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Author | Bogaerts, A.; Yusupov, M.; Razzokov, J.; Van der Paal, J. | ||||
Title | Plasma for cancer treatment: How can RONS penetrate through the cell membrane? Answers from computer modeling | Type | A1 Journal article | ||
Year | 2019 | Publication | Frontiers of Chemical Science and Engineering | Abbreviated Journal | Front Chem Sci Eng |
Volume | Issue | Pages | |||
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Plasma is gaining increasing interest for cancer treatment, but the underlying mechanisms are not yet fully understood. Using computer simulations at the molecular level, we try to gain better insight in how plasma-generated reactive oxygen and nitrogen species (RONS) can penetrate through the cell membrane. Specifically, we compare the permeability of various (hydrophilic and hydrophobic) RONS across both oxidized and nonoxidized cell membranes. We also study pore formation, and how it is hampered by higher concentrations of cholesterol in the cell membrane, and we illustrate the much higher permeability of H2O2 through aquaporin channels. Both mechanisms may explain the selective cytotoxic effect of plasma towards cancer cells. Finally, we also discuss the synergistic effect of plasma-induced oxidation and electric fields towards pore formation. Keywords plasma medicine, cancer treatment, computer modelling, cell membrane, reactive oxygen and nitrogen species |
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Publisher | Place of Publication | Editor | |||
Language | Wos | 000468848400004 | Publication Date | 2019-03-22 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 2095-0179 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 1.712 | Times cited | 5 | Open Access | Not_Open_Access: Available from 23.05.2020 |
Notes | We acknowledge financial support from the Research Foundation–Flanders (FWO; Grant Nos. 1200216N and 11U5416N). 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. We are also very thankful to R. Cordeiro for the very interesting discussions. | Approved ![]() |
Most recent IF: 1.712 | ||
Call Number | PLASMANT @ plasmant @UA @ admin @ c:irua:159977 | Serial | 5172 | ||
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Author | Vanmeert, M.; Razzokov, J.; Mirza, M.U.; Weeks, S.D.; Schepers, G.; Bogaerts, A.; Rozenski, J.; Froeyen, M.; Herdewijn, P.; Pinheiro, V.B.; Lescrinier, E. | ||||
Title | Rational design of an XNA ligase through docking of unbound nucleic acids to toroidal proteins | Type | A1 Journal article | ||
Year | 2019 | Publication | Nucleic acids research | Abbreviated Journal | Nucleic Acids Res |
Volume | 47 | Issue | 13 | Pages | 7130-7142 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Xenobiotic nucleic acids (XNA) are nucleic acid analogues not present in nature that can be used for the storage of genetic information. In vivo XNA applications could be developed into novel biocontainment strategies, but are currently limited by the challenge of developing XNA processing enzymes such as polymerases, ligases and nucleases. Here, we present a structure-guided modelling-based strategy for the rational design of those enzymes essential for the development of XNA molecular biology. Docking of protein domains to unbound double-stranded nucleic acids is used to generate a first approximation of the extensive interaction of nucleic acid processing enzymes with their substrate. Molecular dynamics is used to optimise that prediction allowing, for the first time, the accurate prediction of how proteins that form toroidal complexes with nucleic acids interact with their substrate. Using the Chlorella virus DNA ligase as a proof of principle, we recapitulate the ligase's substrate specificity and successfully predict how to convert it into an XNA-templated XNA ligase. | ||||
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Language | Wos | 000490556600047 | Publication Date | 2019-07-26 | |
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Series Volume | Series Issue | Edition | |||
ISSN | 0305-1048 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 10.162 | Times cited | 1 | Open Access | |
Notes | European Research Council, FP7/2007-2013 ERC-2012-ADG 20120216/320683 ; KU Leuven, OT/14/128 ; Biotechnology and Biosciences Research Council, BB/N01023X/1 BB/N010221/1 ; Authors are grateful to Prof. Dr A.M.J.J. (Alexandre) Bonvin from the University of Utrecht and the WeNMR institute for his expert contribution. We have greatly benefited from discussions and help from numerous postdocs over the years (in particular, Dr E. Groaz, Dr E. Eremeeva, Dr J. Masschelein, Dr S. Xiaoping and Dr M. Renders) as well as graduate student D. Kestemont and undergraduate student M. Abdel Fattah Ismail. We express our gratitude to L. Margamuljana for helpful discussions and excellent technical assistance on in vitro experiments. | Approved ![]() |
Most recent IF: 10.162 | ||
Call Number | PLASMANT @ plasmant @c:irua:162105 | Serial | 5359 | ||
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Author | Razzokov, J.; Yusupov, M.; Cordeiro, R.M.; Bogaerts, A. | ||||
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 |
Volume | 51 | Issue | 36 | Pages | 365203 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
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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Language | Wos | 000441182400002 | Publication Date | 2018-08-08 | |
