Publications by year

2024

  • MinActionPath2: path generation between different conformations of large macromolecular assemblies by action minimization
    Koehl Patrice, Navaza Rafael, Tekpinar Mustafa, Delarue Marc
    Nucleic Acids Res. 2024 Jul 5;52(W1):W256-W263. DOI: 10.1093/nar/gkae421 PubMeb: 38783081 PubMed Central: PMC11223808

2023

  • Analyzing the Geometry and Dynamics of Viral Structures: A Review of Computational Approaches Based on Alpha Shape Theory, Normal Mode Analysis, and Poisson-Boltzmann Theories
    Hsieh Yin-Chen, Delarue Marc, Orland Henri, Koehl Patrice
    Viruses. 2023 Jun 13;15(6):1366. DOI: 10.3390/v15061366 PubMeb: 37376665 PubMed Central: PMC10300701
  • Reclassification of family A DNA polymerases reveals novel functional subfamilies and distinctive structural features
    Czernecki Dariusz, Nourisson Antonin, Legrand Pierre, Delarue Marc
    Nucleic Acids Res. 2023 May 22;51(9):4488-4507. DOI: 10.1093/nar/gkad242 PubMeb: 37070157 PubMed Central: PMC10201439
  • DNA-binding mechanism and evolution of replication protein A
    Madru Clément, Martínez-Carranza Markel, Laurent Sébastien, Alberti Alessandra C, Chevreuil Maelenn, Raynal Bertrand, Haouz Ahmed, Le Meur Rémy A, Delarue Marc, Henneke Ghislaine, Flament Didier, Krupovic Mart, Legrand Pierre, Sauguet Ludovic
    Nat Commun. 2023 Apr 22;14(1):2326. DOI: 10.1038/s41467-023-38048-w PubMeb: 37087464 PubMed Central: PMC10122647
  • Computing the Gromov-Wasserstein Distance between Two Surface Meshes Using Optimal Transport
    Koehl Patrice, Delarue Marc, Orland Henri
    Algorithms. 2023 Feb 28;16(3):131. DOI: 10.3390/a16030131

2021

  • Characterization of a triad of genes in cyanophage S-2L sufficient to replace adenine by 2-aminoadenine in bacterial DNA
    Czernecki Dariusz, Bonhomme Frédéric, Kaminski Pierre-Alexandre, Delarue Marc
    Nat Commun. 2021 Aug 5;12(1):4710. DOI: 10.1038/s41467-021-25064-x PubMeb: 34354070 PubMed Central: PMC8342488
  • Parameterizing elastic network models to capture the dynamics of proteins
    Koehl Patrice, Orland Henri, Delarue Marc
    J Comput Chem. 2021 Jun 11;(1):10.1002/jcc.26701. DOI: 10.1002/jcc.26701 PubMeb: 34117647
  • Fast and efficient purification of SARS-CoV-2 RNA dependent RNA polymerase complex expressed in Escherichia coli
    Madru Clément, Tekpinar Ayten Dizkirici, Rosario Sandrine, Czernecki Dariusz, Brûlé Sébastien, Sauguet Ludovic, Delarue Marc
    PLoS One. 2021 Apr 29;16(4):e0250610. DOI: 10.1371/journal.pone.0250610 PubMeb: 33914787 PubMed Central: PMC8084133
  • How cyanophage S-2L rejects adenine and incorporates 2-aminoadenine to saturate hydrogen bonding in its DNA
    Czernecki Dariusz, Legrand Pierre, Tekpinar Mustafa, Rosario Sandrine, Kaminski Pierre-Alexandre, Delarue Marc
    Nat Commun. 2021 Apr 23;12(1):2420. DOI: 10.1038/s41467-021-22626-x PubMeb: 33893297 PubMed Central: PMC8065100
  • Physics approach to the variable-mass optimal-transport problem
    Koehl Patrice, Delarue Marc, Orland Henri
    Phys Rev E. 2021 Jan;103(1-1):012113. DOI: 10.1103/PhysRevE.103.012113 PubMeb: 33601576

