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  1. Article ; Online: Situating the phosphonated calixarene-cytochrome C association by molecular dynamics simulations.

    Bartocci, Alessio / Dumont, Elise

    The Journal of chemical physics

    2024  Volume 160, Issue 10

    Abstract: Protein-calixarenes binding plays an increasingly central role in many applications, spanning from molecular recognition to drug delivery strategies and protein inhibition. These ligands obey a specific bio-supramolecular chemistry, which can be revealed ...

    Abstract Protein-calixarenes binding plays an increasingly central role in many applications, spanning from molecular recognition to drug delivery strategies and protein inhibition. These ligands obey a specific bio-supramolecular chemistry, which can be revealed by computational approaches, such as molecular dynamics simulations. In this paper, we rely on all-atom, explicit-solvent molecular dynamics simulations to capture the electrostatically driven association of a phosphonated calix-[4]-arene with cytochome-C, which critically relies on surface-exposed paired lysines. Beyond two binding sites identified in direct agreement with the x-ray structure, the association has a larger structural impact on the protein dynamics. Then, our simulations allow a direct comparison to analogous calixarenes, namely, sulfonato, similarly reported as "molecular glue." Our work can contribute to a robust in silico predictive tool to assess binding sites for any given protein of interest for crystallization, with the specificity of a macromolecular cage whose endo/exo orientation plays a role in the binding.
    MeSH term(s) Molecular Dynamics Simulation ; Cytochromes c/chemistry ; Calixarenes/chemistry ; Calixarenes/metabolism ; Binding Sites ; Proteins/chemistry
    Chemical Substances Cytochromes c (9007-43-6) ; Calixarenes (130036-26-9) ; Proteins
    Language English
    Publishing date 2024-03-11
    Publishing country United States
    Document type Journal Article
    ZDB-ID 3113-6
    ISSN 1089-7690 ; 0021-9606
    ISSN (online) 1089-7690
    ISSN 0021-9606
    DOI 10.1063/5.0198522
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Book ; Online: Radiation-induced and oxidative DNA damages

    Dumont, Elise / Chatgilialoglu, Chryssostomos / Monari, Antonio

    2015  

    Abstract: DNA stores and passes the genetic information of almost all living organisms. Its molecular structure and their intramolecular interactions are particularly suitable to maximize stability against oxidative stress and UV-light absorption. Yet the ... ...

    Abstract DNA stores and passes the genetic information of almost all living organisms. Its molecular structure and their intramolecular interactions are particularly suitable to maximize stability against oxidative stress and UV-light absorption. Yet the protection and repair strategies are still error-prone: DNA lesions are produced, including the most complex and highly mutagenic ones. An important threat to DNA stability comes from photosensitization, i.e. from the dramatic multiplication of radiation-induced defects mediated by the presence of organic or organometallic dyes compared to the direct exposure to UVA radiation. Moreover, the photo-induced production of singlet oxygen generates an extremely high oxidative stress on DNA that, in vivo, normally results in extended cellular apoptosis.-

    Elucidating the processes leading to DNA damages, from the production of a simple radical entity to deleterious lesions, as well as the opportunities of repair by devoted enzymes, is a cornerstone towards the development of more efficient protection strategies. Sensitization and selective production of DNA lesions can also be exploited to induce the selective apoptosis of cancer cells upon exposition to radiation or to oxidative stress, for instance in the field of photodynamic therapy. The importance and relevance of the field is witnessed by the impressive amount of high-level papers dealing with this complex subject, and notably tackling the structural elucidation of DNA and DNA-drug adducts, the mechanisms of formation of DNA lesions (including the precise detection of the final lesion products), as well as the influence of the lesions on the DNA stability and dynamics and the consequences on the ease of repair.-

