB-I00/AEI/10.13039/501100011033 ; We thank Gonzalo Rodríguez Cañada and Xavier Solé-Martí (Universitat Politècnica de Catalunya) for help in collecting some of the experimental data and for the useful discussions. This work has been primarily funded by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 714793). The authors acknowledge MINECO for PID2019103892RB-I00/AEI/10.13039/501100011033 project (CC). The authors belong to SGR2022-1368 (FT, AEN, CL, MPG, CC) and acknowledge Generalitat de Catalunya for the ICREA Academia Award for Excellence in Research of CC. We thank also COST Actions CA20114 (Therapeutical Applications of Cold Plasmas) and CA19110 (Plasma Applications for Smart and Sustainable Agriculture) for the stimulating environment provided. |
Approved |
Most recent IF: 6.6; 2023 IF: 4.21 |
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Call Number |
PLASMANT @ plasmant @c:irua:196773 |
Serial |
8794 |
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Permanent link to this record |
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Author |
Oliveira, M.C.; Yusupov, M.; Bogaerts, A.; Cordeiro, R.M. |
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Title |
Distribution of lipid aldehydes in phase-separated membranes: A molecular dynamics study |
Type |
A1 Journal article |
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Year |
2022 |
Publication |
Archives Of Biochemistry And Biophysics |
Abbreviated Journal |
Arch Biochem Biophys |
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Volume |
717 |
Issue |
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Pages |
109136 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
It is well established that lipid aldehydes (LAs) are able to increase the permeability of cell membranes and induce their rupture. However, it is not yet clear how LAs are distributed in phase-separated membranes (PSMs), which are responsible for the transport of selected molecules and intracellular signaling. Thus, we investigate here the distribution of LAs in a PSM by coarse-grained molecular dynamics simulations. Our results reveal that LAs derived from mono-unsaturated lipids tend to accumulate at the interface between the liquid-ordered/liquiddisordered domains, whereas those derived from poly-unsaturated lipids remain in the liquid-disordered domain. These results are important for understanding the effects caused by oxidized lipids in membrane structure, properties and organization. |
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Place of Publication |
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Editor |
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Language |
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Wos |
000767632000001 |
Publication Date |
2022-01-24 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0003-9861 |
ISBN |
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Additional Links |
UA library record; WoS full record |
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Impact Factor |
3.9 |
Times cited |
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Open Access |
OpenAccess |
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Notes |
We thank the University of Antwerp and the Coordination of Superior Level Staff Improvement (CAPES, Brazil) for the scholarship granted. The calculations were performed using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UAntwerpen), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UAntwerpen. |
Approved |
Most recent IF: 3.9 |
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Call Number |
PLASMANT @ plasmant @c:irua:185874 |
Serial |
6905 |
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Permanent link to this record |
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Author |
Tit, N.; Al Ezzi, M.M.; Abdullah, H.M.; Yusupov, M.; Kouser, S.; Bahlouli, H.; Yamani, Z.H. |
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Title |
Detection of CO2 using CNT-based sensors: Role of Fe catalyst on sensitivity and selectivity |
Type |
A1 Journal article |
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Year |
2017 |
Publication |
Materials chemistry and physics |
Abbreviated Journal |
Mater Chem Phys |
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Volume |
186 |
Issue |
186 |
Pages |
353-364 |
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|
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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|
Abstract |
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. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
Lausanne |
Editor |
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Language |
|
Wos |
000390621200044 |
Publication Date |
2016-11-04 |
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Series Editor |
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Series Title |
|
Abbreviated Series Title |
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Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
0254-0584 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
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|
Impact Factor |
2.084 |
Times cited |
17 |
Open Access |
Not_Open_Access |
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|
Notes |
|
Approved |
Most recent IF: 2.084 |
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|
Call Number |
UA @ lucian @ c:irua:140333 |
Serial |
4465 |
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Permanent link to this record |
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Author |
Neyts, E.C.; Yusupov, M.; Verlackt, C.C.; Bogaerts, A. |
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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 |
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|
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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|
Abstract |
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. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
London |
Editor |
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Language |
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Wos |
000338860300001 |
Publication Date |
2014-06-26 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
|
Series Issue |
|
Edition |
|
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|
ISSN |
0022-3727;1361-6463; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
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|
Impact Factor |
2.588 |
Times cited |
28 |
Open Access |
|
|
|
Notes |
|
Approved |
Most recent IF: 2.588; 2014 IF: 2.721 |
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|
