RNA Tertiary Structure and Cooperative Assembly of a Large Ribonucleoprotein Complex, Journal of Molecular Biology, vol.344, issue.2, pp.395-407, 2004. ,
DOI : 10.1016/j.jmb.2004.09.009
Effects of polyvalent cations on the folding of an rRNA three-way junction and binding of ribosomal protein S15, RNA, vol.4, issue.8, pp.984-997, 1998. ,
DOI : 10.1017/S1355838298980426
Crystal structure of the S15-rRNA complex, Nat. Struct. Biol, vol.7, pp.273-277, 2000. ,
The crystal structure of UUCG tetraloop, J. Mol. Biol, vol.304, pp.34-42, 2000. ,
Solution structure of the ribosomal RNA binding protein S15 from Thermus thermophilus, Nature Structural & Molecular Biology, vol.1, issue.1, pp.20-23, 1997. ,
DOI : 10.1016/S0263-7855(98)80030-1
Conformational variability of the N-terminal helix in the structure of ribosomal protein S15, Structure, vol.6, issue.4, pp.429-438, 1998. ,
DOI : 10.1016/S0969-2126(98)00045-8
Importance of magnesium ions in the mechanism of catalysis by a hammerhead ribozyme: strictly linear relationship between the ribozyme activity and the concentration of magnesium ions, Magnes. Res, vol.16, pp.210-217, 2003. ,
Identifying Kinetic Barriers to Mechanical Unfolding of the T. thermophila Ribozyme, Science, vol.299, issue.5614, pp.1892-1895, 2003. ,
DOI : 10.1126/science.1081338
Solution structure and thermodynamics of a divalent metal ion binding site in an RNA pseudoknot, 1999. ,
HIERARCHY AND DYNAMICS OF RNA FOLDING, Annual Review of Biophysics and Biomolecular Structure, vol.26, issue.1, pp.113-137, 1997. ,
DOI : 10.1146/annurev.biophys.26.1.113
Argininamide Binding Arrests Global Motions in HIV-1 TAR RNA: Comparison with Mg2+-induced Conformational Stabilization, Journal of Molecular Biology, vol.338, issue.1, pp.7-16, 2004. ,
DOI : 10.1016/j.jmb.2004.02.031
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4694592
Mg 21 -induced variations in the conformation and dynamics of HIV-1 TAR RNA probed using NMR residual dipolar couplings, 2003. ,
The contribution of metal ions to the structural stability of the large ribosomal subunit, RNA, vol.10, issue.9, pp.1366-1379, 2004. ,
DOI : 10.1261/rna.7390804
Magnesium ions mediate contacts between phosphoryl oxygens at positions 2122 and 2176 of the 23S rRNA and ribosomal protein L1, RNA, vol.6, issue.12, pp.1714-1726, 2000. ,
DOI : 10.1017/S1355838200001436
Crystallization and preliminary X-ray diffraction studies of the metal-ion-mediated ternary complex of the HutP protein with l-histidine and its cognate RNA, Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, vol.1702, issue.1, pp.125-128, 2004. ,
DOI : 10.1016/j.bbapap.2004.07.003
Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets, Nucleic Acids Research, vol.31, issue.23, pp.6942-6952, 2003. ,
DOI : 10.1093/nar/gkg880
The Mg2+ Binding Sites of the 5S rRNA Loop E Motif as Investigated by Molecular Dynamics Simulations, Chemistry & Biology, vol.10, issue.6, pp.551-561, 2003. ,
DOI : 10.1016/S1074-5521(03)00121-2
Long-Residency Hydration, Cation Binding, and Dynamics of Loop E/Helix IV rRNA-L25 Protein Complex, Biophysical Journal, vol.87, issue.5, pp.3397-3412, 2003. ,
DOI : 10.1529/biophysj.104.047126
Binding of Helix-Threading Peptides to E. coli 16S Ribosomal RNA and Inhibition of the S15-16S Complex, ChemBioChem, vol.3, issue.12, pp.2247-2254, 2005. ,
DOI : 10.1021/cc010003n
Identification of an RNA-Protein Bridge Spanning the Ribosomal Subunit Interface, Science, vol.285, issue.5436, pp.2133-2135, 1999. ,
DOI : 10.1126/science.285.5436.2133
