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Numerical Encodings of Amino Acids in Multivariate Gaussian Modeling of Protein Multiple Sequence Alignments.

Koehl P, Orland H, Delarue M.

Molecules. 2018 Dec 28;24(1). pii: E104. doi: 10.3390/molecules24010104.


Electrostatics, proton sensor, and networks governing the gating transition in GLIC, a proton-gated pentameric ion channel.

Hu H, Ataka K, Menny A, Fourati Z, Sauguet L, Corringer PJ, Koehl P, Heberle J, Delarue M.

Proc Natl Acad Sci U S A. 2018 Dec 26;115(52):E12172-E12181. doi: 10.1073/pnas.1813378116. Epub 2018 Dec 12.


Coarse-grained dynamics of supramolecules: Conformational changes in outer shells of Dengue viruses.

Koehl P, Delarue M.

Prog Biophys Mol Biol. 2018 Sep 28. pii: S0079-6107(18)30138-X. doi: 10.1016/j.pbiomolbio.2018.09.004. [Epub ahead of print]


Mechano-chemostats to study the effects of compressive stress on yeast.

Holt LJ, Hallatschek O, Delarue M.

Methods Cell Biol. 2018;147:215-231. doi: 10.1016/bs.mcb.2018.06.010. Epub 2018 Jul 19.


Combined approaches from physics, statistics, and computer science for ab initio protein structure prediction: ex unitate vires (unity is strength)?

Delarue M, Koehl P.

F1000Res. 2018 Jul 24;7. pii: F1000 Faculty Rev-1125. doi: 10.12688/f1000research.14870.1. eCollection 2018. Review.


mTORC1 Controls Phase Separation and the Biophysical Properties of the Cytoplasm by Tuning Crowding.

Delarue M, Brittingham GP, Pfeffer S, Surovtsev IV, Pinglay S, Kennedy KJ, Schaffer M, Gutierrez JI, Sang D, Poterewicz G, Chung JK, Plitzko JM, Groves JT, Jacobs-Wagner C, Engel BD, Holt LJ.

Cell. 2018 Jul 12;174(2):338-349.e20. doi: 10.1016/j.cell.2018.05.042. Epub 2018 Jun 21.


Enzymatic synthesis of random sequences of RNA and RNA analogues by DNA polymerase theta mutants for the generation of aptamer libraries.

Randrianjatovo-Gbalou I, Rosario S, Sismeiro O, Varet H, Legendre R, Coppée JY, Huteau V, Pochet S, Delarue M.

Nucleic Acids Res. 2018 Jul 6;46(12):6271-6284. doi: 10.1093/nar/gky413.


Structural Basis for a Bimodal Allosteric Mechanism of General Anesthetic Modulation in Pentameric Ligand-Gated Ion Channels.

Fourati Z, Howard RJ, Heusser SA, Hu H, Ruza RR, Sauguet L, Lindahl E, Delarue M.

Cell Rep. 2018 Apr 24;23(4):993-1004. doi: 10.1016/j.celrep.2018.03.108.


Terminal deoxynucleotidyltransferase: the story of an untemplated DNA polymerase capable of DNA bridging and templated synthesis across strands.

Loc'h J, Delarue M.

Curr Opin Struct Biol. 2018 Dec;53:22-31. doi: 10.1016/ Epub 2018 Apr 12. Review.


Crystal structures of a pentameric ion channel gated by alkaline pH show a widely open pore and identify a cavity for modulation.

Hu H, Nemecz Á, Van Renterghem C, Fourati Z, Sauguet L, Corringer PJ, Delarue M.

Proc Natl Acad Sci U S A. 2018 Apr 24;115(17):E3959-E3968. doi: 10.1073/pnas.1717700115. Epub 2018 Apr 9.


Meet-U: Educating through research immersion.

Abdollahi N, Albani A, Anthony E, Baud A, Cardon M, Clerc R, Czernecki D, Conte R, David L, Delaune A, Djerroud S, Fourgoux P, Guiglielmoni N, Laurentie J, Lehmann N, Lochard C, Montagne R, Myrodia V, Opuu V, Parey E, Polit L, Privé S, Quignot C, Ruiz-Cuevas M, Sissoko M, Sompairac N, Vallerix A, Verrecchia V, Delarue M, Guérois R, Ponty Y, Sacquin-Mora S, Carbone A, Froidevaux C, Le Crom S, Lespinet O, Weigt M, Abboud S, Bernardes J, Bouvier G, Dequeker C, Ferré A, Fuchs P, Lelandais G, Poulain P, Richard H, Schweke H, Laine E, Lopes A.

