H. K. Huang, H. Yoon, E. M. Hannig, and T. F. Donahue, GTP hydrolysis controls stringent selection of the AUG start codon during translation initiation in Saccharomyces??cerevisiae, Genes & Development, vol.11, issue.18, pp.2396-2413, 1997.
DOI : 10.1101/gad.11.18.2396

M. A. Algire, D. Maag, and J. R. Lorsch, Pi Release from eIF2, Not GTP Hydrolysis, Is the Step Controlled by Start-Site Selection during Eukaryotic Translation Initiation, Molecular Cell, vol.20, issue.2, pp.251-262, 2005.
DOI : 10.1016/j.molcel.2005.09.008

E. Schmitt, S. Blanquet, and Y. Mechulam, The large subunit of initiation factor aIF2 is a close structural homologue of elongation factors, The EMBO Journal, vol.21, issue.7, pp.1821-1832, 2002.
DOI : 10.1093/emboj/21.7.1821

URL : https://hal.archives-ouvertes.fr/hal-00770921

A. Roll-mecak, P. Alone, C. Cao, T. E. Dever, and S. K. Burley, X-ray Structure of Translation Initiation Factor eIF2??: IMPLICATIONS FOR tRNA AND eIF2?? BINDING, Journal of Biological Chemistry, vol.279, issue.11, pp.10634-10642, 2004.
DOI : 10.1074/jbc.M310418200

P. Nissen, M. Kjeldgaard, S. Thirup, G. Polekhina, L. Reshetnikova et al., Crystal Structure of the Ternary Complex of Phe-tRNAPhe, EF-Tu, and a GTP Analog, Science, vol.270, issue.5241, pp.1464-1472, 1995.
DOI : 10.1126/science.270.5241.1464

E. Schmitt, M. Panvert, C. Lazennec-schurdevin, P. D. Coureux, J. Perez et al., Structure of the ternary initiation complex aIF2???GDPNP???methionylated initiator tRNA, Nature Structural & Molecular Biology, vol.430, issue.4, pp.450-454, 2012.
DOI : 10.1107/S0021889895007047

URL : https://hal.archives-ouvertes.fr/hal-00764443

L. Phan, L. W. Schoenfeld, L. Valasek, K. H. Nielsen, and A. G. Hinnebusch, A subcomplex of three eIF3 subunits binds eIF1 and eIF5 and stimulates ribosome binding of mRNA and tRNAiMet, The EMBO Journal, vol.20, issue.11, pp.2954-2965, 2001.
DOI : 10.1093/emboj/20.11.2954

C. A. Fekete, D. J. Applefield, S. A. Blakely, N. Shirokikh, T. Pestova et al., The eIF1A C-terminal domain promotes initiation complex assembly, scanning and AUG selection in vivo, The EMBO Journal, vol.21, issue.20, pp.3588-3601, 2005.
DOI : 10.1128/MCB.24.21.9437-9455.2004

D. S. Olsen, E. M. Savner, A. Mathew, F. Zhang, T. Krishnamoorthy et al., Domains of eIF1A that mediate binding to eIF2, eIF3 and eIF5B and promote ternary complex recruitment in vivo, The EMBO Journal, vol.22, issue.2, pp.193-204, 2003.
DOI : 10.1093/emboj/cdg030

D. Maag, C. A. Fekete, Z. Gryczynski, and J. R. Lorsch, A Conformational Change in the Eukaryotic Translation Preinitiation Complex and Release of eIF1 Signal Recognition of the Start Codon, Molecular Cell, vol.17, issue.2, pp.265-275, 2005.
DOI : 10.1016/j.molcel.2004.11.051

T. V. Pestova, S. I. Borukhov, and C. U. Hellen, Eukaryotic ribosomes require initiation factors 1 and 1A to locate initiation codons, Nature, vol.394, issue.6696, pp.854-859, 1998.
DOI : 10.1038/29703

T. V. Pestova and V. G. Kolupaeva, The roles of individual eukaryotic translation initiation factors in ribosomal scanning and initiation codon selection, Genes & Development, vol.16, issue.22, pp.2906-2922, 2002.
DOI : 10.1101/gad.1020902

L. A. Passmore, T. M. Schmeing, D. Maag, D. J. Applefield, M. G. Acker et al., The Eukaryotic Translation Initiation Factors eIF1 and eIF1A Induce an Open Conformation of the 40S Ribosome, Molecular Cell, vol.26, issue.1, pp.41-50, 2007.
DOI : 10.1016/j.molcel.2007.03.018

