Records |
Author ![sorted by Author field, ascending order (up)](img/sort_asc.gif) |
Ghasemitarei, M.; Yusupov, M.; Razzokov, J.; Shokri, B.; Bogaerts, A. |
Title |
Transport of cystine across xC-antiporter |
Type |
A1 Journal article |
Year |
2019 |
Publication |
Archives of biochemistry and biophysics |
Abbreviated Journal |
Arch Biochem Biophys |
Volume |
664 |
Issue |
|
Pages |
117-126 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
Extracellular cystine (CYC) uptake by xC antiporter is important for the cell viability. Especially in cancer cells, the upregulation of xC activity is observed, which protects these cells from intracellular oxidative stress. Hence, inhibition of the CYC uptake may eventually lead to cancer cell death. Up to now, the molecular level mechanism of the CYC uptake by xC antiporter has not been studied in detail. In this study, we applied several different simulation techniques to investigate the transport of CYC through xCT, the light subunit of the xC antiporter, which is responsible for the CYC and glutamate translocation. Specifically, we studied the permeation of CYC across three model systems, i.e., outward facing (OF), occluded (OCC) and inward facing (IF) configurations of xCT. We also investigated the effect of mutation of Cys327 to Ala within xCT, which was also studied experimentally in literature. This allowed us to qualitatively compare our computation results with experimental observations, and thus, to validate our simulations. In summary, our simulations provide a molecular level mechanism of the transport of CYC across the xC antiporter, more specifically, which amino acid residues in the xC antiporter play a key role in the uptake, transport and release of CYC. |
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Wos |
000461411200014 |
Publication Date |
2019-02-07 |
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; WoS citing articles |
Impact Factor |
3.165 |
Times cited |
3 |
Open Access |
OpenAccess |
Notes |
Research Foundation − FlandersResearch Foundation − Flanders (FWO), 1200216N 1200219N ; Hercules FoundationHercules Foundation; Flemish GovernmentFlemish Government (department EWI); UAUA; M. Y. gratefully acknowledges financial support from the Research Foundation − Flanders (FWO), grant numbers 1200216N and 1200219N. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen, a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. Finally, we thank A. S. Mashayekh Esfehan and A. Mohseni for their important comments on the manuscript. |
Approved |
Most recent IF: 3.165 |
Call Number |
PLASMANT @ plasmant @UA @ admin @ c:irua:158571 |
Serial |
5183 |
Permanent link to this record |
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Author ![sorted by Author field, ascending order (up)](img/sort_asc.gif) |
Ghasemitarei, M.; Yusupov, M.; Razzokov, J.; Shokri, B.; Bogaerts, A. |
Title |
Effect of oxidative stress on cystine transportation by xC‾ antiporter |
Type |
A1 Journal article |
Year |
2019 |
Publication |
Archives of biochemistry and biophysics |
Abbreviated Journal |
Arch Biochem Biophys |
Volume |
674 |
Issue |
|
Pages |
108114 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
Abstract |
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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Wos |
000525439700011 |
Publication Date |
2019-09-23 |
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; WoS citing articles |
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 |
Call Number |
PLASMANT @ plasmant @c:irua:163474 |
Serial |
5372 |
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Author ![sorted by Author field, ascending order (up)](img/sort_asc.gif) |
Oliveira, M.C.; Cordeiro, R.M.; Bogaerts, A. |
Title |
Effect of lipid oxidation on the channel properties of Cx26 hemichannels : a molecular dynamics study |
Type |
A1 Journal article |
Year |
2023 |
Publication |
Archives of biochemistry and biophysics |
Abbreviated Journal |
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Volume |
746 |
Issue |
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Pages |
109741-12 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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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Wos |
001079100300001 |
Publication Date |
2023-09-07 |
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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; 1096-0384 |
ISBN |
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Additional Links |
UA library record; WoS full record |
Impact Factor |
3.9 |
Times cited |
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Open Access |
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Notes |
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Approved |
Most recent IF: 3.9; 2023 IF: 3.165 |
Call Number |
UA @ admin @ c:irua:200282 |
Serial |
9028 |
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Author ![sorted by Author field, ascending order (up)](img/sort_asc.gif) |
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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Wos |
000594173400010 |
Publication Date |
0000-00-00 |
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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; 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 ![sorted by Author field, ascending order (up)](img/sort_asc.gif) |
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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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 |
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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 |
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Author ![sorted by Author field, ascending order (up)](img/sort_asc.gif) |
Rezaei, M.; Ghasemitarei, M.; Razzokov, J.; Yusupov, M.; Ghorbanalilu, M.; Ejtehadi, M.R. |
Title |
In silico study of the impact of oxidation on pyruvate transmission across the hVDAC1 protein channel |
Type |
A1 Journal article |
Year |
2024 |
Publication |
Archives of biochemistry and biophysics |
Abbreviated Journal |
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Volume |
751 |
Issue |
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Pages |
109835-109837 |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
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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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 |
001127850500001 |
Publication Date |
2023-11-23 |
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; 1096-0384 |
ISBN |
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Additional Links |
UA library record; WoS full record |
Impact Factor |
3.9 |
Times cited |
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Open Access |
Not_Open_Access |
Notes |
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Approved |
Most recent IF: 3.9; 2024 IF: 3.165 |
Call Number |
UA @ admin @ c:irua:202185 |
Serial |
9046 |
Permanent link to this record |