PLoS Comput Biol. 2018 Mar 15;14(3):e1005992. doi: 10.1371/journal.pcbi.1005992. eCollection 2018 Mar.


Full mutational mapping of titratable residues helps to identify proton-sensors involved in the control of channel gating in the Gloeobacter violaceus pentameric ligand-gated ion channel.

Nemecz Á, Hu H, Fourati Z, Van Renterghem C, Delarue M, Corringer PJ.

PLoS Biol. 2017 Dec 27;15(12):e2004470. doi: 10.1371/journal.pbio.2004470. eCollection 2017 Dec.


SCWISh network is essential for survival under mechanical pressure.

Delarue M, Poterewicz G, Hoxha O, Choi J, Yoo W, Kayser J, Holt L, Hallatschek O.

Proc Natl Acad Sci U S A. 2017 Dec 19;114(51):13465-13470. doi: 10.1073/pnas.1711204114. Epub 2017 Nov 29.


Ab initio sampling of transition paths by conditioned Langevin dynamics.

Delarue M, Koehl P, Orland H.

J Chem Phys. 2017 Oct 21;147(15):152703. doi: 10.1063/1.4985651.


A simple molecular mechanism explains multiple patterns of cell-size regulation.

Delarue M, Weissman D, Hallatschek O.

PLoS One. 2017 Aug 16;12(8):e0182633. doi: 10.1371/journal.pone.0182633. eCollection 2017.


Microfluidic-Based Generation of 3D Collagen Spheres to Investigate Multicellular Spheroid Invasion.

Bertillot F, Attieh Y, Delarue M, Gurchenkov BG, Descroix S, Vignjevic DM, Ferraro D.

Methods Mol Biol. 2017;1612:269-279. doi: 10.1007/978-1-4939-7021-6_20.


String method solution of the gating pathways for a pentameric ligand-gated ion channel.

Lev B, Murail S, Poitevin F, Cromer BA, Baaden M, Delarue M, Allen TW.

Proc Natl Acad Sci U S A. 2017 May 23;114(21):E4158-E4167. doi: 10.1073/pnas.1617567114. Epub 2017 May 9.


Neuron-to-Neuron Transfer of FUS in Drosophila Primary Neuronal Culture Is Enhanced by ALS-Associated Mutations.

Feuillette S, Delarue M, Riou G, Gaffuri AL, Wu J, Lenkei Z, Boyer O, Frébourg T, Campion D, Lecourtois M.

J Mol Neurosci. 2017 May;62(1):114-122. doi: 10.1007/s12031-017-0908-y. Epub 2017 Apr 20.


Identification of a pre-active conformation of a pentameric channel receptor.

Menny A, Lefebvre SN, Schmidpeter PA, Drège E, Fourati Z, Delarue M, Edelstein SJ, Nimigean CM, Joseph D, Corringer PJ.

Elife. 2017 Mar 15;6. pii: e23955. doi: 10.7554/eLife.23955.


The Renormalization Group and Its Applications to Generating Coarse-Grained Models of Large Biological Molecular Systems.

Koehl P, Poitevin F, Navaza R, Delarue M.

J Chem Theory Comput. 2017 Mar 14;13(3):1424-1438. doi: 10.1021/acs.jctc.6b01136. Epub 2017 Feb 24.


Cell-like pressure sensors reveal increase of mechanical stress towards the core of multicellular spheroids under compression.

Dolega ME, Delarue M, Ingremeau F, Prost J, Delon A, Cappello G.

Nat Commun. 2017 Jan 27;8:14056. doi: 10.1038/ncomms14056.


Comparative Normal Mode Analysis of the Dynamics of DENV and ZIKV Capsids.

Hsieh YC, Poitevin F, Delarue M, Koehl P.

Front Mol Biosci. 2016 Dec 27;3:85. doi: 10.3389/fmolb.2016.00085. eCollection 2016.


Barbiturates Bind in the GLIC Ion Channel Pore and Cause Inhibition by Stabilizing a Closed State.

Fourati Z, Ruza RR, Laverty D, Drège E, Delarue-Cochin S, Joseph D, Koehl P, Smart T, Delarue M.

J Biol Chem. 2017 Feb 3;292(5):1550-1558. doi: 10.1074/jbc.M116.766964. Epub 2016 Dec 16.


Plant programmed cell death from a chromatin point of view.

Latrasse D, Benhamed M, Bergounioux C, Raynaud C, Delarue M.

J Exp Bot. 2016 Oct;67(20):5887-5900. Epub 2016 Sep 17. Review.


Self-Driven Jamming in Growing Microbial Populations.