    Due to the complexity of the field lying at the frontiers between chemistry, physics and biology, multidisciplinary strategies allying modeling and experience are needed. This topic aims at giving an extended overview of the current research in the domain, with fundamental contribution from the leading groups in the field of DNA reactivity, structural characterization, photo-chemistry and photo-physics, as well as repair mechanism. It will therefore be a fundamental guide for scientists wanting to address the field of DNA lesion and repair, but also more generally for researchers working in rational drug design or in the development of biomarkers and medical imaging techniques
    Keywords Science (General) ; Chemistry
    Size 1 electronic resource (93 p.)
    Publisher Frontiers Media SA
    Document type Book ; Online
    Note English ; Open Access
    HBZ-ID HT020091848
    ISBN 9782889196609 ; 2889196607
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  3. Article ; Online: Probing the dynamical interaction of the

    Bartocci, Alessio / Dumont, Elise

    Physical chemistry chemical physics : PCCP

    2023  Volume 25, Issue 27, Page(s) 18067–18074

    Abstract: Calixarenes are hallmark molecules in supramolecular chemistry as hosts for small ligands. They have also conversely proved their interest as ligands toward assisted co-crystallization of proteins. These functionalized macrocycles target positively- ... ...

    Abstract Calixarenes are hallmark molecules in supramolecular chemistry as hosts for small ligands. They have also conversely proved their interest as ligands toward assisted co-crystallization of proteins. These functionalized macrocycles target positively-charged residues, and notably surface-exposed lysines, with a site-selectivity finely characterized experimentally, but that remains to be assessed. Relying on a tailored molecular dynamics simulations protocol, we explore the association of
    MeSH term(s) Antifungal Agents/pharmacology ; Ligands ; Proteins/chemistry ; Calixarenes/chemistry ; Lysine
    Chemical Substances calix(4)arene ; Antifungal Agents ; Ligands ; Proteins ; Calixarenes (130036-26-9) ; Lysine (K3Z4F929H6)
    Language English
    Publishing date 2023-07-12
    Publishing country England
    Document type Journal Article
    ZDB-ID 1476244-4
    ISSN 1463-9084 ; 1463-9076
    ISSN (online) 1463-9084
    ISSN 1463-9076
    DOI 10.1039/d3cp01202f
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Dynamics and energetics of PCBP1 binding to severely oxidized RNA.

    Gillet, Natacha / Dumont, Elise

    Frontiers in molecular biosciences

    2022  Volume 9, Page(s) 994915

    Abstract: Oxidatively generated lesions such as 8-oxo-7, 8-dihydroguanine (8-oxoG) on RNA strands constitute a hallmark marker of the oxidative stress in the cell. Poly-C binding protein 1 (PCBP1) is able to specifically recognize severely damaged RNA strands ... ...

    Abstract Oxidatively generated lesions such as 8-oxo-7, 8-dihydroguanine (8-oxoG) on RNA strands constitute a hallmark marker of the oxidative stress in the cell. Poly-C binding protein 1 (PCBP1) is able to specifically recognize severely damaged RNA strands containing two 8-oxoG lesions separated by five nucleobases, which trigger a signaling pathway leading to cell apoptosis. We apply an
    Language English
    Publishing date 2022-11-03
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2814330-9
    ISSN 2296-889X
    ISSN 2296-889X
    DOI 10.3389/fmolb.2022.994915
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Reactivity of Singlet Oxygen with DNA, an Update.

    Ravanat, Jean-Luc / Dumont, Elise

    Photochemistry and photobiology

    2022  Volume 98, Issue 3, Page(s) 564–571

    Abstract: The reactivity of singlet oxygen with DNA constituents and in particular with the guanine base has been studied during more than four decades but the exact mechanisms by which such a reactive oxygen species reacts with DNA is still a matter of debate. In ...

