Emmanuelle Bignon

Publications

Article dans une revue (46)

Communication pathway analysis within protein-nucleic acid complexes Sneha Bheemireddy,Roy González-Alemán,Emmanuelle Bignon,Yasaman Karami Journal of Chemical Theory and Computation, 2025, 21 (17), pp.8255-8266. ⟨10.1101/2025.02.14.638259⟩ Article dans une revue hal-05041556v1
DynaRepo: the repository of macromolecular conformational dynamics Omid Mokhtari,Emmanuelle Bignon,Hamed Khakzad,Yasaman Karami Nucleic Acids Research, 2025, pp.gkaf1130. ⟨10.1093/nar/gkaf1130⟩ Article dans une revue hal-05404177v1
Specific Binding Modes of the SIRT6 C-Terminal Domain to the Nucleosome Core Particle Influence DNA Unwrapping and H3K27 Accessibility Yuya Qiu,Gabor Papai,Adam Ben Shem,Emmanuelle Bignon Journal of Physical Chemistry B, 2025, 129 (39), pp.9855-9861. ⟨10.1021/acs.jpcb.5c02221⟩ Article dans une revue hal-05368086v1
Dynamical Resolution of QM/MM Near-UV Circular Dichroism Spectra of Low-Symmetry Systems Jérémy Morere,Tanguy Leyder,Catherine Michaux,Claude Millot,Emmanuelle Bignonet al. Chemistry, 2025, 7 (2), pp.63. ⟨10.3390/chemistry7020063⟩ Article dans une revue hal-05216295v1
Cysteine hyperoxidation rewires communication pathways in the nucleosome and destabilizes the dyad Yasaman Karami,Emmanuelle Bignon Computational and Structural Biotechnology Journal, 2024, 23, pp.1387-1396. ⟨10.1016/j.csbj.2024.03.025⟩ Article dans une revue hal-04567034v1
DNA damage and repair in the nucleosome: insights from computational methods Natacha Gillet,Elise Dumont,Emmanuelle Bignon Biophysical Reviews, 2024, 16 (3), pp.345-356. ⟨10.1007/s12551-024-01183-9⟩ Article dans une revue hal-04743222v1
Binding to nucleosome poises human SIRT6 for histone H3 deacetylation Ekaterina Smirnova,Emmanuelle Bignon,Patrick Schultz,Gabor Papai,Adam Ben Shem eLife, 2024, 12, ⟨10.7554/elife.87989⟩ Article dans une revue hal-04487439v1
Molecular Bases and Specificity behind the Activation of the Immune System OAS/RNAse L Pathway by Viral RNA Emma Jung-Rodriguez,Florent Barbault,Emmanuelle Bignon,Antonio Monari Viruses, 2024, 16 (8), pp.1246. ⟨10.3390/v16081246⟩ Article dans une revue hal-04746925v1
Synthesis of Original Cyclic Dinucleotide Analogues Using the Sulfo-click Reaction Romain Amador,Jean-Jacques Vasseur,Gabriel Birkuš,Emmanuelle Bignon,Antonio Monariet al. Organic Letters, 2024, 26 (4), pp.819-823. ⟨10.1021/acs.orglett.3c03908⟩ Article dans une revue hal-04426596v1
Robust AMBER Force Field Parameters for Glutathionylated Cysteines Zineb Elftmaoui,Emmanuelle Bignon International Journal of Molecular Sciences, 2023, 24 (19), pp.15022. ⟨10.3390/ijms241915022⟩ Article dans une revue hal-04487434v1
Revealing the Molecular Interactions between Human ACE2 and the Receptor Binding Domain of the SARS-CoV-2 Wild-Type, Alpha and Delta Variants Cécilia Hognon,Emmanuelle Bignon,Antonio Monari,Marco Marazzi,Cristina Garcia-Iriepa International Journal of Molecular Sciences, 2023, 24 (3), pp.2517. ⟨10.3390/ijms24032517⟩ Article dans une revue hal-04150197v1
Predicting the three-dimensional structure of the c-KIT proto-oncogene promoter and the dynamics of its strongly coupled guanine quadruplexes Emmanuelle Bignon,Angelo Spinello,Tom Miclot,Luisa D’anna,Cosimo Ducaniet al. Journal of Physical Chemistry Letters, 2023, 14 (20), pp.4704-4710. ⟨10.1021/acs.jpclett.3c00765⟩ Article dans une revue hal-04258965v1