Series Editor | Series Title | Abbreviated Series Title | |||
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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Author | Razzokov, J.; Yusupov, M.; Vanuytsel, S.; Neyts, E.C.; Bogaerts, A. | ||||
Title | Phosphatidylserine flip-flop induced by oxidation of the plasma membrane: a better insight by atomic scale modeling | Type | A1 Journal article | ||
Year | 2017 | Publication | Plasma processes and polymers | Abbreviated Journal | Plasma Process Polym |
Volume | 14 | Issue | 10 | Pages | 1700013 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | We perform molecular dynamics simulations to study the flip-flop motion of phosphatidylserine (PS) across the plasma membrane upon increasing oxidation degree of the membrane. Our computational results show that an increase of the oxidation degree in the lipids leads to a decrease of the free energy barrier for translocation of PS through the membrane. In other words, oxidation of the lipids facilitates PS flip-flop motion across the membrane, because in native phospholipid bilayers this is only a “rare event” due to the high energy barriers for the translocation of PS. The present study provides an atomic-scale insight into the mechanisms of the PS flip-flop upon oxidation of lipids, as produced for example by cold atmospheric plasma, in living cells. | ||||
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Language | Wos | 000413045800010 | Publication Date | 2017-04-05 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 1612-8850 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 2.846 | Times cited | 9 | Open Access | Not_Open_Access |
Notes | Fonds Wetenschappelijk Onderzoek, 1200216N ; | Approved ![]() |
Most recent IF: 2.846 | ||
Call Number | PLASMANT @ plasmant @c:irua:149567 | Serial | 4910 | ||
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Author | Yusupov, M.; Lackmann, J.-W.; Razzokov, J.; Kumar, S.; Stapelmann, K.; Bogaerts, A. | ||||
Title | Impact of plasma oxidation on structural features of human epidermal growth factor | Type | A1 Journal article | ||
Year | 2018 | Publication | Plasma processes and polymers | Abbreviated Journal | Plasma Process Polym |
Volume | 15 | Issue | 8 | Pages | 1800022 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
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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Publisher | Place of Publication | Editor | |||
Language | Wos | 000441895700004 | Publication Date | 2018-05-07 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 1612-8850 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 2.846 | Times cited | 7 | Open Access | Not_Open_Access |
Notes | Fonds Wetenschappelijk Onderzoek, 1200216N ; Bundesministerium für Bildung und Forschung, 03Z22DN12 ; | Approved ![]() |
Most recent IF: 2.846 | ||
Call Number | PLASMANT @ plasmant @c:irua:152815 | Serial | 5008 | ||
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Author | Kumar, N.; Shaw, P.; Razzokov, J.; Yusupov, M.; Attri, P.; Uhm, H.S.; Choi, E.H.; Bogaerts, A. | ||||
Title | Enhancement of cellular glucose uptake by reactive species: a promising approach for diabetes therapy | Type | A1 Journal article | ||
Year | 2018 | Publication | RSC advances | Abbreviated Journal | Rsc Adv |
Volume | 8 | Issue | 18 | Pages | 9887-9894 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
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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Language | Wos | 000430451800036 | Publication Date | 2018-03-08 | |
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Series Volume | Series Issue | Edition | |||
ISSN | 2046-2069 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 3.108 | Times cited | 1 | Open Access | OpenAccess |
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 | ||
Call Number | PLASMANT @ plasmant @c:irua:149564 | Serial | 4909 | ||
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Author | 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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Language | Wos | 000461411200014 | Publication Date | 2019-02-07 | |
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Series Volume | Series Issue | Edition | |||
ISSN | 0003-9861 | ISBN | 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 | ||
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Author | 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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Language | Wos | 000525439700011 | Publication Date | 2019-09-23 | |
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ISSN | 0003-9861 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 3.165 | Times cited | Open Access | ||
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 | Cordeiro, R.M.; Yusupov, M.; Razzokov, J.; Bogaerts, A. | ||||
Title | Parametrization and Molecular Dynamics Simulations of Nitrogen Oxyanions and Oxyacids for Applications in Atmospheric and Biomolecular Sciences | Type | A1 Journal article | ||
Year | 2020 | Publication | Journal Of Physical Chemistry B | Abbreviated Journal | J Phys Chem B |