30S ribosomal subunits can be assembled in vivo without primary binding ribosomal protein S15, RNA, vol.12, issue.7, pp.1-11, 2006. ,
DOI : 10.1261/rna.2262106
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1484426
Molecular dynamics simulations of RNA: Anin silico single molecule approach, Biopolymers, vol.81, issue.2, pp.169-184, 2007. ,
DOI : 10.1080/07391102.2001.10506748
Theoretical Study of Binding of Hydrated Zn(II) and Mg(II) Cations to 5???-Guanosine Monophosphate. Toward Polarizable Molecular Mechanics for DNA and RNA, The Journal of Physical Chemistry B, vol.107, issue.33, pp.8669-8681, 2003. ,
DOI : 10.1021/jp022659s
Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. ii: sequence context effects on the dynamical structures of the 10 unique dinucleotide steps, Biophys. J, vol.89, pp.3721-3740, 2005. ,
URL : https://hal.archives-ouvertes.fr/hal-00313393
Force Field with Improved Sugar Pucker Phases and Helical Repeat, Journal of Biomolecular Structure and Dynamics, vol.16, issue.4, pp.845-861, 1999. ,
DOI : 10.1080/07391102.1998.10508245
Quantum and statistical mechanical studies of liquids. 10. Transferable intermolecular potential functions for water, alcohols, and ethers. Application to liquid water, Journal of the American Chemical Society, vol.103, issue.2, pp.335-340, 1981. ,
DOI : 10.1021/ja00392a016
) method for Ewald sums in large systems, The Journal of Chemical Physics, vol.9, issue.12, pp.10089-10092, 1993. ,
DOI : 10.1126/science.2548279
Ion-water interaction potentials derived from free energy perturbation simulations, The Journal of Physical Chemistry, vol.94, issue.21, pp.8021-8024, 1990. ,
DOI : 10.1021/j100384a009
Molecular dynamics with coupling to an external bath, The Journal of Chemical Physics, vol.15, issue.8, 1984. ,
DOI : 10.1039/fs9821700055
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes, Journal of Computational Physics, vol.23, issue.3, pp.327-341, 1977. ,
DOI : 10.1016/0021-9991(77)90098-5
Automated Assignment of Ambiguous Nuclear Overhauser Effects with ARIA, Methods Enzymol, vol.339, pp.71-90, 2001. ,
DOI : 10.1016/S0076-6879(01)39310-2
RECOORD: A recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank, Proteins: Structure, Function, and Bioinformatics, vol.19, issue.4, pp.662-672, 2005. ,
DOI : 10.1002/prot.20408
Influence of non-bonded parameters on the quality of NMR structures: A new force field for NMR structure calculation, Journal of Biomolecular NMR, vol.13, issue.1, pp.51-59, 1999. ,
DOI : 10.1023/A:1008365802830
PROCHECK: a program to check the stereochemical quality of protein structures, Journal of Applied Crystallography, vol.26, issue.2, pp.283-291, 1993. ,
DOI : 10.1107/S0021889892009944
Errors in protein structures, Nature, vol.381, issue.6580, p.272, 1996. ,
DOI : 10.1038/381272a0
Torsion-Angle Molecular Dynamics as a New Efficient Tool for NMR Structure Calculation, Journal of Magnetic Resonance, vol.124, issue.1, 1997. ,
DOI : 10.1006/jmre.1996.1027
Comparison of Different Torsion Angle Approaches for NMR Structure Determination, Journal of Biomolecular NMR, vol.18, issue.3, pp.1-15, 2006. ,
DOI : 10.1080/07391102.1989.10507739
Refinement of protein structures in explicit solvent, Proteins: Structure, Function, and Bioinformatics, vol.8, issue.3, pp.496-506, 2003. ,
DOI : 10.1002/prot.10299
Structures of the Bacterial Ribosome at 3.5 A Resolution, Science, vol.310, issue.5749, pp.827-834, 2005. ,
DOI : 10.1126/science.1117230