2020

  • Structural Studies of HNA Substrate Specificity in Mutants of an Archaeal DNA Polymerase Obtained by Directed Evolution
    Samson Camille, Legrand Pierre, Tekpinar Mustafa, Rozenski Jef, Abramov Mikhail, Holliger Philipp, Pinheiro Vitor B, Herdwijn Piet, Delarue Marc
    Biomolecules. 2020 Dec 8;10(12):1647. DOI: 10.3390/biom10121647 PubMeb: 33302546 PubMed Central: PMC7763228
  • Structural basis for allosteric transitions of a multidomain pentameric ligand-gated ion channel
    Hu Haidai, Howard Rebecca J, Bastolla Ugo, Lindahl Erik, Delarue Marc
    Proc Natl Acad Sci U S A. 2020 Jun 16;117(24):13437-13446. DOI: 10.1073/pnas.1922701117 PubMeb: 32482881 PubMed Central: PMC7306758
  • Structural evidence for the binding of monocarboxylates and dicarboxylates at pharmacologically relevant extracellular sites of a pentameric ligand-gated ion channel
    Fourati Zaineb, Sauguet Ludovic, Delarue Marc
    Acta Crystallogr D Struct Biol. 2020 Jul 1;76(Pt 7):668-675. DOI: 10.1107/S205979832000772X PubMeb: 32627739 PubMed Central: PMC7336382
  • Structural basis for the increased processivity of D-family DNA polymerases in complex with PCNA
    Madru Clément, Henneke Ghislaine, Raia Pierre, Hugonneau-Beaufet Inès, Pehau-Arnaudet Gérard, England Patrick, Lindahl Erik, Delarue Marc, Carroni Marta, Sauguet Ludovic
    Nat Commun. 2020 Mar 27;11(1):1591. DOI: 10.1038/s41467-020-15392-9 PubMeb: 32221299 PubMed Central: PMC7101311

2019

  • Statistical Physics Approach to the Optimal Transport Problem
    Koehl Patrice, Delarue Marc, Orland Henri
    Phys Rev Lett. 2019 Jul 26;123(4):040603. DOI: 10.1103/PhysRevLett.123.040603 PubMeb: 31491256
  • Optimal transport at finite temperature
    Koehl Patrice, Delarue Marc, Orland Henri
    Phys Rev E. 2019 Jul;100(1-1):013310. DOI: 10.1103/PhysRevE.100.013310 PubMeb: 31499816
  • Structural evidence for an in trans base selection mechanism involving Loop1 in polymerase μ at an NHEJ double-strand break junction
    Loc'h Jérôme, Gerodimos Christina A, Rosario Sandrine, Tekpinar Mustafa, Lieber Michael R, Delarue Marc
    J Biol Chem. 2019 Jul 5;294(27):10579-10595. DOI: 10.1074/jbc.RA119.008739 PubMeb: 31138645 PubMed Central: PMC6615693 Faculty Opinions (F1000 Prime): 735848655
  • Structure of the DP1-DP2 PolD complex bound with DNA and its implications for the evolutionary history of DNA and RNA polymerases
    Raia Pierre, Carroni Marta, Henry Etienne, Pehau-Arnaudet Gérard, Brûlé Sébastien, Béguin Pierre, Henneke Ghislaine, Lindahl Erik, Delarue Marc, Sauguet Ludovic
    PLoS Biol. 2019 Jan 18;17(1):e3000122. DOI: 10.1371/journal.pbio.3000122 PubMeb: 30657780 PubMed Central: PMC6355029
  • An updated structural classification of replicative DNA polymerases
    Raia Pierre, Delarue Marc, Sauguet Ludovic
    Biochem Soc Trans. 2019 Feb 28;47(1):239-249. DOI: 10.1042/BST20180579 PubMeb: 30647142
  • Coarse-grained dynamics of supramolecules: Conformational changes in outer shells of Dengue viruses
    Koehl Patrice, Delarue Marc
    Prog Biophys Mol Biol. 2019 May;143(1):20-37. DOI: 10.1016/j.pbiomolbio.2018.09.004 PubMeb: 30273615

