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Author | Ghasemitarei, M.; Privat-Maldonado, A.; Yusupov, M.; Rahnama, S.; Bogaerts, A.; Ejtehadi, M.R. | ||||
Title | Effect of Cysteine Oxidation in SARS-CoV-2 Receptor-Binding Domain on Its Interaction with Two Cell Receptors: Insights from Atomistic Simulations | Type | A1 Journal article | ||
Year | 2022 | Publication | Journal Of Chemical Information And Modeling | Abbreviated Journal | J Chem Inf Model |
Volume | 62 | Issue | 1 | Pages | 129-141 |
Keywords | A1 Journal article; Pharmacology. Therapy; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Binding of the SARS-CoV-2 S-glycoprotein to cell receptors is vital for the entry of the virus into cells and subsequent infection. ACE2 is the main cell receptor for SARS-CoV-2, which can attach to the C-terminal receptor-binding domain (RBD) of the SARS-CoV-2 S-glycoprotein. The GRP78 receptor plays an anchoring role, which attaches to the RBD and increases the chance of other RBDs binding to ACE2. Although high levels of reactive oxygen and nitrogen species (RONS) are produced during viral infections, it is not clear how they affect the RBD structure and its binding to ACE2 and GRP78. In this research, we apply molecular dynamics simulations to study the effect of oxidation of the highly reactive cysteine (Cys) amino acids of the RBD on its binding to ACE2 and GRP78. The interaction energy of both ACE2 and GRP78 with the whole RBD, as well as with the RBD main regions, is compared in both the native and oxidized RBDs. Our results show that the interaction energy between the oxidized RBD and ACE2 is strengthened by 155 kJ/mol, increasing the binding of the RBD to ACE2 after oxidation. In addition, the interaction energy between the RBD and GRP78 is slightly increased by 8 kJ/mol after oxidation, but this difference is not significant. Overall, these findings highlight the role of RONS in the binding of the SARS-CoV-2 S-glycoprotein to host cell receptors and suggest an alternative mechanism by which RONS could modulate the entrance of viral particles into the cells. | ||||
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Publisher | Place of Publication | Editor | |||
Language | Wos | 000740019000001 | Publication Date | 2022-01-10 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN ![]() |
1549-9596 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 5.6 | Times cited | Open Access | Not_Open_Access | |
Notes | Fonds Wetenschappelijk Onderzoek, 1200219N ; Binding of the SARS-CoV-2 S-glycoprotein to cell receptors is vital for the entry of the virus into cells and subsequent infection. ACE2 is the main cell receptor for SARS-CoV-2, which can attach to the C-terminal receptor-binding domain (RBD) of the SARS-CoV-2 S-glycoprotein. The GRP78 receptor plays an anchoring role, which attaches to the RBD and increases the chance of other RBDs binding to ACE2. Although high levels of reactive oxygen and nitrogen species (RONS) are produced during viral infections, it is not clear how they affect the RBD structure and its binding to ACE2 and GRP78. In this research, we apply molecular dynamics simulations to study the effect of oxidation of the highly reactive cysteine (Cys) amino acids of the RBD on its binding to ACE2 and GRP78. The interaction energy of both ACE2 and GRP78 with the whole RBD, as well as with the RBD main regions, is compared in both the native and oxidized RBDs. Our results show that the interaction energy between the oxidized RBD and ACE2 is strengthened by 155 kJ/mol, increasing the binding of the RBD to ACE2 after oxidation. In addition, the interaction energy between the RBD and GRP78 is slightly increased by 8 kJ/mol after oxidation, but this difference is not significant. Overall, these findings highlight the role of RONS in the binding of the SARS-CoV-2 S-glycoprotein to host cell receptors and suggest an alternative mechanism by which RONS could modulate the entrance of viral particles into the cells. | Approved | Most recent IF: 5.6 | ||
Call Number | PLASMANT @ plasmant @c:irua:185485 | Serial | 7050 | ||
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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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Publisher | Place of Publication | Editor | |||
Language | Wos | 000512222500015 | Publication Date | 2020-02-13 | |
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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 | Van der Paal, J.; Hong, S.-H.; Yusupov, M.; Gaur, N.; Oh, J.-S.; Short, R.D.; Szili, E.J.; Bogaerts, A. | ||||
Title | How membrane lipids influence plasma delivery of reactive oxygen species into cells and subsequent DNA damage : an experimental and computational study | Type | A1 Journal article | ||
Year | 2019 | Publication | Physical chemistry, chemical physics | Abbreviated Journal | Phys Chem Chem Phys |
Volume | 21 | Issue | 35 | Pages | 19327-19341 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | The mechanisms of plasma in medicine are broadly attributed to plasma-derived reactive oxygen and nitrogen species (RONS). In order to exert any intracellular effects, these plasma-derived RONS must first traverse a major barrier in the cell membrane. The cell membrane lipid composition, and thereby the magnitude of this barrier, is highly variable between cells depending on type and state (e.g. it is widely accepted that healthy and cancerous cells have different membrane lipid compositions). In this study, we investigate how plasma-derived RONS interactions with lipid membrane components can potentially be exploited in the future for treatment of diseases. We couple phospholipid vesicle experiments, used as simple cell models, with molecular dynamics (MD) simulations of the lipid membrane to provide new insights into how the interplay between phospholipids and cholesterol may influence the response of healthy and diseased cell membranes to plasma-derived RONS. We focus on the (i) lipid tail saturation degree, (ii) lipid head group type, and (iii) membrane cholesterol