Team members
#[plugannuaireteam]EquipeA-6
Publications
2025
Exploring RNA destabilization mechanisms in biomolecular condensates through atomistic simulations
Boccalini M, Berezovska Y, Bussi G, Paloni M, Barducci A, Proc Natl Acad Sci U S A, 2025
Incoherent feedback from coupled amino acids and ribosome pools generates damped oscillations in growing E. coli
Droghetti R, Fuchs P, Iuliani I, Firmano V, Tallarico G, Calabrese L, Grilli J, Sclavi B, Ciandrini L, Cosentino Lagomarsino M, Nat Commun, 2025
2024
In situfate of Chikungunya virus replication organelles
Girard J, Le Bihan O, Lai-Kee-Him J, Girleanu M, Bernard E, Castellarin C, Chee M, Neyret A, Spehner D, Holy X, Favier A-L, Briant L, Bron P, J Virol, 2024
How total mRNA influences cell growth
Calabrese L, Ciandrini L, Cosentino Lagomarsino M, Proc Natl Acad Sci U S A, 2024
Optimal control of ribosome population for gene expression under periodic nutrient intake
Soubrier C, Foxall E, Ciandrini L, Dao Duc K, J R Soc Interface, 2024
2023
Structural Insights into the Activation of Human Aryl Hydrocarbon Receptor by the Environmental Contaminant Benzo[a]pyrene and Structurally Related Compounds
Kwong HS, Paloni M, Grandvuillemin L, Sirounian S, Ancelin A, Lai-Kee-Him J, Grimaldi M, Carivenc C, Lancey C, Ragan TJ, Hesketh EL, Balaguer P, Barducci A, Gruszczyk J, Bourguet W, J Mol Biol, 2023
A cyclin-dependent kinase-mediated phosphorylation switch of disordered protein condensation
Valverde JM, Dubra G, Phillips M, Haider A, Elena-Real C, Fournet A, Alghoul E, Chahar D, Andres-Sanchez N, Paloni M, Bernado P, van Mierlo G, Vermeulen M, van den Toorn H, Heck AJR, Constantinou A, Barducci A, Ghosh K, Sibille N, Knipscheer P, Krasinska L, Fisher D, Altelaar M, Nat Commun, 2023
Data-driven large-scale genomic analysis reveals an intricate phylogenetic and functional landscape in J-domain proteins
Malinverni D, Zamuner S, Rebeaud ME, Barducci A, Nillegoda NB, De Los Rios P, Proc Natl Acad Sci U S A, 2023
Compartmentalization of the SUMO/RNF4 pathway by SLX4 drives DNA repair
Alghoul E, Paloni M, Takedachi A, Urbach S, Barducci A, Gaillard PH, Basbous J, Constantinou A, Mol Cell, 2023
The structure of pathogenic huntingtin exon 1 defines the bases of its aggregation propensity
Elena-Real CA, Sagar A, Urbanek A, Popovic M, Morato A, Estana A, Fournet A, Doucet C, Lund XL, Shi ZD, Costa L, Thureau A, Allemand F, Swenson RE, Milhiet PE, Crehuet R, Barducci A, Cortes J, Sinnaeve D, Sibille N, Bernado P, Nat Struct Mol Biol, 2023
Nucleation of Biomolecular Condensates from Finite-Sized Simulations
Li L, Paloni M, Finney AR, Barducci A, Salvalaglio M, J Phys Chem Lett, 2023
TASEPy: A Python-based package to iteratively solve the inhomogeneous exclusion process
Ciandrini L, Crisostomo RL, Szavitz-Nossan J, SciPost Physics Codebases, 2023
Codebase release 1.1 for TASEPy
Ciandrini L, Crisostomo RL, Szavitz-Nossan J, SciPost Physics Codebases, 2023
2022
Cryo-EM structure of the agonist-bound Hsp90-XAP2-AHR cytosolic complex
Gruszczyk J, Grandvuillemin L, Lai-Kee-Him J, Paloni M, Savva CG, Germain P, Grimaldi M, Boulahtouf A, Kwong HS, Bous J, Ancelin A, Bechara C, Barducci A, Balaguer P, Bourguet W, Nat Commun, 2022
Viro-fluidics: Real-time analysis of virus production kinetics at the single-cell level
Eid J, Socol M, Naillon A, Feuillard J, Ciandrini L, Margeat E, Charlot B, Mougel M, Biophys Rep (N Y), 2022
Protein degradation sets the fraction of active ribosomes at vanishing growth
Calabrese L, Grilli J, Osella M, Kempes CP, Lagomarsino MC, Ciandrini L, PLoS Comput Biol, 2022
Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR
Gauto DF, Macek P, Malinverni D, Fraga H, Paloni M, Sucec I, Hessel A, Bustamante JP, Barducci A, Schanda P, Nat Commun, 2022
2021
The diversity of molecular interactions involving intrinsically disordered proteins: A molecular modeling perspective
Clerc I, Sagar A, Barducci A, Sibille N, Bernado P, Cortes J, Comput Struct Biotechnol J, 2021
Arginine multivalency stabilizes protein/RNA condensates
Paloni M, Bussi G, Barducci A, Protein Sci, 2021
Author Correction: Molecular dissection of amyloid disaggregation by human HSP70
Wentink AS, Nillegoda NB, Feufel J, Ubartaite G, Schneider CP, De Los Rios P, Hennig J, Barducci A, Bukau B, Nature, 2021
2020
Molecular dissection of amyloid disaggregation by human HSP70
Wentink AS, Nillegoda NB, Feufel J, Ubartaite G, Schneider CP, De Los Rios P, Hennig J, Barducci A, Bukau B, Nature, 2020
Unraveling Molecular Interactions in Liquid-Liquid Phase Separation of Disordered Proteins by Atomistic Simulations
Paloni M, Bailly R, Ciandrini L, Barducci A, J Phys Chem B, 2020
Rational programming of history-dependent logic in cellular populations
Zuniga A, Guiziou S, Mayonove P, Meriem ZB, Camacho M, Moreau V, Ciandrini L, Hersen P, Bonnet J, Nat Commun, 2020
Inferring efficiency of translation initiation and elongation from ribosome profiling
Szavits-Nossan J, Ciandrini L, Nucleic Acids Res, 2020
Coevolutionary Analysis of Protein Subfamilies by Sequence Reweighting
Malinverni D, Barducci A, Entropy (Basel), 2020
2019
Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones
Assenza S, Sassi AS, Kellner R, Schuler B, De Los Rios P, Barducci A, Elife, 2019
Insights into the activation mechanism of human estrogen-related receptor gamma by environmental endocrine disruptors
Thouennon E, Delfosse V, Bailly R, Blanc P, Boulahtouf A, Grimaldi M, Barducci A, Bourguet W, Balaguer P, Cell Mol Life Sci, 2019
Interplay of Protein Disorder in Retinoic Acid Receptor Heterodimer and Its Corepressor Regulates Gene Expression
Cordeiro TN, Sibille N, Germain P, Barthe P, Boulahtouf A, Allemand F, Bailly R, Vivat V, Ebel C, Barducci A, Bourguet W, le Maire A, Bernado P, Structure, 2019
DNA-segment-capture model for loop extrusion by structural maintenance of chromosome (SMC) protein complexes
Marko JF, De Los Rios P, Barducci A, Gruber S, Nucleic Acids Res, 2019
Aromatic Ring Dynamics, Thermal Activation, and Transient Conformations of a 468 kDa Enzyme by Specific
Gauto DF, Macek P, Barducci A, Fraga H, Hessel A, Terauchi T, Gajan D, Miyanoiri Y, Boisbouvier J, Lichtenecker R, Kainosho M, Schanda P, J Am Chem Soc, 2019
Structural basis for chemically-induced homodimerization of a single domain antibody
Lesne J, Chang HJ, De Visch A, Paloni M, Barthe P, Guichou JF, Mayonove P, Barducci A, Labesse G, Bonnet J, Cohen-Gonsaud M, Sci Rep, 2019
Function, evolution, and structure of J-domain proteins
Kampinga HH, Andreasson C, Barducci A, Cheetham ME, Cyr D, Emanuelsson C, Genevaux P, Gestwicki JE, Goloubinoff P, Huerta-Cepas J, Kirstein J, Liberek K, Mayer MP, Nagata K, Nillegoda NB, Pulido P, Ramos C, De Los Rios P, Rospert S, Rosenzweig R, Sahi C, Taipale M, Tomiczek B, Ushioda R, Young JC, Zimmermann R, Zylicz A, Zylicz M, Craig EA, Marszalek J, Cell Stress Chaperones, 2019
Driven transport on a flexible polymer with particle recycling: a model inspired by transcription and translation
Fernandes LD, Ciandrini L, Physical Review E, 2019
An equilibrium model for ribosome competition
Rogalla PS, Rudge TJ, Ciandrini L, Physical Biology, 2019
Exclusion process subject to conformational size changes
Rousset Y, Ciandrini L, Kern N, SciPost Phys, 2019
Accurate measures of translation efficiency and traffic using ribosome profiling