Volume | 124 | Issue | 6 | Pages | 1082-1089 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Nitrogen oxyanions and oxyacids are important agents in atmospheric chemistry and medical biology. Although their chemical behavior in solution is relatively well understood, they may behave very differently at the water/air interface of atmospheric aerosols or at the membrane/water interface of cells. Here, we developed a fully classical model for molecular dynamics simulations of NO3−, NO2−, HNO3, and HNO2 in the framework of the GROMOS 53A6 and 54A7 force field versions. The model successfully accounted for the poorly structured solvation shell and ion pairing tendency of NO3−. Accurate pure-liquid properties and hydration free energies were obtained for the oxyacids. Simulations at the water/air interface showed a local enrichment of HNO3 and depletion of NO3−. The effect was discussed in light of earlier spectroscopic data and ab initio calculations, suggesting that HNO3 behaves as a weaker acid at the surface of water. Our model will hopefully allow for efficient and accurate simulations of nitrogen oxyanions and oxyacids in solution and at microheterogeneous interface environments. | ||||
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Language | Wos | 000512222500015 | Publication Date | 2020-02-13 | |
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Series Volume | Series Issue | Edition | |||
ISSN | 1520-6106 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 3.3 | Times cited | Open Access | ||
Notes | We thank Universidade Federal do ABC for providing the computational resources needed for completion of this work. This study was financed in part by the Coordenaçaõ de Aperfeiçoamento de Pessoal de Nı ́vel Superior – Brasil (CAPES) – Finance Code 001. | Approved ![]() |
Most recent IF: 3.3; 2020 IF: 3.177 | ||
Call Number | PLASMANT @ plasmant @c:irua:166488 | Serial | 6340 | ||
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Author | 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 | |
Volume | 751 | Issue | 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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Language | Wos | 001127850500001 | Publication Date | 2023-11-23 | |
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Series Volume | Series Issue | Edition | |||
ISSN | 0003-9861; 1096-0384 | ISBN | Additional Links | UA library record; WoS full record | |
Impact Factor | 3.9 | Times cited | Open Access | Not_Open_Access | |
Notes | Approved ![]() |
Most recent IF: 3.9; 2024 IF: 3.165 | |||
Call Number | UA @ admin @ c:irua:202185 | Serial | 9046 | ||
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Author | Razzokov, J.; Yusupov, M.; Bogaerts, A. | ||||
Title | Oxidation destabilizes toxic amyloid beta peptide aggregation | Type | A1 Journal article | ||
Year | 2019 | Publication | Scientific reports | Abbreviated Journal | Sci Rep-Uk |
Volume | 9 | Issue | 1 | Pages | 5476 |
Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | The aggregation of insoluble amyloid beta (Aβ) peptides in the brain is known to trigger the onset of neurodegenerative diseases, such as Alzheimer’s disease. In spite of the massive number of investigations, the underlying mechanisms to destabilize the Aβ aggregates are still poorly understood. Some studies indicate the importance of oxidation to destabilize the Aβ aggregates. In particular, oxidation induced by cold atmospheric plasma (CAP) has demonstrated promising results in eliminating these toxic aggregates. In this paper, we investigate the effect of oxidation on the stability of an Aβ pentamer. By means of molecular dynamics simulations and umbrella sampling, we elucidate the conformational changes of Aβ pentamer in the presence of oxidized residues, and we estimate the dissociation free energy of the terminal peptide out of the pentamer form. The calculated dissociation free energy of the terminal peptide is also found to decrease with increasing oxidation. This indicates that Aβ pentamer aggregation becomes less favorable upon oxidation. Our study contributes to a better insight in one of the potential mechanisms for inhibition of toxic Aβ peptide aggregation, which is considered to be the main culprit to Alzheimer’s disease. | ||||
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Language | Wos | 000462990000018 | Publication Date | 2019-04-02 | |
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Series Volume | Series Issue | Edition | |||
ISSN | 2045-2322 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 4.259 | Times cited | 5 | Open Access | OpenAccess |
Notes | M.Y. gratefully acknowledges financial support from the Research Foundation – Flanders (FWO), grant 1200216N and 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. | Approved ![]() |
Most recent IF: 4.259 | ||
Call Number | PLASMANT @ plasmant @UA @ admin @ c:irua:159367 | Serial | 5182 | ||
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Author | Yusupov, M.; Razzokov, J.; Cordeiro, R.M.; Bogaerts, A. | ||||
Title | Transport of Reactive Oxygen and Nitrogen Species across Aquaporin: A Molecular Level Picture | Type | A1 Journal article | ||
Year | 2019 | Publication | Oxidative medicine and cellular longevity | Abbreviated Journal | Oxid Med Cell Longev |