fraction. Using encapsulated molecular probes, we study the influence of the above membrane components on the ingress of RONS into the vesicles, and subsequent DNA damage. Our results indicate that all of the above membrane components can enhance or suppress RONS uptake, depending on their relative concentration within the membrane. Further, we show that higher RONS uptake into the vesicles does not always correlate with increased DNA damage, which is attributed to ROS reactivity and lifetime. The MD simulations indicate the multifactorial chemical and physical processes at play, including (i) lipid oxidation, (ii) lipid packing, and (iii) lipid rafts formation. The methods and findings presented here provide a platform of knowledge that could be leveraged in the development of therapies relying on the action of plasma, in which the cell membrane and oxidative stress response in cells is targeted. | ||||
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Language | Wos | 000486175400045 | Publication Date | 2019-08-21 | |
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1463-9076; 1463-9084 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 4.123 | Times cited | 1 | Open Access | |
Notes | Approved | Most recent IF: 4.123 | |||
Call Number | UA @ admin @ c:irua:162782 | Serial | 6303 | ||
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Author | Yusupov, M.; Neyts, E.C.; Khalilov, U.; Snoeckx, R.; van Duin, A.C.T.; Bogaerts, A. | ||||
Title | Atomic-scale simulations of reactive oxygen plasma species interacting with bacterial cell walls | Type | A1 Journal article | ||
Year | 2012 | Publication | New journal of physics | Abbreviated Journal | New J Phys |
Volume | 14 | Issue | 9 | Pages | 093043 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | In recent years there has been growing interest in the use of low-temperature atmospheric pressure plasmas for biomedical applications. Currently, however, there is very little fundamental knowledge regarding the relevant interaction mechanisms of plasma species with living cells. In this paper, we investigate the interaction of important plasma species, such as O3, O2 and O atoms, with bacterial peptidoglycan (or murein) by means of reactive molecular dynamics simulations. Specifically, we use the peptidoglycan structure to model the gram-positive bacterium Staphylococcus aureus murein. Peptidoglycan is the outer protective barrier in bacteria and can therefore interact directly with plasma species. Our results demonstrate that among the species mentioned above, O3 molecules and especially O atoms can break important bonds of the peptidoglycan structure (i.e. CO, CN and CC bonds), which subsequently leads to the destruction of the bacterial cell wall. This study is important for gaining a fundamental insight into the chemical damaging mechanisms of the bacterial peptidoglycan structure on the atomic scale. | ||||
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Publisher | Place of Publication | Bristol | Editor | ||
Language | Wos | 000309393400001 | Publication Date | 2012-09-27 | |
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1367-2630; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 3.786 | Times cited | 47 | Open Access | |
Notes | Approved | Most recent IF: 3.786; 2012 IF: 4.063 | |||
Call Number | UA @ lucian @ c:irua:101014 | Serial | 189 | ||
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Author | Yusupov, M.; Bultinck, E.; Depla, D.; Bogaerts, A. | ||||
Title | Behavior of electrons in a dual-magnetron sputter deposition system : a Monte Carlo model | Type | A1 Journal article | ||
Year | 2011 | Publication | New journal of physics | Abbreviated Journal | New J Phys |
Volume | 13 | Issue | Pages | 033018-033018,17 | |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | A Monte Carlo model has been developed for investigating the electron behavior in a dual-magnetron sputter deposition system. To describe the three-dimensional (3D) geometry, different reference frames, i.e. a local and a global coordinate system, were used. In this study, the influence of both closed and mirror magnetic field configurations on the plasma properties is investigated. In the case of a closed magnetic field configuration, the calculated electron trajectories show that if an electron is emitted in (or near) the center of the cathode, where the influence of the magnetic field is low, it is able to travel from one magnetron to the other. On the other hand, when an electron is created at the race track area, it is more or less trapped in the strong magnetic field and cannot easily escape to the second magnetron region. In the case of a mirror magnetic field configuration, irrespective of where the electron is emitted from the cathode, it cannot travel from one magnetron to the other because the magnetic field lines guide the electron to the substrate. Moreover, the electron density and electron impact ionization rate have been calculated and studied in detail for both configurations. | ||||
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Publisher | Place of Publication | Bristol | Editor | ||
Language | Wos | 000289064600001 | Publication Date | 2011-03-15 | |
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1367-2630; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 3.786 | Times cited | 12 | Open Access | |
Notes | Approved | Most recent IF: 3.786; 2011 IF: 4.177 | |||
Call Number | UA @ lucian @ c:irua:87544 | Serial | 224 | ||
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Author | Yusupov, M.; Saraiva, M.; Depla, D.; Bogaerts, A. | ||||
Title | Sputter deposition of MgxAlyOz thin films in a dual-magnetron device : a multi-species Monte Carlo model | Type | A1 Journal article | ||
Year | 2012 | Publication | New journal of physics | Abbreviated Journal | New J Phys |
