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Publications 2005

G. Archontis, T. Simonson. Proton binding to proteins : a self-consistent dielectric continuum analysis. Biophys. J. (2005) 88, 3888-3904.

M. Fromant, E. Schmitt, Y. Mechulam, C. Lazennec, P. Plateau, S. Blanquet. Crystal structure at 1.8 Å resolution and identification of active residues ofSulfolobus solfataricus peptidyl-tRNA hydrolase. Biochemistry (2005) 44, 4294-4301. 

S. Blanquet, P. Plateau, S. Onesti. Class II aminoacyl-tRNA synthetases : lysyl-tRNA synthetase. In The aminoacyl-tRNA synthetases, C. Francklyn, M. Ibba & S. Cusack (eds). Landes Biosciences (2005), p. 227-240.

S. Blanquet, T. Crepin, Y. Mechulam, E. Schmitt. Class I aminoacyl-tRNA synthetases : methionyl-tRNA synthetase. In The aminoacyl-tRNA synthetases, C. Francklyn, M. Ibba & S. Cusack (eds). Landes Biosciences (2005).

A. Jaramillo, S. Wodak. Computational protein design is a challenge for implicit solvatation models. Biophys. J. (2005) 88, 156-171.

L. Yatime, E. Schmitt, S. Blanquet, Y. Mechulam. Structure-function relationships of the intact aIF2alpha subumit from the archaeon Pyrococcus abyssi. Biochemistry (2005) 44, 8749-8756. 

E. Schmitt, S. Blanquet, Y. Mechulam. Structural basis for tRNA-dependent amidotransferase function. Structure (2005) 13, 1421-1433. 

L. Guillon, E. Schmitt, S. Blanquet, Y. Mechulam. Initiator tRNA binding by e/aIF5B, the eukaryotic/archaeal homologue of bacterial initiation factor IF2.Biochemistry (2005) 44, 15594-15601. 

T. Simonson. Le problème du repliement : peut-on prédire la structure des protéines ? Med. Sci. (2005) 21, 609-612. 

G. Archontis, T. Simonson. A pairwise generalized Born method suitable for protein calculations. J. Phys. Chem. B (2005) 109, 22667-22673. 


Publications 2006 

L. Yatime, Y. Mechulam, S. Blanquet, E. Schmitt. Structural switch of the gamma subunit in an archaeal aIF2 alpha gamma heterodimer. Structure(2006) 14, 119-128. 

N. Calimet, T. Simonson. Cys(x)His(y)-Zn(2+) interactions : possibilities and limitations of a simple pairwise force field. J. Mol. Graph. Model. (2006) 24, 404-411. 

H. Oshikane, K. Sheppard, S. Fukai, Y. Nakamura, R. Ishitani, T. Numata, R.L. Sherrer, L. Feng, E. Schmitt, M. Panvert, S. Blanquet, Y. Mechulam, D. Söll, O. Nureki. Structural basis of RNA-dependent recruitment of glutamine to the genetic code. Science (2006) 312, 1950-1954. 

D. Thompson, T. Simonson. (2006) Molecular dynamics simulations show that bound Mg(2+) contributes to amino acid and aminoacyl adenylate binding specificity in aspartyl-tRNA synthetase through long range electrostatic interactions. J. Biol. Chem. 281, 23792-23803. 

M.L Ferri-Fioni, M. Fromant, A.P Bouin, C. Aubard, C. Lazennec, P. Plateau, S. Blanquet. Identification in archaea of a novel D-Tyr-tRNA(Tyr) deacylase. J. Biol. Chem. (2006) 281, 27575-27585. 

D. Thompson, P. Plateau, T. Simonson. Free energy simulations and experiments reveal long-range electrostatic interactions and substrate-assisted specificity in an aminoacyl-tRNA synthetase. (2006) ChemBioChem 7, 337-344.