Volume | 2019 | Issue | Pages | 1-11 | |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Aquaporins (AQPs) are transmembrane proteins that conduct not only water molecules across the cell membrane but also other solutes, such as reactive oxygen and nitrogen species (RONS), produced (among others) by cold atmospheric plasma (CAP). These RONS may induce oxidative stress in the cell interior, which plays a role in cancer treatment. The underlying mechanisms of the transport of RONS across AQPs, however, still remain obscure. We apply molecular dynamics simulations to investigate the permeation of both hydrophilic (H<sub>2</sub>O<sub>2</sub>and OH) and hydrophobic (NO<sub>2</sub>and NO) RONS through AQP1. Our simulations show that these RONS can all penetrate across the pores of AQP1. The permeation free energy barrier of OH and NO is lower than that of H<sub>2</sub>O<sub>2</sub>and NO<sub>2</sub>, indicating that these radicals may have easier access to the pore interior and interact with the amino acid residues of AQP1. We also study the effect of RONS-induced oxidation of both the phospholipids and AQP1 (i.e., sulfenylation of Cys<sub>191</sub>) on the transport of the above-mentioned RONS across AQP1. Both lipid and protein oxidation seem to slightly increase the free energy barrier for H<sub>2</sub>O<sub>2</sub>and NO<sub>2</sub>permeation, while for OH and NO, we do not observe a strong effect of oxidation. The simulation results help to gain insight in the underlying mechanisms of the noticeable rise of CAP-induced RONS in cancer cells, thereby improving our understanding on the role of AQPs in the selective anticancer capacity of CAP. | ||||
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Language | Wos | 000492999000001 | Publication Date | 2019-06-17 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 1942-0900 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 4.593 | Times cited | 5 | Open Access | OpenAccess |
Notes | The authors acknowledge the Turing HPC infrastructure at the CalcUA core facility of the University of Antwerp (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI), and the UA, where all computational work was performed. M.Y. gratefully acknowledges Dr. U. Khalilov for the fruitful discussions. This work was financially supported by the Research Foundation Flanders (FWO) (grant number 1200219N). | Approved ![]() |
Most recent IF: 4.593 | ||
Call Number | PLASMANT @ plasmant @UA @ admin @ c:irua:160118 | Serial | 5180 | ||
Permanent link to this record | |||||
Author | De Backer, J.; Razzokov, J.; Hammerschmid, D.; Mensch, C.; Hafideddine, Z.; Kumar, N.; van Raemdonck, G.; Yusupov, M.; Van Doorslaer, S.; Johannessen, C.; Sobott, F.; Bogaerts, A.; Dewilde, S. | ||||
Title | The effect of reactive oxygen and nitrogen species on the structure of cytoglobin: A potential tumor suppressor | Type | A1 Journal article | ||
Year | 2018 | Publication | Redox Biology | Abbreviated Journal | Redox Biol |
Volume | 19 | Issue | Pages | 1-10 | |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Molecular Spectroscopy (MolSpec) | ||||
Abstract | Many current anti-cancer therapies rely on increasing the intracellular reactive oxygen and nitrogen species (RONS) contents with the aim to induce irreparable damage, which subsequently results in tumor cell death. A novel tool in cancer therapy is the use of cold atmospheric plasma (CAP), which has been found to be very effective in the treatment of many different cancer cell types in vitro as well as in vivo, mainly through the vast generation of RONS. One of the key determinants of the cell's fate will be the interaction of RONS, generated by CAP, with important proteins, i.e. redox-regulatory proteins. One such protein is cytoglobin (CYGB), a recently discovered globin proposed to be involved in the protection of the cell against oxidative stress. In this study, the effect of plasma-produced RONS on CYGB was investigated through the treatment of CYGB with CAP for different treatment times. Spectroscopic analysis of CYGB showed that although chemical modifications occur, its secondary structure remains intact. Mass spectrometry experiments identified these modifications as oxidations of mainly sulfur-containing and aromatic amino acids. With longer treatment time, the treatment was also found to induce nitration of the heme. Furthermore, the two surface-exposed cysteine residues of CYGB were oxidized upon treatment, leading to the formation of intermolecular disulfide bridges, and potentially also intramolecular disulfide bridges. In addition, molecular dynamics and docking simulations confirmed, and further show, that the formation of an intramolecular disulfide bond, due to oxidative conditions, affects the CYGB 3D structure, thereby opening the access to the heme group, through gate functioning of His117. Altogether, the results obtained in this study (1) show that plasma-produced RONS can extensively oxidize proteins and (2) that the oxidation status of two redox-active cysteines lead to different conformations of CYGB. | ||||
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Corporate Author | Thesis | ||||
Publisher | Place of Publication | Editor | |||
Language | Wos | 000449722100002 | Publication Date | 2018-07-24 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 2213-2317 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 6.337 | Times cited | Open Access | OpenAccess | |
Notes | M.Y. and N.K. gratefully acknowledge financial support from the Research Foundation – Flanders (FWO), Grant nos. 1200216N and 12J5617N. 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). C.M acknowledges the financial support provided by the Flemish Community and the University of Antwerp (BOF-NOI) for the pre-doctoral scholarship is under grant number/project ID: 28465. S.V.D., S. D. and Z.H. acknowledge the FWO (Grant G.0687.13) and the GOA-BOF UA 2013–2016 (project-ID 28312) for funding. The computational resources and services used in this work were provided by the HPC core facility CalcUA of the Universiteit Antwerpen, and VSC (Flemish Supercomputer Center), funded by the Research Foundation – Flanders (FWO) and the Flemish Government – department EWI. | Approved ![]() |
