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2010-2014

 

Publications 2010

Naveau M, Lazennec-Schurdevin C, Panvert M, Mechulam Y, Schmitt E. tRNA binding properties of eukaryotic translation initiation factor 2 from Encephalitozoon cuniculi. Biochemistry. 2010 , 49, 8680-8688.

Schmitt E, Naveau M, Mechulam Y. Eukaryotic and archaeal translation initiation factor 2 : a heterotrimeric tRNA carrier. FEBS Lett. 2010, 548, 405-412.

Lazard M, Blanquet S, Fisicaro P, Labarraque G, Plateau P. Uptake of selenite by Saccharomyces cerevisiae involves the high and low affinity orthophosphate transporters. J Biol Chem. 2010, 285, 32029-32037.

Bougot-Robin K, Reverchon JL, Fromant M, Mugherli L, Plateau P, Benisty H. 2D label-free imaging of resonant grating biochips in ultraviolet. Opt Express. 2010, 18, 11472-11482.

Bhalt TK, Yogarel M, Wydau S, Berwal R, Sharma A. Ligand-bound structures provide atomic snapshots for the catalytic mechanism of D-amino acid deacylase. J.Biol.Chem. 2010, 285,5917-5930.

Trivella A, Gaillard T, Stote RH, Hellwig P. Far infrared spectra of solid state aliphatic amino acids in different protonation states. J. Chem. Phy, 2010, 132,115105.

A. Aleksandrov, S. Polydorides, G. Archontis & T. Simonson (2010) Journal of Physical Chemistry B, 114, 10634-10648. Predicting the acid/base behavior of proteins : a constant-pH Monte Carlo approach with generalized Born solvent.

M. Schmidt am Busch, A. Sedano & T. Simonson (2010) Plos One, 5(5), e10410. Computational protein design : validation and possible relevance as a tool for homology searching and fold recognition.

A. Aleksandrov & T. Simonson (2010) Journal of Biological Chemistry, 285, 13807-13815. Molecular dynamics simulations show that conformational selection governs the binding preferences of imatinib for several tyrosine kinases.

D. Dalm, G. Palm, A. Aleksandrov, T. Simonson & W. Hinrichs (2010) Journal of Molecular Biology, 398, 83-96. Non-antibiotic properties of tetracyclines : structural basis for inhibition of secretory Phospholipase A2.

A. Aleksandrov, D. Thompson & T. Simonson (2010) Journal of Molecular Recognition, 23, 117-127. Alchemical free energy simulations for biological complexes : powerful but temperamental...

A. Aleksandrov & T. Simonson (2010) Journal of Computational Chemistry, 31, 1550-1560. A molecular mechanics model for imatinib and imatinib:kinase binding.

A. Lopes, M. Schmidt am Busch & T. Simonson (2010) Journal of Computational Chemistry, 31, 1273-1286. Computational design of protein:ligand binding : modifying the specificity of asparaginyl-tRNA synthetase.

Suarez M., Tortosa P., Garcia-Mira M.M., Rodriguez-Larrea D., Godoy-Ruiz R., Ibarra-Molero B., Sanchez-Ruiz J.M., Jaramillo A. Using multi-objective computational design to extend protein promiscuity. Biophysical Chemistry, 2010, 147, 13-19.

 

Publications 2011

Galimand M, Schmitt E, Panvert M, Desmolaize B, Douthwaite S, Mechulam Y, Courvalin P. Intrinsic resistance to aminoglycosides in Enterococcus faecium is conferred by the 16S rRNA m5C1404-specific methyltransferase EfmM. RNA. 2011 Feb ;17(2):251-62

G. Launay, T. Simonson. A large decoy set of protein-protein complexes produced by flexible docking. Journal of Computational Chemistry, 2011 Jan 15, 32, 106-120

N. V. Valeyev & A. Aleksandrov (2011). An atomistic model for simulations of nilotinib and nilotinib/kinase binding. Theoretical Chemistry Accounts, Jan 31, 129, 747-756.

P. Satpati, C. Clavaguera, G. Ohanessian & T. Simonson. Free energy simulations of a GTPase : GTP and GDP binding to archaeal Initiation Factor 2. Journal of Physical Chemistry B, 2011 Mai 2, 115, 6749-63.

Y. Mechulam, S. Blanquet and E. Schmitt. 9 June 2011, posting date. Chapter 4.2.2, Translation Initiation. In A. Böck, R. Curtiss III, J. B. Kaper, P. D. Karp, F. C. Neidhardt, J. M. Slauch, and C. L. Squires (ed.), EcoSal—Escherichia coli and Salmonella : cellular and molecular biology. http://www.ecosal.org. ASM Press, Washington, DC. doi : 10.1128/ecosal.4.2.2. revue invitée.