Relative stability of protein structures determined by X-ray crystallography or NMR spectroscopy: A molecular dynamics simulation study, Proteins: Structure, Function, and Bioinformatics, vol.22, issue.1, pp.111-120, 2003. ,
DOI : 10.1007/978-94-015-7658-1_21
Refined solution structure and backbone dynamics of 15 Nlabeled C12A-p8MTCP1 studied by NMR relaxation, Journal of Biomolecular NMR, vol.15, issue.4, pp.271-288, 1999. ,
DOI : 10.1023/A:1008336418418
Helix motion in protein C12A-p8MTCP1: Comparison of molecular dynamics simulations and multifield NMR relaxation data, Journal of Computational Chemistry, vol.9, issue.16, pp.1577-1586, 2002. ,
DOI : 10.1002/pro.5560070314
Structure refinement of flexible proteins using dipolar couplings: application to the protein p8MTCP1, Journal of Biomolecular NMR, vol.22, issue.1, pp.47-56, 2002. ,
DOI : 10.1023/A:1013821123201
RNA backbone is rotameric, Proc. Natl. Acad. Sci. USA, pp.13904-13909, 2003. ,
DOI : 10.1002/pro.5560060807
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC283519
Theoretical studies of an exceptionally stable RNA tetraloop: observation of convergence from an incorrect NMR structure to the correct one using unrestrained molecular dynamics, Journal of Molecular Biology, vol.270, issue.3, pp.436-450, 1997. ,
DOI : 10.1006/jmbi.1997.1113
Combined Locally Enhanced Sampling and Particle Mesh Ewald as a Strategy To Locate the Experimental Structure of a Nonhelical Nucleic Acid, Journal of the American Chemical Society, vol.120, issue.29, pp.7149-7155, 1998. ,
DOI : 10.1021/ja9727023
Solution structure of an unusually stable RNA hairpin, 5'GGAC(UUCG)GUCC, Nature, vol.346, pp.613-614, 1990. ,
DOI : 10.1038/346680a0
Structure of the P1 Helix from Group I Self-splicing Introns, Journal of Molecular Biology, vol.250, issue.3, pp.333-353, 1995. ,
DOI : 10.1006/jmbi.1995.0381
Detailed analysis of RNA-protein interactions within the ribosomal protein S8-rRNA complex from the archaeon Methanococcus jannaschii, Journal of Molecular Biology, vol.311, issue.2, pp.311-324, 2001. ,
DOI : 10.1006/jmbi.2001.4877
Symmetric K+ and Mg2+ Ion-binding Sites in the 5S rRNA Loop E Inferred from Molecular Dynamics Simulations, Journal of Molecular Biology, vol.335, issue.2, pp.555-571, 2004. ,
DOI : 10.1016/j.jmb.2003.10.057
URL : https://hal.archives-ouvertes.fr/hal-00104364
Satisfying Hydrogen Bonding Potential in Proteins, Journal of Molecular Biology, vol.238, issue.5, pp.777-793, 2003. ,
DOI : 10.1006/jmbi.1994.1334
Binding interactions between the core central domain of 16S rRNA and the ribosomal protein S15 determined by molecular dynamics simulations, Nucleic Acids Research, vol.31, issue.2, pp.629-638, 2003. ,
DOI : 10.1093/nar/gkg149
Role of conserved nucleotides in building the 16 S rRNA binding site for ribosomal protein S15, Journal of Molecular Biology, vol.305, issue.4, pp.785-803, 2001. ,
DOI : 10.1006/jmbi.2000.4354
Residual Dipolar Couplings in Protein Structure Determination, Methods Mol. Biol, vol.278, pp.89-106, 2004. ,
DOI : 10.1385/1-59259-809-9:089
Role of N-terminal helix in interaction of ribosomal protein S15 with 16S rRNA, Biochemistry (Moscow), vol.320, issue.12, pp.1319-1323, 2004. ,
DOI : 10.1007/s10541-005-0076-5
Analysis of RNA motifs, Current Opinion in Structural Biology, vol.13, issue.3, pp.300-308, 2003. ,
DOI : 10.1016/S0959-440X(03)00076-9
Sequence to Structure (S2S): display, manipulate and interconnect RNA data from sequence to structure, Bioinformatics, vol.21, issue.15, pp.3320-3321, 2005. ,
DOI : 10.1093/bioinformatics/bti504
The PyMOL Molecular Graphics System, 2002. ,