Search

Your search keyword '"Chen-Hui Chan"' showing total 13 results
Start Over Author "Chen-Hui Chan"
13 results on '"Chen-Hui Chan"'

1. Recognition of a tandem lesion by DNA bacterial formamidopyrimidine glycosylases explored combining molecular dynamics and machine learning

Author

Emmanuelle Bignon, Natacha Gillet, Chen-Hui Chan, Tao Jiang, Antonio Monari, and Elise Dumont

Subjects
MutM, DNA repair glycosylase, Tandem lesion, Molecular dynamics simulations, Biotechnology, TP248.13-248.65
Abstract

The combination of several closely spaced DNA lesions, which can be induced by a single radical hit, constitutes a hallmark in the DNA damage landscape and radiation chemistry. The occurrence of such a tandem base lesion gives rise to a strong coupling with the double helix degrees of freedom and induces important structural deformations, in contrast to DNA strands containing a single oxidized nucleobase. Although such complex lesions are known to be refractory to repair by DNA glycosylases, there is still a lack of structural evidence to rationalize these phenomena. In this contribution, we explore, by numerical modeling and molecular simulations, the behavior of the bacterial glycosylase responsible for base excision repair (MutM), specialized in excising oxidatively-damaged defects such as 7,8-dihydro-8-oxoguanine (8-oxoG). The difference in lesion recognition between a simple damage and a tandem lesion featuring an additional abasic site is assessed at atomistic resolution owing to microsecond molecular dynamics simulations and machine learning postprocessing, allowing to extensively pinpoint crucial differences in the interaction patterns of the damaged bases. Our results reveal substantial changes in the interaction network surrounding the 8-oxoG upon addition of an adjacent abasic site, leading to the perturbation of the intercalation triad which is crucial for lesion recognition and processing. The recognition process might also be impacted by a more constrained MutM-DNA binding upon tandem damage, as shown by the machine learning post-processing. This work advocates for the use of such high throughput numerical simulations for exploring the complex combinatorial chemistry of tandem DNA lesions repair and more generally local multiple damaged sites of the utmost significance in radiation chemistry.

Published
2021
Full Text
View/download PDF

2. Probing interaction of a trilysine peptide with DNA underlying formation of guanine–lysine cross-links: insights from molecular dynamics

Author

Antonio Monari, Chen-Hui Chan, Elise Dumont, Jean-Luc Ravanat, Laboratoire de Chimie - UMR5182 (LC), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS Lyon)-Institut de Chimie du CNRS (INC), Laboratoire de Physique et Chimie Théoriques (LPCT), Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Chimie Interface Biologie pour l’Environnement, la Santé et la Toxicologie (CIBEST ), SYstèmes Moléculaires et nanoMatériaux pour l’Energie et la Santé (SYMMES), Institut de Chimie du CNRS (INC)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)

Subjects
Guanine, Stereochemistry, education, Oligonucleotides, General Physics and Astronomy, Peptide, 02 engineering and technology, Molecular Dynamics Simulation, 010402 general chemistry, complex mixtures, 01 natural sciences, chemistry.chemical_compound, Molecular dynamics, [CHIM]Chemical Sciences, Molecule, Physical and Theoretical Chemistry, ComputingMilieux_MISCELLANEOUS, chemistry.chemical_classification, Binding Sites, [CHIM.ORGA]Chemical Sciences/Organic chemistry, Oligonucleotide, Lysine, 021001 nanoscience & nanotechnology, 0104 chemical sciences, chemistry, Radical ion, Covalent bond, Quantum Theory, Thermodynamics, bacteria, 0210 nano-technology, Oligopeptides, DNA
Abstract

