We present extensive explicit solvent molecular dynamics analysis of three RNA three-way junctions (3WJs) from the large ribosomal subunit: the 3WJ formed by Helices 90-92 (H90-H92) of 23S rRNA; the 3WJ formed by H42-H44 organizing the GTPase associated center (GAC) of 23S rRNA; and the 3WJ of 5S rRNA. H92 near the peptidyl transferase center binds the 3'-CCA end of amino-acylated tRNA. The GAC binds protein factors and stimulates GTP hydrolysis driving protein synthesis. The 5S rRNA binds the central protuberance and A-site finger (ASF) involved in bridges with the 30S subunit. The simulations reveal that all three 3WJs possess significant anisotropic hinge-like flexibility between their stacked stems and dynamics within the compact regions of their adjacent stems. The A-site 3WJ dynamics may facilitate accommodation of tRNA, while the 5S 3WJ flexibility appears to be essential for coordinated movements of ASF and 5S rRNA. The GAC 3WJ may support large-scale dynamics of the L7/L12-stalk region. The simulations reveal that H42-H44 rRNA segments are not fully relaxed and in the X-ray structures they are bent towards the large subunit. The bending may be related to L10 binding and is distributed between the 3WJ and the H42-H97 contact.

Institute of Biophysics Academy of Sciences of the Czech Republic 61265 Brno Czech Republic

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Lescoute A, Westhof E. Topology of three-way junctions in folded RNAs. RNA. 2006;12:83–93. PubMed PMC

McDowell SE, Spackova N, Sponer J, Walter NG. Molecular dynamics simulations of RNA: an in silico single molecule approach. Biopolymers. 2007;85:169–184. PubMed PMC

Hall KB. RNA in motion. Curr. Opin. Chem. Biol. 2008;12:612–618. PubMed PMC

Auffinger P, Hashem Y. Nucleic acid solvation: from outside to insight. Curr. Opin. Struct. Biol. 2007;17:325–333. PubMed

Cheatham TE. Simulation and modeling of nucleic acid structure, dynamics and interactions. Curr. Opin. Struct. Biol. 2004;14:360–367. PubMed

Banas P, Jurecka P, Walter NG, Sponer J, Otyepka M. Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM. Methods. 2009;49:202–216. PubMed PMC

Ditzler MA, Otyepka M, Šponer J, Walter NG. Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in. Acc. Chem. Res. 2010;43:40–47. PubMed PMC

Trabuco LG, Villa E, Mitra K, Frank J, Schulten K. Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Structure. 2008;16:673–683. PubMed PMC

Villa A, Wöhnert J, Stock G. Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch. Nucleic Acids Res. 2009;37:4774–4786. PubMed PMC

Auffinger P, Bielecki L, Westhof E. Symmetric K+ and Mg2+ ion-binding sites in the 5 S rRNA loop E inferred from molecular dynamics simulations. J. Mol. Biol. 2004;335:555–571. PubMed

Reblova K, Lankas F, Razga F, Krasovska MV, Koca J, Sponer J. Structure, dynamics, and elasticity of free 16S rRNA helix 44 studied by molecular dynamics simulations. Biopolymers. 2006;82:504–520. PubMed

Li W, Ma BY, Shapiro BA. Binding interactions between the core central domain of 16S rRNA and the ribosomal protein S15 determined by molecular dynamics simulations. Nucleic Acids Res. 2003;31:629–638. PubMed PMC

Li PTX, Vieregg J, Tinoco I. How RNA unfolds and refolds. Annu. Rev. Biochem. 2008;77:77–100. PubMed

Razga F, Koca J, Sponer J, Leontis NB. Hinge-like motions in RNA kink-turns: the role of the second A-minor motif and nominally unpaired bases. Biophys. J. 2005;88:3466–3485. PubMed PMC

Besseova I, Otyepka M, Reblova K, Sponer J. Dependence of A-RNA simulations on the choice of the force field and salt strength. Phys. Chem. Chem. Phys. 2009;11:10701–10711. PubMed

Orozco M, Perez A, Noy A, Luque FJ. Theoretical methods for the simulation of nucleic acids. Chem. Soc. Rev. 2003;32:350–364. PubMed