Most recent IF: 6.337 | ||
Call Number | PLASMANT @ plasmant @c:irua:152818 | Serial | 5006 | ||
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Author | Yusupov, M.; Privat-Maldonado, A.; Cordeiro, R.M.; Verswyvel, H.; Shaw, P.; Razzokov, J.; Smits, E.; Bogaerts, A. | ||||
Title | Oxidative damage to hyaluronan–CD44 interactions as an underlying mechanism of action of oxidative stress-inducing cancer therapy | Type | A1 Journal article | ||
Year | 2021 | Publication | Redox Biology | Abbreviated Journal | Redox Biol |
Volume | 43 | Issue | Pages | 101968 | |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Center for Oncological Research (CORE) | ||||
Abstract | Multiple cancer therapies nowadays rely on oxidative stress to damage cancer cells. Here we investigated the biological and molecular effect of oxidative stress on the interaction between CD44 and hyaluronan (HA), as interrupting their binding can hinder cancer progression. Our experiments demonstrated that the oxidation of HA decreased its recognition by CD44, which was further enhanced when both CD44 and HA were oxidized. The reduction of CD44–HA binding negatively affected the proliferative state of cancer cells. Our multi-level atomistic simulations revealed that the binding free energy of HA to CD44 decreased upon oxidation. The effect of HA and CD44 oxidation on CD44–HA binding was similar, but when both HA and CD44 were oxidized, the effect was much larger, in agreement with our experiments. Hence, our experiments and computations support our hypothesis on the role of oxidation in the disturbance of CD44–HA interaction, which can lead to the inhibition of proliferative signaling pathways inside the tumor cell to induce cell death. | ||||
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Publisher | Place of Publication | Editor | |||
Language | Wos | 000657371800005 | Publication Date | 2021-04-14 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 2213-2317 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 6.337 | Times cited | Open Access | OpenAccess | |
Notes | Fwo; The authors acknowledge the Turing HPC infrastructure at the CalcUA core facility of the University of Antwerp (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA, where all computational work was performed. | Approved ![]() |
Most recent IF: 6.337 | ||
Call Number | PLASMANT @ plasmant @c:irua:177780 | Serial | 6750 | ||
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Author | Attri, P.; Razzokov, J.; Yusupov, M.; Koga, K.; Shiratani, M.; Bogaerts, A. | ||||
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 | ||
Year | 2020 | Publication | International Journal Of Biological Macromolecules | Abbreviated Journal | Int J Biol Macromol |
Volume | 148 | Issue | Pages | 657-665 | |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
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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Publisher | Place of Publication | Editor | |||
Language | Wos | 000522094600066 | Publication Date | 2020-01-20 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 0141-8130 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 8.2 | Times cited | Open Access | ||
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 | ||
Call Number | PLASMANT @ plasmant @c:irua:165585 | Serial | 5444 | ||
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Author | Marimuthu, P.; Razzokov, J.; Eshonqulov, G. | ||||
Title | Disruption of conserved polar interactions causes a sequential release of Bim mutants from the canonical binding groove of Mcl1 | Type | A1 Journal article | ||
Year | 2020 | Publication | International Journal Of Biological Macromolecules | Abbreviated Journal | Int J Biol Macromol |
Volume | 158 | Issue | Pages | 364-374 | |
Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Mcl1 is an important anti-apoptotic member of the Bcl2 family proteins that are upregulated in several cancer malignancies. The canonical binding groove (CBG) located at the surface of Mcl1 exhibits a critical role in binding partners selectively via the BH3-domain of pro-apoptotic Bcl2 family members that trigger the downregulation of Mcl1 function. There are several crystal structures of point-mutated pro-apoptotic Bim peptides in complex with Mcl1. However, the mechanistic effects of such point-mutations towards peptide binding and complex stability still remain unexplored. Here, the effects of the reported point mutations in Bim peptides and their binding mechanisms to Mcl1 were computationally evaluated using atomistic-level steered molecular dynamics (SMD) simulations. A range of external-forces and constant-velocities were applied to the Bim peptides to uncover the mechanistic basis of peptide dissociation from the CBG of Mcl1. Although the peptides showed similarities in their dissociation pathways, the peak rupture forces varied significantly. According to simulations results, the disruption of the conserved polar contacts at the complex interface causes a sequential release of the peptides from the CBG of Mcl1. Overall, the results obtained from the current study may provide valuable insights for the development of novel anti-cancer peptide-inhibitors that can downregulate Mcl1’s function. | ||||