Understanding the interactions of Guanine‐Quadruplexes with peptides as novel strategies for diagnosis or tuning biological functions Tom Miclot,Aurane Froux,Luisa d’Anna,Emmanuelle Bignon,Stéphanie Grandemangeet al. ChemBioChem, 2023, 24 (6), pp.e202200624. ⟨10.1002/cbic.202200624⟩ Article dans une revue hal-03925526v1
Resolving a guanine-quadruplex structure in the SARS-CoV-2 genome through circular dichroism and multiscale molecular modeling Luisa d'Anna,Tom Miclot,Emmanuelle Bignon,Ugo Perricone,Giampaolo Baroneet al. Chemical Science, 2023, 14 (41), pp.11332-11339. ⟨10.1039/d3sc04004f⟩ Article dans une revue hal-04487444v1
Mechanism of the covalent inhibition of human transmembrane protease serine 2 as an original antiviral strategy Angelo Spinello,Luisa D’anna,Emmanuelle Bignon,Tom Miclot,Stéphanie Grandemangeet al. Journal of Physical Chemistry B, 2023, 127 (28), pp.6287-6295. ⟨10.1021/acs.jpcb.3c02910⟩ Article dans une revue hal-04258941v1
Molecular Basis of the pH-Controlled Maturation of the Tick-Borne Encephalitis Flavivirus Emmanuelle Bignon,Elise Dumont,Antonio Monari Journal of Physical Chemistry Letters, 2023, 14 (7), pp.1977-1982. ⟨10.1021/acs.jpclett.2c03551⟩ Article dans une revue hal-04487441v1
How SARS-CoV-2 alters the regulation of gene expression in infected cells Emmanuelle Bignon,Stéphanie Grandemange,Elise Dumont,Antonio Monari Journal of Physical Chemistry Letters, 2023, 14 (13), pp.3199-3207. ⟨10.1021/acs.jpclett.3c00582⟩ Article dans une revue hal-04258968v1
G‐quadruplex recognition by DARPIns through epitope/paratope analogy Tom Miclot,Emmanuelle Bignon,Alessio Terenzi,Stéphanie Grandemange,Giampaolo Baroneet al. Chemistry - A European Journal, 2022, 28 (57), pp.e202201824. ⟨10.1002/chem.202201824⟩ Article dans une revue hal-03925664v1
Specific Recognition of the 5′-Untranslated Region of West Nile Virus Genome by Human Innate Immune System Emmanuelle Bignon,Marco Marazzi,Tom Miclot,Giampaolo Barone,Antonio Monari Viruses, 2022, 14 (6), pp.1282. ⟨10.3390/v14061282⟩ Article dans une revue hal-04487450v1
How Fragile We Are: Influence of Stimulator of Interferon Genes (STING) Variants on Pathogen Recognition and Immune Response Efficiency Jeremy Morere,Cécilia Hognon,Tom Miclot,Tao Jiang,Elise Dumontet al. Journal of Chemical Information and Modeling, 2022, 62 (12), pp.3096-3106. ⟨10.1021/acs.jcim.2c00315⟩ Article dans une revue hal-04157319v1
Hijacking of Cellular Functions by Severe Acute Respiratory Syndrome Coronavirus-2. Permeabilization and Polarization of the Host Lipid Membrane by Viroporins Emmanuelle Bignon,Marco Marazzi,Antonio Monari Journal of Physical Chemistry Letters, 2022, 13 (21), pp.4642-4649. ⟨10.1021/acs.jpclett.2c01102⟩ Article dans une revue hal-04487448v1
Autophagy and evasion of the immune system by SARS-CoV-2. Structural features of the non-structural protein 6 from wild type and Omicron viral strains interacting with a model lipid bilayer Emmanuelle Bignon,Marco Marazzi,Stéphanie Grandemange,Antonio Monari Chemical Science, 2022, 13 (20), pp.6098-6105. ⟨10.1039/d2sc00108j⟩ Article dans une revue hal-03925667v1
Structure of the 5′ untranslated region in SARS-CoV-2 genome and its specific recognition by innate immune system via the human oligoadenylate synthase 1 Emmanuelle Bignon,Tom Miclot,Alessio Terenzi,Giampaolo Barone,Antonio Monari Chemical Communications, 2022, 58 (13), pp.2176-2179. ⟨10.1039/D1CC07006A⟩ Article dans une revue hal-04487446v1