2018

  • Numerical Encodings of Amino Acids in Multivariate Gaussian Modeling of Protein Multiple Sequence Alignments
    Koehl Patrice, Orland Henri, Delarue Marc
    Molecules. 2018 Dec 28;24(1):104. DOI: 10.3390/molecules24010104 PubMeb: 30597916 PubMed Central: PMC6337344
  • Combined approaches from physics, statistics, and computer science for ab initio protein structure prediction: ex unitate vires (unity is strength)?
    Delarue Marc, Koehl Patrice
    F1000Res. 2018 Jul 24;7(1):F1000 Faculty Rev-1125. DOI: 10.12688/f1000research.14870.1 PubMeb: 30079234 PubMed Central: PMC6058471
  • Electrostatics, proton sensor, and networks governing the gating transition in GLIC, a proton-gated pentameric ion channel
    Hu Haidai, Ataka Kenichi, Menny Anaïs, Fourati Zaineb, Sauguet Ludovic, Corringer Pierre-Jean, Koehl Patrice, Heberle Joachim, Delarue Marc
    Proc Natl Acad Sci U S A. 2018 Dec 26;115(52):E12172-E12181. DOI: 10.1073/pnas.1813378116 PubMeb: 30541892 PubMed Central: PMC6310827
  • Crystal structures of a pentameric ion channel gated by alkaline pH show a widely open pore and identify a cavity for modulation
    Hu Haidai, Nemecz Ákos, Van Renterghem Catherine, Fourati Zaineb, Sauguet Ludovic, Corringer Pierre-Jean, Delarue Marc
    Proc Natl Acad Sci U S A. 2018 Apr 24;115(17):E3959-E3968. DOI: 10.1073/pnas.1717700115 PubMeb: 29632192 PubMed Central: PMC5924894
  • Structural Basis for a Bimodal Allosteric Mechanism of General Anesthetic Modulation in Pentameric Ligand-Gated Ion Channels
    Fourati Zaineb, Howard Rebecca J, Heusser Stephanie A, Hu Haidai, Ruza Reinis R, Sauguet Ludovic, Lindahl Erik, Delarue Marc
    Cell Rep. 2018 Apr 24;23(4):993-1004. DOI: 10.1016/j.celrep.2018.03.108 PubMeb: 29694907 Faculty Opinions (F1000 Prime): 733109264
  • Terminal deoxynucleotidyltransferase: the story of an untemplated DNA polymerase capable of DNA bridging and templated synthesis across strands
    Loc'h Jérôme, Delarue Marc
    Curr Opin Struct Biol. 2018 Dec;53(1):22-31. DOI: 10.1016/j.sbi.2018.03.019 PubMeb: 29656238 Faculty Opinions (F1000 Prime): 733048842
  • Enzymatic synthesis of random sequences of RNA and RNA analogues by DNA polymerase theta mutants for the generation of aptamer libraries
    Randrianjatovo-Gbalou Irina, Rosario Sandrine, Sismeiro Odile, Varet Hugo, Legendre Rachel, Coppée Jean-Yves, Huteau Valérie, Pochet Sylvie, Delarue Marc
    Nucleic Acids Res. 2018 Jul 6;46(12):6271-6284. DOI: 10.1093/nar/gky413 PubMeb: 29788485 PubMed Central: PMC6158600