S. Das, R. Ghosh, and U. Maitra, Eukaryotic Translation Initiation Factor 5 Functions as a GTPase-activating Protein, Journal of Biological Chemistry, vol.276, issue.9, pp.6720-6726, 2001.
DOI : 10.1074/jbc.M008863200

F. E. Paulin, L. E. Campbell, K. O-'brien, J. Loughlin, and C. G. Proud, Eukaryotic translation initiation factor 5 (eIF5) acts as a classical GTPase-activator protein, Current Biology, vol.11, issue.1, pp.55-59, 2001.
DOI : 10.1016/S0960-9822(00)00025-7

R. Majumdar and U. Maitra, Regulation of GTP hydrolysis prior to ribosomal AUG selection during eukaryotic translation initiation, The EMBO Journal, vol.262, issue.21, pp.3737-3746, 2005.
DOI : 10.1101/gad.1255704

Y. N. Cheung, D. Maag, S. F. Mitchell, C. A. Fekete, M. A. Algire et al., Dissociation of eIF1 from the 40S ribosomal subunit is a key step in start codon selection in vivo, Genes & Development, vol.21, issue.10, pp.1217-1230, 2007.
DOI : 10.1101/gad.1528307

N. Tolstrup, C. W. Sensen, R. A. Garrett, and I. G. Clausen, Two different and highly organized mechanisms of translation initiation in the archaeon Sulfolobus solfataricus, Extremophiles, vol.4, issue.3, pp.175-179, 2000.
DOI : 10.1007/s007920070032

N. C. Kyrpides and C. R. Woese, Universally conserved translation initiation factors, Proceedings of the National Academy of Sciences, vol.95, issue.1, pp.224-228, 1998.
DOI : 10.1073/pnas.95.1.224

N. Pedulla, R. Palermo, D. Hasenohrl, U. Blasi, P. Cammarano et al., The archaeal eIF2 homologue: functional properties of an ancient translation initiation factor, Nucleic Acids Research, vol.33, issue.6, pp.1804-1812, 2005.
DOI : 10.1093/nar/gki321

R. M. Voorhees, T. M. Schmeing, A. C. Kelley, and V. Ramakrishnan, The Mechanism for Activation of GTP Hydrolysis on the Ribosome, Science, vol.330, issue.6005, pp.835-838, 2010.
DOI : 10.1126/science.1194460

Y. Chen, S. Feng, V. Kumar, R. Ero, and Y. G. Gao, Structure of EF-G???ribosome complex in a pretranslocation state, Nature Structural & Molecular Biology, vol.13, issue.9, pp.1077-1084, 2013.
DOI : 10.1107/S0907444994003112

D. S. Tourigny, I. S. Fernandez, A. C. Kelley, and V. Ramakrishnan, Elongation Factor G Bound to the Ribosome in an Intermediate State of Translocation, Science, vol.340, issue.6140, p.1235490, 2013.
DOI : 10.1126/science.1235490

A. Aleksandrov and M. Field, Mechanism of activation of elongation factor Tu by ribosome: Catalytic histidine activates GTP by protonation, RNA, vol.19, issue.9, pp.1218-1225, 2013.
DOI : 10.1261/rna.040097.113

URL : https://hal.archives-ouvertes.fr/hal-00866971

A. Liljas, M. Ehrenberg, and J. Aqvist, Comment on "The Mechanism for Activation of GTP Hydrolysis on the Ribosome", Science, vol.333, issue.6038, p.37, 2011.
DOI : 10.1126/science.1202472

G. Wallin, S. C. Kamerlin, and J. Aqvist, Energetics of activation of GTP hydrolysis on the ribosome, Nature Communications, vol.42, 1733.
DOI : 10.1038/ncomms2741

L. Yatime, Y. Mechulam, S. Blanquet, and E. Schmitt, Structural Switch of the ?? Subunit in an Archaeal aIF2???? Heterodimer, Structure, vol.14, issue.1, pp.119-128, 2006.
DOI : 10.1016/j.str.2005.09.020

URL : https://hal.archives-ouvertes.fr/hal-00502073

Y. Mechulam, L. Guillon, L. Yatime, S. Blanquet, and E. Schmitt, Protection-Based Assays to Measure Aminoacyl-tRNA Binding to Translation Initiation Factors, Methods Enzymol, vol.430, pp.265-281, 2007.
DOI : 10.1016/S0076-6879(07)30011-6