Delarue M, Hartung J, Schreck C, Gniewek P, Hu L, Herminghaus S, Hallatschek O.

Nat Phys. 2016 Aug;12(8):762-766. Epub 2016 May 9.


Shared active site architecture between archaeal PolD and multi-subunit RNA polymerases revealed by X-ray crystallography.

Sauguet L, Raia P, Henneke G, Delarue M.

Nat Commun. 2016 Aug 22;7:12227. doi: 10.1038/ncomms12227. [Epub ahead of print]


Structural Basis for a New Templated Activity by Terminal Deoxynucleotidyl Transferase: Implications for V(D)J Recombination.

Loc'h J, Rosario S, Delarue M.

Structure. 2016 Sep 6;24(9):1452-63. doi: 10.1016/j.str.2016.06.014. Epub 2016 Aug 4.


Beyond Poisson-Boltzmann: Numerical Sampling of Charge Density Fluctuations.

Poitevin F, Delarue M, Orland H.

J Phys Chem B. 2016 Jul 7;120(26):6270-7. doi: 10.1021/acs.jpcb.6b02650. Epub 2016 Apr 26.


Sites of Anesthetic Inhibitory Action on a Cationic Ligand-Gated Ion Channel.

Laurent B, Murail S, Shahsavar A, Sauguet L, Delarue M, Baaden M.

Structure. 2016 Apr 5;24(4):595-605. doi: 10.1016/j.str.2016.02.014. Epub 2016 Mar 24.


Structural Basis for Xenon Inhibition in a Cationic Pentameric Ligand-Gated Ion Channel.

Sauguet L, Fourati Z, Prangé T, Delarue M, Colloc'h N.

PLoS One. 2016 Feb 24;11(2):e0149795. doi: 10.1371/journal.pone.0149795. eCollection 2016.


Chloroplast Activity and 3'phosphadenosine 5'phosphate Signaling Regulate Programmed Cell Death in Arabidopsis.

Bruggeman Q, Mazubert C, Prunier F, Lugan R, Chan KX, Phua SY, Pogson BJ, Krieger-Liszkay A, Delarue M, Benhamed M, Bergounioux C, Raynaud C.

Plant Physiol. 2016 Mar;170(3):1745-56. doi: 10.1104/pp.15.01872. Epub 2016 Jan 8.


Effect of an osmotic stress on multicellular aggregates.

Monnier S, Delarue M, Brunel B, Dolega ME, Delon A, Cappello G.

Methods. 2016 Feb 1;94:114-9. doi: 10.1016/j.ymeth.2015.07.009. Epub 2015 Jul 22.


Involvement of Arabidopsis Hexokinase1 in Cell Death Mediated by Myo-Inositol Accumulation.

Bruggeman Q, Prunier F, Mazubert C, de Bont L, Garmier M, Lugan R, Benhamed M, Bergounioux C, Raynaud C, Delarue M.

Plant Cell. 2015 Jun;27(6):1801-14. doi: 10.1105/tpc.15.00068. Epub 2015 Jun 5.


Structural basis for a novel mechanism of DNA bridging and alignment in eukaryotic DSB DNA repair.

Gouge J, Rosario S, Romain F, Poitevin F, Béguin P, Delarue M.

EMBO J. 2015 Apr 15;34(8):1126-42. doi: 10.15252/embj.201489643. Epub 2015 Mar 11.


Genuine open form of the pentameric ligand-gated ion channel GLIC.

Fourati Z, Sauguet L, Delarue M.

Acta Crystallogr D Biol Crystallogr. 2015 Mar;71(Pt 3):454-60. doi: 10.1107/S1399004714026698. Epub 2015 Feb 26.


Allosteric and hyperekplexic mutant phenotypes investigated on an α1 glycine receptor transmembrane structure.

Moraga-Cid G, Sauguet L, Huon C, Malherbe L, Girard-Blanc C, Petres S, Murail S, Taly A, Baaden M, Delarue M, Corringer PJ.

Proc Natl Acad Sci U S A. 2015 Mar 3;112(9):2865-70. doi: 10.1073/pnas.1417864112. Epub 2015 Feb 17.


To die or not to die? Lessons from lesion mimic mutants.

Bruggeman Q, Raynaud C, Benhamed M, Delarue M.

Front Plant Sci. 2015 Jan 30;6:24. doi: 10.3389/fpls.2015.00024. eCollection 2015. Review.


Stress distributions and cell flows in a growing cell aggregate.

Delarue M, Joanny JF, Jülicher F, Prost J.