2017

  • Ab initio sampling of transition paths by conditioned Langevin dynamics
    Delarue Marc, Koehl Patrice, Orland Henri
    J Chem Phys. 2017 Oct 21;147(15):152703. DOI: 10.1063/1.4985651 PubMeb: 29055326
  • The Renormalization Group and Its Applications to Generating Coarse-Grained Models of Large Biological Molecular Systems
    Koehl Patrice, Poitevin Frédéric, Navaza Rafael, Delarue Marc
    J Chem Theory Comput. 2017 Mar 14;13(3):1424-1438. DOI: 10.1021/acs.jctc.6b01136 PubMeb: 28170254
  • String method solution of the gating pathways for a pentameric ligand-gated ion channel
    Lev Bogdan, Murail Samuel, Poitevin Frédéric, Cromer Brett A, Baaden Marc, Delarue Marc, Allen Toby W
    Proc Natl Acad Sci U S A. 2017 May 23;114(21):E4158-E4167. DOI: 10.1073/pnas.1617567114 PubMeb: 28487483 PubMed Central: PMC5448215 Faculty Opinions (F1000 Prime): 727600609
  • Barbiturates Bind in the GLIC Ion Channel Pore and Cause Inhibition by Stabilizing a Closed State
    Fourati Zaineb, Ruza Reinis Reinholds, Laverty Duncan, Drège Emmanuelle, Delarue-Cochin Sandrine, Joseph Delphine, Koehl Patrice, Smart Trevor, Delarue Marc
    J Biol Chem. 2017 Feb 3;292(5):1550-1558. DOI: 10.1074/jbc.M116.766964 PubMeb: 27986812 PubMed Central: PMC5290934

2016

  • Comparative Normal Mode Analysis of the Dynamics of DENV and ZIKV Capsids
    Hsieh Yin-Chen, Poitevin Frédéric, Delarue Marc, Koehl Patrice
    Front Mol Biosci. 2016 Dec 27;3(1):85. DOI: 10.3389/fmolb.2016.00085 PubMeb: 28083537 PubMed Central: PMC5187361
  • Shared active site architecture between archaeal PolD and multi-subunit RNA polymerases revealed by X-ray crystallography
    Sauguet Ludovic, Raia Pierre, Henneke Ghislaine, Delarue Marc
    Nat Commun. 2016;7(1):12227. DOI: 10.1038/ncomms12227 PubMeb: 27548043 PubMed Central: PMC4996933 Faculty Opinions (F1000 Prime): 726663708
  • Structural Basis for a New Templated Activity by Terminal Deoxynucleotidyl Transferase: Implications for V(D)J Recombination
    Loc'h Jérôme, Rosario Sandrine, Delarue Marc
    Structure. 2016 Sep 6;24(9):1452-63. DOI: 10.1016/j.str.2016.06.014 PubMeb: 27499438 Faculty Opinions (F1000 Prime): 726620136
  • Structural Basis for Xenon Inhibition in a Cationic Pentameric Ligand-Gated Ion Channel
    Sauguet Ludovic, Fourati Zeineb, Prangé Thierry, Delarue Marc, Colloc'h Nathalie
    PLoS One. 2016 Feb 24;11(2):e0149795. DOI: 10.1371/journal.pone.0149795 PubMeb: 26910105 PubMed Central: PMC4765991
  • Sites of Anesthetic Inhibitory Action on a Cationic Ligand-Gated Ion Channel
    Laurent Benoist, Murail Samuel, Shahsavar Azadeh, Sauguet Ludovic, Delarue Marc, Baaden Marc
    Structure. 2016 Apr 5;24(4):595-605. DOI: 10.1016/j.str.2016.02.014 PubMeb: 27021161

2015

  • Structural basis for a novel mechanism of DNA bridging and alignment in eukaryotic DSB DNA repair
    Gouge Jérôme, Rosario Sandrine, Romain Félix, Poitevin Frédéric, Béguin Pierre, Delarue Marc
    EMBO J. 2015 Apr 15;34(8):1126-42. DOI: 10.15252/embj.201489643 PubMeb: 25762590 PubMed Central: PMC4406656
  • Allosteric and hyperekplexic mutant phenotypes investigated on an α1 glycine receptor transmembrane structure
    Moraga-Cid Gustavo, Sauguet Ludovic, Huon Christèle, Malherbe Laurie, Girard-Blanc Christine, Petres Stéphane, Murail Samuel, Taly Antoine, Baaden Marc, Delarue Marc, Corringer Pierre-Jean
    Proc Natl Acad Sci U S A. 2015 Mar 3;112(9):2865-70. DOI: 10.1073/pnas.1417864112 PubMeb: 25730860 PubMed Central: PMC4352774
  • Genuine open form of the pentameric ligand-gated ion channel GLIC
    Fourati Zaineb, Sauguet Ludovic, Delarue Marc
    Acta Crystallogr D Biol Crystallogr. 2015 Mar;71(Pt 3):454-60. DOI: 10.1107/S1399004714026698 PubMeb: 25760595 Faculty Opinions (F1000 Prime): 725386230
  • Crystallographic studies of pharmacological sites in pentameric ligand-gated ion channels
    Sauguet Ludovic, Shahsavar Azadeh, Delarue Marc
    Biochim Biophys Acta. 2015 Mar;1850(3):511-23. DOI: 10.1016/j.bbagen.2014.05.007 PubMeb: 24836522