URL : https://hal.archives-ouvertes.fr/hal-00502061

F. Dardel, MC-Fit: Using Monte-Carlo methods to get accurate confidence limits on enzyme parameters, Bioinformatics, vol.10, issue.3, pp.273-275, 1994.
DOI : 10.1093/bioinformatics/10.3.273

W. J. Kabsch, Evaluation of single-crystal X-ray diffraction data from a position-sensitive detector, Journal of Applied Crystallography, vol.21, issue.6, pp.916-924, 1988.
DOI : 10.1107/S0021889888007903

L. C. Storoni, A. J. Mccoy, and R. J. Read, Likelihood-enhanced fast rotation functions, Acta Crystallographica Section D Biological Crystallography, vol.60, issue.3, pp.432-438, 2004.
DOI : 10.1107/S0907444903028956

P. Emsley, B. Lohkamp, W. G. Scott, and K. Cowtan, Features and development of Coot, Acta Crystallogr, vol.66, pp.486-501, 2010.

P. D. Adams, P. V. Afonine, G. Bunkóczibunk´bunkóczi, V. B. Chen, I. W. Davis et al., PHENIX: a comprehensive Python-based system for macromolecular structure solution, Acta Cryst, vol.66, pp.213-221, 2010.

T. Darden, Treatment of Long-Range Forces and Potential Computational Biochemistry & Biophysics, 2001.

N. Foloppe and A. Mackerell, All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data, Journal of Computational Chemistry, vol.7, issue.2, pp.86-104, 2000.
DOI : 10.1002/(SICI)1096-987X(20000130)21:2<86::AID-JCC2>3.0.CO;2-G

A. D. Mackerell, . Jr, N. Banavali, and N. Foloppe, Development and current status of the CHARMM force field for nucleic acids, Biopolymers, vol.40, issue.4, pp.257-265, 2000.
DOI : 10.1002/1097-0282(2000)56:4<257::AID-BIP10029>3.0.CO;2-W

W. Jorgensen, J. Chandrasekhar, J. Madura, R. Impey, and M. Klein, Comparison of simple potential functions for simulating liquid water, The Journal of Chemical Physics, vol.79, issue.2, pp.926-935, 1983.
DOI : 10.1063/1.445869

J. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid et al., Scalable molecular dynamics with NAMD, Journal of Computational Chemistry, vol.84, issue.16, pp.1781-1802, 2005.
DOI : 10.1002/jcc.20289

A. Aleksandrov, J. Proft, W. Hinrichs, and T. Simonson, Protonation Patterns in Tetracycline:Tet Repressor Recognition: Simulations and Experiments, ChemBioChem, vol.53, issue.6, pp.675-685, 2007.
DOI : 10.1002/cbic.200600535

URL : https://hal.archives-ouvertes.fr/hal-00488201

T. Simonson, A. Aleksandrov, and P. Satpati, Electrostatic free energies in translational GTPases: Classic allostery and the rest, Biochimica et Biophysica Acta (BBA) - General Subjects, vol.1850, issue.5, 2014.
DOI : 10.1016/j.bbagen.2014.07.006

URL : https://hal.archives-ouvertes.fr/hal-01152238

P. M. Gill, B. G. Johnson, J. A. Pople, and M. J. Frisch, The performance of the Becke???Lee???Yang???Parr (B???LYP) density functional theory with various basis sets, Chemical Physics Letters, vol.197, issue.4-5, pp.499-505, 1992.
DOI : 10.1016/0009-2614(92)85807-M

F. Weigend and R. Ahlrichs, Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy, Physical Chemistry Chemical Physics, vol.110, issue.16, pp.3297-3305, 2005.
DOI : 10.1039/b508541a

M. Field, The pDynamo Program for Molecular Simulations using Hybrid Quantum Chemical and Molecular Mechanical Potentials, Journal of Chemical Theory and Computation, vol.4, issue.7, pp.1151-1161, 2008.
DOI : 10.1021/ct800092p

F. Neese, The ORCA program system, Wiley Interdisciplinary Reviews: Computational Molecular Science, vol.132, issue.1, pp.73-78, 2012.
DOI : 10.1002/wcms.81

A. Aleksandrov and M. Field, A hybrid elastic band string algorithm for studies of enzymatic reactions, Physical Chemistry Chemical Physics, vol.115, issue.36, pp.12544-12553, 2012.
DOI : 10.1039/c2cp40918f