Volume | 14 | Issue | 7 | Pages | 073043 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | A multi-species Monte Carlo (MC) model, combined with an analytical surface model, has been developed in order to investigate the general plasma processes occurring during the sputter deposition of complex oxide films in a dual-magnetron sputter deposition system. The important plasma species, such as electrons, Ar+ ions, fast Ar atoms and sputtered metal atoms (i.e. Mg and Al atoms) are described with the so-called multi-species MC model, whereas the deposition of MgxAlyOz films is treated by an analytical surface model. Targetsubstrate distances for both magnetrons in the dual-magnetron setup are varied for the purpose of growing stoichiometric complex oxide thin films. The metal atoms are sputtered from pure metallic targets, whereas the oxygen flux is only directed toward the substrate and is high enough to obtain fully oxidized thin films but low enough to avoid target poisoning. The calculations correspond to typical experimental conditions applied to grow these complex oxide films. In this paper, some calculation results are shown, such as the densities of various plasma species, their fluxes toward the targets and substrate, the deposition rates, as well as the film stoichiometry. Moreover, some results of the combined model are compared with experimental observations. Note that this is the first complete model, which can be applied for large and complicated magnetron reactor geometries, such as dual-magnetron configurations. With this model, we are able to describe all important plasma species as well as the deposition process. It can also be used to predict film stoichiometries of complex oxide films on the substrate. | ||||
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Publisher | Place of Publication | Bristol | Editor | ||
Language | Wos | 000307072500003 | Publication Date | 2012-07-21 | |
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1367-2630; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 3.786 | Times cited | 2 | Open Access | |
Notes | Approved | Most recent IF: 3.786; 2012 IF: 4.063 | |||
Call Number | UA @ lucian @ c:irua:100100 | Serial | 3111 | ||
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Author | Matnazarova, S.; Khalilov, U.; Yusupov, M. | ||||
Title | Effect of endohedral nickel atoms on the hydrophilicity of carbon nanotubes | Type | A1 Journal article | ||
Year | 2023 | Publication | Molecular simulation | Abbreviated Journal | |
Volume | 49 | Issue | 17 | Pages | 1575-1581 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Carbon nanotubes (CNTs) have been successfully used in biomedicine, including cancer therapy, due to their unique physico-chemical properties. Because pristine CNTs exhibit hydrophobic behaviour, they can have a cytotoxic effect on cells, which limits their practical use in biomedicine. The toxicity of CNTs can be reduced by adding water-soluble functional radicals to their surface, i.e. by increasing their hydrophilicity. Another possibility for increasing the hydrophilicity of CNTs is probably filling them with endohedral metal atoms, which has not yet been studied. Thus, in this study, we use computer simulations to investigate the combined effect of endohedral nickel atoms and functional groups on the hydrophilicity of CNTs. Our simulation results show that the introduction of endohedral nickel atoms into CNTs increases their binding energy with functional groups. We also find that the addition of functional groups to the surface of CNT, along with filling it with endohedral nickel atoms, leads to an increase in the dipole moment of the CNT as well as its interaction energy with water, thereby increasing the hydrophilicity of the CNT and, consequently, its solubility in water. This, in turn, can lead to a decrease in CNT toxicity. | ||||
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Language | Wos | 001059544800001 | Publication Date | 2023-09-06 | |
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ISSN ![]() |
0892-7022 | ISBN | Additional Links | UA library record; WoS full record | |
Impact Factor | 2.1 | Times cited | Open Access | ||
Notes | Approved | Most recent IF: 2.1; 2023 IF: 1.254 | |||
Call Number | UA @ admin @ c:irua:199261 | Serial | 9027 | ||
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Author | Khalilov, U.; Uljayev, U.; Mehmonov, K.; Nematollahi, P.; Yusupov, M.; Neyts, E.C.; Neyts, E.C. | ||||
Title | Can endohedral transition metals enhance hydrogen storage in carbon nanotubes? | Type | A1 Journal article | ||
Year | 2024 | Publication | International journal of hydrogen energy | Abbreviated Journal | |
Volume | 55 | Issue | Pages | 640-610 | |
Keywords | A1 Journal article; Engineering sciences. Technology; Modelling and Simulation in Chemistry (MOSAIC); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | The safe and efficient use of hydrogen energy, which is in high demand worldwide today, requires efficient hydrogen storage. Despite significant advances in hydrogen storage using carbon-based nanomaterials, including carbon nanotubes (CNTs), efforts to substantially increase the storage capacity remain less effective. In this work, we demonstrate the effect of endohedral transition metal atoms on the hydrogen storage capacity of CNTs using reactive molecular dynamics simulations. We find that an increase in the volume fraction of endohedral nickel atoms leads to an increase in the concentration of physisorbed hydrogen molecules around single-walled CNTs (SWNTs) by approximately 1.6 times compared to pure SWNTs. The obtained results provide insight into the underlying mechanisms of how endohedral transition metal atoms enhance the hydrogen storage ability of SWNTs under nearly ambient conditions. | ||||
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Publisher | Place of Publication | Editor | |||
Language | Wos | 001142427400001 | Publication Date | 2023-11-24 | |
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ISSN ![]() |
0360-3199 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 7.2 | Times cited | Open Access | Not_Open_Access | |
Notes | Approved | Most recent IF: 7.2; 2024 IF: 3.582 | |||
Call Number | UA @ admin @ c:irua:202315 | Serial | 9006 | ||