Exploring Dihydroflavonol‐4‐Reductase Reactivity and Selectivity by QM/MM‐MD Simulations Julien Diharce,Emmanuelle Bignon,Sébastien Fiorucci,Serge Antonczak ChemBioChem, 2022, 23 (3), ⟨10.1002/cbic.202100553⟩ Article dans une revue hal-03599132v1
Never cared for what they do: High structural stability of Guanine-Quadruplexes in the presence of strand-break damage Tom Miclot,Cécilia Hognon,Emmanuelle Bignon,Alessio Terenzi,Stéphanie Grandemangeet al. Molecules, 2022, 27 (10), pp.3256. ⟨10.3390/molecules27103256⟩ Article dans une revue hal-03925687v1
Modeling the Enzymatic Mechanism of the SARS-CoV-2 RNA-Dependent RNA Polymerase by DFT/MM-MD: An Unusual Active Site Leading to High Replication Rates Emmanuelle Bignon,Antonio Monari Journal of Chemical Information and Modeling, 2022, 62 (17), pp.4261-4269. ⟨10.1021/acs.jcim.2c00802⟩ Article dans une revue hal-04487454v1
Molecular Mechanisms Associated with Clustered Lesion-Induced Impairment of 8-oxoG Recognition by the Human Glycosylase OGG1 Tao Jiang,Antonio Monari,Elise Dumont,Emmanuelle Bignon Molecules, 2021, 26 (21), pp.6465. ⟨10.3390/molecules26216465⟩ Article dans une revue hal-03786798v1
The iron maiden. Cytosolic aconitase/IRP1 conformational transition in the regulation of ferritin translation and iron hemostasis Cécilia Hognon,Emmanuelle Bignon,Guillaume Harle,Nadège Touche,Stéphanie Grandemangeet al. Biomolecules, 2021, 11 (9), pp.1329. ⟨10.3390/biom11091329⟩ Article dans une revue hal-03503702v1
Recent smell loss is the best predictor of COVID-19 among individuals with recent respiratory symptoms Richard C. Gerkin,Kathrin Ohla,Maria G. Veldhuizen,Paule V. Joseph,Christine E. Kellyet al. Chemical Senses, 2021, 46, pp.bjaa081. ⟨10.1093/chemse/bjaa081⟩ Article dans une revue hal-03367315v1
Recognition of a tandem lesion by DNA bacterial formamidopyrimidine glycosylases explored combining molecular dynamics and machine learning Emmanuelle Bignon,Natacha Gillet,Chen-Hui Chan,Tao Jiang,Antonio Monariet al. Computational and Structural Biotechnology Journal, 2021, 19, pp.2861-2869. ⟨10.1016/j.csbj.2021.04.055⟩ Article dans une revue hal-03326585v1
A Dynamic View of the Interaction of Histone Tails with Clustered Abasic Sites in a Nucleosome Core Particle Emmanuelle Bignon,Natacha Gillet,Tao Jiang,Christophe Morell,Elise Dumont Journal of Physical Chemistry Letters, 2021, 12 (25), pp.6014-6019. ⟨10.1021/acs.jpclett.1c01058⟩ Article dans une revue hal-03279410v1
Structure and Dynamics of RNA Guanine Quadruplexes in SARS-CoV-2 Genome. Original Strategies against Emerging Viruses Tom Miclot,Cécilia Hognon,Emmanuelle Bignon,Alessio Terenzi,Marco Marazziet al. Journal of Physical Chemistry Letters, 2021, 12 (42), pp.10277--10283. ⟨10.1021/acs.jpclett.1c03071⟩ Article dans une revue hal-03786805v1
Nucleosomal embedding reshapes the dynamics of abasic sites Emmanuelle Bignon,Victor Claerbout,Tao Jiang,Christophe Morell,Natacha Gilletet al. Scientific Reports, 2020, 10 (1), pp.17314. ⟨10.1038/s41598-020-73997-y⟩ Article dans une revue hal-03157466v1
Smell and taste changes are early indicators of the COVID-19 pandemic and political decision effectiveness Denis Pierron,Veronica Pereda-Loth,Marylou Mantel,Maëlle Moranges,Emmanuelle Bignonet al. Nature Communications, 2020, 11 (1), pp.5152. ⟨10.1038/s41467-020-18963-y⟩ Article dans une revue hal-02978603v2
Impact of the Nucleosome Histone Core on the Structure and Dynamics of DNA-Containing Pyrimidine–Pyrimidone (6–4) Photoproduct Eva Matoušková,Emmanuelle Bignon,Victor Claerbout,Tomáš Dršata,Natacha Gilletet al. Journal of Chemical Theory and Computation, 2020, 16 (9), pp.5972-5981. ⟨10.1021/acs.jctc.0c00593⟩ Article dans une revue hal-03157488v1
