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2015-2019

PUBLICATIONS 2017

A Simple PB/LIE Free Energy Function Accurately Predicts the Peptide Binding Specificity of the Tiam1 PDZ Domain. Panel N, Sun YJ, Fuentes EJ, Simonson T. Front Mol Biosci. 2017. doi : 10.3389/fmolb.2017.00065

A unique surface on Pat1 C-terminal domain directly interacts with Dcp2 decapping enzyme and Xrn1 5’-3’ mRNA exonuclease in yeast. Charenton C, Gaudon-Plesse C, Fourati Z, Taverniti V, Back R, Kolesnikova O, Séraphin B, Graille M. Proc Natl Acad Sci U S A. 2017 . doi : 10.1073/pnas.1418718112. Epub 2017 Oct 24. doi: 10.1073/pnas.1711680114

Full Protein Sequence Redesign with an MMGBSA Energy Function. Gaillard T, Simonson T. J Chem Theory Comput. 2017. doi : 10.1021/acs.jctc.7b00202

Comparing pairwise-additive and many-body generalized Born models for acid/base calculations and protein design. Villa F, Mignon D, Polydorides S, Simonson T. J Comput Chem. 2017 . doi: 10.1002/jcc.24898

Computational Design of the Tiam1 PDZ Domain and Its Ligand Binding. Mignon D, Panel N, Chen X, Fuentes EJ, Simonson T. J Chem Theory Comput, 2017 . doi: 10.1021/acs.jctc.6b01255

Trm112, a protein activator of methyltransferases modifying actors of eukaryotic translational apparatus. Bourgeois G, Létoquart J, Tran N.V, Graille M. Biomolecules. 2017; 7(1). doi: 10.3390/biom7010007

Activation mode of the eukaryotic m2G10 tRNA methyltransferase Trm11 by its partner protein Trm112. Bourgeois G, Marcoux J, Saliou JM,Cianférani S, Graille M. Nucleic Acids Res. 2017; 45(4); 1971-1982. doi: 10.1093/nar/gkw1271

The structure of an E. coli tRNAfMet A1-U72 variant shows an unusual conformation of the A1-U72 base pair. Monestier A, Aleksandrov A, Coureux PD, Panvert M, Mechulam Y, Schmitt E. RNA. 2017 in press. doi: 10.1261/rna.057877.116

 

PUBLICATIONS 2016

Cryo-EM study of start codon selection during archaeal translation initiation. Coureux PD, Lazennec-Schurdevin C, Monestier A, Larquet E, Cladière L, Klaholz BP, Schmitt E, Mechulam Y. Nat Commun. 2016. doi: 10.1038/ncomms13366.

WASP and WAVE Team Up at the Leading Edge. Molinie N, Gautreau A. Dev Cell. 2016 Oct 24;39(2):135-136. doi: 10.1016/j.devcel.2016.10.008.

A hybrid Monte Carlo scheme for multibackbone protein design. Druart K, Bigot J, Audit E, Simonson T. J Chem Theory Comput. 2016 Oct 24. [Epub ahead of print]

Direct interaction between exocyst and Wave complexes promotes cell protrusions and motility. Biondini M, Sadou-Dubourgnoux A, Paul-Gilloteaux P, Zago G, Arslanhan MD, Waharte F, Formstecher E, Hertzog M, Yu J, Guerois R, Gautreau A, Scita G, Camonis J, Parrini MC. J Cell Sci. 2016 Oct 15;129(20):3756-3769.

Structure of the active form of Dcp1-Dcp2 decapping enzyme bound to m7GDP and its Edc3 activator. Charenton C, Taverniti V, Gaudon-Plesse C, Back R, Séraphin B, Graille M. Nat. Struct. Mol. Biol. 2016 Oct 3;23(11); 982-986. doi: 10.1038/nsmb.3300.

Studies of the B-Z transition of DNA: The temperature dependence of the free-energy difference, the composition of the counterion sheath in mixed salt, and the preparation of a sample of the 5'-d[T-(m(5) C-G)12 -T] duplex in pure B-DNA or Z-DNA form. Guéron M, Plateau P, Filoche M. Biopolymers. 2016 Jul;105(7):369-84. doi: 10.1002/bip.22824.

