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Author |
Khosravian, N.; Kamaraj, B.; Neyts, E.C.; Bogaerts, A. |
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Title |
Structural modification of P-glycoprotein induced by OH radicals: Insights from atomistic simulations |
Type |
A1 Journal article |
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Year |
2016 |
Publication |
Scientific reports |
Abbreviated Journal |
Sci Rep-Uk |
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Volume |
6 |
Issue |
6 |
Pages |
19466 |
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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 reports on the possible effects of OH radical impact on the transmembrane domain 6 of P-glycoprotein, TM6, which plays a crucial role in drug binding in human cells. For the first time, we employ molecular dynamics (MD) simulations based on the self-consistent charge density functional tight binding (SCC-DFTB) method to elucidate the potential sites of fragmentation and mutation in this domain upon impact of OH radicals, and to obtain fundamental information about the underlying reaction mechanisms. Furthermore, we apply non-reactive MD simulations to investigate the long-term effect of this mutation, with possible implications for drug binding. Our simulations indicate that the interaction of OH radicals with TM6 might lead to the breaking of C-C and C-N peptide bonds, which eventually cause fragmentation of TM6. Moreover, according to our simulations, the OH radicals can yield mutation in the aromatic ring of phenylalanine in TM6, which in turn affects its structure. As TM6 plays an important role in the binding of a range of cytotoxic drugs with P-glycoprotein, any changes in its structure are likely to affect the response of the tumor cell in chemotherapy. This is crucial for cancer therapies based on reactive oxygen species, such as plasma treatment. |
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Address  |
Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium |
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English |
Wos |
000369573900001 |
Publication Date |
2016-02-09 |
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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 |
7 |
Open Access |
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Notes |
The authors acknowledge financial support from the Fund for Scientific Research (FWO) Flanders, grant number G012413N. The calculations were performed in part using the Turing HPC infrastructure of 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 Universiteit Antwerpen.” |
Approved |
Most recent IF: 4.259 |
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Call Number |
c:irua:131610 |
Serial |
4031 |
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Author |
Attri, P.; Yusupov, M.; Park, J.H.; Lingamdinne, L.P.; Koduru, J.R.; Shiratani, M.; Choi, E.H.; Bogaerts, A. |
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Title |
Mechanism and comparison of needle-type non-thermal direct and indirect atmospheric pressure plasma jets on the degradation of dyes |
Type |
A1 Journal article |
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Year |
2016 |
Publication |
Scientific reports |
Abbreviated Journal |
Sci Rep-Uk |
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Volume |
6 |
Issue |
6 |
Pages |
34419 |
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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 |
Purified water supply for human use, agriculture and industry is the major global priority nowadays. The advanced oxidation process based on atmospheric pressure non-thermal plasma (NTP) has been used for purification of wastewater, although the underlying mechanisms of degradation of organic pollutants are still unknown. In this study we employ two needle-type atmospheric pressure non-thermal plasma jets, i.e., indirect (ID-APPJ) and direct (D-APPJ) jets operating at Ar feed gas, for the treatment of methylene blue, methyl orange and congo red dyes, for two different times (i.e., 20 min and 30 min). Specifically, we study the decolorization/degradation of all three dyes using the above mentioned plasma sources, by means of UV-Vis spectroscopy, HPLC and a density meter. We also employ mass spectroscopy to verify whether only decolorization or also degradation takes place after treatment of the dyes by the NTP jets. Additionally, we analyze the interaction of OH radicals with all three dyes using reactive molecular dynamics simulations, based on the density functional-tight binding method. This investigation represents the first report on the degradation of these three different dyes by two types of NTP setups, analyzed by various methods, and based on both experimental and computational studies. |
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Address |
Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium |
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Corporate Author |
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Thesis |
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Publisher |
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Editor |
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Language |
English |
Wos |
000385172300001 |
Publication Date |
2016-10-06 |
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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 |
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 |
23 |
Open Access |
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Notes |
We gratefully acknowledge the grant received from the SRC program of the National Research Foundation of Korea (NRF), funded by the Korean Government (MEST) (No. 20100029418). PA is thankful to FY 2015 Japan Society for the Promotion of Science (JSPS) invitation fellowship. This work was partly supported by MEXT KAKENHI Grant Number 24108009 and JSPS KAKENHI Grant Number JP16H03895. M. Y. gratefully acknowledges financial support from the Research Foundation – Flanders (FWO), grant number 1200216N. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. |
Approved |
Most recent IF: 4.259 |
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Call Number |
PLASMANT @ plasmant @ c:irua:135847 |
Serial |
4283 |
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