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Oliveira, M.C.; Cordeiro, R.M.; Bogaerts, A. |
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Title |
Effect of lipid oxidation on the channel properties of Cx26 hemichannels : a molecular dynamics study |
Type |
A1 Journal article |
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Year  |
2023 |
Publication |
Archives of biochemistry and biophysics |
Abbreviated Journal |
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Volume |
746 |
Issue |
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Pages |
109741-12 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
Intercellular communication plays a crucial role in cancer, as well as other diseases, such as inflammation, tissue degeneration, and neurological disorders. One of the proteins responsible for this, are connexins (Cxs), which come together to form a hemichannel. When two hemichannels of opposite cells interact with each other, they form a gap junction (GJ) channel, connecting the intracellular space of these cells. They allow the passage of ions, reactive oxygen and nitrogen species (RONS), and signaling molecules from the interior of one cell to another cell, thus playing an essential role in cell growth, differentiation, and homeostasis. The importance of GJs for disease induction and therapy development is becoming more appreciated, especially in the context of oncology. Studies have shown that one of the mechanisms to control the formation and disruption of GJs is mediated by lipid oxidation pathways, but the underlying mechanisms are not well understood. In this study, we performed atomistic molecular dynamics simulations to evaluate how lipid oxidation influences the channel properties of Cx26 hemichannels, such as channel gating and permeability. Our results demonstrate that the Cx26 hemichannel is more compact in the presence of oxidized lipids, decreasing its pore diameter at the extracellular side and increasing it at the amino terminus domains, respectively. The permeability of the Cx26 hemichannel for water and RONS molecules is higher in the presence of oxidized lipids. The latter may facilitate the intracellular accumulation of RONS, possibly increasing oxidative stress in cells. A better understanding of this process will help to enhance the efficacy of oxidative stress-based cancer treatments. |
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001079100300001 |
Publication Date |
2023-09-07 |
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0003-9861; 1096-0384 |
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UA library record; WoS full record |
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no |
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Call Number |
UA @ admin @ c:irua:200282 |
Serial |
9028 |
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Author |
Abduvokhidov, D.; Yusupov, M.; Shahzad, A.; Attri, P.; Shiratani, M.; Oliveira, M.C.; Razzokov, J. |
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Title |
Unraveling the Transport Properties of RONS across Nitro-Oxidized Membranes |
Type |
A1 Journal Article |
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Year |
2023 |
Publication |
Biomolecules |
Abbreviated Journal |
Biomolecules |
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Volume |
13 |
Issue |
7 |
Pages |
1043 |
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Keywords |
A1 Journal Article; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ; |
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Abstract |
The potential of cold atmospheric plasma (CAP) in biomedical applications has received significant interest, due to its ability to generate reactive oxygen and nitrogen species (RONS). Upon exposure to living cells, CAP triggers alterations in various cellular components, such as the cell membrane. However, the permeation of RONS across nitrated and oxidized membranes remains understudied. To address this gap, we conducted molecular dynamics simulations, to investigate the permeation capabilities of RONS across modified cell membranes. This computational study investigated the translocation processes of less hydrophilic and hydrophilic RONS across the phospholipid bilayer (PLB), with various degrees of oxidation and nitration, and elucidated the impact of RONS on PLB permeability. The simulation results showed that less hydrophilic species, i.e., NO, NO2, N2O4, and O3, have a higher penetration ability through nitro-oxidized PLB compared to hydrophilic RONS, i.e., HNO3, s-cis-HONO, s-trans-HONO, H2O2, HO2, and OH. In particular, nitro-oxidation of PLB, induced by, e.g., cold atmospheric plasma, has minimal impact on the penetration of free energy barriers of less hydrophilic species, while it lowers these barriers for hydrophilic RONS, thereby enhancing their translocation across nitro-oxidized PLB. This research contributes to a better understanding of the translocation abilities of RONS in the field of plasma biomedical applications and highlights the need for further analysis of their role in intracellular signaling pathways. |
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001035160000001 |
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2023-06-27 |
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2218-273X |
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UA library record; WoS full record; WoS citing articles |
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Not_Open_Access |
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Notes |
This research was funded by the Innovative Development Agency of the Republic of Uzbekistan, grant number FZ-2020092817. |
Approved |
Most recent IF: NA |
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Call Number |
PLASMANT @ plasmant @c:irua:198154 |
Serial |
8803 |
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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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Wos |
000767632000001 |
Publication Date |
2022-01-24 |
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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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Author |
Oliveira, M.C.; Verswyvel, H.; Smits, E.; Cordeiro, R.M.; Bogaerts, A.; Lin, A. |
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Title |
The pro- and anti-tumoral properties of gap junctions in cancer and their role in therapeutic strategies |
Type |
A1 Journal article |
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Year |
2022 |
Publication |
Redox Biology |
Abbreviated Journal |
Redox Biol |
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Volume |
57 |
Issue |
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Pages |
102503 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Center for Oncological Research (CORE) |
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Abstract |