A. Aleksandrov & M. Field (2011) Efficient solvent boundary potential for hybrid potential simulations. Physical Chemistry Chemical Physics, Juin 14, 13, 10503-9.

Lazard M, Ha-Duong NT, Mounié S, Perrin R, Plateau P, Blanquet S. Selenodiglutathione uptake by the Saccharomyces cerevisiae vacuolar ATP-binding cassette transporter Ycf1p. FEBS J. 2011 Aug 31. doi : 10.1111/j.1742-4658.2011 08318.x.

T. Gaillard & D. A. Case (2011) Evaluation of DNA Force Fields in Implicit Solvation. Journal of Chemical Theory and Computation, 7, 3181-3198.

S. Polydorides, N. Amara, T. Simonson & G. Archontis (2011) Computational protein design with a generalized Born solvent model : application to Asparaginyl-tRNA synthetase. Proteins, 79, 3448-3468.

Giorgi L, Bontems F, Fromant M, Aubard C, Blanquet S, Plateau P. The RNA binding site of Escherichia coli peptidyl-tRNA hydrolase. J Biol Chem. 2011 286(45):39585-94.

Bouthier de la Tour C., Boisnard S., Norais C., Toueille M., Bentchikou E., Vannier F., Cox M.M., Sommer S., Servant P. The deinococcal DdrB protein is involved in an early step of DNA double strand break repair and in plasmid transformation through its single-strand annealing activity. DNA Repair, 2011, 10(12), 1223-1231.

Satpati P. Stable complex C2H4Al4Li3- and its similarity with bicyclo[2.2.0]hex-2-ene : A DFT study International Journal of Quantum Chemistry, 2011, 111, 4241-4246.

Satpati P. Possibility of proton passage through all metal aromatic Al 42- ring in HAl4- International Journal of Quantum Chemistry, 2011, 111, 3816-3820.

Kotov, Nikolay V. ; Bates, Declan G. ; Gizatullina, Antonina N. ; Gilaziev, Bulat ; Khairullin, Rustem N. ; Chen, Michael Z. Q. ; Drozdov, Ignat ; Umezawa, Yoshinori ; Hundhausen, Christian ; Aleksandrov, Alexey ; Yan, Xing-gang ; Spurgeon, Sarah K. ; Smales, C. Mark ; Valeyev, Najl V. Computational modelling elucidates the mechanism of ciliary regulation in health and disease. BMC SYSTEMS BIOLOGY, 2011, 5.

L. Giorgi, P. Plateau, G. O’Mahony, C. Aubard, M. Fromant, A. Thureau, M. Grøtli, S. Blanquet, F. Bontems. NMR-based substrate analog docking to Escherichia coli peptidyl-tRNA hydrolase. Journal of Molecular Biology, 2011, 619-633.

 

Publications 2012

E. Schmitt, M. Panvert, C. Lazennec-Schurdevin, P-D Coureux, J. Perez, A. Thompson and Y. Mechulam. Structure of the ternary initiation complex aIF2–GDPNP–methionylated initiator tRNA. Nat. Struct. Mol. Biol., 9, 450-454, 2012.

Aleksandrov A., M. Field. A hybrid elastic band string algorithm for studies of enzymatic reactions. Physical Chemistry Chemical Physics, 14, 12544-53, 2012

J-P. Colletier, A. Aleksandrov, N. Coquelle, S. Mraihi, E. Mendoza-Barber, M. Field, D. Madern. Sampling the conformational energy landscape of a hyperthermophilic protein by engineering key substitutions. Molecular Biology and Evolution, 29, 1683-94, 2012

M. Schmidt am Busch, A. Lopes, D. Mignon, T. Gaillard, T. Simonson 
The inverse protein folding problem : protein design and structure prediction in the genomic era. in J. Zeng, R. Zhang, H. Treutlein (Ed.) Quantum Simulations of Materials and Biological Systems. Springer Verlag, New York, 2012.

Peyroche G, Saveanu C, Dauplais M, Lazard M, Beuneu F, Decourty L, Malabat C, Jacquier A, Blanquet S, Plateau P. Sodium selenide toxicity is mediated by O2-dependent DNA breaks. PLoS One. 2012 ;7(5):e36343.