Call Number |
UA @ lucian @ c:irua:117853 |
Serial |
472 |
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Permanent link to this record |
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Author |
Khalilov, U.; Uljayev, U.; Mehmonov, K.; Nematollahi, P.; Yusupov, M.; Neyts, E.C.; Neyts, E.C. |
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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 |
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|
Keywords |
A1 Journal article; Engineering sciences. Technology; Modelling and Simulation in Chemistry (MOSAIC); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
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. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Editor |
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Language |
|
Wos |
001142427400001 |
Publication Date |
2023-11-24 |
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Series Editor |
|
Series Title |
|
Abbreviated Series Title |
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|
Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
0360-3199 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
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|
Impact Factor |
7.2 |
Times cited |
|
Open Access |
Not_Open_Access |
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|
Notes |
|
Approved |
Most recent IF: 7.2; 2024 IF: 3.582 |
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|
Call Number |
UA @ admin @ c:irua:202315 |
Serial |
9006 |
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Permanent link to this record |
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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. |
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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 |
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Keywords |
A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
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. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
|
Editor |
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Language |
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Wos |
000897762100001 |
Publication Date |
2022-11-14 |
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Series Editor |
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Series Title |
|
Abbreviated Series Title |
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Series Volume |
|
Series Issue |
|
Edition |
|
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|
ISSN |
2192-2640 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
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|
Impact Factor |
10 |
Times cited |
|
Open Access |
OpenAccess |
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|
Notes |
National Research Foundation of Korea; Kementerian Pendidikan, 2020R1I1A1A01073071 2021R1A6A1A03038785 ; |
Approved |
Most recent IF: 10; 2023 IF: 5.11 |
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|
Call Number |
PLASMANT @ plasmant @c:irua:192804 |
Serial |
7242 |
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Permanent link to this record |
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Author |
Yusupov, M.; Bultinck, E.; Depla, D.; Bogaerts, A. |
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Title |
Behavior of electrons in a dual-magnetron sputter deposition system : a Monte Carlo model |
Type |
A1 Journal article |
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Year |
2011 |
Publication |
New journal of physics |
Abbreviated Journal |
New J Phys |
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Volume |
13 |
Issue |
|
Pages |
033018-033018,17 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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|
Abstract |
A Monte Carlo model has been developed for investigating the electron behavior in a dual-magnetron sputter deposition system. To describe the three-dimensional (3D) geometry, different reference frames, i.e. a local and a global coordinate system, were used. In this study, the influence of both closed and mirror magnetic field configurations on the plasma properties is investigated. In the case of a closed magnetic field configuration, the calculated electron trajectories show that if an electron is emitted in (or near) the center of the cathode, where the influence of the magnetic field is low, it is able to travel from one magnetron to the other. On the other hand, when an electron is created at the race track area, it is more or less trapped in the strong magnetic field and cannot easily escape to the second magnetron region. In the case of a mirror magnetic field configuration, irrespective of where the electron is emitted from the cathode, it cannot travel from one magnetron to the other because the magnetic field lines guide the electron to the substrate. Moreover, the electron density and electron impact ionization rate have been calculated and studied in detail for both configurations. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
Bristol |
Editor |
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Language |
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Wos |
000289064600001 |
Publication Date |
2011-03-15 |
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Series Editor |
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Series Title |
|
Abbreviated Series Title |
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Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
1367-2630; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
|
Impact Factor |
3.786 |
Times cited |
12 |
Open Access |
|
|
|
Notes |
|
Approved |
Most recent IF: 3.786; 2011 IF: 4.177 |
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|
Call Number |
UA @ lucian @ c:irua:87544 |
Serial |
224 |
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Permanent link to this record |
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Author |
Yusupov, M.; Neyts, E.C.; Khalilov, U.; Snoeckx, R.; van Duin, A.C.T.; Bogaerts, A. |
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Title |
Atomic-scale simulations of reactive oxygen plasma species interacting with bacterial cell walls |
Type |
A1 Journal article |
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Year |
2012 |
Publication |
New journal of physics |
Abbreviated Journal |
New J Phys |
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|
Volume |
14 |
Issue |
9 |
Pages |
093043 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