DNA-protein cross-links constitute bulky DNA lesions that interfere with the cellular machinery. Amongst these stable covalently tethered adducts, the efficient nucleophilic addition of the free amino group of lysines onto the guanine radical cation has been evidenced. In vitro addition of a trilysine peptide onto a guanine radical cation generated in a TGT oligonucleotide is so efficient that competitive addition of a water molecule, giving rise to 8-oxo-7,8-dihydroguanine, is not observed. This suggests a spatial proximity between guanine and lysine for the stabilization of the prereactive complex. We report all-atom microsecond scale molecular dynamics simulations that probe the structure and interactions of the trilysine peptide (KKK) with two oligonucleotides. Our simulations reveal a strong, electrostatically driven yet dynamic interaction, spanning several association modes. Furthermore, the presence of neighbouring cytosines has been identified as a factor favoring KKK binding. Relying on ab initio molecular dynamics on a model system constituted of guanine and methylammonium, we also corroborate a mechanistic pathway involving fast deprotonation of the guanine radical cation followed by hydrogen transfer from ammonium leaving as a result a nitrogen reactive species that can subsequently cross-link with guanine. Our study sheds new light on a ubiquitous mechanism for DNA-protein cross-links also stressing out possible sequence dependences.

Published
2019

3. Monte Carlo simulation of free radical production under keV photon irradiation of gold nanoparticle aqueous solution. Part II: Local primary chemical boost

Author

Floriane Poignant, Hela Charfi, Chen-Hui Chan, Elise Dumont, David Loffreda, Benoit Gervais, Michaël Beuve, Institut de Physique des 2 Infinis de Lyon (IP2I Lyon), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie - UMR5182 (LC), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS Lyon)-Institut de Chimie du CNRS (INC), Centre de recherche sur les Ions, les MAtériaux et la Photonique (CIMAP - UMR 6252), Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Normandie Université (NU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Caen Normandie (UNICAEN), Normandie Université (NU), ANR-11-LABX-0063,PRIMES,Physique, Radiobiologie, Imagerie Médicale et Simulation(2011), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche sur les Matériaux Avancés (IRMA), Normandie Université (NU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Rouen Normandie (UNIROUEN), and Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Radiation, [PHYS.PHYS]Physics [physics]/Physics [physics], 7. Clean energy, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Water radiolysis, 030218 nuclear medicine & medical imaging, 03 medical and health sciences, 0302 clinical medicine, 030220 oncology & carcinogenesis, Free radical production, Gold nanoparticles, [CHIM]Chemical Sciences, Photon irradiation, Monte Carlo simulation
Abstract

International audience; Highlights• We calculated radical production around gold/water nanoparticle (GNP/WNP) in water.• Calculations were performed for single keV photon absorption.• In the micrometer range, radicals are overproduced by GNP compared to WNP.• In the nanometer range, radicals are overproduced by small GNP compared to WNP due to Auger electrons.• In the nanometer range, radical production is comparable for large NP.

Published
2021

4. Recognition of a Tandem Lesion by DNA Glycosylases Explored Combining Molecular Dynamics and Machine Learning

Author

Antonio Monari, Chen-Hui Chan, Elise Dumont, Tao Jiang, Natacha Gillet, and Emmanuelle Bignon

Subjects
Tandem, DNA damage, business.industry, Base excision repair, Machine learning, computer.software_genre, Nucleobase, chemistry.chemical_compound, chemistry, DNA glycosylase, Helix, AP site, Artificial intelligence, business, computer, DNA
Abstract

The combination of several closely spaced DNA lesions, which can be induced by a single radical hit, constitutes a hallmark in the DNA damage landscape and radiation chemistry. The occurrence of such tandem base lesions give rise to a strong coupling with the double helix degrees of freedom and induce important structural deformations, in contrast to DNA strands containing a single oxidized nucleobase. Although such complex lesions are known to be refractory to repair by DNA glycosylases, there is still a lack of structural evidence to rationalize these phenomena. In this contribution, we explore, by numerical modeling and molecular simulations, the behavior of the bacterial glycosylase responsible for base excision repair (MutM), specialized in excising oxidatively-damaged defects such as 7,8-dihydro-8-oxoguanine (8-oxoG). The difference in lesion recognition between a simple damage and a tandem lesions featuring an additional abasic site is assessed at atomistic resolution owing to microsecond molecular dynamics simulation and machine learning postprocessing, allowing to extensively pinpoint crucial differences in the interaction patterns of the damaged bases. This work advocates for the use of such high throughput numerical simulations for exploring the complex combinatorial chemistry of tandem DNA lesions repair and more generally multiple damaged sites of the utmost significance in radiation chemistry.