P. Satpati & T. Simonson. Conformational selection through electrostatics : free energy simulations of GTP and GDP binding to archaeal Initiation Factor 2.Proteins, 80, 1264–82. 2012

P. Satpati & T. Simonson. Conformational selection by the aIF2 GTPase : a molecular dynamics study of functional pathways. Biochemistry, 51, 353–61. 2012

T. Simonson. Protein:ligand recognition : simple models for electrostatic effects.Current Pharmaceutical Design 2012

T. Simonson & P. Satpati. Nucleotide recognition by the initiation factor aIF5B : free energy simulations of a neo-classical GTPase. Proteins, 2012

Graille M. and Séraphin B. Surveilance pathways rescuing eukaryotic ribosomes lost in translation. Nat. Rev. Mol. Cell. Biol., 2012.

George, Nicholas P. ; Ngo, Khanh V. ; Chitteni-Pattu, Sindhu ; Norais, Cedric A. ; Battista, John R. ; Cox, Michael M. ; Keck, James L. Structure and Cellular Dynamics of Deinococcus radiodurans Single-stranded DNA (ssDNA)-binding Protein (SSB)-DNA Complexes. J. Biol. Chem, 2012, 287(26), 22123-22132.

 

Publications 2013

Naveau M, Lazennec-Schurdevin C, Panvert M, Dubiez E, Mechulam Y, Schmitt E. Roles of yeast eIF2α and eIF2β subunits in the binding of the initiator methionyl-tRNA. Nucleic Acids Res. 2013, 41(2):1047-57.

Norais C, Moisan A, Gaspin C, Clouet-d’Orval B. Diversity of CRISPR systems in the euryarchaeal Pyrococcales. RNA Biol. 2013, 10(5):659-70.

T. Simonson. Protein:ligand recognition : simple models for electrostatic effects.Curr. Pharm. Des. 2013, 19:4241-4256.

Norais C, Servant P, Bouthier-de-la-Tour C, Coureux PD, Ithurbide S, Vannier F, Guerin PP, Dulberger CL, Satyshur KA, Keck JL, Armengaud J, Cox MM, Sommer S. The Deinococcus radiodurans DR1245 protein, a DdrB partner homologous to YbjN proteins and reminiscent of type III secretion system chaperones. PLoS One. 2013 ;8(2):e56558.

T. Simonson, P. Satpati. Simulating GTP:Mg and GDP:Mg with a simple force field : a structural and thermodynamic analysis. J. Comp. Chem., 34:836-46

Dauplais M, Lazard M, Blanquet S, Plateau P. Neutralization by metal ions of the toxicity of sodium selenide. PLoS One. 2013 ;8(1):e54353

Leulliot N, Quevillon-Cheruel C, Graille M, Geslin C, Flament D, Le Romancer M, van Tilbeurgh H. Crystal structure of PAV1-137, a protein from the virus PAV1 that infects Pyrococcus abyssi. Archaea 2013, 2013:568053.

Aleksandrov A. & Field M. Mechanism of activation of elongation factor Tu by ribosome : Catalytic histidine activates GTP by protonation. RNA, 2013, 19(9):1218-25.

T. Simonson, T. Gaillard, D. Mignon, M. Schmidt am Busch, A. Lopes, N. Amara, S. Polydorides, A. Sedano, K. Druart, G. Archontis. Computational Protein Design : The Proteus Software and Selected Applications J. Comp. Chem.2013, 34:2472-2484.

T. Gaillard, B.B.L. Schwarz, Y. Chebaro, R.H. Stote, A. Dejaegere. Protein Structural Statistics with PSS. J. Chem. Inf. Model. 2013, 53:2471-2482

Guellouz A, Valerio-Lepiniec M, Urvoas A, Chevrel A, Graille M, Fourati-Kammoun Z, Desmadril M, van Tilbeurgh H, Minard P. Selection of specific protein binders for pre-defined targets from an optimized library of artificial helicoidal repeat proteins (alphaRep). Plos One 2013, 8(8):e71512..

Kolesnikova O, Back R, Graille M , Séraphin B. Identification of the Rps28 binding motif from yeast Edc3 involved in the autoregulatory feedback loop controlling RPS28B mRNA decay. Nucleic Acids Res 2013, 41:9514-9523.

Jacquier H, Birgy A, Le Nagard H, Mechulam Y, Schmitt E, Glodt J, Bercot B, Petit E, Poulain J, Barnaud G, Gros PA, Tenaillon O. Capturing the mutational landscape of the beta-lactamase TEM-1. Proc Natl Acad Sci U S A. 2013, 110(32):13067-72.

