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

A. Aleksandrov, J. Proft, W. Hinrichs, and T. Simonson, Protonation patterns in tetracycline:tet repressor recognition: simulations and experiments, Chembiochem, vol.8, pp.675-685, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00488201

P. Barraud, E. Schmitt, Y. Mechulam, F. Dardel, and C. Tisné, A unique conformation of the anticodon stem-loop is associated with the capacity of tRNA f Met to initiate protein synthesis, Nucleic Acids Res, vol.36, pp.4894-4901, 2008.

R. Basavappa and P. B. Sigler, The 3 Å crystal structure of yeast initiator tRNA: functional implications in initiator/elongator discrimination, EMBO J, vol.10, pp.3105-3111, 1991.

D. J. Battle and J. A. Doudna, Specificity of RNA-RNA helix recognition, Proc Natl Acad Sci, vol.99, pp.11676-11681, 2002.

B. R. Brooks, C. L. Brooks, . Iii, A. D. Mackerell, L. Nilsson et al., CHARMM: the biomolecular simulation program, J Comp Chem, vol.30, pp.1545-1614, 2009.

S. H. Chen, R. T. Byrne, E. A. Wood, and M. M. Cox, Escherichia coli radD (yejH) gene: a novel function involved in radiation resistance and double-strand break repair, Mol Microbiol, vol.95, pp.754-768, 2015.

P. D. Coureux, C. Lazennec-schurdevin, A. Monestier, E. Larquet, L. Cladière et al., Cryo-EM study of start codon selection during archaeal translation initiation, Nat Commun, vol.7, p.13366, 2016.

G. E. Crooks, G. Hon, J. M. Chandonia, and S. E. Brenner, WebLogo: a sequence logo generator, Genome Res, vol.14, pp.1188-1190, 2004.

T. Darden and O. Becker, Treatment of long-range forces and potential, Computational biochemistry & biophysics, 2001.

M. Dekker,

K. A. Datsenko and B. L. Wanner, One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products, Proc Natl Acad Sci, vol.97, pp.6640-6645, 2000.

K. Diederichs and P. A. Karplus, Better models by discarding data?, Acta Crystallogr D Biol Crystallogr, vol.69, pp.1215-1222, 2013.

P. C. Durant and D. R. Davis, Stabilization of the anticodon stem-loop of tRNA Lys,3 by an A +-C base-pair and by pseudouridine, J Mol Biol, vol.285, pp.115-131, 1999.

S. Dutka, T. Meinnel, C. Lazennec, Y. Mechulam, and S. Blanquet, Role of the 1-72 base pair in tRNAs for the activity of Escherichia coli peptidyl-tRNA hydrolase, Nucleic Acids Res, vol.21, pp.4025-4030, 1993.

F. Eckert and A. Klamt, Fast solvent screening via quantum chemistry: COSMO-RS approach, AlChE J, vol.48, pp.369-385, 2002.

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

D. Farruggio, J. Chaudhuri, U. Maitra, and U. L. Rajbhandary, The A1 ? U72 base pair conserved in eukaryotic initiator tRNAs is important specifically for binding to the eukaryotic translation initiation factor eIF2, Mol Cell Biol, vol.16, pp.4248-4256, 1996.

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, J Comput Chem, vol.21, pp.86-104, 2000.

F. Guerra, C. Bickelhaupt, F. M. Saha, S. Wang, and F. , Adenine tautomers: relative stabilities, ionization energies, and mismatch with cytosine, J Phys Chem A, vol.110, pp.4012-4020, 2006.

R. Giege, Toward a more complete view of tRNA biology, Nat Struct Mol Biol, vol.15, pp.1007-1014, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00341708

J. M. Guillon, T. Meinnel, Y. Mechulam, C. Lazennec, S. Blanquet et al., Nucleotides of tRNA governing the specificity of Escherichia coli methionyl-tRNA f Met formyltransferase, J Mol Biol, vol.224, pp.359-367, 1992.

J. M. Guillon, Y. Mechulam, S. Blanquet, and G. Fayat, Importance of formylability and anticodon stem sequence to give tRNA Met an initiator identity in Escherichia coli, J Bacteriol, vol.175, pp.4507-4514, 1993.

M. S. Guyer, R. R. Reed, J. A. Steitz, and K. B. Low, Identification of a sex-factor-affinity site in E. coli as ??, Cold Spring Harb Symp Quant Biol, vol.45, pp.135-140, 1981.