Published
2021

5. Low-energy electron transport in gold: mesoscopic potential calculation and its impact on electron emission yields

Author

Chen-Hui Chan, Floriane Poignant, Andrei Ipatov, David Loffreda, Michael Beuve, Elise Dumont, Benoit Gervais, Ricardo Martins Ramos, Institut de Physique des 2 Infinis de Lyon (IP2I Lyon), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie - UMR5182 (LC), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS Lyon)-Institut de Chimie du CNRS (INC), Centre de recherche sur les Ions, les MAtériaux et la Photonique (CIMAP - UMR 6252), Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Normandie Université (NU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Caen Normandie (UNICAEN), Normandie Université (NU), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche sur les Matériaux Avancés (IRMA), Normandie Université (NU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Rouen Normandie (UNIROUEN), and Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[PHYS]Physics [physics], Mesoscopic physics, Materials science, Mean free path, Monte Carlo method, General Physics and Astronomy, Fermi energy, 02 engineering and technology, Electron, 021001 nanoscience & nanotechnology, Molecular physics, Secondary electrons, 030218 nuclear medicine & medical imaging, 03 medical and health sciences, 0302 clinical medicine, Density functional theory, 0210 nano-technology, Plasmon
Abstract

International audience; In a previous work, we extended and benchmarked the MDM Monte Carlo code with available data for gold metallic media irradiated by electron beams. In this paper, we worked with the aim of improving the cross sections on which our Monte Carlo simulation is based, and which are essential for an accurate description of the transport of electrons in gold. The mesoscopic potential of solid gold has been predicted, and its sensitivity toward electron emission has been evaluated. This potential was derived from the calculation of the electrostatic and atomistic potential by density functional theory and used to calculate inelastic inverse mean free path for electron transport. After integrating these results into our Monte Carlo code, we evaluated the impact of these new cross sections on yields of electron emission from solid gold irradiated by monoenergetic electron beams. We obtained a mesoscopic potential value of − 12.77 eV for our model of bulk metal gold, 27% lower than the one commonly estimated from the Fermi energy. This result impacted on the inverse mean free path for plasmon excitations with a 10% decrease for electrons in the range of 6–30 eV. Regarding electron emission yields, there was no impact of the new mesoscopic potential on the primary electron yields, but for secondary electrons, the emission yields were increased by a factor of up to two depending on the primary beam energy and thickness of the gold foil.

Published
2021

7. Monte Carlo simulation of free radical production under keV photon irradiation of gold nanoparticle aqueous solution. Part I: Global primary chemical boost

Author

Benoit Gervais, Etienne Testa, David Loffreda, Hela Charfi, Elise Dumont, Michael Beuve, Chen-Hui Chan, Floriane Poignant, Institut de Physique des 2 Infinis de Lyon (IP2I Lyon), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie - UMR5182 (LC), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS Lyon)-Institut de Chimie du CNRS (INC), Centre de recherche sur les Ions, les MAtériaux et la Photonique (CIMAP - UMR 6252), Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Normandie Université (NU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Caen Normandie (UNICAEN), Normandie Université (NU), ANR-11-LABX-0063,PRIMES,Physique, Radiobiologie, Imagerie Médicale et Simulation(2011), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-École Nationale Supérieure d'Ingénieurs de Caen (ENSICAEN), Normandie Université (NU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche sur les Matériaux Avancés (IRMA), Normandie Université (NU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Rouen Normandie (UNIROUEN), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), and ANR: 11-LABX-0063,PRIMES,Physique, Radiobiologie, Imagerie Médicale et Simulation(2011)

Subjects
Radiation, Aqueous solution, Materials science, Radiation-chemical yields, 010308 nuclear & particles physics, Radical, Monte Carlo method, Nanoparticle, Photon energy, 01 natural sciences, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Water radiolysis, 030218 nuclear medicine & medical imaging, 03 medical and health sciences, Chemical species, 0302 clinical medicine, Colloidal gold, Chemical physics, Yield (chemistry), 0103 physical sciences, [PHYS.PHYS.PHYS-MED-PH]Physics [physics]/Physics [physics]/Medical Physics [physics.med-ph], Gold nanoparticles, Photon irradiation, Monte Carlo simulation
Abstract