Gap junctions (GJs), essential structures for cell-cell communication, are made of two hemichannels (commonly called connexons), one on each adjacent cell. Found in almost all cells, GJs play a pivotal role in many physiological and cellular processes, and have even been linked to the progression of diseases, such as cancer. Modulation of GJs is under investigation as a therapeutic strategy to kill tumor cells. Furthermore, GJs have also been studied for their key role in activating anti-cancer immunity and propagating radiation- and oxidative stress-induced cell death to neighboring cells, a process known as the bystander effect. While, gap junction (GJ)based therapeutic strategies are being developed, one major challenge has been the paradoxical role of GJs in both tumor progression and suppression, based on GJ composition, cancer factors, and tumoral context. Therefore, understanding the mechanisms of action, regulation, and the dual characteristics of GJs in cancer is critical for developing effective therapeutics. In this review, we provide an overview of the current under standing of GJs structure, function, and paradoxical pro- and anti-tumoral role in cancer. We also discuss the treatment strategies to target these GJs properties for anti-cancer responses, via modulation of GJ function. |
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Wos |
000871090800004 |
Publication Date |
0000-00-00 |
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Edition |
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ISSN |
2213-2317 |
ISBN |
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Additional Links |
UA library record; WoS full record |
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Impact Factor |
11.4 |
Times cited |
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Open Access |
OpenAccess |
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Notes |
We thank Coordination of Superior Level Staff Improvement (CAPES, Brazil) for the scholarship granted, and the Turing HPC infrastructure at the CalcUA core facility of the University of Antwerp, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the University of Antwerp, for providing the computational resources needed for running the simulations. This work was also funded in part by the funded by the Research Foundation – Flanders (FWO) and the Flemish Government. The FWO fellowships and grants that funded this work include: 12S9221N (Abraham Lin), G044420N (Abraham Lin and Annemie Bogaerts), and 1S67621N (Hanne Verswyvel). Figs. 1, 4 and 5 were created in BioRender.com. |
Approved |
Most recent IF: 11.4 |
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Call Number |
PLASMANT @ plasmant @c:irua:191362 |
Serial |
7112 |
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Author |
Oliveira, M.C. |
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Title |
Influence of phase-separated domains on the permeability of oxidized lipid membranes |
Type |
Doctoral thesis |
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Year |
2022 |
Publication |
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Abbreviated Journal |
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Volume |
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Issue |
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Pages |
151 p. |
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Keywords |
Doctoral thesis; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
Biological membranes are under constant attack of reactive oxygen and nitrogen species (RONS), which may lead to a complex mixture of nitro-oxidized lipids that are responsible for structural and dynamic changes on the membrane. Because of that, nitro-oxidized lipids are also associated with several tumors and inflammatory and neurodegenerative diseases. Moreover, lipid oxidation may induce membrane phase-separated domains, which also drastically affect the membrane function. Evidence suggests that domain interfaces are “hot spots” for pore formation, but the underlying mechanisms remain elusive. There is an urgent need for an improved understanding of oxidation-induced phase separation on membrane properties. Likewise, the molecular structure at domain interfaces still needs to be elucidated. To evaluate the effect of lipid nitro-oxidation on the permeability of single-phase (homogeneous) and phase-separated (heterogeneous) phospholipid bilayers (PLBs), we performed atomistic molecular dynamics (MD) simulations using: (1) single-phase PLBs composed of several isomers of nitrated and/or oxidized lipids; (2) phase-separated PLBs composed of coexisting liquid ordered (Lo) and liquid disordered (Ld) domains, where the Ld domain is composed of non-oxidized and/or oxidized lipids. Our results show that nitrated lipids increase the membrane permeability of single-phase PLBs by three-fold compared to oxidized lipids. In addition, we show that oxidized lipids in the presence of nitrated lipids decrease the membrane permeability, suggesting an interaction between nitrated and oxidized lipids. Overall, the permeability of single-phase and phase-separated PLBs was comparable, and the presence of oxidized lipids increases the membrane permeability only in single-phase PLBs. Despite the latter, the presence of only 1.5% of lipid aldehydes at the Lo/Ld domain interfaces of phase-separated PLBs was able to increase the membrane permeability. In consequence of this, we also performed coarse-grained MD simulations to evaluate whether lipid aldehydes have a preference to accumulate at the interface between Lo/Ld domains. Our results show that lipid aldehydes derived from mono-unsaturated lipids accumulate at the interface, but those derived from poly-unsaturated lipids remain in the Ld domain. This study is of interest for photodynamic therapy and plasma medicine for cancer treatment, to understand the effects caused by RONS in cell membranes. |
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UA library record |
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Notes |
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Approved |
Most recent IF: NA |
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Call Number |
UA @ admin @ c:irua:191039 |
Serial |
7173 |
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Author |
Oliveira, M.C.; Yusupov, M.; Cordeiro, R.M.; Bogaerts, A. |
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Title |
Unraveling the permeation of reactive species across nitrated membranes by computer simulations |
Type |
A1 Journal Article;Reactive oxygen and nitrogen species |
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Year |
2021 |
Publication |
Computers In Biology And Medicine |
Abbreviated Journal |
Comput Biol Med |
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Volume |
136 |
Issue |
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Pages |
104768 |
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Keywords |