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 Dev, vol.11, pp.2396-2413, 1997.

W. Jorgensen, J. Chandrasekhar, J. Madura, R. Impey, and M. Klein, Comparison of simple potential functions for simulating liquid water, J Chem Phys, vol.79, pp.926-935, 1983.

G. Kampf, L. E. Kapinos, R. Griesser, B. Lippert, and H. Sigel, Comparison of the acid-base properties of purine derivatives in aqueous solution. Determination of intrinsic proton affinities of various basic sites, J Chem Soc Perkin Trans, vol.2, pp.1320-1327, 2002.

S. Kapoor, G. Das, and U. Varshney, Crucial contribution of the multiple copies of the initiator tRNA genes in the fidelity of tRNA f Met selection on the ribosomal P-site in Escherichia coli, Nucleic Acids Res, vol.39, pp.202-212, 2011.

L. D. Kapp and J. R. Lorsch, GTP-dependent recognition of the methionine moiety on initiator tRNA by translation factor eIF2, J Mol Biol, vol.335, pp.923-936, 2004.

L. D. Kapp, S. E. Kolitz, and J. R. Lorsch, Yeast initiator tRNA identity elements cooperate to influence multiple steps of translation initiation, RNA, vol.12, pp.751-764, 2006.

P. A. Karplus and K. Diederichs, Linking crystallographic model and data quality, Science, vol.336, pp.1030-1033, 2012.

G. Keith, J. Heitzler, C. El-adlouni, A. L. Glasser, C. Fix et al., The primary structure of cytoplasmic initiator tRNA Met from Schizosaccharomyces pombe, Nucleic Acids Res, vol.21, p.2949, 1993.

T. Kenri, K. Kohno, N. Goshima, F. Imamoto, and Y. Kano, Construction and characterization of an Escherichia coli mutant with a deletion of the metZ gene encoding tRNA f1 Met, Gene, vol.103, pp.31-36, 1991.

S. E. Kolitz and J. R. Lorsch, Eukaryotic initiator tRNA: finely tuned and ready for action, FEBS Lett, vol.584, pp.396-404, 2010.

A. Korostelev, S. Trakhanov, M. Laurberg, and H. F. Noller, Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements, Cell, vol.126, pp.1065-1077, 2006.

C. P. Lee, B. L. Seong, and U. L. Ralbhandary, Structural and sequence elements important for recognition of Escherichia coli formylmethionine tRNA by methionyl-tRNA transformylase are clustered in the acceptor stem, J Biol Chem, vol.266, pp.18012-18017, 1991.

J. A. Liberman, M. Guo, J. L. Jenkins, J. Krucinska, Y. Chen et al., A transition-state interaction shifts nucleobase ionization toward neutrality to facilitate small ribozyme catalysis, J Am Chem Soc, vol.134, pp.16933-16936, 2012.

T. M. Lowe and S. R. Eddy, tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence, Nucleic Acids Res, vol.25, pp.955-964, 1997.

X. J. Lu, H. J. Bussemaker, and W. K. Olson, DSSR: an integrated software tool for dissecting the spatial structure of RNA, Nucleic Acids Res, vol.43, p.142, 2015.

D. Mangroo and U. L. Rajbhandary, Mutants of Escherichia coli initiator tRNA defective in initiation, J Biol Chem, vol.270, pp.12203-12209, 1995.

C. Marck and H. Grosjean, tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features, RNA, vol.8, pp.1189-1232, 2002.

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

F. Neese, The ORCA program system, WIREs Comput Mol Sci, vol.2, pp.73-78, 2012.

P. Nissen, J. A. Ippolito, N. Ban, P. B. Moore, and T. A. Steitz, RNA tertiary interactions in the large ribosomal subunit: the A-minor motif, Proc Natl Acad Sci, vol.98, pp.4899-4903, 2001.

J. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid et al., Scalable molecular dynamics with NAMD, J Comput Chem, vol.26, pp.1781-1802, 2005.

S. Ravindranathan, S. E. Butcher, and J. Feigon, Adenine protonation in domain B of the hairpin ribozyme, Biochemistry, vol.39, pp.16026-16032, 2000.

A. Rozov, N. Demeshkina, E. Westhof, M. Yusupov, and G. Yusupova, New structural insights into translational miscoding, Trends Biochem Sci, vol.41, pp.798-814, 2016.
URL : https://hal.archives-ouvertes.fr/hal-02294531

J. Rudinger, R. Hillenbrandt, M. Sprinzl, and R. Giege, Antideterminants present in minihelix(Sec) hinder its recognition by prokaryotic elongation factor Tu, EMBO J, vol.15, pp.650-657, 1996.