International audience; The use of gold nanoparticles to enhance radiation therapy efficiency has been thoroughly investigated over the past two decades. While theoretical studies have mostly focused on physical mechanisms and dose enhancement, studies of free radical production are scarce. In this work, we investigated the primary yield of free radicals ( and ) induced by 20–90 keV monoenergetic photons, for small GNPs concentrations. Our study is based on a Monte Carlo approach which enables electron transport down to low energy, both in water and in gold. We obtained, for a gold concentration of 1 , an average chemical enhancement varying from 6 to 14%, depending mostly on the photon energy and, to a lesser extent, on the chemical species and size of the GNP. This enhancement is strongly correlated to the dose deposition enhancement, although not strictly proportional. While supporting the hypothesis that therapeutic efficiency of GNPs may not simply be explained by an overproduction of free radicals in the early stage, our simulation provides inputs for further macroscopic simulations, including cumulative track effects and potentially GNP chemical reactivity.

Published
2020

8. Effect of the Ligand Binding Strength on the Morphology of Functionalized Gold Nanoparticles

Author

Floriane Poignant, Elise Dumont, David Loffreda, Michael Beuve, Chen-Hui Chan, Laboratoire de Chimie - UMR5182 (LC), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS Lyon)-Institut de Chimie du CNRS (INC), Institut de Physique des 2 Infinis de Lyon (IP2I Lyon), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Materials science, Nanoparticle, Metal Nanoparticles, Context (language use), 02 engineering and technology, Polyethylene glycol, 010402 general chemistry, Ligands, 7. Clean energy, 01 natural sciences, Polyethylene Glycols, chemistry.chemical_compound, Monolayer, [CHIM]Chemical Sciences, General Materials Science, Physical and Theoretical Chemistry, Density Functional Theory, Nanotubes, 021001 nanoscience & nanotechnology, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, 0104 chemical sciences, chemistry, Octahedron, Chemical engineering, Models, Chemical, Colloidal gold, PEGylation, Nanorod, Adsorption, Gold, 0210 nano-technology, Nanospheres
Abstract

International audience; Functionalized gold nanoparticles are investigated by density functional theory calculations in the context of cancer radiotherapy. Several typical experimental shapes, including nanostars, nanospheres, and nanorods, are modeled by optimizing Au clusters covered by organic monolayers composed of hydrated short-chain polyethylene glycol (PEG) ligands. The PEGylation stabilizes significantly the stellation of decahedral Au54 by deforming significantly its geometry at the spikes. The higher stability of the PEG molecules adsorbed on this stellated nanocluster with respect to the more spherical icosahedral Au55 and Au79 leads to a larger energy cost to desorb them and thus a weaker propensity for the starred nanoparticle to exchange ligands with the cell membrane, in agreement with experiments. These results open interesting possibilities for advancing our understanding of the cellular uptake of gold nanoparticles.

Published
2020

9. A Water Solvation Shell Can Transform Gold Metastable Nanoparticles in the Fluxional Regime

Author

Michael Beuve, Floriane Poignant, Elise Dumont, David Loffreda, Chen-Hui Chan, Laboratoire de Chimie - UMR5182 (LC), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de Physique Nucléaire de Lyon (IPNL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), ANR-11-LABX-0063,PRIMES,Physique, Radiobiologie, Imagerie Médicale et Simulation(2011), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS Lyon)-Institut de Chimie du CNRS (INC), and Université de Lyon-Université de Lyon-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)

Subjects
Materials science, 010308 nuclear & particles physics, Physics::Optics, Nanoparticle, 02 engineering and technology, 021001 nanoscience & nanotechnology, 01 natural sciences, London dispersion force, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Solvation shell, Chemical physics, Colloidal gold, Metastability, 0103 physical sciences, [CHIM]Chemical Sciences, General Materials Science, Density functional theory, Physics::Chemical Physics, Physical and Theoretical Chemistry, 0210 nano-technology
Abstract