A. Aleksandrov, T. Simonson. The tetracycline:Mg(2+) complex : a molecular mechanics force field. (2006) J. Comput. Chem. 27, 1517-1533. 

T. Simonson. Free energy calculations : approximate methods for biological macromolecules. In Free energy calculations : theory and applications in chemistry and biology. C. Chipot & A. Pohorille (eds), Springer Verlag, New York (2006).

C. Chipot, A.E. Mark, V.S. Pande, T. Simonson. Applications of free energy calculations to chemistry and biology. In Free energy calculations : theory and applications in chemistry and biology. C. Chipot & A. Pohorille (eds), Springer Verlag, New York (2006).


Publications 2007

L. Yatime, Y. Mechulam, S. Blanquet E. Schmitt. Structure of an archaeal homotrimericinitiation factor 2 reveals a nucleotide state between the GTP and the GDP states. Proc. Natl. Acad. Sci. USA, (2007), 104, 18445-18450.

S. Wydau, M.L. Ferri-Fioni, S. Blanquet, P. Plateau P. GEK1, a gene product ofArabidopsis thaliana involved in ethanol tolerance, is a D-aminoacyl-tRNA deacylase. Nucleic Acids Res. (2007) 35, 930-938. 

A. Tarze, M. Dauplais, I. Grigoras, M. Lazard M, N.T. Ha-Duong, F. Barbier, S. Blanquet S. Extracellular production of hydrogen selenide accounts for thiol-assisted toxicity of selenite against Saccharomyces cerevisiae. J. Biol. Chem. (2007), 282(12):8759-67.

J. Noirel & T. Simonson (2007). Neutral evolution of protein-protein interactions : a computational study using simple models. BMC Structural Biology, 7, 79-93.

D. Thompson, C. Lazennec, P. Plateau & T. Simonson (2007). Ammonium scanning in an enzyme active site : the chiral specificity of aspartyl-tRNA synthetase. Journal of Biological Chemistry, 282, 30856-308

G. Launay, R. Mendez, S. Wodak, T. Simonson (2007) Recognizing protein-protein interfaces with empirical potentials and reduced amino. BMC Bioinformatics, 8, 270-278

A. Lopes, A. Alexandrov, C. Bathelt, G. Archontis & T. Simonson (2007) Computational sidechain placement and protein mutagenesis with implicit solvent models Proteins, 67, 853-867

A. Alexandrov, J. Proft, W. Hinrichs & T. Simonson (2007). Protonation patterns in tetracycline:Tet Repressor recognition : simulations and experiments.ChemBioChem, 8, 675- 68.

Rodrigo G., Montagud A., Aparici A., Aroca M.C., Baguena M., Carrera J., Edo C., Fernandez-De-Cordoba P., Ferrando A., Fuertes G., Gimenez D., Mata C., Medrano J.V., Navarrete C., Navarro E., Salgado J., Tortosa P., Urchueguia J., Jaramillo A. Vanillin cell sensor. IET Synthetic Biology, 2007, 1, 74-78.

Rodrigo G., Carrera J., Jaramillo A. Genetdes : Automatic design of transcriptional networks. Bioinformatics, 2007, 23, 1857-1858.

Rodrigo G., Carrera J., Jaramillo A. Evolutionary mechanisms of circadian clocks. Central European Journal of Biology, 2007, 2, 233-253.

Rodrigo G., Jaramillo A. Computational design of digital and memory biological devices.Systems and Synthetic Biology, 2007, 1, 183-195.

Rodrigo G., Carrera J., Jaramillo A. Asmparts : Assembly of biological model parts Systems and Synthetic Biology, 2007, 1, 167-170.


Publications 2008

Barraud P, Schmitt E, Mechulam Y, Dardel F, Tisné C. A unique conformation of the anticodon stem-loop is associated with the capacity of tRNAfMet to initiate protein synthesis. Nucleic Acids Res. 36:4894-901. 