Szavits-Nossan J, Ciandrini L, bioRxiv, 2019
Coevolutionary Analysis of Protein Sequences for Molecular Modeling
Malinverni D, Barducci A, Methods Mol Biol, 2019
2018
Emerging fields in chaperone proteins: a French workshop
Mileo E, Ilbert M, Barducci A, Bordes P, Castanie-Cornet MP, Garnier C, Genevaux P, Gillet R, Goloubinoff P, Ochsenbein F, Richarme G, Iobbi-Nivol C, Giudici-Orticoni MT, Gontero B, Genest O, Biochimie, 2018
Lipid tempering simulation of model biological membranes on parallel platforms
Cardelli C, Barducci A, Procacci P, Biochim Biophys Acta, 2018
Chaperones convert the energy from ATP into the nonequilibrium stabilization of native proteins
Goloubinoff P, Sassi AS, Fauvet B, Barducci A, De Los Rios P, Nat Chem Biol, 2018
2017
Catch bond drives stator mechanosensitivity in the bacterial flagellar motor
Nord AL, Gachon E, Perez-Carrasco R, Nirody JA, Barducci A, Berry RM, Pedaci F, Proc Natl Acad Sci USA, 2017
Prion protein beta2-alpha2 loop conformational landscape
Caldarulo E, Barducci A, Wuthrich K, Parrinello M, Proc Natl Acad Sci USA, 2017
Evolution of an intricate J-protein network driving protein disaggregation in eukaryotes
Nillegoda NB, Stank A, Malinverni D, Alberts N, Szlachcic A, Barducci A, De Los Rios P, Wade RC, Bukau B, Elife, 2017
Modeling Hsp70/Hsp40 interaction by multi-scale molecular simulations and co-evolutionary sequence analysis
Malinverni D, Jost Lopez A, De Los Rios P, Hummer G, Barducci A, Elife, 2017
2016
Communication: Role of explicit water models in the helix folding/unfolding processes
Palazzesi F, Salvalaglio M, Barducci A, Parrinello M, J Chem Phys, 2016
Effect of the Synaptic Plasma Membrane on the Stability of the Amyloid Precursor Protein Homodimer
Audagnotto M, Lemmin T, Barducci A, Dal Peraro M, J Phys Chem Lett, 2016
Research
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2025
Exploring RNA destabilization mechanisms in biomolecular condensates through atomistic simulations
Boccalini M, Berezovska Y, Bussi G, Paloni M, Barducci A, Proc Natl Acad Sci U S A, 2025
Incoherent feedback from coupled amino acids and ribosome pools generates damped oscillations in growing E. coli
Droghetti R, Fuchs P, Iuliani I, Firmano V, Tallarico G, Calabrese L, Grilli J, Sclavi B, Ciandrini L, Cosentino Lagomarsino M, Nat Commun, 2025
2024
In situfate of Chikungunya virus replication organelles
Girard J, Le Bihan O, Lai-Kee-Him J, Girleanu M, Bernard E, Castellarin C, Chee M, Neyret A, Spehner D, Holy X, Favier A-L, Briant L, Bron P, J Virol, 2024
How total mRNA influences cell growth
Calabrese L, Ciandrini L, Cosentino Lagomarsino M, Proc Natl Acad Sci U S A, 2024
Optimal control of ribosome population for gene expression under periodic nutrient intake
Soubrier C, Foxall E, Ciandrini L, Dao Duc K, J R Soc Interface, 2024
2023
Structural Insights into the Activation of Human Aryl Hydrocarbon Receptor by the Environmental Contaminant Benzo[a]pyrene and Structurally Related Compounds
Kwong HS, Paloni M, Grandvuillemin L, Sirounian S, Ancelin A, Lai-Kee-Him J, Grimaldi M, Carivenc C, Lancey C, Ragan TJ, Hesketh EL, Balaguer P, Barducci A, Gruszczyk J, Bourguet W, J Mol Biol, 2023
A cyclin-dependent kinase-mediated phosphorylation switch of disordered protein condensation
Valverde JM, Dubra G, Phillips M, Haider A, Elena-Real C, Fournet A, Alghoul E, Chahar D, Andres-Sanchez N, Paloni M, Bernado P, van Mierlo G, Vermeulen M, van den Toorn H, Heck AJR, Constantinou A, Barducci A, Ghosh K, Sibille N, Knipscheer P, Krasinska L, Fisher D, Altelaar M, Nat Commun, 2023
Data-driven large-scale genomic analysis reveals an intricate phylogenetic and functional landscape in J-domain proteins