URL : https://hal.archives-ouvertes.fr/hal-00764439

J. Kästner, H. M. Senn, S. Thiel, N. Otte, and W. Thiel, QM/MM Free-Energy Perturbation Compared to Thermodynamic Integration and Umbrella Sampling:?? Application to an Enzymatic Reaction, Journal of Chemical Theory and Computation, vol.2, issue.2, pp.452-461, 2006.
DOI : 10.1021/ct050252w

A. Aleksandrov, E. Zvereva, and M. Field, The Mechanism of Citryl-Coenzyme A Formation Catalyzed by Citrate Synthase, The Journal of Physical Chemistry B, vol.118, issue.17, pp.4505-4513, 2014.
DOI : 10.1021/jp412346g

URL : https://hal.archives-ouvertes.fr/hal-00998107

O. Nikonov, E. Stolboushkina, V. Arkhipova, O. Kravchenko, S. Nikonov et al., Conformational transitions in the ?? subunit of the archaeal translation initiation factor 2, Acta Crystallographica Section D Biological Crystallography, vol.104, issue.3, pp.658-667, 2014.
DOI : 10.1107/S1399004713032240/mn5043sup1.pdf

H. Berchtold, L. Reshtnikova, C. O. Reiser, N. K. Schirmer, M. Sprinzl et al., Crystal structure of active elongation factor Tu reveals major domain rearrangements, Nature, vol.365, issue.6442, pp.126-132, 1993.
DOI : 10.1038/365126a0

I. R. Vetter and A. Wittinghofer, The Guanine Nucleotide-Binding Switch in Three Dimensions, Science, vol.294, issue.5545, pp.1299-1304, 2001.
DOI : 10.1126/science.1062023

T. Daviter, H. J. Wieden, and M. V. Rodnina, Essential Role of Histidine 84 in Elongation Factor Tu for the Chemical Step of GTP Hydrolysis on the Ribosome, Journal of Molecular Biology, vol.332, issue.3, pp.689-699, 2003.
DOI : 10.1016/S0022-2836(03)00947-1

V. Hauryliuk, S. Hansson, and M. Ehrenberg, Cofactor Dependent Conformational Switching of GTPases, Biophysical Journal, vol.95, issue.4, pp.1704-1715, 2008.
DOI : 10.1529/biophysj.107.127290

B. Wilden, A. Savelsbergh, M. V. Rodnina, and W. Wintermeyer, Role and timing of GTP binding and hydrolysis during EF-G-dependent tRNA translocation on the ribosome, Proceedings of the National Academy of Sciences, vol.103, issue.37, pp.13670-13675, 2006.
DOI : 10.1073/pnas.0606099103

J. F. Eccleston and M. R. Webb, Characterization of the GTPase reaction of elongation factor Tu. Determination of the stereochemical course in the presence of antibiotic X5108, J. Biol. Chem, vol.257, pp.5046-5049, 1982.

A. C. Storer and A. Cornish-bowden, - and other ions in solution. Calculation of the true concentrations of species present in mixtures of associating ions, Biochemical Journal, vol.159, issue.1, pp.1-5, 1976.
DOI : 10.1042/bj1590001

A. J. Adamczyk and A. Warshel, Converting structural information into an allosteric-energy-based picture for elongation factor Tu activation by the ribosome, Proceedings of the National Academy of Sciences, vol.108, issue.24, pp.9827-9832, 2011.
DOI : 10.1073/pnas.1105714108

P. Gouet, E. Courcelle, D. I. Stuart, and F. Metoz, ESPript: analysis of multiple sequence alignments in PostScript, Bioinformatics, vol.15, issue.4, pp.305-308, 1999.
DOI : 10.1093/bioinformatics/15.4.305

URL : https://hal.archives-ouvertes.fr/hal-00314288

K. Scheffzek, M. R. Ahmadian, W. Kabsch, L. Wiesmuller, A. Lautwein et al., The Ras-RasGAP Complex: Structural Basis for GTPase Activation and Its Loss in Oncogenic Ras Mutants, Science, vol.277, issue.5324, pp.333-338, 1997.
DOI : 10.1126/science.277.5324.333

B. Kuhle and R. Ficner, A monovalent cation acts as structural and catalytic cofactor in translational GTPases, The EMBO Journal, vol.33, issue.21, pp.2547-2563, 2014.
DOI : 10.15252/embj.201488517

C. Maracci, F. Peske, E. Dannies, C. Pohl, and M. V. Rodnina, Ribosome-induced tuning of GTP hydrolysis by a translational GTPase, Proceedings of the National Academy of Sciences, vol.111, issue.40, pp.14418-14423, 2014.
DOI : 10.1073/pnas.1412676111