M. Ruff, S. Krishnaswamy, M. Boeglin, A. Poterszman, A. Mitschler et al., Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNA Asp, Science, vol.252, pp.1682-1689, 1991.

W. Saenger, Principles of nucleic acid structure, 1984.

L. Samhita, S. Shetty, and U. Varshney, Unconventional initiator tRNAs sustain Escherichia coli, Proc Natl Acad Sci, vol.109, pp.13058-13063, 2012.

L. Samhita, V. Nanjundiah, and U. Varshney, How many initiator tRNA genes does Escherichia coli need?, J Bacteriol, vol.196, pp.2607-2615, 2014.

S. Sarkhel, A. Rich, and M. Egli, Water-nucleobase "stacking": H-? and lone pair-? interactions in the atomic resolution crystal structure of an RNA pseudoknot, J Am Chem Soc, vol.125, pp.8998-8999, 2003.

E. Schmitt, M. Panvert, S. Blanquet, and Y. Mechulam, Crystal structure of methionyl-tRNA f Met transformylase complexed with the initiator formyl-methionyl-tRNA f Met, EMBO J, vol.17, pp.6819-6826, 1998.

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, Nat Struct Mol Biol, vol.19, pp.450-454, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00764443

T. D. Schneider and R. M. Stephens, Sequence logos: a new way to display consensus sequences, Nucleic Acids Res, vol.18, pp.6097-6100, 1990.

L. Schrodinger, The PyMOL Molecular Graphics System, Version 1.3r1, 2010.

L. H. Schulman and H. Pelka, The structural basis for the resistance of Escherichia coli formylmethionyl transfer ribonucleic acid to cleavage by Escherichia coli peptidyl transfer ribonucleic acid hydrolase, J Biol Chem, vol.250, pp.542-547, 1975.

M. Selmer, C. M. Dunham, F. V. Murphy, . Iv, A. Weixlbaumer et al., Structure of the 70S ribosome complexed with mRNA and tRNA, Science, vol.313, pp.1935-1942, 2006.

J. F. Senecoff, P. J. Rossmeissl, and M. M. Cox, DNA recognition by the FLP recombinase of the yeast 2 ? plasmid. A mutational analysis of the FLP binding site, J Mol Biol, vol.201, pp.405-421, 1988.

Y. Y. Sham, Z. T. Chu, and A. Warshel, Consistent calculations of pKa's of ionizable residues in proteins: semi-microscopic and microscopic approaches, J Phys Chem B, vol.101, pp.4458-4472, 1997.

H. Shi and P. B. Moore, The crystal structure of yeast phenylalanine tRNA at 1.93 Å resolution: a classic structure revisited, RNA, vol.6, pp.1091-1105, 2000.

J. Tao, J. P. Perdew, V. N. Staroverov, and G. E. Scuseria, Climbing the density functional ladder: nonempirical meta-generalized gradient approximation designed for molecules and solids, Phys Rev Lett, vol.91, p.146401, 2003.

U. Von-pawel-rammingen, S. Astrom, and A. S. Bystrom, Mutational analysis of conserved positions potentially important for initiator tRNA function in Saccharomyces cerevisiae, Mol Cell Biol, vol.12, pp.1432-1442, 1992.

A. Warshel and G. Naray-szabo, Computational approaches to biochemical reactivity, 1997.

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, Phys Chem Chem Phys, vol.7, pp.3297-3305, 2005.

J. L. Wilcox, A. K. Ahluwalia, and P. C. Bevilacqua, Charged nucleobases and their potential for RNA catalysis, Acc Chem Res, vol.44, pp.1270-1279, 2011.

L. Yatime, E. Schmitt, S. Blanquet, and Y. Mechulam, Functional molecular mapping of archaeal translation initiation factor 2, J Biol Chem, vol.279, pp.15984-15993, 2004.
URL : https://hal.archives-ouvertes.fr/hal-00770710

J. Zhang and A. R. Ferre-d'amare, Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA, Nature, vol.500, pp.363-366, 2013.

J. Zhang and A. R. Ferre-d'amare, The tRNA elbow in structure, recognition and evolution, Life, vol.6, p.3, 2016.

G. Zubay, The isolation and fractionation of soluble ribonucleic acids, J Mol Biol, vol.4, pp.347-356, 1962.