Spackova N, Sponer J. Molecular dynamics simulations of sarcin-ricin rRNA motif. Nucleic Acids Res. 2006;34:697–708. PubMed PMC

Ninio J. Multiple stages in codon-anticodon recognition: double-trigger mechanisms and geometric constraints. Biochimie. 2006;88:963–992. PubMed

Blanchard SC, Kim HD, Gonzalez RL, Puglisi JD, Chu S. tRNA dynamics on the ribosome during translation. Proc. Natl Acad. Sci. USA. 2004;101:12893–12898. PubMed PMC

Mitra K, Frank J. Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps. Annu. Rev. Biophys. Biomol. Struct. 2006;35:299–317. PubMed

Frank J, Spahn CMT. The ribosome and the mechanism of protein synthesis. Rep. Prog. Phys. 2006;69:1383–1417.

Blanchard SC, Gonzalez RL, Kim HD, Chu S, Puglisi JD. tRNA selection and kinetic proofreading in translation. Nat. Struct. Mol. Biol. 2004;11:1008–1014. PubMed

Dorywalska M, Blanchard SC, Gonzalez RL, Kim HD, Chu S, Puglisi JD. Site-specific labeling of the ribosome for single-molecule spectroscopy. Nucleic Acids Res. 2005;33:182–189. PubMed PMC

Spirin AS. Ribosome as a molecular machine. FEBS Lett. 2002;514:2–10. PubMed

Krasovska MV, Sefcikova J, Reblova K, Schneider B, Walter NG, Sponer J. Cations and hydration in catalytic RNA: molecular dynamics of the hepatitis delta virus ribozyme. Biophys. J. 2006;91:626–638. PubMed PMC

Auffinger P, Bielecki L, Westhof E. The Mg2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations. Chem. Biol. 2003;10:551–561. PubMed

Reblova K, Spackova N, Stefl R, Csaszar K, Koca J, Leontis NB, Sponer J. Non-Watson-Crick basepairing and hydration in RNA motifs: molecular dynamics of 5S rRNA loop E. Biophys. J. 2003;84:3564–3582. PubMed PMC

Shankar N, Kennedy SD, Chen G, Krugh TR, Turner DH. The NMR structure of an internal loop from 23S ribosomal RNA differs from its structure in crystals of 50S ribosomal subunits. Biochemistry. 2006;45:11776–11789. PubMed PMC

Leontis NB, Stombaugh J, Westhof E. The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Res. 2002;30:3497–3531. PubMed PMC

Brunelle JL, Youngman EM, Sharma D, Green R. The interaction between C75 of tRNA and the A loop of the ribosome stimulates peptidyl transferase activity. RNA. 2006;12:33–39. PubMed PMC

Voorhees RM, Weixlbaumer A, Loakes D, Kelley AC, Ramakrishnan V. Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome. Nat. Struct. Mol. Biol. 2009;16:528–533. PubMed PMC

Hansen MA, Kirpekar F, Ritterbusch W, Vester B. Posttranscriptional modifications in the A-loop of 23S rRNAs from selected archaea and eubacteria. RNA. 2002;8:202–213. PubMed PMC

Widerak M, Kern R, Malki A, Richarme G. U2552 methylation at the ribosomal A-site is a negative modulator of translational accuracy. Gene. 2005;347:109–114. PubMed

Razga F, Spackova N, Reblova K, Koca J, Leontis NB, Sponer J. Ribosomal RNA kink-turn motif - a flexible molecular hinge. J. Biomol. Struct. Dyn. 2004;22:183–193. PubMed

Goody TA, Melcher SE, Norman DG, Lilley DMJ. The kink-turn motif in RNA is dimorphic, and metal ion-dependent. RNA. 2004;10:254–264. PubMed PMC

Klein DJ, Schmeing TM, Moore PB, Steitz TA. The kink-turn: a new RNA secondary structure motif. EMBO J. 2001;20:4214–4221. PubMed PMC

Frank J, Agrawal RK. A ratchet-like inter-subunit reorganization of the ribosome during translocation. Nature. 2000;406:318–322. PubMed