International audience; Solvated gold nanoparticles have been modeled in the fluxional regime by density functional theory including dispersion forces for an extensive set of conventional morphologies. The study of isolated adsorption of one water molecule shows that the most stable adsorption forms are similar (corners and edges) regardless of the nanoparticle shape and size, although the adsorption strength differs significantly (0.15 eV). When a complete and explicit water solvation shell interacts with gold nanoclusters, metastable in vacuum and presenting a predominance of (100) square facets (ino-decahedra Au55 and Au147), these nanoparticles are found unstable and transform into the closest morphologies exhibiting mainly (111) triangular facets and symmetries. The corresponding adsorption strength per water molecule becomes independent of shape and size and is enhanced by the formation of two hydrogen bonds on average. For applications in radiotherapy, this study suggests that the shapes of small gold nanoparticles should be homogenized by interacting with the biological environment.

Published
2019

10. Bond dissociation energies of carbonyl gold complexes: a new descriptor of ligand effects in gold(i) complexes?

Author

Héloïse Dossmann, Richard B. Cole, Antony Memboeuf, Yves Gimbert, Anne Milet, Hervé Clavier, Chen-Hui Chan, Denis Lesage, David Gatineau, Institut des Sciences Moléculaires de Marseille (ISM2), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut Parisien de Chimie Moléculaire (IPCM), Chimie Moléculaire de Paris Centre (FR 2769), Institut de Chimie du CNRS (INC)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Chimie Structurale Organique et Biologique (CSOB), Institut de Chimie du CNRS (INC)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie - UMR5182 (LC), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS Lyon)-Institut de Chimie du CNRS (INC), Département de Chimie Moléculaire (DCM), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Chimie, Electrochimie Moléculaires et Chimie Analytique (CEMCA), Université de Brest (UBO)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut Brestois Santé Agro Matière (IBSAM), Université de Brest (UBO), Département de Chimie Moléculaire - Synthèse Et Réactivité en Chimie Organique (DCM - SeRCO ), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Nationale Supérieure de Chimie de Paris - Chimie ParisTech-PSL (ENSCP), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), and ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017)

Subjects
010405 organic chemistry, Ligand, Bond strength, Chemistry, 010402 general chemistry, Tandem mass spectrometry, 01 natural sciences, Bond-dissociation energy, Dissociation (chemistry), 0104 chemical sciences, Catalysis, Inorganic Chemistry, chemistry.chemical_compound, Computational chemistry, Electronic effect, [CHIM.COOR]Chemical Sciences/Coordination chemistry, Carbene
Abstract

International audience; Ligand electronic effects in gold(I) chemistry have been evaluated by means of the experimental determination of M-CO bond dissociation energies for 16 [L-Au-CO] + complexes, bearing L ligands widely used in gold catalysis. Energy-resolved analyzes have been achieved using tandem mass spectrometry with collision induced dissociation. Coupled to DFT calculations, this approach enables the quantification of ligand effects based on the LAu-CO bond strength. Further energy decomposition analysis gives access to detailed insights of this bond's properties. Whereas small differences are observed between phosphine-and phosphite-containing gold complexes, carbene ligands are shown to stabilize much more efficiently the gold-carbonyl bond.