2014

  • Crystal structures of a pentameric ligand-gated ion channel provide a mechanism for activation
    Sauguet Ludovic, Shahsavar Azadeh, Poitevin Frédéric, Huon Christèle, Menny Anaïs, Nemecz Àkos, Haouz Ahmed, Changeux Jean-Pierre, Corringer Pierre-Jean, Delarue Marc
    Proc Natl Acad Sci U S A. 2014 Jan 21;111(3):966-71. DOI: 10.1073/pnas.1314997111 PubMeb: 24367074 PubMed Central: PMC3903189 Faculty Opinions (F1000 Prime): 718216322

2013

  • Structural basis for ion permeation mechanism in pentameric ligand-gated ion channels
    Sauguet Ludovic, Poitevin Frédéric, Murail Samuel, Van Renterghem Catherine, Moraga-Cid Gustavo, Malherbe Laurie, Thompson Andrew W, Koehl Patrice, Corringer Pierre-Jean, Baaden Marc, Delarue Marc
    EMBO J. 2013 Mar 6;32(5):728-41. DOI: 10.1038/emboj.2013.17 PubMeb: 23403925 PubMed Central: PMC3590989
  • Structural basis for potentiation by alcohols and anaesthetics in a ligand-gated ion channel
    Sauguet Ludovic, Howard Rebecca J, Malherbe Laurie, Lee Ui S, Corringer Pierre-Jean, Harris R Adron, Delarue Marc
    Nat Commun. 2013;4(1):1697. DOI: 10.1038/ncomms2682 PubMeb: 23591864 PubMed Central: PMC4204805 Faculty Opinions (F1000 Prime): 718001360
  • Structures of intermediates along the catalytic cycle of terminal deoxynucleotidyltransferase: dynamical aspects of the two-metal ion mechanism
    Gouge Jérôme, Rosario Sandrine, Romain Félix, Beguin Pierre, Delarue Marc
    J Mol Biol. 2013 Nov 15;425(22):4334-52. DOI: 10.1016/j.jmb.2013.07.009 PubMeb: 23856622
  • New nucleotide-competitive non-nucleoside inhibitors of terminal deoxynucleotidyl transferase: discovery, characterization, and crystal structure in complex with the target
    Costi Roberta, Crucitti Giuliana Cuzzucoli, Pescatori Luca, Messore Antonella, Scipione Luigi, Tortorella Silvano, Amoroso Alessandra, Crespan Emmanuele, Campiglia Pietro, Maresca Bruno, Porta Amalia, Granata Ilaria, Novellino Ettore, Gouge Jérôme, Delarue Marc, Maga Giovanni, Di Santo Roberto
    J Med Chem. 2013 Sep 26;56(18):7431-41. DOI: 10.1021/jm4010187 PubMeb: 23968551

