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	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
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	001071356400001	Publication Date	2023-09-11
	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 received no external funding.			Approved	Most recent IF: NA
	Call Number	PLASMANT @ plasmant @c:irua:200380			Serial	8958
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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
	Corporate Author				Thesis
	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
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	Author	Cotte, M.; Gonzalez, V.; Vanmeert, F.; Monico, L.; Dejoie, C.; Burghammer, M.; Huder, L.; de Nolf, W.; Fisher, S.; Fazlic, I.; Chauffeton, C.; Wallez, G.; Jimenez, N.; Albert-Tortosa, F.; Salvado, N.; Possenti, E.; Colombo, C.; Ghirardello, M.; Comelli, D.; Avranovich Clerici, E.; Vivani, R.; Romani, A.; Costantino, C.; Janssens, K.; Taniguchi, Y.; McCarthy, J.; Reichert, H.; Susini, J.
	Title	The “Historical Materials BAG” : a new facilitated access to synchrotron X-ray diffraction analyses for cultural heritage materials at the European Synchrotron Radiation Facility			Type	A1 Journal article
	Year	2022	Publication	Molecules: a journal of synthetic chemistry and natural product chemistry	Abbreviated Journal	Molecules
	Volume	27	Issue	6	Pages	1997-21
	Keywords	A1 Journal article; Antwerp X-ray Imaging and Spectroscopy (AXIS)
	Abstract	The European Synchrotron Radiation Facility (ESRF) has recently commissioned the new Extremely Brilliant Source (EBS). The gain in brightness as well as the continuous development of beamline instruments boosts the beamline performances, in particular in terms of accelerated data acquisition. This has motivated the development of new access modes as an alternative to standard proposals for access to beamtime, in particular via the “block allocation group” (BAG) mode. Here, we present the recently implemented “historical materials BAG”: a community proposal giving to 10 European institutes the opportunity for guaranteed beamtime at two X-ray powder diffraction (XRPD) beamlines-ID13, for 2D high lateral resolution XRPD mapping, and ID22 for high angular resolution XRPD bulk analyses-with a particular focus on applications to cultural heritage. The capabilities offered by these instruments, the specific hardware and software developments to facilitate and speed-up data acquisition and data processing are detailed, and the first results from this new access are illustrated with recent applications to pigments, paintings, ceramics and wood.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000776369800001	Publication Date	2022-03-21
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1420-3049	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	4.6	Times cited		Open Access	OpenAccess
	Notes				Approved	Most recent IF: 4.6
	Call Number	UA @ admin @ c:irua:188053			Serial	7218
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	Author	Fuoco, T.; Cuartero, M.; Parrilla, M.; García-Guzmán, J.J.; Crespo, G.A.; Finne-Wistrand, A.
	Title	Capturing the real-time hydrolytic degradation of a library of biomedical polymers by combining traditional assessment and electrochemical sensors			Type	A1 Journal article
	Year	2021	Publication	Biomacromolecules	Abbreviated Journal	Biomacromolecules
	Volume	22	Issue	2	Pages	949-960
	Keywords	A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
	Abstract	We have developed an innovative methodology to overcome the lack of techniques for real-time assessment of degradable biomedical polymers at physiological conditions. The methodology was established by combining polymer characterization techniques with electrochemical sensors. The in vitro hydrolytic degradation of a series of aliphatic polyesters was evaluated by following the molar mass decrease and the mass loss at different incubation times while tracing pH and l-lactate released into the incubation media with customized miniaturized electrochemical sensors. The combination of different analytical approaches provided new insights into the mechanistic and kinetics aspects of the degradation of these biomedical materials. Although molar mass had to reach threshold values for soluble oligomers to be formed and specimens’ resorption to occur, the pH variation and l-lactate concentration were direct evidence of the resorption of the polymers and indicative of the extent of chain scission. Linear models were found for pH and released l-lactate as a function of mass loss for the l-lactide-based copolymers. The methodology should enable the sequential screening of degradable polymers at physiological conditions and has potential to be used for preclinical material’s evaluation aiming at reducing animal tests.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos		Publication Date	2021-01-27
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	1525-7797	ISBN		Additional Links	UA library record
	Impact Factor	5.246	Times cited		Open Access	OpenAccess
	Notes				Approved	Most recent IF: 5.246
	Call Number	UA @ admin @ c:irua:175296			Serial	7575
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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
	Corporate Author				Thesis
	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
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	Author	Zhang, X.B.; Van Tendeloo, G.; van Landuyt, J.; van Dyck, D.; Briers, J.; Bao, Y.; Geise, H.J.
	Title	An electron microscopic study of highly oriented undoped and FeCl₃-doped poly (p-phenylenevinylene)			Type	A1 Journal article
	Year	1996	Publication	Macromolecules	Abbreviated Journal	Macromolecules
	Volume	29	Issue	5	Pages	1554-1561
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Washington, D.C.	Editor
	Language		Wos	A1996TY13900024	Publication Date	2002-07-26
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0024-9297;1520-5835;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	5.8	Times cited	10	Open Access
	Notes				Approved	no
	Call Number	UA @ lucian @ c:irua:15452			Serial	939
Permanent link to this record