Alessandro Barducci
Modélisation Moléculaire Multi-échelle
04 67 41 79 11
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Liste des publications
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
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
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
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
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
2015
Large-Scale Conformational Transitions and Dimerization Are Encoded in the Amino-Acid Sequences of Hsp70 Chaperones
Malinverni D, Marsili S, Barducci A, De Los Rios P, Plos Computational Biology, 2015
Theoretical and Experimental Characterization of Amino-PEG-Phosphonate-Terminated Polyphosphorhydrazone Dendrimers: Influence of Size and PEG Capping on Cytotoxicity Profiles
Hameau A, Fruchon S, Bijani C, Barducci A, Blanzat M, Poupot R, Pavan GM, Caminade A, Turrin C, Journal Of Polymer Science Part A-polymer Chemistry, 2015
Non-equilibrium conformational dynamics in the function of molecular chaperones
Barducci A, De Los Rios P, Current Opinion In Structural Biology, 2015
Accuracy of Current All-Atom Force-Fields in Modeling Protein Disordered States
Palazzesi F, Prakash MK, Bonomi M, Barducci A, Journal Of Chemical Theory And Computation, 2015
Quantifying the role of chaperones in protein translocation by computational modeling.
Assenza S, De Los Rios P, Barducci A, Frontiers In Molecular Biosciences, 2015
Tackling sampling challenges in biomolecular simulations.
Barducci A, Pfaendtner J, Bonomi M, Methods In Molecular Biology (clifton, N.j.), 2015
2014
Single-molecule spectroscopy reveals chaperone-mediated expansion of substrate protein
Kellner R, Hofmann H, Barducci A, Wunderlich B, Nettels D, Schuler B, Proceedings Of The National Academy Of Sciences Of The United States Of America, 2014
Hsp70 chaperones are non-equilibrium machines that achieve ultra-affinity by energy consumption
De Los Rios P, Barducci A, Elife, 2014
The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems
Sterpone F, Melchionna S, Tuffery P, Pasquali S, Mousseau N, Cragnolini T, Chebaro Y, St-Pierre J, Kalimeri M, Barducci A, Laurin Y, Tek A, Baaden M, Phuong Hoang Nguyen , Derreumaux P, Chemical Society Reviews, 2014
2013
Free-energy landscape of protein oligomerization from atomistic simulations
Barducci A, Bonomi M, Prakash MK, Parrinello M, Proceedings Of The National Academy Of Sciences Of The United States Of America, 2013
The allosteric communication pathways in KIX domain of CBP
Palazzesi F, Barducci A, Tollinger M, Parrinello M, Proceedings Of The National Academy Of Sciences Of The United States Of America, 2013
Structural and energetic basis for hybridization limits in high-density DNA monolayers
Doni G, Ngavouka MDN, Barducci A, Parisse P, De Vita A, Scoles G, Casalis L, Pavan GM, Nanoscale, 2013
Combining metadynamics simulation and experiments to characterize dendrimers in solution
Pavan GM, Barducci A, Albertazzi L, Parrinello M, Soft Matter, 2013
2011
Effect of Urea on the beta-Hairpin Conformational Ensemble and Protein Denaturation Mechanism
Berteotti A, Barducci A, Parrinello M, Journal Of The American Chemical Society, 2011
Replica Temperatures for Uniform Exchange and Efficient Roundtrip Times in Explicit Solvent Parallel Tempering Simulations
Prakash MK, Barducci A, Parrinello M, Journal Of Chemical Theory And Computation, 2011
Assessing the Quality of the OPEP Coarse-Grained Force Field
Barducci A, Bonomi M, Derreumaux P, Journal Of Chemical Theory And Computation, 2011
Metadynamics
Barducci A, Bonomi M, Parrinello M, Wiley Interdisciplinary Reviews-computational Molecular Science, 2011
2010
Multiple Routes and Milestones in the Folding of HIV-1 Protease Monomer
Bonomi M, Barducci A, Gervasio FL, Parrinello M, Plos One, 2010
Probing the Mechanism of pH-Induced Large-Scale Conformational Changes in Dengue Virus Envelope Protein Using Atomistic Simulations
Prakash MK, Barducci A, Parrinello M, Biophysical Journal, 2010
Linking Well-Tempered Metadynamics Simulations with Experiments
Barducci A, Bonomi M, Parrinello M, Biophysical Journal, 2010
2009
2008
2007
Numerical verification of the generalized Crooks nonequilibrium work theorem for non-Hamiltonian molecular dynamics simulations
Chelli R, Marsili S, Barducci A, Procacci P, Journal Of Chemical Physics, 2007
Generalization of the Jarzynski and Crooks nonequilibrium work theorems in molecular dynamics simulations
Chelli R, Marsili S, Barducci A, Procacci P, Physical Review E, 2007
Problems in molecular dynamics of condensed phases
Schettino V, Chelli R, Marsili S, Barducci A, Faralli C, Pagliai M, Procacci P, Cardini G, Theoretical Chemistry Accounts, 2007
Recovering the Crooks equation for dynamical systems in the isothermal-isobaric ensemble: A strategy based on the equations of motion
Chelli R, Marsili S, Barducci A, Procacci P, Journal Of Chemical Physics, 2007
2006
Crooks equation for steered molecular dynamics using a Nose-Hoover thermostat
Procacci P, Marsili S, Barducci A, Signorini GF, Chelli R, Journal Of Chemical Physics, 2006
Self-healing umbrella sampling: A non-equilibrium approach for quantitative free energy calculations
Marsili S, Barducci A, Chelli R, Procacci P, Schettino V, Journal Of Physical Chemistry B, 2006
Metadynamics simulation of prion protein: beta-structure stability and the early stages of misfolding
Barducci A, Chelli R, Procacci P, Schettino V, Gervasio F, Parrinello M, Journal Of The American Chemical Society, 2006
2005
Behavior of polarizable models in presence of strong electric fields. I. Origin of nonlinear effects in water point-charge systems
Chelli R, Barducci A, Bellucci L, Schettino V, Procacci P, Journal Of Chemical Physics, 2005
Misfolding pathways of the prion protein probed by molecular dynamics Simulations
Barducci A, Chelli R, Procacci P, Schettino V, Biophysical Journal, 2005