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Author | Yusupov, M.; Van der Paal, J.; Neyts, E.C.; Bogaerts, A. | ||||
Title | Synergistic effect of electric field and lipid oxidation on the permeability of cell membranes | Type | A1 Journal article | ||
Year | 2017 | Publication | Biochimica et biophysica acta : G : general subjects | Abbreviated Journal | Bba-Gen Subjects |
Volume | 1861 | Issue | 1861 | Pages | 839-847 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Background: Strong electric fields are knownto affect cell membrane permeability,which can be applied for therapeutic purposes, e.g., in cancer therapy. A synergistic enhancement of this effect may be accomplished by the presence of reactive oxygen species (ROS), as generated in cold atmospheric plasmas. Little is known about the synergy between lipid oxidation by ROS and the electric field, nor on howthis affects the cell membrane permeability. Method: We here conduct molecular dynamics simulations to elucidate the dynamics of the permeation process under the influence of combined lipid oxidation and electroporation. A phospholipid bilayer (PLB), consisting of di-oleoyl-phosphatidylcholine molecules covered with water layers, is used as a model system for the plasma membrane. Results and conclusions:Weshow howoxidation of the lipids in the PLB leads to an increase of the permeability of the bilayer to ROS, although the permeation free energy barriers still remain relatively high. More importantly, oxidation of the lipids results in a drop of the electric field threshold needed for pore formation (i.e., electroporation) in the PLB. The created pores in the membrane facilitate the penetration of reactive plasma species deep into the cell interior, eventually causing oxidative damage. General significance: This study is of particular interest for plasma medicine, as plasma generates both ROS and electric fields, but it is also of more general interest for applications where strong electric fields and ROS both come into play. |
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Publisher | Place of Publication | Editor | |||
Language | Wos | 000397366200012 | Publication Date | 2017-01-27 | |
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0304-4165 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 4.702 | Times cited | Open Access | OpenAccess | |
Notes | This work is financially supported by the Fund for Scientific Research Flanders (FWO; grant numbers: 1200216N and 11U5416N). The work was carried out 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 Flem | Approved | Most recent IF: 4.702 | ||
Call Number | PLASMANT @ plasmant @ c:irua:140095 | Serial | 4413 | ||
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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. | ||||
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Publisher | Place of Publication | Editor | |||
Language | Wos | 000502890900015 | Publication Date | 2019-09-13 | |
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0301-4622 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 2.402 | Times cited | Open Access | ||
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 | ||
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Author | Tit, N.; Al Ezzi, M.M.; Abdullah, H.M.; Yusupov, M.; Kouser, S.; Bahlouli, H.; Yamani, Z.H. | ||||
Title | Detection of CO2 using CNT-based sensors: Role of Fe catalyst on sensitivity and selectivity | Type | A1 Journal article | ||
Year | 2017 | Publication | Materials chemistry and physics | Abbreviated Journal | Mater Chem Phys |
Volume | 186 | Issue | 186 | Pages | 353-364 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | The adsorption of CO2 on surfaces of graphene and carbon nanotubes (CNTs), decorated with Fe atoms, are investigated using the self-consistent-charge density-functional tight-binding (SCC-DFTB) method, neglecting the heat effects. Fe ad-atoms are more stable when they are dispersed on hollow sites. They introduce a large density of states at the Fermi level (N-F); where keeping such density low would help in gas sensing. Furthermore, the Fe ad-atom can weaken the C=O double bonds of the chemisorbed CO2 molecule, paving the way for oxygen atoms to drain more charges from Fe. Consequently, chemisorption of CO2 molecules reduces both N-F and the conductance while it enhances the sensitivity with the increasing gas dose. Conducting armchair CNTs (ac-CNTs) have higher sensitivity than graphene and semiconducting zigzag CNTs (zz-CNT5). Comparative study of sensitivity of ac-CNT-Fe composite towards various gases (e.g., O-2, N-2, H-2, H2O, CO and CO2) has shown high sensitivity and selectivity towards CO, CO2 and H2O gases. (C) 2016 Elsevier B.V. All rights reserved. | ||||
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Publisher | Place of Publication | Lausanne | Editor | ||
Language | Wos | 000390621200044 | Publication Date | 2016-11-04 | |
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0254-0584 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 2.084 | Times cited | 17 | Open Access | Not_Open_Access |
Notes | Approved | Most recent IF: 2.084 | |||
Call Number | UA @ lucian @ c:irua:140333 | Serial | 4465 | ||
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Author | Kovács, A.; Yusupov, M.; Cornet, I.; Billen, P.; Neyts, E.C. | ||||
Title | Effect of natural deep eutectic solvents of non-eutectic compositions on enzyme stability | Type | A1 Journal article | ||
Year | 2022 | Publication | Journal Of Molecular Liquids | Abbreviated Journal | J Mol Liq |
Volume | 366 | Issue | Pages | 120180-17 | |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Biochemical Wastewater Valorization & Engineering (BioWaVE); Intelligence in PRocesses, Advanced Catalysts and Solvents (iPRACS) | ||||