2012

  • Molecular recognition of canonical and deaminated bases by P. abyssi family B DNA polymerase
    Gouge Jérôme, Ralec Céline, Henneke Ghislaine, Delarue Marc
    J Mol Biol. 2012 Oct 26;423(3):315-36. DOI: 10.1016/j.jmb.2012.07.025 PubMeb: 22902479
  • Structure and pharmacology of pentameric receptor channels: from bacteria to brain
    Corringer Pierre-Jean, Poitevin Frédéric, Prevost Marie S, Sauguet Ludovic, Delarue Marc, Changeux Jean-Pierre
    Structure. 2012 Jun 6;20(6):941-56. DOI: 10.1016/j.str.2012.05.003 PubMeb: 22681900
  • A locally closed conformation of a bacterial pentameric proton-gated ion channel
    Prevost Marie S, Sauguet Ludovic, Nury Hugues, Van Renterghem Catherine, Huon Christèle, Poitevin Frederic, Baaden Marc, Delarue Marc, Corringer Pierre-Jean
    Nat Struct Mol Biol. 2012 May 13;19(6):642-9. DOI: 10.1038/nsmb.2307 PubMeb: 22580559 Faculty Opinions (F1000 Prime): 717248063

2011

  • X-ray structures of general anaesthetics bound to a pentameric ligand-gated ion channel
    Nury Hugues, Van Renterghem Catherine, Weng Yun, Tran Alphonso, Baaden Marc, Dufresne Virginie, Changeux Jean-Pierre, Sonner James M, Delarue Marc, Corringer Pierre-Jean
    Nature. 2011 Jan 20;469(7330):428-31. DOI: 10.1038/nature09647 PubMeb: 21248852 Faculty Opinions (F1000 Prime): 7989960
  • AquaSAXS: a web server for computation and fitting of SAXS profiles with non-uniformally hydrated atomic models
    Poitevin Frédéric, Orland Henri, Doniach Sebastian, Koehl Patrice, Delarue Marc
    Nucleic Acids Res. 2011 Jul;39(Web Server issue):W184-9. DOI: 10.1093/nar/gkr430 PubMeb: 21665925 PubMed Central: PMC3125794

2010

  • One-microsecond molecular dynamics simulation of channel gating in a nicotinic receptor homologue
    Nury Hugues, Poitevin Frédéric, Van Renterghem Catherine, Changeux Jean-Pierre, Corringer Pierre-Jean, Delarue Marc, Baaden Marc
    Proc Natl Acad Sci U S A. 2010 Apr 6;107(14):6275-80. DOI: 10.1073/pnas.1001832107 PubMeb: 20308576 PubMed Central: PMC2852019 Faculty Opinions (F1000 Prime): 4176956
  • Crystal structure of the extracellular domain of a bacterial ligand-gated ion channel
    Nury Hugues, Bocquet Nicolas, Le Poupon Chantal, Raynal Bertrand, Haouz Ahmed, Corringer Pierre-Jean, Delarue Marc
    J Mol Biol. 2010 Feb 5;395(5):1114-27. DOI: 10.1016/j.jmb.2009.11.024 PubMeb: 19917292

2009

  • X-ray structure of a pentameric ligand-gated ion channel in an apparently open conformation
    Bocquet Nicolas, Nury Hugues, Baaden Marc, Le Poupon Chantal, Changeux Jean-Pierre, Delarue Marc, Corringer Pierre-Jean
    Nature. 2009 Jan 1;457(7225):111-4. DOI: 10.1038/nature07462 PubMeb: 18987633 Faculty Opinions (F1000 Prime): 1135958
  • Conferring a template-dependent polymerase activity to terminal deoxynucleotidyltransferase by mutations in the Loop1 region
    Romain Félix, Barbosa Isabelle, Gouge Jérôme, Rougeon François, Delarue Marc
    Nucleic Acids Res. 2009 Aug;37(14):4642-56. DOI: 10.1093/nar/gkp460 PubMeb: 19502493 PubMed Central: PMC2724280
  • Beyond the Poisson-Boltzmann model: modeling biomolecule-water and water-water interactions
    Koehl Patrice, Orland Henri, Delarue Marc
    Phys Rev Lett. 2009 Feb 27;102(8):087801. DOI: 10.1103/PhysRevLett.102.087801 PubMeb: 19257790 PubMed Central: PMC2664224 Faculty Opinions (F1000 Prime): 13540956