Records |
Author |
Oliveira, M.C.; Yusupov, M.; Bogaerts, A.; Cordeiro, R.M. |
Title |
Molecular dynamics simulations of mechanical stress on oxidized membranes |
Type |
A1 Journal article |
Year |
2019 |
Publication |
Biophysical chemistry |
Abbreviated Journal |
Biophys Chem |
Volume |
254 |
Issue |
|
Pages |
106266 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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. |
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 |
000502890900015 |
Publication Date |
2019-09-13 |
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 |
0301-4622 |
ISBN ![sorted by ISBN field, ascending order (up)](img/sort_asc.gif) |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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 |
Call Number |
PLASMANT @ plasmant @c:irua:163477 |
Serial |
5374 |
Permanent link to this record |
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Author |
Oliveira, M.C.; Yusupov, M.; Bogaerts, A.; Cordeiro, R.M. |
Title |
How do nitrated lipids affect the properties of phospholipid membranes? |
Type |
A1 Journal article |
Year |
2020 |
Publication |
Archives Of Biochemistry And Biophysics |
Abbreviated Journal |
Arch Biochem Biophys |
Volume |
695 |
Issue |
|
Pages |
108548 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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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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 |
000594173400010 |
Publication Date |
0000-00-00 |
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 ![sorted by ISBN field, ascending order (up)](img/sort_asc.gif) |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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 |
Call Number |
PLASMANT @ plasmant @c:irua:173861 |
Serial |
6440 |
Permanent link to this record |
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Author |
Oliveira, M.C.; Yusupov, M.; Bogaerts, A.; Cordeiro, R.M. |
Title |
Lipid Oxidation: Role of Membrane Phase-Separated Domains |
Type |
A1 Journal Article |
Year |
2021 |
Publication |
Journal Of Chemical Information And Modeling |
Abbreviated Journal |
J Chem Inf Model |
Volume |
61 |
Issue |
6 |
Pages |
2857-2868 |
Keywords |
A1 Journal Article; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ; |
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. |
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 |
000669541400034 |
Publication Date |
2021-06-28 |
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 ![sorted by ISBN field, ascending order (up)](img/sort_asc.gif) |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
Impact Factor |
3.76 |
Times cited |
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Open Access |
OpenAccess |
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 |
Call Number |
PLASMANT @ plasmant @c:irua:179766 |
Serial |
6806 |
Permanent link to this record |
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Author |
Oliveira, M.C.; Yusupov, M.; Bogaerts, A.; Cordeiro, R.M. |
Title |
Distribution of lipid aldehydes in phase-separated membranes: A molecular dynamics study |
Type |
A1 Journal article |
Year |
2022 |
Publication |
Archives Of Biochemistry And Biophysics |
Abbreviated Journal |
Arch Biochem Biophys |
Volume |
717 |
Issue |
|
Pages |
109136 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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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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 |
000767632000001 |
Publication Date |
2022-01-24 |
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 ![sorted by ISBN field, ascending order (up)](img/sort_asc.gif) |
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Additional Links |
UA library record; WoS full record |
Impact Factor |
3.9 |
Times cited |
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Open Access |
OpenAccess |
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 |
Call Number |
PLASMANT @ plasmant @c:irua:185874 |
Serial |
6905 |
Permanent link to this record |