Abstract | Natural deep eutectic solvents (NADES) represent a green alternative to common organic solvents in the biochemical industry due to their benign behavior and tailorable properties, in particular as media for enzymatic reactions. However, to fully exploit their potential in enzymatic reactions, there is a need for a more fundamental understanding of how these neoteric solvents influence the course of these reac-tions. Thus, the aim of this study is to investigate the influence of NADES with various molar composi-tions on the stability and structure of enzymes, applying molecular dynamics simulations. This can help to better understand the effect of individual compounds of NADES, in addition to eutectic mixtures. More specifically, we simulate the behavior of Candida antarctica lipase B (CALB) enzyme in NADES com-posed of choline chloride with either urea, ethylene glycol or glycerol. Hereto, we monitor the NADES microstructure, the general stability of the enzyme and changes in the structure of its active sites and sur-face residues. Our simulations show that none of the studied NADES systems significantly disrupt the microstructure of the solvent or the stability of the CALB enzyme within the time scales of the simula-tions. The enzyme preserves its initial structure, size and intra-chain hydrogen bonds in all investigated compositions and, for the first time reported, also in NADES with increased hydrogen bond donating com-pound ratios. As the main novelty, our results indicate that, in addition to the composition, the molar ratio can be an additional variable to fine-tune the physicochemical properties of NADES without altering the enzyme characteristics. These findings could facilitate the development and application of task -tailored NADES media for biocatalytic processes. (c) 2022 Elsevier B.V. All rights reserved. | ||||
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Language | Wos | 000865431800010 | Publication Date | 2022-08-25 | |
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Series Volume | Series Issue | Edition | |||
ISSN ![]() |
0167-7322 | ISBN | Additional Links | UA library record; WoS full record | |
Impact Factor | 6 | Times cited | Open Access | Not_Open_Access | |
Notes | Approved | Most recent IF: 6 | |||
Call Number | UA @ admin @ c:irua:191538 | Serial | 7265 | ||
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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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Corporate Author | Thesis | ||||
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 | Neyts, E.C.; Yusupov, M.; Verlackt, C.C.; Bogaerts, A. | ||||
Title | Computer simulations of plasmabiomolecule and plasmatissue interactions for a better insight in plasma medicine | Type | A1 Journal article | ||
Year | 2014 | Publication | Journal of physics: D: applied physics | Abbreviated Journal | J Phys D Appl Phys |
Volume | 47 | Issue | 29 | Pages | 293001 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Plasma medicine is a rapidly evolving multidisciplinary field at the intersection of chemistry, biochemistry, physics, biology, medicine and bioengineering. It holds great potential in medical, health care, dentistry, surgical, food treatment and other applications. This multidisciplinary nature and variety of possible applications come along with an inherent and intrinsic complexity. Advancing plasma medicine to the stage that it becomes an everyday tool in its respective fields requires a fundamental understanding of the basic processes, which is lacking so far. However, some major advances have already been made through detailed experiments over the last 15 years. Complementary, computer simulations may provide insight that is difficultif not impossibleto obtain through experiments. In this review, we aim to provide an overview of the various simulations that have been carried out in the context of plasma medicine so far, or that are relevant for plasma medicine. We focus our attention mostly on atomistic simulations dealing with plasmabiomolecule interactions. We also provide a perspective and tentative list of opportunities for future modelling studies that are likely to further advance the field. | ||||
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Corporate Author | Thesis | ||||
Publisher | Place of Publication | London | Editor | ||
Language | Wos | 000338860300001 | Publication Date | 2014-06-26 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN ![]() |
0022-3727;1361-6463; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 2.588 | Times cited | 28 | Open Access | |
Notes | Approved | Most recent IF: 2.588; 2014 IF: 2.721 | |||
Call Number | UA @ lucian @ c:irua:117853 | Serial | 472 | ||
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Author | Yusupov, M.; Neyts, E.C.; Simon, P.; Berdiyorov, G.; Snoeckx, R.; van Duin, A.C.T.; Bogaerts, A. | ||||
Title | Reactive molecular dynamics simulations of oxygen species in a liquid water layer of interest for plasma medicine | Type | A1 Journal article | ||
Year | 2014 | Publication | Journal of physics: D: applied physics | Abbreviated Journal | J Phys D Appl Phys |
Volume | 47 | Issue | 2 | Pages | 025205-25209 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | The application of atmospheric pressure plasmas in medicine is increasingly gaining attention in recent years, although very little is currently known about the plasma-induced processes occurring on the surface of living organisms. It is known that most bio-organisms, including bacteria, are coated by a liquid film surrounding them, and there might be many interactions between plasma species and the liquid layer before the plasma species reach the surface of the bio-organisms. Therefore, it is essential to study the behaviour of the reactive species in a liquid film, in order to determine whether these species can travel through this layer and reach the biomolecules, or whether new species are formed along the way. In this work, we investigate the interaction of reactive oxygen species (i.e. O, OH, HO2 and H2O2) with water, which is assumed as a simple model system for the liquid layer surrounding biomolecules. Our computational investigations show that OH, HO2 and H2O2 can travel deep into the liquid layer and are hence in principle able to reach the bio-organism. Furthermore, O, OH and HO2 radicals react with water molecules through hydrogen-abstraction reactions, whereas no H-abstraction reaction takes place in the case of H2O2. This study is important to gain insight into the fundamental operating mechanisms in plasma medicine, in general, and the interaction mechanisms of plasma species with a liquid film, in particular. | ||||