    Abstract The reactivity of singlet oxygen with DNA constituents and in particular with the guanine base has been studied during more than four decades but the exact mechanisms by which such a reactive oxygen species reacts with DNA is still a matter of debate. In this review article, a summary of the data that were obtained from several laboratories and using complementary experimental and theoretical approaches are presented. Reaction mechanisms of
    MeSH term(s) DNA/metabolism ; Guanine ; Oxidation-Reduction ; Oxygen ; Reactive Oxygen Species ; Singlet Oxygen
    Chemical Substances Reactive Oxygen Species ; Singlet Oxygen (17778-80-2) ; Guanine (5Z93L87A1R) ; DNA (9007-49-2) ; Oxygen (S88TT14065)
    Language English
    Publishing date 2022-01-05
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 123540-0
    ISSN 1751-1097 ; 0031-8655
    ISSN (online) 1751-1097
    ISSN 0031-8655
    DOI 10.1111/php.13581
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.B 1686: Show issues Location:
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    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  6. Article ; Online: Rationalizing the environment-dependent photophysical behavior of a DNA luminescent probe by classical and non-adiabatic molecular dynamics simulations.

    Monari, Antonio / Burger, Alain / Dumont, Elise

    Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology

    2023  Volume 22, Issue 9, Page(s) 2081–2092

    Abstract: Environment-sensitive fluorescent nucleoside analogs are of utmost importance to investigate the structure of nucleic acids, their intrinsic flexibility, and sequence-specific DNA- and RNA-binding proteins. The latter play indeed a key role in ... ...

    Abstract Environment-sensitive fluorescent nucleoside analogs are of utmost importance to investigate the structure of nucleic acids, their intrinsic flexibility, and sequence-specific DNA- and RNA-binding proteins. The latter play indeed a key role in transcription, translation as well as in the regulation of RNA stability, localization and turnover, and many other cellular processes. The sensitivity of the embedded fluorophore to polarity, hydration, and base stacking is clearly dependent on the specific excited-state relaxation mechanism and can be rationalized combining experimental and computational techniques. In this work, we elucidate the mechanisms leading to the population of the triplet state manifold for a versatile nucleobase surrogate, namely the 2-thienyl-3-hydroxychromone in gas phase, owing to non-adiabatic molecular dynamics simulations. Furthermore, we analyze its behavior in the B-DNA environment via classical molecular dynamics simulations, which evidence a rapid extrusion of the adenine facing the 2-thienyl-3-hydroxychromone nucleobase surrogate. Our simulations provide new insights into the dynamics of this family of chromophores, which could give rise to an integrated view and a fine tuning of their photochemistry, and namely the role of excited-state intramolecular proton transfer for the rational design of the next generation of fluorescent nucleoside analogs.
    MeSH term(s) Molecular Dynamics Simulation ; Nucleosides/chemistry ; DNA/chemistry ; Nucleic Acids ; Protons ; DNA Probes
    Chemical Substances Nucleosides ; DNA (9007-49-2) ; Nucleic Acids ; Protons ; DNA Probes
    Language English
    Publishing date 2023-05-11
    Publishing country England
    Document type Journal Article
    ZDB-ID 2072584-X
    ISSN 1474-9092 ; 1474-905X
    ISSN (online) 1474-9092
    ISSN 1474-905X
    DOI 10.1007/s43630-023-00431-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: How SARS-CoV-2 Alters the Regulation of Gene Expression in Infected Cells.

    Bignon, Emmanuelle / Grandemange, Stéphanie / Dumont, Elise / Monari, Antonio

    The journal of physical chemistry letters

    2023  Volume 14, Issue 13, Page(s) 3199–3207

    Abstract: Nonstructural accessory proteins in viruses play a key role in hijacking the basic cellular mechanisms, which is essential to promote the virus survival and evasion of the immune system. The immonuglobulin-like open reading frame 8 (ORF8) protein ... ...