Interface Focus. 2014 Dec 6;4(6):20140033. doi: 10.1098/rsfs.2014.0033.


Compressive stress inhibits proliferation in tumor spheroids through a volume limitation.

Delarue M, Montel F, Vignjevic D, Prost J, Joanny JF, Cappello G.

Biophys J. 2014 Oct 21;107(8):1821-1828. doi: 10.1016/j.bpj.2014.08.031.


Crystallographic studies of pharmacological sites in pentameric ligand-gated ion channels.

Sauguet L, Shahsavar A, Delarue M.

Biochim Biophys Acta. 2015 Mar;1850(3):511-23. doi: 10.1016/j.bbagen.2014.05.007. Epub 2014 May 14. Review.


The Polyadenylation Factor Subunit CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR30: A Key Factor of Programmed Cell Death and a Regulator of Immunity in Arabidopsis.

Bruggeman Q, Garmier M, de Bont L, Soubigou-Taconnat L, Mazubert C, Benhamed M, Raynaud C, Bergounioux C, Delarue M.

Plant Physiol. 2014 Jun;165(2):732-746. Epub 2014 Apr 4.


The BAF60 subunit of the SWI/SNF chromatin-remodeling complex directly controls the formation of a gene loop at FLOWERING LOCUS C in Arabidopsis.

Jégu T, Latrasse D, Delarue M, Hirt H, Domenichini S, Ariel F, Crespi M, Bergounioux C, Raynaud C, Benhamed M.

Plant Cell. 2014 Feb;26(2):538-51. doi: 10.1105/tpc.113.114454. Epub 2014 Feb 7.


Chromatin meets the cell cycle.

Raynaud C, Mallory AC, Latrasse D, Jégu T, Bruggeman Q, Delarue M, Bergounioux C, Benhamed M.

J Exp Bot. 2014 Jun;65(10):2677-89. doi: 10.1093/jxb/ert433. Epub 2014 Feb 4. Review.


Enhanced amino acid selection in fully evolved tryptophanyl-tRNA synthetase, relative to its urzyme, requires domain motion sensed by the D1 switch, a remote dynamic packing motif.

Weinreb V, Li L, Chandrasekaran SN, Koehl P, Delarue M, Carter CW Jr.

J Biol Chem. 2014 Feb 14;289(7):4367-76. doi: 10.1074/jbc.M113.538660. Epub 2014 Jan 6.


Crystal structures of a pentameric ligand-gated ion channel provide a mechanism for activation.

Sauguet L, Shahsavar A, Poitevin F, Huon C, Menny A, Nemecz À, Haouz A, Changeux JP, Corringer PJ, Delarue M.

Proc Natl Acad Sci U S A. 2014 Jan 21;111(3):966-71. doi: 10.1073/pnas.1314997111. Epub 2013 Dec 23.


New nucleotide-competitive non-nucleoside inhibitors of terminal deoxynucleotidyl transferase: discovery, characterization, and crystal structure in complex with the target.

Costi R, Crucitti GC, Pescatori L, Messore A, Scipione L, Tortorella S, Amoroso A, Crespan E, Campiglia P, Maresca B, Porta A, Granata I, Novellino E, Gouge J, Delarue M, Maga G, Di Santo R.

J Med Chem. 2013 Sep 26;56(18):7431-41. doi: 10.1021/jm4010187. Epub 2013 Sep 12.


Structures of intermediates along the catalytic cycle of terminal deoxynucleotidyltransferase: dynamical aspects of the two-metal ion mechanism.

Gouge J, Rosario S, Romain F, Beguin P, Delarue M.

J Mol Biol. 2013 Nov 15;425(22):4334-52. doi: 10.1016/j.jmb.2013.07.009. Epub 2013 Jul 13.


Structural basis for potentiation by alcohols and anaesthetics in a ligand-gated ion channel.

Sauguet L, Howard RJ, Malherbe L, Lee US, Corringer PJ, Harris RA, Delarue M.

Nat Commun. 2013;4:1697. doi: 10.1038/ncomms2682.


Mechanical control of cell flow in multicellular spheroids.

Delarue M, Montel F, Caen O, Elgeti J, Siaugue JM, Vignjevic D, Prost J, Joanny JF, Cappello G.

Phys Rev Lett. 2013 Mar 29;110(13):138103. Epub 2013 Mar 26.


Computational assembly of polymorphic amyloid fibrils reveals stable aggregates.

Smaoui MR, Poitevin F, Delarue M, Koehl P, Orland H, Waldispühl J.

Biophys J. 2013 Feb 5;104(3):683-93. doi: 10.1016/j.bpj.2012.12.037.

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