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Corporate Author | Thesis | ||||
Publisher | Place of Publication | London | Editor | ||
Language | Wos | 000329108000013 | Publication Date | 2013-12-13 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN ![]() |
0022-3727;1361-6463; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 2.588 | Times cited | 51 | Open Access | |
Notes | Approved | Most recent IF: 2.588; 2014 IF: 2.721 | |||
Call Number | UA @ lucian @ c:irua:112286 | Serial | 2823 | ||
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Author | Van der Paal, J.; Verlackt, C.C.; Yusupov, M.; Neyts, E.C.; Bogaerts, A. | ||||
Title | Structural modification of the skin barrier by OH radicals : a reactive molecular dynamics study for plasma medicine | Type | A1 Journal article | ||
Year | 2015 | Publication | Journal of physics: D: applied physics | Abbreviated Journal | J Phys D Appl Phys |
Volume | 48 | Issue | 48 | Pages | 155202 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | While plasma treatment of skin diseases and wound healing has been proven highly effective, the underlying mechanisms, and more generally the effect of plasma radicals on skin tissue, are not yet completely understood. In this paper, we perform ReaxFF-based reactive molecular dynamics simulations to investigate the interaction of plasma generated OH radicals with a model system composed of free fatty acids, ceramides, and cholesterol molecules. This model system is an approximation of the upper layer of the skin (stratum corneum). All interaction mechanisms observed in our simulations are initiated by H-abstraction from one of the ceramides. This reaction, in turn, often starts a cascade of other reactions, which eventually lead to the formation of aldehydes, the dissociation of ceramides or the elimination of formaldehyde, and thus eventually to the degradation of the skin barrier function. | ||||
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Corporate Author | Thesis | ||||
Publisher | Place of Publication | London | Editor | ||
Language | Wos | 000351856600007 | Publication Date | 2015-03-25 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN ![]() |
0022-3727;1361-6463; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 2.588 | Times cited | 20 | Open Access | |
Notes | Approved | Most recent IF: 2.588; 2015 IF: 2.721 | |||
Call Number | c:irua:124230 | Serial | 3242 | ||
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Author | Bogaerts, A.; Khosravian, N.; Van der Paal, J.; Verlackt, C.C.W.; Yusupov, M.; Kamaraj, B.; Neyts, E.C. | ||||
Title | Multi-level molecular modelling for plasma medicine | Type | A1 Journal article | ||
Year | 2016 | Publication | Journal of physics: D: applied physics | Abbreviated Journal | J Phys D Appl Phys |
Volume | 49 | Issue | 49 | Pages | 054002 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Modelling at the molecular or atomic scale can be very useful for obtaining a better insight in plasma medicine. This paper gives an overview of different atomic/molecular scale modelling approaches that can be used to study the direct interaction of plasma species with biomolecules or the consequences of these interactions for the biomolecules on a somewhat longer time-scale. These approaches include density functional theory (DFT), density functional based tight binding (DFTB), classical reactive and non-reactive molecular dynamics (MD) and united-atom or coarse-grained MD, as well as hybrid quantum mechanics/molecular mechanics (QM/MM) methods. Specific examples will be given for three important types of biomolecules, present in human cells, i.e. proteins, DNA and phospholipids found in the cell membrane. The results show that each of these modelling approaches has its specific strengths and limitations, and is particularly useful for certain applications. A multi-level approach is therefore most suitable for obtaining a global picture of the plasma–biomolecule interactions. | ||||
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Corporate Author | Thesis | ||||
Publisher | Place of Publication | Editor | |||
Language | Wos | 000368944100003 | Publication Date | 2015-12-16 | |
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 | 11 | Open Access | |
Notes | This work is financially supported by the Fund for Scientific Research Flanders (FWO) and the Francqui Foundation. The calculations were carried out 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: 2.588 | ||
Call Number | c:irua:131571 | Serial | 3985 | ||
Permanent link to this record | |||||
Author | Bogaerts, A.; Khosravian, N.; Van der Paal, J.; Verlackt, C.C.W.; Yusupov, M.; Kamaraj, B.; Neyts, E.C. | ||||
Title | Multi-level molecular modelling for plasma medicine | Type | A1 Journal article | ||
Year | 2016 | Publication | Journal Of Physics D-Applied Physics | Abbreviated Journal | J Phys D Appl Phys |
Volume | 49 | Issue | 5 | Pages | 054002-54019 |
Keywords | A1 Journal article; Plasma, laser ablation and surface modeling – Antwerp (PLASMANT) | ||||
Abstract | |||||
Address | |||||
Corporate Author | Thesis | ||||
Publisher | Place of Publication | London | Editor | ||
Language | Wos | Publication Date | 0000-00-00 | ||
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN ![]() |
0022-3727 | ISBN | Additional Links | UA library record | |
Impact Factor | 2.588 | Times cited | Open Access | ||
Notes | Approved | Most recent IF: 2.588 | |||
Call Number | UA @ lucian @ c:irua:129798 | Serial | 4467 | ||
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Author | Yusupov, M.; Yan, D.; Cordeiro, R.M.; Bogaerts, A. | ||||
Title | Atomic scale simulation of H2O2permeation through aquaporin: toward the understanding of plasma cancer treatment | Type | A1 Journal article | ||