In recent years there has been growing interest in the use of low-temperature atmospheric pressure plasmas for biomedical applications. Currently, however, there is very little fundamental knowledge regarding the relevant interaction mechanisms of plasma species with living cells. In this paper, we investigate the interaction of important plasma species, such as O3, O2 and O atoms, with bacterial peptidoglycan (or murein) by means of reactive molecular dynamics simulations. Specifically, we use the peptidoglycan structure to model the gram-positive bacterium Staphylococcus aureus murein. Peptidoglycan is the outer protective barrier in bacteria and can therefore interact directly with plasma species. Our results demonstrate that among the species mentioned above, O3 molecules and especially O atoms can break important bonds of the peptidoglycan structure (i.e. CO, CN and CC bonds), which subsequently leads to the destruction of the bacterial cell wall. This study is important for gaining a fundamental insight into the chemical damaging mechanisms of the bacterial peptidoglycan structure on the atomic scale. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
Bristol |
Editor |
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Language |
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Wos |
000309393400001 |
Publication Date |
2012-09-27 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
1367-2630; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
|
Impact Factor |
3.786 |
Times cited |
47 |
Open Access |
|
|
|
Notes |
|
Approved |
Most recent IF: 3.786; 2012 IF: 4.063 |
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|
Call Number |
UA @ lucian @ c:irua:101014 |
Serial |
189 |
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Permanent link to this record |
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Author |
Razzokov, J.; Yusupov, M.; Cordeiro, R.M.; Bogaerts, A. |
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Title |
Atomic scale understanding of the permeation of plasma species across native and oxidized membranes |
Type |
A1 Journal article |
|
Year |
2018 |
Publication |
Journal of physics: D: applied physics |
Abbreviated Journal |
J Phys D Appl Phys |
|
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Volume |
51 |
Issue |
36 |
Pages |
365203 |
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|
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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|
Abstract |
Cold atmospheric plasmas (CAPs) have attracted significant interest for their potential benefits in medical applications, including cancer therapy. The therapeutic effects of CAPs are related to reactive oxygen and nitrogen species (ROS and RNS) present in the plasma. The impact of ROS has been extensively studied, but the role of RNS in CAP-treatment remains poorly understood at the molecular level. Here, we investigate the permeation of RNS and ROS across native and oxidized phospholipid bilayers (PLBs) by means of computer simulations. The results reveal significantly lower free energy barriers for RNS (i.e. NO, NO2, N2O4) and O3 compared to hydrophilic ROS, such as OH, HO2 and H2O2. This suggests that the investigated RNS and O3 can permeate more easily through both native and oxidized PLBs in comparison to hydrophilic ROS, indicating their potentially important role in plasma medicine. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Editor |
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Language |
|
Wos |
000441182400002 |
Publication Date |
2018-08-08 |
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Series Editor |
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Series Title |
|
Abbreviated Series Title |
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Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
0022-3727 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
|
Impact Factor |
2.588 |
Times cited |
10 |
Open Access |
OpenAccess |
|
|
Notes |
M Y gratefully acknowledges financial support from the Research Foundation—Flanders (FWO), grant 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. RMC thanks FAPESP and CNPq for financial support (grants 2012/50680-5 and 459270/2014-1, respectively). |
Approved |
Most recent IF: 2.588 |
|
|
Call Number |
PLASMANT @ plasmant @c:irua:152824 |
Serial |
5005 |
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Permanent link to this record |
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Author |
Yusupov, M. |
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Title |
Atomic scale simulations for a better insight in plasma medicine |
Type |
Doctoral thesis |
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Year |
2014 |
Publication |
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Abbreviated Journal |
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Volume |
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Issue |
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Pages |
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Keywords |
Doctoral thesis; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
Antwerpen |
Editor |
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Language |
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Wos |
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Publication Date |
0000-00-00 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
|
ISBN |
|
Additional Links |
UA library record |
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|
Impact Factor |
|
Times cited |
|
Open Access |
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|
Notes |
|
Approved |
Most recent IF: NA |
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|
Call Number |
UA @ lucian @ c:irua:117837 |
Serial |
188 |
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Permanent link to this record |
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Author |
Yusupov, M.; Yan, D.; Cordeiro, R.M.; Bogaerts, A. |
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Title |
Atomic scale simulation of H2O2permeation through aquaporin: toward the understanding of plasma cancer treatment |
Type |
A1 Journal article |
|
Year |
2018 |
Publication |
Journal of physics: D: applied physics |
Abbreviated Journal |
J Phys D Appl Phys |
|
|
Volume |
51 |
Issue |
12 |
Pages |
125401 |
|
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