Published
2018

11. Molecular Dynamics Insights into Polyamine-DNA Binding Modes: Implications for Cross-Link Selectivity

Author

Jean-Luc Ravanat, Christophe Morell, Elise Dumont, Antonio Monari, Emmanuelle Bignon, Chen-Hui Chan, Laboratoire de Chimie - UMR5182 (LC), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences Analytiques (ISA), Université Claude Bernard Lyon 1 (UCBL), Structure et Réactivité des Systèmes Moléculaires Complexes (SRSMC), Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), SYstèmes Moléculaires et nanoMatériaux pour l’Energie et la Santé (SYMMES), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), This work was supported by the LABEX PRIMES (ANR-11-LABX-0063) of Universite de Lyon, within the program 'Investissements d'Avenir' (ANR-11-IDEX-0007) operated by the French National Research Agency (ANR) through the PhD fellowship of C.H.C., ANR-11-LABX-0063,PRIMES,Physique, Radiobiologie, Imagerie Médicale et Simulation(2011), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS Lyon)-Institut de Chimie du CNRS (INC), Institut de Chimie du CNRS (INC)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie du CNRS (INC)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Spermidine, Guanine, Stereochemistry, polyamines, Molecular Dynamics Simulation, 010402 general chemistry, DNA condensation, 01 natural sciences, Catalysis, Nucleobase, 03 medical and health sciences, Molecular dynamics, chemistry.chemical_compound, noncovalent interactions, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, Putrescine, cross-coupling, Non-covalent interactions, Binding site, chemistry.chemical_classification, Binding Sites, Organic Chemistry, Isothermal titration calorimetry, General Chemistry, DNA, Biogenic Polyamines, molecular dynamics, 0104 chemical sciences, Crystallography, 030104 developmental biology, chemistry, Nucleic Acid Conformation, Thermodynamics, Spermine
Abstract

We acknowledge the Pole Scientifique de Modeisation Numerique (PSMN) for computational resources.; International audience; Biogenic polyamines, which play a role in DNA condensation and stabilization, are ubiquitous and are found at millimolar concentration in the nucleus of eukaryotic cells. The interaction modes of three polyamines-putrescine (Put), spermine (Spm), and spermidine (Spd)-with a self-complementary 16 base pair (bp) duplex, are investigated by all-atom explicit-solvent molecular dynamics. The length of the amine aliphatic chain leads to a change of the interaction mode from minor groove binding to major groove binding. Through all-atom dynamics, noncovalent interactions that stabilize the polyamine-DNA complex and prefigure the reactivity, leading to the low-barrier formation of deleterious DNA-polyamine cross-links, after one-electron oxidation of a guanine nucleobase, are unraveled. The binding strength is quantified from the obtained trajectories by molecular mechanics generalized Born surface area post-processing (MM-GBSA). The values of binding free energies provide the same affinity order, Put

Published
2017

13. Epigallocatechin-3-Gallate Reduces Hepatic Oxidative Stress and Lowers CYP-Mediated Bioactivation and Toxicity of Acetaminophen in Rats

Author

Hsien-Tsung Yao, Chien-Chun Li, and Chen-Hui Chang

Subjects
epigallocatechin-3-gallate, acetaminophen, cytochrome P-450, bioactivation, apoptosis, autophagy, hepatotoxicity, Nutrition. Foods and food supply, TX341-641
Abstract

Epigallocatechin-3-gallate (EGCG) is the most abundant polyphenol in green tea. To investigate the effects of dietary EGCG on oxidative stress and the metabolism and toxicity of acetaminophen in the liver, rats were fed diets with (0.54%) or without EGCG supplementation for four weeks and were then injected intraperitoneally with acetaminophen (1 g/kg). The results showed that EGCG lowered hepatic oxidative stress and cytochrome P450 (CYP) 1A2, 2E1, and 3A, and UDP-glucurosyltransferase activities prior to acetaminophen injection. After acetaminophen challenge, the elevations in plasma alanine aminotransferase activity and histological changes in the liver were ameliorated by EGCG treatment. EGCG reduced acetaminophen-induced apoptosis by lowering the Bax/Bcl2 ratio in the liver. EGCG mildly increased autophagy by increasing the LC3B II/I ratio. Lower hepatic acetaminophen−glutathione and acetaminophen−protein adducts contents were observed after EGCG treatment. EGCG increased glutathione peroxidase and NAD(P)H quinone 1 oxidoreductase activities and reduced organic anion-transporting polypeptides 1a1 expression in the liver after acetaminophen treatment. Our results indicate that EGCG may reduce oxidative stress and lower the metabolism and toxicity of acetaminophen. The reductions in CYP-mediated acetaminophen bioactivation and uptake transporter, as well as enhanced antioxidant enzyme activity, may limit the accumulation of toxic products in the liver and thus lower hepatotoxicity.

Published
2019
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results