Year | 2018 | Publication | Journal of physics: D: applied physics | Abbreviated Journal | J Phys D Appl Phys |
Volume | 51 | Issue | 12 | Pages | 125401 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | Experiments have demonstrated the potential selective anticancer capacity of cold atmospheric plasmas (CAPs), but the underlying mechanisms remain unclear. Using computer simulations, we try to shed light on the mechanism of selectivity, based on aquaporins (AQPs), i.e. transmembrane protein channels transferring external H 2 O 2 and other reactive oxygen species, created e.g. by CAPs, to the cell interior. Specifically, we perform molecular dynamics simulations for the permeation of H 2 O 2 through AQP1 (one of the members of the AQP family) and the palmitoyl-oleoyl-phosphatidylcholine (POPC) phospholipid bilayer (PLB). The free energy barrier of H 2 O 2 across AQP1 is lower than for the POPC PLB, while the permeability coefficient, calculated using the free energy and diffusion rate profiles, is two orders of magnitude higher. This indicates that the delivery of H 2 O 2 into the cell interior should be through AQP. Our study gives a better insight into the role of AQPs in the selectivity of CAPs for treating cancer cells. | ||||
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Corporate Author | Thesis | ||||
Publisher | Place of Publication | Editor | |||
Language | Wos | 000426378100001 | Publication Date | 2018-02-28 | |
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 | 7 | Open Access | OpenAccess |
Notes | MY gratefully acknowledges financial support from the Research Foundation—Flanders (FWO) via Grant No. 1200216N and a travel grant to George Washington University (GWU). 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 Super- computer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. Work at GWU was supported by the National Science Foundation, grant 1465061. RMC thanks FAPESP and CNPq for finan- cial support (Grant Nos. 2012/50680-5 and 459270/2014-1, respectively). | Approved | Most recent IF: 2.588 | ||
Call Number | PLASMANT @ plasmant @c:irua:149382 | Serial | 4811 | ||
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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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Corporate Author | Thesis | ||||
Publisher | Place of Publication | Editor | |||
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 | Mehmonov, K.; Ergasheva, A.; Yusupov, M.; Khalilov, U. | ||||
Title | The role of carbon monoxide in the catalytic synthesis of endohedral carbyne | Type | A1 Journal article | ||
Year | 2023 | Publication | Journal of applied physics | Abbreviated Journal | |
Volume | 134 | Issue | 14 | Pages | 144303-144307 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | The unique physical properties of carbyne, a novel carbon nanostructure, have attracted considerable interest in modern nanotechnology. While carbyne synthesis has been accomplished successfully using diverse techniques, the underlying mechanisms governing the carbon monoxide-dependent catalytic synthesis of endohedral carbyne remain poorly understood. In this simulation-based study, we investigate the synthesis of endohedral carbyne from carbon and carbon monoxide radicals in the presence of a nickel catalyst inside double-walled carbon nanotubes with a (5,5)@(10,10) structure. The outcome of our investigation demonstrates that the incorporation of the carbon atom within the Ni-n@(5,5)@(10,10) model system initiates the formation of an elongated carbon chain. In contrast, upon the introduction of carbon monoxide radicals, the growth of the carbyne chain is inhibited as a result of the oxidation of endohedral nickel clusters by oxygen atoms after the initial steps of nucleation. Our findings align with prior theoretical, simulation, and experimental investigations, reinforcing their consistency and providing valuable insights into the synthesis of carbyne-based nanodevices that hold promising potential for future advancements in nanotechnology. | ||||
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Corporate Author | Thesis | ||||
Publisher | Place of Publication | Editor | |||
Language | Wos | 001083993400003 | Publication Date | 2023-10-10 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN ![]() |
0021-8979; 1089-7550 | ISBN | Additional Links | UA library record; WoS full record | |
Impact Factor | 3.2 | Times cited | Open Access | ||
Notes | Approved | Most recent IF: 3.2; 2023 IF: 2.068 | |||
Call Number | UA @ admin @ c:irua:201233 | Serial | 9106 | ||
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Author | Oliveira, M.C.; Yusupov, M.; Cordeiro, R.M.; Bogaerts, A. | ||||
Title | Unraveling the permeation of reactive species across nitrated membranes by computer simulations | Type | A1 Journal Article;Reactive oxygen and nitrogen species | ||
Year | 2021 | Publication | Computers In Biology And Medicine | Abbreviated Journal | Comput Biol Med |
Volume | 136 | Issue | Pages | 104768 | |
Keywords | A1 Journal Article;Reactive oxygen and nitrogen species; Nitro-oxidative stress; Molecular dynamics simulations; Nitrated membranes; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ; | ||||
Abstract | Reactive oxygen and nitrogen species (RONS) are involved in many biochemical processes, including nitrooxidative stress that causes cancer cell death, observed in cancer therapies such as photodynamic therapy and cold atmospheric plasma. However, their mechanisms of action and selectivity still remain elusive due to the complexity of biological cells. For example, it is not well known how RONS generated by cancer therapies permeate the cell membrane to cause nitro-oxidative damage. There are many studies dedicated to the permeation of RONS across native and oxidized membranes, but not across nitrated membranes, another lipid product also generated during nitro-oxidative stress. Herein, we performed molecular dynamics (MD) simulations to calculate the free energy barrier of RONS permeation across nitrated membranes. Our results show that hydrophilic RONS, such as hydroperoxyl radical (HO2) and peroxynitrous acid (ONOOH), have relatively low barriers compared to hydrogen peroxide (H2O2) and hydroxyl radical (HO), and are more prone to permeate the membrane than for the native or peroxidized membranes, and similar to aldehyde-oxidized membranes. Hydrophobic RONS like molecular oxygen (O2), nitrogen dioxide (NO2) and nitric oxide (NO) even have insignificant barriers for permeation. Compared to native and peroxidized membranes, nitrated membranes are more permeable, suggesting that we must not only consider oxidized membranes during nitro-oxidative stress, but also nitrated membranes, and their role in cancer therapies. | ||||