G. Rodrigo, J. Carrera, K.J. Prather, and A. Jaramillo. DESHARKY : Automatic design of metabolic pathways for optimal cell growth. Bioinformatics Advance Access published onSeptember 5, 2008. DOI:10.1093/bioinformatics/btn471.

P. Agudelo-Romero, P. Carbonell, F. de la Iglesia, J. Carrera, G. Rodrigo, A. Jaramillo, M.A. Pérez-Amador and S.F. Elena. Changes in the gene expression profile of Arabidopsis thaliana after infection with Tobacco etch virus. Virology Journal 2008, 5:92. DOI:10.1186/1743-422X-5-92

Daniele Sciretti, Pierpaolo Bruscolini, Alessandro Pelizzola, Marco Pretti and Alfonso Jaramillo. Computational protein design with side-chain conformational entropy. Proteins. 2008. DOI : 10.1002/prot.22145.

M. Suarez, P. Tortosa, J. Carrera and A. Jaramillo. Pareto Optimization in Computational Protein Design with Multiple Objectives. J. Comp. Chem 2008. DOI : 10.1002/jcc.20981

Suarez M., Tortosa P., Jaramillo A. PROTDES : CHARMM toolbox for computational protein design. Systems and Synthetic Biology, 2008, 2, 105-113.

G. Rodrigo, J. Carrera and A. Jaramillo. In silico evolution of the oscillatory response under light-dark cycles. Biochimie. 2008, 90(6):888-97. DOI : 10.1016/j.biochi.2008.02.012

J. Noirel, S.Y. Ow, G. Sanguinetti, A. Jaramillo and P.C. Wright. Automated extraction of meaningful pathways from quantitative proteomics data. Briefings in Functional Genomics and Proteomics 2008 Mar ;7(2):136-46. DOI : 10.1093/bfgp/eln011

Thompson D, Lazennec C, Plateau P, Simonson T. Probing electrostatic interactions and ligand binding in aspartyl-tRNA synthetase through site-directed mutagenesis and computer simulations. Proteins (2008) 71, 1450-1460.

Grigoras I, Lazard M, Plateau P, Blanquet S. Functional characterization of the Saccharomyces cerevisiae ABC-transporter Yor1p overexpressed in plasma membranes. Biochim. Biophys. Acta. (2008) 1778, 68-78

A. Aleksandrov, L. Schuldt, W. Hinrichs & T. Simonson. T repressor induction by tetracycline : a molecular dynamics, continuum electrostatics, and crystallographic study. (2008) Journal of Molecular Biology, 378, 896-910.

A. Aleksandrov & T. Simonson. Molecular dynamics simulations of the 30S ribosomal subunit reveal a preferred tetracycline binding site. (2008) Journal of the American Chemical Society, 130, 1114-1115.

J. Noirel & T. Simonson. Neutral evolution of proteins : the superfunnel in sequence space and its relation to mutational robustness. (2008) Journal of Chemical Physics, 129, 185104-185112.

G. Launay & T. Simonson. Homology modelling of protein-protein complexes : a simple method and its possibilities and limitations. (2008) BMC Bioinformatics, 9, 427-443.

M. Schmidt am Busch, A. Lopes, N. Amara, C. Bathelt & T. Simonson. Testing the Coulomb/Accessible Surface Area solvent model for protein stability, ligand binding, and protein design. (2008) BMC Bioinformatics, 9, 148-163.

M. Schmidt am Busch, A. Lopes, D. Mignon & T. Simonson. Computational protein design : software implementation, parameter optimization, and performance of a simple method. (2008) Journal of Computational Chemistry, 29, 1092-1102.

T. Simonson. Dielectric relaxation in proteins : the computational perspective.
(2008) Photosynthesis Research, 97, 21-32.

D. Thompson, C. Lazennec, P. Plateau & T. Simonson. Probing electrostatic interactions and ligand binding in aspartyl-tRNA synthetase through site-directed mutagenesis and computer simulations. (2008) Proteins, 71, 1450-1460.