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Publisher | Place of Publication | Editor | |||
Language | Wos | 000564486400010 | Publication Date | 2020-05-03 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 0141-8130 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 8.2 | Times cited | Open Access | ||
Notes | P.M. gratefully acknowledges the Sigrid Jusélius Foundation, Joe, Pentti and Tor Borg Memorial Fund for computational and laboratory infrastructure, the Bioinformatics infrastructure facility supported by Biocenter Finland, CSC-IT Center for Science (Project: 2000461) for the high performance computational facility; Prof. Outi Salo-Ahen, SBL, Pharmacy, Åbo Akademi University and Prof. Olli Pentikäinen, MedChem, University of Turku for valuable discussion; Dr. Jukka Lehtonen for the IT support; and specially thanks Prof. Mark Johnson, SBL, Åbo Akademi University, for providing the lab facility. | Approved ![]() |
Most recent IF: 8.2; 2020 IF: 3.671 | ||
Call Number | PLASMANT @ plasmant @c:irua:169231 | Serial | 6365 | ||
Permanent link to this record | |||||
Author | Razzokov, J.; Yusupov, M.; Bogaerts, A. | ||||
Title | Possible Mechanism of Glucose Uptake Enhanced by Cold Atmospheric Plasma: Atomic Scale Simulations | Type | A1 Journal article | ||
Year | 2018 | Publication | Plasma | Abbreviated Journal | |
Volume | 1 | Issue | 1 | Pages | |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Cold atmospheric plasma (CAP) has shown its potential in biomedical applications, such as wound healing, cancer treatment and bacterial disinfection. Recent experiments have provided evidence that CAP can also enhance the intracellular uptake of glucose molecules which is important in diabetes therapy. In this respect, it is essential to understand the underlying mechanisms of intracellular glucose uptake induced by CAP, which is still unclear. Hence, in this study we try to elucidate the possible mechanism of glucose uptake by cells by performing computer simulations. Specifically, we study the transport of glucose molecules through native and oxidized membranes. Our simulation results show that the free energy barrier for the permeation of glucose molecules across the membrane decreases upon increasing the degree of oxidized lipids in the membrane. This indicates that the glucose permeation rate into cells increases when the CAP oxidation level in the cell membrane is increased. | ||||
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Publisher | Place of Publication | Editor | |||
Language | Wos | Publication Date | 2018-06-08 | ||
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 2571-6182 | ISBN | Additional Links | UA library record | |
Impact Factor | Times cited | Open Access | OpenAccess | ||
Notes | 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 Universiteit Antwerpen. | Approved ![]() |
Most recent IF: NA | ||
Call Number | PLASMANT @ plasmant @ plasma1010011c:irua:152176 | Serial | 4990 | ||
Permanent link to this record | |||||
Author | Razzokov, J.; Naderi, S.; van der Schoot, P. | ||||
Title | Nanoscale insight into silk-like protein self-assembly: effect of design and number of repeat units | Type | A1 Journal article | ||
Year | 2018 | Publication | Physical biology | Abbreviated Journal | Phys. Biol. |
Volume | 15 | Issue | 6 | Pages | 066010 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | By means of replica exchange molecular dynamics simulations we investigate how the length of a silk-like, alternating diblock oligopeptide influences its secondary and quaternary structure. We carry out simulations for two protein sizes consisting of three and five blocks, and study the stability of a single protein, a dimer, a trimer and a tetramer. Initial configurations of our simulations are β-roll and β-sheet structures. We find that for the triblock the secondary and quaternary structures upto and including the tetramer are unstable: the proteins melt into random coil structures and the aggregates disassemble either completely or partially. We attribute this to the competition between conformational entropy of the proteins and the formation of hydrogen bonds and hydrophobic interactions between proteins. This is confirmed by our simulations on the pentablock proteins, where we find that, as the number of monomers in the aggregate increases, individual monomers form more hydrogen bonds whereas their solvent accessible surface area decreases. For the pentablock β-sheet protein, the monomer and the dimer melt as well, although for the β-roll protein only the monomer melts. For both trimers and tetramers remain stable. Apparently, for these the entropy loss of forming β-rolls and β-sheets is compensated for in the free-energy gain due to the hydrogen-bonding and hydrophobic interactions. We also find that the middle monomers in the trimers and tetramers are conformationally much more stable than the ones on the top and the bottom. Interestingly, the latter are more stable on the tetramer than on the trimer, suggesting that as the number of monomers increases protein-protein interactions cooperatively stabilize the assembly. According to our simulations, the β-roll and β-sheet aggregates must be approximately equally stable. |
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Publisher | Place of Publication | Editor | |||