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Corporate Author | Thesis | ||||
Publisher | Place of Publication | Editor | |||
Language | Wos | 000696938800003 | Publication Date | 2021-08-17 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN ![]() |
0010-4825 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 1.836 | Times cited | Open Access | OpenAccess | |
Notes | We thank University of Antwerp and Coordination of Superior Level Staff Improvement (CAPES, Brazil) for the scholarship granted and for providing the computational resources needed for completion of this work. M. Yusupov acknowledges the Flanders Research Foundation (grant 1200219N) for financial support. | Approved | Most recent IF: 1.836 | ||
Call Number | PLASMANT @ plasmant @c:irua:181082 | Serial | 6807 | ||
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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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Publisher | Place of Publication | Editor | |||
Language | Wos | 001127850500001 | Publication Date | 2023-11-23 | |
Series Editor | Series Title | Abbreviated Series Title | |||
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 | 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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Corporate Author | Thesis | ||||
Publisher | Place of Publication | Editor | |||
Language | Wos | 000461411200014 | Publication Date | 2019-02-07 | |
Series Editor | Series Title | Abbreviated Series Title | |||
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 | ||
Permanent link to this record | |||||
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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Corporate Author | Thesis | ||||
Publisher | Place of Publication | Editor | |||
Language | Wos | 000525439700011 | Publication Date | 2019-09-23 | |
Series Editor | Series Title | Abbreviated Series Title | |||
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 | 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 | 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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Publisher | Place of Publication | Editor | |||
Language | Wos | 000594173400010 | Publication Date | 0000-00-00 | |
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ISSN ![]() |
0003-9861 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 3.9 | Times cited | Open Access | ||
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 | ||
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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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Publisher | Place of Publication | Editor | |||
Language | Wos | 000767632000001 | Publication Date | 2022-01-24 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN ![]() |
0003-9861 | ISBN | Additional Links | UA library record; WoS full record | |
Impact Factor | 3.9 | Times cited | 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 | ||
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Author | Yusupov, M.; Bultinck, E.; Depla, D.; Bogaerts, A. | ||||
Title | Elucidating the asymmetric behavior of the discharge in a dual magnetron sputter deposition system | Type | A1 Journal article | ||
Year | 2011 | Publication | Applied physics letters | Abbreviated Journal | Appl Phys Lett |
Volume | 98 | Issue | 13 | Pages | 131502-131502,3 |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | A magnetron discharge is characterized by drifts of the charged particles guiding center, caused by the magnetic field, in contrast to unmagnetized discharges. Because of these drifts, a pronounced asymmetry of the discharge can be observed in a dual magnetron setup. In this work, it is found that the shape of the discharge in a dual magnetron configuration depends on the magnetic field configuration. In a closed configuration, strong drifts were observed in one preferential direction, whereas in a mirror configuration the deflection of the discharge was not so pronounced. Our calculations confirm experimental observations. | ||||
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Publisher | American Institute of Physics | Place of Publication | New York, N.Y. | Editor | |
Language | Wos | 000289153600017 | Publication Date | 2011-04-01 | |
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ISSN ![]() |
0003-6951; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 3.411 | Times cited | 4 | Open Access | |
Notes | Approved | Most recent IF: 3.411; 2011 IF: 3.844 | |||
Call Number | UA @ lucian @ c:irua:87867 | Serial | 1026 | ||
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Author | Yusupov, M. | ||||
Title | Atomic scale simulations for a better insight in plasma medicine | Type | Doctoral thesis | ||
Year | 2014 | Publication | Abbreviated Journal | ||
Volume | Issue | Pages | |||
Keywords | Doctoral thesis; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
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Corporate Author | Thesis | ||||
Publisher | Place of Publication | Antwerpen | Editor | ||
Language | Wos | Publication Date | 0000-00-00 | ||
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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 @ lucian @ c:irua:117837 | Serial | 188 | ||
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