Experiments have demonstrated the potential selective anticancer capacity of cold atmospheric plasmas (CAPs), but the underlying mechanisms remain unclear. Using computer simulations, we try to shed light on the mechanism of selectivity, based on aquaporins (AQPs), i.e. transmembrane protein channels transferring external H 2 O 2 and other reactive oxygen species, created e.g. by CAPs, to the cell interior. Specifically, we perform molecular dynamics simulations for the permeation of H 2 O 2 through AQP1 (one of the members of the AQP family) and the palmitoyl-oleoyl-phosphatidylcholine (POPC) phospholipid bilayer (PLB). The free energy barrier of H 2 O 2 across AQP1 is lower than for the POPC PLB, while the permeability coefficient, calculated using the free energy and diffusion rate profiles, is two orders of magnitude higher. This indicates that the delivery of H 2 O 2 into the cell interior should be through AQP. Our study gives a better insight into the role of AQPs in the selectivity of CAPs for treating cancer cells. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Editor |
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Language |
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Wos |
000426378100001 |
Publication Date |
2018-02-28 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
0022-3727 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
|
Impact Factor |
2.588 |
Times cited |
7 |
Open Access |
OpenAccess |
|
|
Notes |
MY gratefully acknowledges financial support from the Research Foundation—Flanders (FWO) via Grant No. 1200216N and a travel grant to George Washington University (GWU). 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 Super- computer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. Work at GWU was supported by the National Science Foundation, grant 1465061. RMC thanks FAPESP and CNPq for finan- cial support (Grant Nos. 2012/50680-5 and 459270/2014-1, respectively). |
Approved |
Most recent IF: 2.588 |
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|
Call Number |
PLASMANT @ plasmant @c:irua:149382 |
Serial |
4811 |
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Permanent link to this record |
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Author |
Khalilov, U.; Yusupov, M.; Eshonqulov, Gb.; Neyts, Ec.; Berdiyorov, Gr. |
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Title |
Atomic level mechanisms of graphene healing by methane-based plasma radicals |
Type |
A1 Journal article |
|
Year |
2023 |
Publication |
FlatChem |
Abbreviated Journal |
FlatChem |
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Volume |
39 |
Issue |
|
Pages |
100506 |
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Keywords |
A1 Journal article; Condensed Matter Theory (CMT); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Editor |
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Language |
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Wos |
000990342500001 |
Publication Date |
2023-04-19 |
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Series Editor |
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Series Title |
|
Abbreviated Series Title |
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Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
2452-2627 |
ISBN |
|
Additional Links |
UA library record; WoS full record |
|
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Impact Factor |
6.2 |
Times cited |
|
Open Access |
OpenAccess |
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|
Notes |
U.K., M.Y. and G.B.E. acknowledge the support of the Agency for Innovative Development of the Republic of Uzbekistan (Grant numbers F-FA-2021-512 and FZ-2020092435). The computational resources and services used in this work were partially provided by the HPC core facility CalcUA of the Universiteit Antwerpen and VSC (Flemish Supercomputer Center), funded by the FWO and the Flemish Government. |
Approved |
Most recent IF: 6.2; 2023 IF: NA |
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Call Number |
PLASMANT @ plasmant @c:irua:197442 |
Serial |
8813 |
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Permanent link to this record |
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Author |
Hoon Park, J.; Kumar, N.; Hoon Park, D.; Yusupov, M.; Neyts, E.C.; Verlackt, C.C.W.; Bogaerts, A.; Ho Kang, M.; Sup Uhm, H.; Ha Choi, E.; Attri, P.; |
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Title |
A comparative study for the inactivation of multidrug resistance bacteria using dielectric barrier discharge and nano-second pulsed plasma |
Type |
A1 Journal article |
|
Year |
2015 |
Publication |
Scientific reports |
Abbreviated Journal |
Sci Rep-Uk |
|
|
Volume |
5 |
Issue |
5 |
Pages |
13849 |
|
|
Keywords |
A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
|
|
Abstract |
Bacteria can be inactivated through various physical and chemical means, and these have always been the focus of extensive research. To further improve the methodology for these ends, two types of plasma systems were investigated: nano-second pulsed plasma (NPP) as liquid discharge plasma and an Argon gas-feeding dielectric barrier discharge (Ar-DBD) as a form of surface plasma. To understand the sterilizing action of these two different plasma sources, we performed experiments with Staphylococcus aureus (S. aureus) bacteria (wild type) and multidrug resistant bacteria (Penicillum-resistant, Methicillin-resistant and Gentamicin-resistant). We observed that both plasma sources can inactivate both the wild type and multidrug-resistant bacteria to a good extent. Moreover, we observed a change in the surface morphology, gene expression and β-lactamase activity. Furthermore, we used X-ray photoelectron spectroscopy to investigate the variation in functional groups (C-H/C-C, C-OH and C=O) of the peptidoglycan (PG) resulting from exposure to plasma species. To obtain atomic scale insight in the plasma-cell interactions and support our experimental observations, we have performed molecular dynamics simulations to study the effects of plasma species, such as OH, H2O2, O, O3, as well as O2 and H2O, on the dissociation/formation of above mentioned functional groups in PG. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
Nature Publishing Group |
Place of Publication |
London |
Editor |
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Language |
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Wos |
000360909000001 |
Publication Date |
2015-09-09 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
2045-2322; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
4.259 |
Times cited |
32 |
Open Access |
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Notes |
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Approved |
Most recent IF: 4.259; 2015 IF: 5.578 |
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Call Number |
c:irua:127410 |
Serial |
419 |
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Permanent link to this record |