| Records |
| Author |
Ghasemitarei, M.; Ghorbi, T.; Yusupov, M.; Zhang, Y.; Zhao, T.; Shali, P.; Bogaerts, A. |
| Title |
Effects of Nitro-Oxidative Stress on Biomolecules: Part 1—Non-Reactive Molecular Dynamics Simulations |
Type |
A1 Journal Article |
Year  |
2023 |
Publication |
Biomolecules |
Abbreviated Journal |
Biomolecules |
| Volume |
13 |
Issue |
9 |
Pages |
1371 |
| Keywords |
A1 Journal Article; plasma medicine; reactive oxygen and; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ; |
| Abstract |
Plasma medicine, or the biomedical application of cold atmospheric plasma (CAP), is an expanding field within plasma research. CAP has demonstrated remarkable versatility in diverse biological applications, including cancer treatment, wound healing, microorganism inactivation, and skin disease therapy. However, the precise mechanisms underlying the effects of CAP remain incompletely understood. The therapeutic effects of CAP are largely attributed to the generation of reactive oxygen and nitrogen species (RONS), which play a crucial role in the biological responses induced by CAP. Specifically, RONS produced during CAP treatment have the ability to chemically modify cell membranes and membrane proteins, causing nitro-oxidative stress, thereby leading to changes in membrane permeability and disruption of cellular processes. To gain atomic-level insights into these interactions, non-reactive molecular dynamics (MD) simulations have emerged as a valuable tool. These simulations facilitate the examination of larger-scale system dynamics, including protein-protein and protein-membrane interactions. In this comprehensive review, we focus on the applications of non-reactive MD simulations in studying the effects of CAP on cellular components and interactions at the atomic level, providing a detailed overview of the potential of CAP in medicine. We also review the results of other MD studies that are not related to plasma medicine but explore the effects of nitro-oxidative stress on cellular components and are therefore important for a broader understanding of the underlying processes. |
| Address |
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| Corporate Author |
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Thesis |
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| Publisher |
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Place of Publication |
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Editor |
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| Language |
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Wos |
001071356400001 |
Publication Date |
2023-09-11 |
| Series Editor |
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Series Title |
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Abbreviated Series Title |
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| Series Volume |
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Series Issue |
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Edition |
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| ISSN |
2218-273X |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
| Impact Factor |
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Times cited |
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Open Access |
Not_Open_Access |
| Notes |
This research received no external funding. |
Approved |
Most recent IF: NA |
| Call Number |
PLASMANT @ plasmant @c:irua:200380 |
Serial |
8958 |
| Permanent link to this record |
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| 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. |
| Address |
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| Corporate Author |
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Thesis |
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| Publisher |
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Place of Publication |
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Editor |
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| Language |
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Wos |
001035160000001 |
Publication Date |
2023-06-27 |
| Series Editor |
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Series Title |
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Abbreviated Series Title |
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| Series Volume |
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Series Issue |
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Edition |
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| ISSN |
2218-273X |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
| Impact Factor |
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Times cited |
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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 |
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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. |
| Address |
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| Corporate Author |
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Thesis |
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| Publisher |
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Place of Publication |
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Editor |
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| Language |
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Wos |
000578895600001 |
Publication Date |
2020-07-28 |
| Series Editor |
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Series Title |
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Abbreviated Series Title |
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| Series Volume |
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Series Issue |
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Edition |
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| ISSN |
2218-273X |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
| Impact Factor |
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Times cited |
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Open Access |
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| 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 |