Publications 2009

Wydau S, Van der Rest G, Aubard C, Plateau P, Blanquet S. Widespread distribution of cell defense against D-aminoacyl-tRNAs. J. Biol. Chem. 2009, 284, 14096-14104

Robin K, Reverchon JL, Mugherli L, Fromant M, Plateau P, Benisty H. Detection of biological macromolecules on a biochip dedicated to UV specific absorption. Biosens. Bioelectron. 2009, 24,1585-1591.

Baouz S, Schmitter JM, Chenoune L, Beauvallet C, Blanquet S, Woisard A, Hountondji C. Primary Structure Revision and Active Site Mapping of E. Coli Isoleucyl-tRNA. Synthetase by Means of Maldi Mass Spectrometry. Open Biochem J. 2009 Mar 6 ;3:26-38.

Schmitt E, Galimand M, Panvert M, Courvalin P, Mechulam Y. Structural bases for 16 S rRNA methylation catalyzed by ArmA and RmtB methyltransferases. J Mol Biol. 2009 ; 388(3):570-82.

Tanrikulu IC, Schmitt E, Mechulam Y, Goddard WA 3rd, Tirrell DA. Discovery of Escherichia coli methionyl-tRNA synthetase mutants for efficient labeling of proteins with azidonorleucine in vivo. Proc Natl Acad Sci U S A. 2009 ;106(36):15285-90.

Schmitt E, Tanrikulu IC, Yoo TH, Panvert M, Tirrell DA, Mechulam Y. Switching from an Induced-Fit to a Lock-and-Key Mechanism in an Aminoacyl-tRNA Synthetase with Modified Specificity. J Mol Biol. 2009, 394 :843-851.

J. Carrera, G. Rodrigo, A. Jaramillo, S.F. Elena. Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions. Genome Biol. 2009 ;10(9):R96. DOI:10.1186/gb-2009-10-9-r96.

T.E. Landrain, J. Carrera, B. Kirov, G. Rodrigo, A. Jaramillo. Modular Model-based Design for Heterologous Bioproduction in Bacteria. Current Opinion in Biotechnology. 2009. DOI:10.1016/j.copbio.2009.06.003.

J. Carrera, G. Rodrigo, A. Jaramillo ? Towards the automated engineering of a synthetic genome. Molecular Biosystems. 2009. DOI : 10.1039/B904400K

G. Molto, M. Suarez, P. Tortosa, J. Alonso, V. Hernandez, A. Jaramillo. Protein Design Based on Parallel Dimensional Reduction. J. Chem. Inf. Model., 2009, 49 (5), pp 1261–1271. DOI : 10.1021/ci8004594.

J. Carrera, G. Rodrigo, A. Jaramillo. Model-based redesign of global transcription regulation. Nucleic Acids Research 2009 37(5):e38 ; doi:10.1093/nar/gkp022

D. Sciretti, P. Bruscolini, A. Pelizzola, M. Pretti, A. Jaramillo. Computational protein design with side-chain conformational entropy. Proteins 2009, 74(1) : 176-91. DOI : 10.1002/prot.22145.

M. Suarez, G. Rodrigo, J. Carrera, A. Jaramillo. Chapter 4 : Computational Design in Synthetic Biology. Synthetic Biology (Eds. Schmidt, M. ; Kelle, A. ; Ganguli, A. ; de Vriend, H.) (2009). ISBN : 978-90-481-2677-4

M. Suarez, P. Tortosa, M.M. Garcia-Mira, D. Rodríguez-Larrea, R. Godoy-Ruiz, B. Ibarra-Molero, J.M. Sanchez-Ruiz, A. Jaramillo. Using multi-objective computational design to extend protein promiscuity. Biophys Chem. 2009 Dec 22.

Suarez M., Jaramillo A. Challenges in the computational design of proteins. Journal of the Royal Society Interface, 2009, 6, S477-S491.