Malinverni D, Zamuner S, Rebeaud ME, Barducci A, Nillegoda NB, De Los Rios P, Proc Natl Acad Sci U S A, 2023
Compartmentalization of the SUMO/RNF4 pathway by SLX4 drives DNA repair
Alghoul E, Paloni M, Takedachi A, Urbach S, Barducci A, Gaillard PH, Basbous J, Constantinou A, Mol Cell, 2023
The structure of pathogenic huntingtin exon 1 defines the bases of its aggregation propensity
Elena-Real CA, Sagar A, Urbanek A, Popovic M, Morato A, Estana A, Fournet A, Doucet C, Lund XL, Shi ZD, Costa L, Thureau A, Allemand F, Swenson RE, Milhiet PE, Crehuet R, Barducci A, Cortes J, Sinnaeve D, Sibille N, Bernado P, Nat Struct Mol Biol, 2023
Nucleation of Biomolecular Condensates from Finite-Sized Simulations
Li L, Paloni M, Finney AR, Barducci A, Salvalaglio M, J Phys Chem Lett, 2023
TASEPy: A Python-based package to iteratively solve the inhomogeneous exclusion process
Ciandrini L, Crisostomo RL, Szavitz-Nossan J, SciPost Physics Codebases, 2023
Codebase release 1.1 for TASEPy
Ciandrini L, Crisostomo RL, Szavitz-Nossan J, SciPost Physics Codebases, 2023
2022
Cryo-EM structure of the agonist-bound Hsp90-XAP2-AHR cytosolic complex
Gruszczyk J, Grandvuillemin L, Lai-Kee-Him J, Paloni M, Savva CG, Germain P, Grimaldi M, Boulahtouf A, Kwong HS, Bous J, Ancelin A, Bechara C, Barducci A, Balaguer P, Bourguet W, Nat Commun, 2022
Viro-fluidics: Real-time analysis of virus production kinetics at the single-cell level
Eid J, Socol M, Naillon A, Feuillard J, Ciandrini L, Margeat E, Charlot B, Mougel M, Biophys Rep (N Y), 2022
Protein degradation sets the fraction of active ribosomes at vanishing growth
Calabrese L, Grilli J, Osella M, Kempes CP, Lagomarsino MC, Ciandrini L, PLoS Comput Biol, 2022
Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR
Gauto DF, Macek P, Malinverni D, Fraga H, Paloni M, Sucec I, Hessel A, Bustamante JP, Barducci A, Schanda P, Nat Commun, 2022
2021
The diversity of molecular interactions involving intrinsically disordered proteins: A molecular modeling perspective
Clerc I, Sagar A, Barducci A, Sibille N, Bernado P, Cortes J, Comput Struct Biotechnol J, 2021
Arginine multivalency stabilizes protein/RNA condensates
Paloni M, Bussi G, Barducci A, Protein Sci, 2021
Author Correction: Molecular dissection of amyloid disaggregation by human HSP70
Wentink AS, Nillegoda NB, Feufel J, Ubartaite G, Schneider CP, De Los Rios P, Hennig J, Barducci A, Bukau B, Nature, 2021
2020
Molecular dissection of amyloid disaggregation by human HSP70
Wentink AS, Nillegoda NB, Feufel J, Ubartaite G, Schneider CP, De Los Rios P, Hennig J, Barducci A, Bukau B, Nature, 2020
Unraveling Molecular Interactions in Liquid-Liquid Phase Separation of Disordered Proteins by Atomistic Simulations
Paloni M, Bailly R, Ciandrini L, Barducci A, J Phys Chem B, 2020
Rational programming of history-dependent logic in cellular populations
Zuniga A, Guiziou S, Mayonove P, Meriem ZB, Camacho M, Moreau V, Ciandrini L, Hersen P, Bonnet J, Nat Commun, 2020
Inferring efficiency of translation initiation and elongation from ribosome profiling
Szavits-Nossan J, Ciandrini L, Nucleic Acids Res, 2020
Coevolutionary Analysis of Protein Subfamilies by Sequence Reweighting
Malinverni D, Barducci A, Entropy (Basel), 2020
2019
Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones
Assenza S, Sassi AS, Kellner R, Schuler B, De Los Rios P, Barducci A, Elife, 2019
Insights into the activation mechanism of human estrogen-related receptor gamma by environmental endocrine disruptors
Thouennon E, Delfosse V, Bailly R, Blanc P, Boulahtouf A, Grimaldi M, Barducci A, Bourguet W, Balaguer P, Cell Mol Life Sci, 2019