 

PUBLICATIONS 2014

Simonson T, Aleksandrov A, Satpati P. Electrostatic free energies in translational GTPases : Classic allostery and the rest. Biochim Biophys Acta. 2014, doi:10.1016/j.bbagen.2014.07.006 ;

Zvereva EE, Grimme S, Katsyuba SA, Ermolaev VV, Arkhipova DA, Yan N, Miluykov VA, Sinyashin OG, Aleksandrov A. Solvation and Stabilization of Palladium Nanoparticles in Phosphonium-Based Ionic Liquids : a Combined Infrared Spectroscopic and Density Functional Theory Study. Phys Chem Chem Phys. 2014, doi:10.1039/C4CP02547D ;

Lin YL, Aleksandrov A, Simonson T, Roux B. An Overview of Electrostatic Free Energy Computations for Solutions and Proteins. J. Chem. Theory Comput. 2014, 10, 7, 2690–2709

Aleksandrov A, Zvereva E, Field M. The mechanism of citryl-coenzyme A formation catalyzed by citrate synthase. J Phys Chem B. 2014, 118, 17, 4505-13 ;

Jackson CJ, Coppin CW, Carr PD, Aleksandrov A, Wilding M, Sugrue E, Ubels J, Paks M, Newman J, Peat TS, Russell RJ, Field M, Weik M, Oakeshott JG, Scott C. 300-Fold Increase in Production of the Zn2+-Dependent Dechlorinase TrzN in Soluble Form via Apoenzyme Stabilization. Appl Environ Microbiol. 2014, 80, 13, 4003-11 ;

Moutiez M, Schmitt E, Seguin J, Thai R, Favry E, Belin P, Mechulam Y, Gondry M. Unravelling the mechanism of non-ribosomal peptide synthesis by cyclodipeptide synthases, Nat. Commun., 2014, 5, 5141.

Létoquart J ; Huvelle E ; Wacheul L ; Bourgeois G ; Zorbas C ; Graille M ; Heurgué-Hamard V ; Lafontaine D.L.J. Structural and functional studies of Bud23-Trm112 reveal 18S rRNA N7-G1575 methylation occurs on late 40S precursor ribosomes. Proc Natl Acad Sci U S A. 111(51), E5518-26.

Tiouajni M ; Durand D ; Blondeau K ; Graille M ; Urvoas A ; Valerio-Lepiniec M ; Guellouz A ; Aumont-Nicaise M ; Minard P ; van Tillbeurgh H. Structural and functional analysis of the fibronectin binding protein FNE from Streptococcus equi subsp. Equi. FEBJS Journal. 281(24), 5513-31.

Fourati Z ; Roy B ; Millan C ; Coureux PD ; Kervestin S ; van Tilbeurgh H ; He F ; Uson I ; Jacobson A ; Graille M. A highly conserved region essential for NMD in the Upf2 N-terminal domain. J Mol. Biol. 426(22), 3689-3702.

Fourati Z ; Kolesnikova O ; Back R ; Keller J ; Charenton C ; Taverniti V ; Gaudon Plesse C ; Lazar N ; Durand D ; van Tilbeurgh H ; Séraphin B ; Graille M. The C-terminal domain from S. cerevisiae Pat1 displays two conserved regions involved in decapping factor recruitment. Plos One, 9(5), e96828.

Fourati Z & Graille M. Cytoplasmic mRNA surveillance pathways. In « Fungal RNA biology » (Springer International Publishing). Editors : A. Sesma and T. von der Haar. ISBN 978-3-319-05687-6. (Book chapter)

Boudes M ; Sanchez D ; Graille M ; van Tilbeurgh H ; Durand D ; Quevillon-Cheruel S. Structural insights into the dimerization of the response regulator ComE from Streptococcus pneumoniae. Nucleic Acids Res, 42(8), 5302-5313.

T. Gaillard, T. Simonson Pairwise Decomposition of an MMGBSA Energy Function for Computational Protein Design. Journal of Computational Chemistry, 2014, 35, 1371-1387.

Kumar M, Simonson T, Ohanessian G, Clavaguéra C. Structure and Thermodynamics of Mg:Phosphate Interactions in Water : A Simulation Study. Chemphyschem. 2014 Dec 21. doi : 10.1002/cphc.201402685 Simonson T, Aleksandrov A, Satpati P. Electrostatic free energies in translational GTPases : Classic allostery and the rest. Biochim Biophys Acta. 2014 Jul 15. pii : S0304-4165(14)00244-X. doi : 10.1016/j.bbagen.2014.07.006

Gaillard T, Simonson T. Pairwise decomposition of an MMGBSA energy function for computational protein design. J Comput Chem. 2014 Jul 5 ;35(18):1371-87. doi : 10.1002/jcc.23637. Epub 2014 May 23.