Language | Wos | 000444467000001 | Publication Date | 2018-09-12 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 1478-3975 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | Times cited | 1 | Open Access | OpenAccess | |
Notes | The work of J Razzokov is supported by Jepa-Limmat Foundation. We thank Sarah Harris (University of Leeds) and Alexey Lyulin (Eindhoven University of Technology), for useful discussions and advice on the simulations. Eindhoven University of Technology is thanked by J Razzokov for their hospitality. We are grateful for computer time provided by the Dutch National Computing Facilities at the LISA facility at SURFsara. The work of S Naderi forms part of the research program of the Dutch Polymer Institute (DPI, Project No. 698). This work was supported by NWO Exacte Wetenschappen (Physical Sciences) for the use of supercomputer facilities, with financial support (Netherlands Organization for Scientific Research, NWO). | Approved ![]() |
Most recent IF: NA | ||
Call Number | PLASMANT @ plasmant @c:irua:153803c:irua:153596 | Serial | 5050 | ||
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Author | Razzokov, J. | ||||
Title | Molecular level simulations for plasma medicine applications | Type | Doctoral thesis | ||
Year | 2019 | Publication | Abbreviated Journal | ||
Volume | Issue | Pages | 173 p. | ||
Keywords | Doctoral thesis; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
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Publisher | Place of Publication | Editor | |||
Language | Wos | Publication Date | |||
Series Editor | Series Title | Abbreviated Series Title | |||
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ISSN | ISBN | Additional Links | UA library record | ||
Impact Factor | Times cited | Open Access | |||
Notes | Approved ![]() |
Most recent IF: NA | |||
Call Number | UA @ admin @ c:irua:159654 | Serial | 5277 | ||
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Author | Privat-Maldonado, A.; Bengtson, C.; Razzokov, J.; Smits, E.; Bogaerts, A. | ||||
Title | Modifying the Tumour Microenvironment: Challenges and Future Perspectives for Anticancer Plasma Treatments | Type | A1 Journal article | ||
Year | 2019 | Publication | Cancers | Abbreviated Journal | Cancers |
Volume | 11 | Issue | 12 | Pages | 1920 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Center for Oncological Research (CORE) | ||||
Abstract | Tumours are complex systems formed by cellular (malignant, immune, and endothelial cells, fibroblasts) and acellular components (extracellular matrix (ECM) constituents and secreted factors). A close interplay between these factors, collectively called the tumour microenvironment, is required to respond appropriately to external cues and to determine the treatment outcome. Cold plasma (here referred as ‘plasma’) is an emerging anticancer technology that generates a unique cocktail of reactive oxygen and nitrogen species to eliminate cancerous cells via multiple mechanisms of action. While plasma is currently regarded as a local therapy, it can also modulate the mechanisms of cell-to-cell and cell-to-ECM communication, which could facilitate the propagation of its effect in tissue and distant sites. However, it is still largely unknown how the physical interactions occurring between cells and/or the ECM in the tumour microenvironment affect the plasma therapy outcome. In this review, we discuss the effect of plasma on cell-to-cell and cell-to-ECM communication in the context of the tumour microenvironment and suggest new avenues of research to advance our knowledge in the field. Furthermore, we revise the relevant state-of-the-art in three-dimensional in vitro models that could be used to analyse cell-to-cell and cell-to-ECM communication and further strengthen our understanding of the effect of plasma in solid tumours. | ||||
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Publisher | Place of Publication | Editor | |||
Language | Wos | 000507382100097 | Publication Date | 2019-12-02 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 2072-6694 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | Times cited | Open Access | |||
Notes | Figure 4 was created using resources from the ‘Mind the Graph’ platform, free trial version. Spheroid image obtained in collaboration with Sander Bekeschus (INP Greifswald, Germany); organoid image kindly provided by Christophe Deben (Center for Oncological Research, University of Antwerp, Belgium). | Approved ![]() |
Most recent IF: NA | ||
Call Number | PLASMANT @ plasmant @c:irua:164892 | Serial | 5437 | ||
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Author | Marimuthu, P.; Razzokov, J.; Singaravelu, K.; Bogaerts, A. | ||||
Title | Predicted Hotspot Residues Involved in Allosteric Signal Transmission in Pro-Apoptotic Peptide—Mcl1 Complexes | Type | A1 Journal article | ||
Year | 2020 | Publication | Biomolecules | Abbreviated Journal | Biomolecules |
Volume | 10 | Issue | 8 | Pages | 1114 |