A1 Journal Article;Reactive oxygen and nitrogen species; Nitro-oxidative stress; Molecular dynamics simulations; Nitrated membranes; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ; |
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Abstract |
Reactive oxygen and nitrogen species (RONS) are involved in many biochemical processes, including nitrooxidative stress that causes cancer cell death, observed in cancer therapies such as photodynamic therapy and cold atmospheric plasma. However, their mechanisms of action and selectivity still remain elusive due to the complexity of biological cells. For example, it is not well known how RONS generated by cancer therapies permeate the cell membrane to cause nitro-oxidative damage. There are many studies dedicated to the permeation of RONS across native and oxidized membranes, but not across nitrated membranes, another lipid product also generated during nitro-oxidative stress. Herein, we performed molecular dynamics (MD) simulations to calculate the free energy barrier of RONS permeation across nitrated membranes. Our results show that hydrophilic RONS, such as hydroperoxyl radical (HO2) and peroxynitrous acid (ONOOH), have relatively low barriers compared to hydrogen peroxide (H2O2) and hydroxyl radical (HO), and are more prone to permeate the membrane than for the native or peroxidized membranes, and similar to aldehyde-oxidized membranes. Hydrophobic RONS like molecular oxygen (O2), nitrogen dioxide (NO2) and nitric oxide (NO) even have insignificant barriers for permeation. Compared to native and peroxidized membranes, nitrated membranes are more permeable, suggesting that we must not only consider oxidized membranes during nitro-oxidative stress, but also nitrated membranes, and their role in cancer therapies. |
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Wos |
000696938800003 |
Publication Date |
2021-08-17 |
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Series Issue |
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Edition |
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ISSN |
0010-4825 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
1.836 |
Times cited |
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Open Access |
OpenAccess |
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Notes |
We thank University of Antwerp and Coordination of Superior Level Staff Improvement (CAPES, Brazil) for the scholarship granted and for providing the computational resources needed for completion of this work. M. Yusupov acknowledges the Flanders Research Foundation (grant 1200219N) for financial support. |
Approved |
Most recent IF: 1.836 |
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Call Number |
PLASMANT @ plasmant @c:irua:181082 |
Serial |
6807 |
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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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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 |
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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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? |
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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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Abbreviated Series Title |
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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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Author |
Oliveira, M.C.; Yusupov, M.; Bogaerts, A.; Cordeiro, R.M. |
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Title |
Molecular dynamics simulations of mechanical stress on oxidized membranes |
Type |
A1 Journal article |
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Year |
2019 |
Publication |
Biophysical chemistry |
Abbreviated Journal |
Biophys Chem |
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Volume |
254 |
Issue |
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Pages |
106266 |
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Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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Abstract |
Biomembranes are under constant attack of free radicals that may lead to lipid oxidation in conditions of oxidative stress. The products generated during lipid oxidation are responsible for structural and dynamical changes which may jeopardize the membrane function. For instance, the local rearrangements of oxidized lipid molecules may induce membrane rupture. In this study, we investigated the effects of mechanical stress on oxidized phospholipid bilayers (PLBs). Model bilayers were stretched until pore formation (or poration) using nonequilibrium molecular dynamics simulations. We studied single-component homogeneous membranes composed of lipid oxidation products, as well as two-component heterogeneous membranes with coexisting native and oxidized domains. In homogeneous membranes, the oxidation products with —OH and —OOH groups reduced the areal strain required for pore formation, whereas the oxidation product with ]O group behaved similarly to the native membrane. In heterogeneous membranes composed of oxidized and non-oxidized domains, we tested the hypothesis according to which poration may be facilitated at the domain interface region. However, results were inconclusive due to their large statistical variance and sensitivity to simulation setup parameters. We pointed out important technical issues that need to be considered in future simulations of mechanically-induced poration of heterogeneous membranes. This research is of interest for photodynamic therapy and plasma medicine, because ruptured and intact plasma membranes are experimentally considered hallmarks of necrotic and apoptotic cell death. |
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Wos |
000502890900015 |
Publication Date |
2019-09-13 |
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Abbreviated Series Title |
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Edition |
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ISSN |
0301-4622 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.402 |
Times cited |
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Open Access |
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Notes |
São Paulo Research Foundation, 2012/50680-5 ; National Counsel of Technological and Scientific Development, 459270/2014-1 ; We are thankful for the financial support received from the São Paulo Research Foundation (FAPESP) (grant no. 2012/50680-5) and from the National Counsel of Technological and Scientific Development (CNPq) (grant no. 459270/2014-1). MCO acknowledges UFABC for the Master's scholarship granted. |
Approved |
Most recent IF: 2.402 |
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Call Number |
PLASMANT @ plasmant @c:irua:163477 |
Serial |
5374 |
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| Permanent link to this record |