Wetting the lock and key enthalpically favours polyelectrolyte binding Emeric Jeamet,Jean Septavaux,Alexandre Héloin,Marion Donnier-Maréchal,Mélissa Dumartinet al. Chemical Science, 2019, 10 (1), pp.277-283. ⟨10.1039/c8sc02966k⟩ Article dans une revue hal-01917669v1
Molecular Dynamics Insights into Polyamine-DNA Binding Modes: Implications for Cross-Link Selectivity Emmanuelle Bignon,Chen-Hui Chan,Christophe Morell,Antonio Monari,Jean-Luc Ravanatet al. Chemistry - A European Journal, 2017, 23 (52), pp.12845-12852. ⟨10.1002/chem.201702065⟩ Article dans une revue hal-01646327v1
Conformational polymorphism or structural invariance in DNA photoinduced lesions: implications for repair rates François Dehez,Hugo Gattuso,Emmanuelle Bignon,Christophe Morell,Elise Dumontet al. Nucleic Acids Research, 2017, 45 (7), pp.3654-3662. ⟨10.1093/nar/gkx148⟩ Article dans une revue hal-01518937v1
Interstrand cross-linking implies contrasting structural consequences for DNA: insights from molecular dynamics Emmanuelle Bignon,Tomáš Dršata,Christophe Morell,Filip Lankaš,Elise Dumont Nucleic Acids Research, 2017, 45 (4), pp.2188-2195. ⟨10.1093/nar/gkw1253⟩ Article dans une revue hal-01449663v1
Ibuprofen and ketoprofen potentiate UVA-induced cell death by a photosensitization process Emmanuelle Bignon,Marco Marazzi,Vanessa Besancenot,Hugo Gattuso,Guillaume Drouotet al. Scientific Reports, 2017, 7, pp.8885. ⟨10.1038/s41598-017-09406-8⟩ Article dans une revue hal-01583391v1
Singlet Oxygen Attack on Guanine: Reactivity and Structural Signature within the B-DNA Helix Elise Dumont,Raymond Grüber,Emmanuelle Bignon,Christophe Morell,Juan Arandaet al. Chemistry - A European Journal, 2016, 22 (35), pp.12358-12362. ⟨10.1002/chem.201601287⟩ Article dans une revue istex hal-01449792v1
Correlation of bistranded clustered abasic DNA lesion processing with structural and dynamic DNA helix distortion Emmanuelle Bignon,Hugo Gattuso,Christophe Morell,François Dehez,Alexandros G. Georgakilaset al. Nucleic Acids Research, 2016, 44 (18), pp.8588-8599. ⟨10.1093/nar/gkw773⟩ Article dans une revue hal-01449647v1
Probing the reactivity of singlet oxygen with purines Elise Dumont,Raymond Grüber,Emmanuelle Bignon,Christophe Morell,Yohann Moreauet al. Nucleic Acids Research, 2016, 44 (1), pp.56-62. ⟨10.1093/nar/gkv1364⟩ Article dans une revue hal-01271590v1
Repair Rate of Clustered Abasic DNA Lesions by Human Endonuclease: Molecular Bases of Sequence Specificity Hugo Gattuso,Elodie Durand,Emmanuelle Bignon,Christophe Morell,Alexandros G. Georgakilaset al. Journal of Physical Chemistry Letters, 2016, 7 (19), pp.3760-3765. ⟨10.1021/acs.jpclett.6b01692⟩ Article dans une revue hal-01449702v1
DNA Photosensitization by an &quot;Insider&quot;: Photophysics and Triplet Energy Transfer of 5-Methyl-2-pyrimidone Deoxyribonucleoside Emmanuelle Bignon,Hugo Gattuso,Christophe Morell,Elise Dumont,Antonio Monari Chemistry - A European Journal, 2015, 21 (32), pp.11509-11516. ⟨10.1002/chem.201501212⟩ Article dans une revue istex hal-01186698v1
Insights into the chemical meanings of the reaction electronic flux Christophe Morell,Vincent Tognetti,Emmanuelle Bignon,Elise Dumont,Noemi Hernandez-Haroet al. Theoretical Chemistry Accounts: Theory, Computation, and Modeling, 2015, 134 (11), pp.133. ⟨10.1007/s00214-015-1730-7⟩ Article dans une revue hal-01363815v1