    Abstract Nonstructural accessory proteins in viruses play a key role in hijacking the basic cellular mechanisms, which is essential to promote the virus survival and evasion of the immune system. The immonuglobulin-like open reading frame 8 (ORF8) protein expressed by SARS-CoV-2 accumulates in the nucleus and may influence the regulation of the gene expression in infected cells. In this contribution, by using microsecond time-scale all-atom molecular dynamics simulations, we unravel the structural bases behind the epigenetic action of ORF8. In particular, we highlight how the protein is able to form stable aggregates with DNA through a histone tail-like motif, and how this interaction is influenced by post-translational modifications, such as acetylation and methylation, which are known epigenetic markers in histones. Our work not only clarifies the molecular mechanisms behind the perturbation of the epigenetic regulation caused by the viral infection but also offers an unusual perspective which may foster the development of original antivirals.
    MeSH term(s) Humans ; SARS-CoV-2/metabolism ; Epigenesis, Genetic ; COVID-19/genetics ; Histones/metabolism ; Methylation
    Chemical Substances Histones
    Language English
    Publishing date 2023-03-27
    Publishing country United States
    Document type Journal Article
    ISSN 1948-7185
    ISSN (online) 1948-7185
    DOI 10.1021/acs.jpclett.3c00582
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Molecular Basis of the pH-Controlled Maturation of the Tick-Borne Encephalitis Flavivirus.

    Bignon, Emmanuelle / Dumont, Elise / Monari, Antonio

    The journal of physical chemistry letters

    2023  Volume 14, Issue 7, Page(s) 1977–1982

    Abstract: Flaviviruses are enveloped viruses causing high public concerns. Their maturation spans several cellular compartments having different pH. Thus, complex control mechanisms are in place to avoid premature maturation. Here we report the dynamical behavior ... ...

    Abstract Flaviviruses are enveloped viruses causing high public concerns. Their maturation spans several cellular compartments having different pH. Thus, complex control mechanisms are in place to avoid premature maturation. Here we report the dynamical behavior at neutral and acidic pH of the precursor of the membrane fusion protein E of tick-borne encephalitis, showing the different stabilizations of the E dimer and the role played by the small fusion-assisting protomer (pr). The comprehension, at atomic resolution, of the fine regulation of viral maturation will be fundamental to the development of efficient strategies against emerging viral threats.
    MeSH term(s) Humans ; Encephalitis, Tick-Borne ; Encephalitis Viruses, Tick-Borne/chemistry ; Encephalitis Viruses, Tick-Borne/metabolism ; Viral Envelope Proteins/chemistry ; Viral Envelope Proteins/metabolism ; Flavivirus Infections ; Hydrogen-Ion Concentration
    Chemical Substances Viral Envelope Proteins
    Language English
    Publishing date 2023-02-15
    Publishing country United States
    Document type Journal Article
    ISSN 1948-7185
    ISSN (online) 1948-7185
    DOI 10.1021/acs.jpclett.2c03551
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Free energy landscape and thermodynamics properties of novel mutations in PncA of pyrazinamide resistance isolates of

    Tahir Khan, Muhammad / Dumont, Elise / Chaudhry, Aijaz Rasool / Wei, Dong-Qing

    Journal of biomolecular structure & dynamics

    2023  , Page(s) 1–12

    Abstract: Pyrazinamide (PZA) is one of the first-line antituberculosis therapy, active against non- ... ...

    Abstract Pyrazinamide (PZA) is one of the first-line antituberculosis therapy, active against non-replicating
    Language English
    Publishing date 2023-10-14
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2023.2268216
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2093: Show issues Location:
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  10. Article ; Online: Capturing the Recognition Dynamics of

    Bartocci, Alessio / Pereira, Gilberto / Cecchini, Marco / Dumont, Elise

    Journal of chemical information and modeling

    2022  

    Abstract: Calix[ ...

    Abstract Calix[
    Language English
    Publishing date 2022-09-02
    Publishing country United States
    Document type Journal Article
    ZDB-ID 190019-5
    ISSN 1549-960X ; 0095-2338
    ISSN (online) 1549-960X
    ISSN 0095-2338
    DOI 10.1021/acs.jcim.2c00483
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