Comparing three stochastic search algorithms for computational protein design: Monte Carlo, replica exchange Monte Carlo, and a multistart, steepest-descent heuristic. Mignon D, Simonson T. J Comput Chem. 2016 Jul 15;37(19):1781-93. doi: 10.1002/jcc.24393.

Proteus and the Design of Ligand Binding Sites. Polydorides S, Michael E, Mignon D, Druart K, Archontis G, Simonson T. Methods Mol Biol. 2016;1414:77-97. doi: 10.1007/978-1-4939-3569-7_6.

Protein side chain conformation predictions with an MMGBSA energy function. Gaillard T, Panel N, Simonson T. Proteins. 2016 Jun;84(6):803-19. doi: 10.1002/prot.25030.

Actin nucleation at the centrosome controls lymphocyte polarity. Obino D, Farina F, Malbec O, Sáez PJ, Maurin M, Gaillard J, Dingli F, Loew D, Gautreau A, Yuseff MI, Blanchoin L, Théry M, Lennon-Duménil AM. Nat Commun. 2016 Mar 18;7:10969. doi: 10.1038/ncomms10969.

Arpin downregulation in breast cancer is associated with poor prognosis. Lomakina ME, Lallemand F, Vacher S, Molinie N, Dang I, Cacheux W, Chipysheva TA, Ermilova VD, de Koning L, Dubois T, Bièche I, Alexandrova AY, Gautreau A. Br J Cancer. 2016 Mar 1;114(5):545-53. doi: 10.1038/bjc.2016.18.

Redesigning the stereospecificity of tyrosyl-tRNA synthetase. Simonson T, Ye-Lehmann S, Palmai Z, Amara N, Wydau-Dematteis S, Bigan E, Druart K, Moch C,Plateau P. Proteins. 2016 Feb;84(2):240-53. doi: 10.1002/prot.24972.

Protein:Ligand binding free energies: A stringent test for computational protein design. Druart K, Palmai Z, Omarjee E, Simonson T. J Comput Chem. 2016 Feb 5;37(4):404-15. doi: 10.1002/jcc.24230.

Hybrid Structural Analysis of the Arp2/3 Regulator Arpin Identifies Its Acidic Tail as a Primary Binding Epitope. Fetics S, Thureau A, Campanacci V, Aumont-Nicaise M, Dang I, Gautreau A, Pérez J, Cherfils J. Structure. 2016 Feb 2;24(2):252-60. doi: 10.1016/j.str.2015.12.001.

Persistent cell migration and adhesion rely on retrograde transport of β(1) integrin. Shafaq-Zadah M, Gomes-Santos CS, Bardin S, Maiuri P, Maurin M, Iranzo J, Gautreau A, Lamaze C, Caswell P, Goud B, Johannes L. Nat Cell Biol. 2016 Jan;18(1):54-64. doi: 10.1038/ncb3287.

AMOTL1 Promotes Breast Cancer Progression and Is Antagonized by Merlin. Couderc C, Boin A, Fuhrmann L, Vincent-Salomon A, Mandati V, Kieffer Y, Mechta-Grigoriou F, Del Maestro L, Chavrier P, Vallerand D, Brito I, Dubois T, De Koning L, Bouvard D, Louvard D, Gautreau A, Lallemand D. Neoplasia. 2016 Jan;18(1):10-24. doi: 10.1016/j.neo.2015.11.010.

 

Publications 2015

Insights into molecular plasticity in protein complexes from Trm9-Trm112 tRNA modifying enzyme crystal structure. Létoquart J, Tran N.V, Caroline V, Alexandrov A, Lazar N, van Tilbeurgh H, Liger D, Graille M. Nucleic Acids Res. 2015; 43(22), 10989-11002.

Cdc123, a Cell Cycle Regulator Needed for eIF2 Assembly, Is an ATP-Grasp Protein with Unique Features. Panvert M, Dubiez E, Arnold L, Perez J, Mechulam Y, Seufert W, Schmitt E. Structure. 2015 Jul 21. pii : S0969-2126(15)00267-1. doi : 10.1016/j.str.2015.06.014.

Structure of a left-handed DNA G-quadruplex. Chung WJ, Heddi B, Schmitt E, Lim KW, Mechulam Y, Phan AT. Proc Natl Acad Sci U S A. 2015 Mar 3 ;112(9):2729-33. doi : 10.1073/pnas.1418718112. Epub 2015 Feb 18.