Communication dans un congrès (10)

Combining solid-state, liquid-state and relaxometry NMR to decipher structure and dynamics of supramolecular hydrogels Corentin Boulogne,Jérémy Morere,Paul Hoschtettler,Marie-Christine Averlant-Petit,Emmanuelle Bignonet al. GERM 2025, GERM, Jun 2025, Autrans (Vercors), France Communication dans un congrès hal-05218199v1
Exploring the epigenetic regulation of DNA compaction with all atom MD simulations Emmanuelle Bignon,Ekaterina Smirnova,Patrick Schultz,Gabor Papai,Adam Ben Shem ThéMoSiA-RCTF2024, Jun 2024, Rouen, France Communication dans un congrès hal-05215703v1
How do DNA lesions impact the structure of a Nucleosome Core Particle? Insights from molecular dynamics simulations Emmanuelle Bignon,Elise Dumont,Natacha Gillet,Tao Jiang,Victor E. P. Claerbout CECAM workshop B-DNA Consortium meeting, Apr 2023, Ascona (CH), Switzerland Communication dans un congrès hal-05215692v1
Structure and reactivity of complex DNA lesions: clustered abasic sites as a case study Emmanuelle Bignon,Christophe Morell,Elise Dumont 21e congrès du GGMM, Apr 2019, Nice, France Communication dans un congrès hal-02308222v1
Molecular dynamics insights for DNA lesions in oligonucleotides and nucleosomal DNA Emmanuelle Bignon,Elise Dumont Huitième réunion annuelle du GdR Architecture et Dynamique Nucléaires (ADN), Mar 2019, Lyon, France Communication dans un congrès hal-02124544v1
Computational insights into DNA lesions: sequence effects in and out of the nucleosome Emmanuelle Bignon,Elise Dumont Network analysis to elucidate natural system dynamics, diversity and performance - CECAM workshop, May 2019, Lyon, France Communication dans un congrès hal-02308301v1
Modélisation de structures d'ADN endommagé : un microscope computationnel Emmanuelle Bignon,Raymond Grüber,Elise Dumont,Christophe Morell,Jean-Luc Ravanat Forum de la recherche en cancérologie Rhône-Alpes Auvergne, Mar 2016, Lyon, France Communication dans un congrès hal-01297487v1
Modelling the structure and triplet-triplet energy transfer of the 6-4 photoproduct Emmanuelle Bignon,Hugo Gattuso,Christophe Morell,Antonio Monari,Elise Dumont Joint Congress of the French and Italian Photochemists and Photobiologists 2016, Sep 2016, Bari, Italy Communication dans un congrès hal-01488339v1
MODELLING THE INTERSTRAND CROSS-LINKS IMPACT ON DNA STRUCTURE Emmanuelle Bignon,Tomáš Dršata,Elise Dumont,Christophe Morell,Filip Lankaš 14th International Workshop on Radiation Damage to DNA, Mar 2016, Melbourne, Australia Communication dans un congrès hal-01490046v1
Abasic Sites Impact on DNA Structure and Interstrand Cross-Links Generation Modelling Emmanuelle Bignon,Christophe Morell,Elise Dumont COST Action CM1201 : Biomimetic Radical Chemistry & ClicGene , Mar 2016, Grenoble, France Communication dans un congrès hal-01490054v1