Interplay of Protein Disorder in Retinoic Acid Receptor Heterodimer and Its Corepressor Regulates Gene Expression
Cordeiro TN, Sibille N, Germain P, Barthe P, Boulahtouf A, Allemand F, Bailly R, Vivat V, Ebel C, Barducci A, Bourguet W, le Maire A, Bernado P, Structure, 2019
DNA-segment-capture model for loop extrusion by structural maintenance of chromosome (SMC) protein complexes
Marko JF, De Los Rios P, Barducci A, Gruber S, Nucleic Acids Res, 2019
Aromatic Ring Dynamics, Thermal Activation, and Transient Conformations of a 468 kDa Enzyme by Specific
Gauto DF, Macek P, Barducci A, Fraga H, Hessel A, Terauchi T, Gajan D, Miyanoiri Y, Boisbouvier J, Lichtenecker R, Kainosho M, Schanda P, J Am Chem Soc, 2019
Structural basis for chemically-induced homodimerization of a single domain antibody
Lesne J, Chang HJ, De Visch A, Paloni M, Barthe P, Guichou JF, Mayonove P, Barducci A, Labesse G, Bonnet J, Cohen-Gonsaud M, Sci Rep, 2019
Function, evolution, and structure of J-domain proteins
Kampinga HH, Andreasson C, Barducci A, Cheetham ME, Cyr D, Emanuelsson C, Genevaux P, Gestwicki JE, Goloubinoff P, Huerta-Cepas J, Kirstein J, Liberek K, Mayer MP, Nagata K, Nillegoda NB, Pulido P, Ramos C, De Los Rios P, Rospert S, Rosenzweig R, Sahi C, Taipale M, Tomiczek B, Ushioda R, Young JC, Zimmermann R, Zylicz A, Zylicz M, Craig EA, Marszalek J, Cell Stress Chaperones, 2019
Driven transport on a flexible polymer with particle recycling: a model inspired by transcription and translation
Fernandes LD, Ciandrini L, Physical Review E, 2019
An equilibrium model for ribosome competition
Rogalla PS, Rudge TJ, Ciandrini L, Physical Biology, 2019
Exclusion process subject to conformational size changes
Rousset Y, Ciandrini L, Kern N, SciPost Phys, 2019
Accurate measures of translation efficiency and traffic using ribosome profiling
Szavits-Nossan J, Ciandrini L, bioRxiv, 2019
Coevolutionary Analysis of Protein Sequences for Molecular Modeling
Malinverni D, Barducci A, Methods Mol Biol, 2019
2018
Emerging fields in chaperone proteins: a French workshop
Mileo E, Ilbert M, Barducci A, Bordes P, Castanie-Cornet MP, Garnier C, Genevaux P, Gillet R, Goloubinoff P, Ochsenbein F, Richarme G, Iobbi-Nivol C, Giudici-Orticoni MT, Gontero B, Genest O, Biochimie, 2018
Lipid tempering simulation of model biological membranes on parallel platforms
Cardelli C, Barducci A, Procacci P, Biochim Biophys Acta, 2018
Chaperones convert the energy from ATP into the nonequilibrium stabilization of native proteins
Goloubinoff P, Sassi AS, Fauvet B, Barducci A, De Los Rios P, Nat Chem Biol, 2018
2017
Catch bond drives stator mechanosensitivity in the bacterial flagellar motor
Nord AL, Gachon E, Perez-Carrasco R, Nirody JA, Barducci A, Berry RM, Pedaci F, Proc Natl Acad Sci USA, 2017
Prion protein beta2-alpha2 loop conformational landscape
Caldarulo E, Barducci A, Wuthrich K, Parrinello M, Proc Natl Acad Sci USA, 2017
Evolution of an intricate J-protein network driving protein disaggregation in eukaryotes
Nillegoda NB, Stank A, Malinverni D, Alberts N, Szlachcic A, Barducci A, De Los Rios P, Wade RC, Bukau B, Elife, 2017
Modeling Hsp70/Hsp40 interaction by multi-scale molecular simulations and co-evolutionary sequence analysis
Malinverni D, Jost Lopez A, De Los Rios P, Hummer G, Barducci A, Elife, 2017
2016
Communication: Role of explicit water models in the helix folding/unfolding processes
Palazzesi F, Salvalaglio M, Barducci A, Parrinello M, J Chem Phys, 2016
Effect of the Synaptic Plasma Membrane on the Stability of the Amyloid Precursor Protein Homodimer
Audagnotto M, Lemmin T, Barducci A, Dal Peraro M, J Phys Chem Lett, 2016