Identification of a second GTP-bound magnesium ion in archaeal initiation factor 2. Dubiez E, Aleksandrov A, Lazennec-Schurdevin C, Mechulam Y, Schmitt E. Nucleic Acids Res. 2015 Mar 11 ;43(5):2946-57. doi : 10.1093/nar/gkv053. Epub 2015 Feb 17.

Trans-sulfuration Pathway Seleno-amino Acids Are Mediators of Selenomethionine Toxicity in Saccharomyces cerevisiae. Lazard M, Dauplais M, Blanquet S, Plateau P. J Biol Chem. 2015 Apr 24 ;290(17):10741-50. doi : 10.1074/jbc.M115.640375. Epub 2015 Mar 5.

Crystal structure of the effector AvrLm4-7 of Leptosphaeria maculans reveals insights into its translocation into plant cells and recognition by resistance proteins. Blondeau K, Blaise F, Graille M, Kale SD, Linglin J, Ollivier B, Labarde A, Lazar N, Daverdin G, Balesdent MH, Choi DH, Tyler BM, Rouxel T, van Tilbeurgh H, Fudal I. Plant J. 2015 Aug ;83(4):610-24. doi : 10.1111/tpj.12913. Epub 2015 Jul 14.

Crystal structures of the Gon7/Pcc1 and Bud32/Cgi121 complexes provide a model for the complete yeast KEOPS complex. Zhang W, Collinet B, Graille M, Daugeron MC, Lazar N, Libri D, Durand D, van Tilbeurgh H. Nucleic Acids Res. 2015 Mar 31 ;43(6):3358-72. doi : 10.1093/nar/gkv155. Epub 2015 Mar 3.

Structure and thermodynamics of Mg:phosphate interactions in water : a simulation study. Kumar M, Simonson T, Ohanessian G, Clavaguéra C. Chemphyschem. 2015 Feb 23 ;16(3):658-65. doi : 10.1002/cphc.201402685. Epub 2014 Dec 21.

Electrostatic free energies in translational GTPases : Classic allostery and the rest. Simonson T, Aleksandrov A, Satpati P. Biochim Biophys Acta. 2015 May ;1850(5):1006-16. doi : 10.1016/j.bbagen.2014.07.006. Epub 2014 Jul 15.

Far infrared spectra of solid state l-serine, l-threonine, l-cysteine, and l-methionine in different protonation states. Gaillard T, Trivella A, Stote RH, Hellwig P. Spectrochim Acta A Mol Biomol Spectrosc. 2015 Nov 5 ;150:301-7. doi : 10.1016/j.saa.2015.05.031. Epub 2015 May 16.

The Arp2/3 inhibitory protein arpin induces cell turning by pausing cell migration. Gorelik R, Gautreau A. Cytoskeleton (Hoboken). 2015 Aug 3. doi : 10.1002/cm.21233. 

Specific GFP-binding artificial proteins (αRep) : a new tool for in vitro to live cell applications. Chevrel A, Urvoas A, de la Sierra-Gallay IL, Aumont-Nicaise M, Moutel S, Desmadril M, Perez F, Gautreau A, van Tilbeurgh H, Minard P, Valerio-Lepiniec M. Biosci Rep. 2015 Jun 12 ;35(4). pii : e00223. doi : 10.1042/BSR20150080.

Membrane protrusion powers clathrin-independent endocytosis of interleukin-2 receptor. Basquin C, Trichet M, Vihinen H, Malardé V, Lagache T, Ripoll L, Jokitalo E, Olivo-Marin JC, Gautreau A, Sauvonnet N. EMBO J. 2015 Aug 13 ;34(16):2147-61. doi : 10.15252/embj.201490788. Epub 2015 Jun 29.

Single-molecule imaging in live cell using gold nanoparticles. Leduc C, Si S, Gautier JJ, Gao Z, Shibu ES, Gautreau A, Giannone G, Cognet L, Lounis B. Methods Cell Biol. 2015 ;125:13-27. doi : 10.1016/bs.mcb.2014.10.002. Epub 2015 Jan 7.

Quantitative analysis of endosome tubulation and microdomain organization mediated by the WASH complex. Derivery E, Gautreau A. Methods Cell Biol. 2015;130:215-34. doi: 10.1016/bs.mcb.2015.03.025.