Poster de conférence (2)

Insights into DNA lesions formation and structural outcome by simulation tools Elise Dumont,Chen-Hui Chan,Emmanuelle Bignon,François Dehez,Antonio Monari Fifteenth edition of the international Workshop on Radiation Damage to DNA, May 2018, Aussois, France Poster de conférence hal-02114267v1
Probing Interstand CrossLinks Impact on DNA Structure by Classical Molecular Dynamics Simulations Emmanuelle Bignon,Christophe Morell,Elise Dumont Forum de la Recherche en Cancérologie Auvergne-Rhône-Alpes 2017, Apr 2017, Lyon, France Poster de conférence hal-01504781v1

Chapitre d'ouvrage (3)

Molecular Dynamics and QM/MM to Understand Genome Organization and Reproduction in Emerging RNA Viruses Emmanuelle Bignon,Antonio Monari Manuel Yáñez; Russell J. Boyd. Comprehensive Computational Chemistry, 3, Elsevier, pp.895-909, 2024, ⟨10.1016/B978-0-12-821978-2.00101-X⟩ Chapitre d'ouvrage hal-04746809v1
A moveable feast. Molecular modeling and simulation unraveling cross-talks between RNA structure and its biological role Aurane Froux,Emmanuelle Bignon,Guillaume Harlé,Stéphanie Grandemange,Antonio Monari RNA Structure and Function, 14, Springer International Publishing, pp.279-294, 2023, RNA Technologies, ⟨10.1007/978-3-031-36390-0_13⟩ Chapitre d'ouvrage hal-04316714v1
CHAPTER 6. Influence of DNA Structure on Lesion Formation and Repair: Role of Modelling and Simulations Natacha Gillet,Emmanuelle Bignon,Elise Dumont,Antonio Monari Improta, Roberto and Douki, Thierry. Comprehensive Series in Photochemical & Photobiological Sciences, Royal Society of Chemistry, pp.105--132, 2021, 978-1-83916-196-4. ⟨10.1039/9781839165580-00105⟩ Chapitre d'ouvrage hal-03786795v1

Pré-publication, Document de travail (4)

InterMap: Accelerated Detection of Interaction Fingerprints on Large-Scale Molecular Ensembles Ernesto Fajardo-Díaz,Emmanuelle Bignon,François Dehez,Yasaman Karami,Roy González-Alemán 2026 Pré-publication, Document de travail hal-05553084v1
Structure, dynamics, and processing of 8oxoG:A in the nucleosome Abigayle F Vito,Justin A Ling,Julia C Ferrara,Caleb S Jacques,Natacha Gilletet al. 2025 Pré-publication, Document de travail hal-05368102v1
Histone H3 as a redox switch in the nucleosome core particle: insights from molecular modeling † Yasaman Karami,Roy González-Alemán,Mailys Duch,Yuya Qiu,Yani Kedjaret al. 2024 Pré-publication, Document de travail hal-04746825v1
The best COVID-19 predictor is recent smell loss: a cross-sectional study Richard C. Gerkin,Kathrin Ohla,Maria Geraldine Veldhuizen,Paule V. Joseph,Christine E Kellyet al. 2020 Pré-publication, Document de travail (preprint/prepublication) hal-02979656v2

Thèse (1)

Theoretical approach of complex DNA lesions : from formation to repair Emmanuelle Bignon Analytical chemistry. Université de Lyon, 2017. English. ⟨NNT : 2017LYSE1085⟩ Thèse tel-01586105v1