Keywords | A1 Journal article; Engineering sciences. Technology; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Mcl1 is a primary member of the Bcl–2 family—anti–apoptotic proteins (AAP)—that is overexpressed in several cancer pathologies. The apoptotic regulation is mediated through the binding of pro-apoptotic peptides (PAPs) (e.g., Bak and Bid) at the canonical hydrophobic binding groove (CBG) of Mcl1. Although all PAPs form amphipathic α-helices, their amino acid sequences vary to different degree. This sequence variation exhibits a central role in the binding partner selectivity towards different AAPs. Thus, constructing a novel peptide or small organic molecule with the ability to mimic the natural regulatory process of PAP is essential to inhibit various AAPs. Previously reported experimental binding free energies (BFEs) were utilized in the current investigation aimed to understand the mechanistic basis of different PAPs targeted to mMcl1. Molecular dynamics (MD) simulations used to estimate BFEs between mMcl1—PAP complexes using Molecular Mechanics-Generalized Born Solvent Accessible (MMGBSA) approach with multiple parameters. Predicted BFE values showed an excellent agreement with the experiment (R2 = 0.92). The van–der Waals (ΔGvdw) and electrostatic (ΔGele) energy terms found to be the main energy components that drive heterodimerization of mMcl1—PAP complexes. Finally, the dynamic network analysis predicted the allosteric signal transmission pathway involves more favorable energy contributing residues. In total, the results obtained from the current investigation may provide valuable insights for the synthesis of a novel peptide or small organic inhibitor targeting Mcl1. | ||||
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Publisher | Place of Publication | Editor | |||
Language | Wos | 000578895600001 | Publication Date | 2020-07-28 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 2218-273X | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | Times cited | Open Access | |||
Notes | P.M. gratefully acknowledges the use of the bioinformatics infrastructure facility supported by Biocenter Finland and the CSC-IT Center for Science (Project: 2000461) for the computational facility; Jukka Lehtonen for the IT support; Mark Johnson (SBL) Åbo Akademi University for providing the lab support and Outi Salo-Ahen (Pharmacy) Åbo Akademi University and Olli T. Pentikäinen (Institute of Biomedicine) University of Turku, for their valuable support and discussion. | Approved ![]() |
Most recent IF: NA | ||
Call Number | PLASMANT @ plasmant @c:irua:170486 | Serial | 6396 | ||
Permanent link to this record | |||||
Author | Lin, A.; Razzokov, J.; Verswyvel, H.; Privat-Maldonado, A.; De Backer, J.; Yusupov, M.; Cardenas De La Hoz, E.; Ponsaerts, P.; Smits, E.; Bogaerts, A. | ||||
Title | Oxidation of Innate Immune Checkpoint CD47 on Cancer Cells with Non-Thermal Plasma | Type | A1 Journal article | ||
Year | 2021 | Publication | Cancers | Abbreviated Journal | Cancers |
Volume | 13 | Issue | 3 | Pages | 579 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Laboratory for Experimental Hematology (LEH); Center for Oncological Research (CORE) | ||||
Abstract | Non-thermal plasma (NTP) therapy has been emerging as a promising cancer treatment strategy, and recently, its ability to locally induce immunogenic cancer cell death is being unraveled. We hypothesized that the chemical species produced by NTP reduce immunosuppressive surface proteins and checkpoints that are overexpressed on cancerous cells. Here, 3D in vitro tumor models, an in vivo mouse model, and molecular dynamics simulations are used to investigate the effect of NTP on CD47, a key innate immune checkpoint. CD47 is immediately modulated after NTP treatment and simulations reveal the potential oxidized salt-bridges responsible for conformational changes. Umbrella sampling simulations of CD47 with its receptor, signal-regulatory protein alpha (SIRPα), demonstrate that the induced-conformational changes reduce its binding affinity. Taken together, this work provides new insight into fundamental, chemical NTP-cancer cell interaction mechanisms and a previously overlooked advantage of present NTP cancer therapy: reducing immunosuppressive signals on the surface of cancer cells. | ||||
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Publisher | Place of Publication | Editor | |||
Language | Wos | 000614960600001 | Publication Date | 2021-02-02 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 2072-6694 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | Times cited | Open Access | OpenAccess | ||
Notes | We thank Erik Fransen (University of Antwerp; Antwerp, Belgium) for his help and guidance on the statistical analysis. | Approved ![]() |
Most recent IF: NA | ||
Call Number | PLASMANT @ plasmant @c:irua:176455 | Serial | 6709 | ||
Permanent link to this record | |||||
Author | Abduvokhidov, D.; Yusupov, M.; Shahzad, A.; Attri, P.; Shiratani, M.; Oliveira, M.C.; Razzokov, J. | ||||
Title | Unraveling the Transport Properties of RONS across Nitro-Oxidized Membranes | Type | A1 Journal Article | ||
Year | 2023 | Publication | Biomolecules | Abbreviated Journal | Biomolecules |
Volume | 13 | Issue | 7 | Pages | 1043 |
Keywords | A1 Journal Article; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ; | ||||
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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Publisher | Place of Publication | Editor | |||
Language | Wos | 001035160000001 | Publication Date | 2023-06-27 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 2218-273X | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | Times cited | Open Access | Not_Open_Access | ||
Notes | This research was funded by the Innovative Development Agency of the Republic of Uzbekistan, grant number FZ-2020092817. | Approved ![]() |
Most recent IF: NA | ||
Call Number | PLASMANT @ plasmant @c:irua:198154 | Serial | 8803 | ||
Permanent link to this record |