Razga F, Koca J, Mokdad A, Sponer J. Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA. Nucleic Acids Res. 2007;35:4007–4017. PubMed PMC

Kouvela EC, Gerbanas GV, Xaplanteri MA, Petropoulos AD, Dinos GP, Kalpaxis DL. Changes in the conformation of 5S rRNA cause alterations in principal functions of the ribosomal nanomachine. Nucleic Acids Res. 2007;35:5108–5119. PubMed PMC

Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham TE, Debolt S, Ferguson D, Seibel G, Kollman PA. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comput. Phys. Commun. 1995;91:1–41.

Case DA, Darden TA, Cheatham TE, Simmerling CL, Wang J, Duke RE, Luo R, Merz KM, Wang B, Pearlman DA, et al. Amber 8. San Francisco, CA: University of California; 2004.

Duke RE, Pedersen LG. PMEMD 3. Chapel Hill: University of North Carolina; 2003. PubMed

Darden T, York D, Pedersen L. Particle mesh Ewald – an N.LOG(N) method for Ewald sums in large systems. J. Chem. Phys. 1993;98:10089–10092.

Ryckaert JP, Ciccotti G, Berendsen HJC. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 1977;23:327–341.

Harvey SC, Tan RKZ, Cheatham TE. The flying ice cube: velocity rescaling in molecular dynamics leads to violation of energy equipartition. J. Comput. Chem. 1998;19:726–740.

Case DA, Darden TA, Cheatham TE, Simmerling CL, Wang J, Duke RE, Luo R, Merz KM, Pearlman DA, Crowley M, et al. Amber 9. San Francisco, CA: University of California; 2006.

Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J. Mol. Graph. 1996;14:33–38. PubMed

Amadei A, Linssen ABM, Berendsen HJC. Essential Dynamics of Proteins. Proteins. 1993;17:412–425. PubMed

Mongan J. Interactive essential dynamics. J. Comput. Aided Mol. Des. 2004;18:433–436. PubMed

Zheng WJ, Doniach S. A comparative study of motor-protein motions by using a simple elastic-network model. Proc. Natl Acad. Sci. USA. 2003;100:13253–13258. PubMed PMC

Suhre K, Sanejouand YH. ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Res. 2004;32:W610–W614. PubMed PMC

Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. A Second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 1995;117:5179–5197.

Wang JM, Cieplak P, Kollman PA. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem. 2000;21:1049–1074.

Perez A, Marchan I, Svozil D, Sponer J, Cheatham TE, Laughton CA, Orozco M. Refinenement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers. Biophys. J. 2007;92:3817–3829. PubMed PMC

Krasilnikov AS, Mondragon A. On the occurrence of the T-loop RNA folding motif in large RNA molecules. RNA. 2003;9:640–643. PubMed PMC

Gutell RR, Cannone JJ, Konings D, Gautheret D. Predicting U-turns in ribosomal RNA with comparative sequence analysis. J. Mol. Biol. 2000;300:791–803. PubMed

Nissen P, Ippolito JA, Ban N, Moore PB, Steitz TA. RNA tertiary interactions in the large ribosomal subunit: the A-minor motif. Proc. Natl Acad. Sci. USA. 2001;98:4899–4903. PubMed PMC

Lescoute A, Westhof E. The A-minor motifs in the decoding recognition process. Biochimie. 2006;88:993–999. PubMed

Tamura M, Holbrook SR. Sequence and structural conservation in RNA ribose zippers. J. Mol. Biol. 2002;320:455–474. PubMed

Korostelev A, Ermolenko DN, Noller HF. Structural dynamics of the ribosome. Curr. Opin. Chem. Biol. 2008;12:674–683. PubMed PMC

Razga F, Zacharias M, Reblova K, Koca J, Sponer J. RNA kink-turns as molecular elbows: hydration, cation binding, and large-scale dynamics. Structure. 2006;14:825–835. PubMed

Schuwirth BS, Borovinskaya MA, Hau CW, Zhang W, Vila-Sanjurjo A, Holton JM, Cate JHD. Structures of the bacterial ribosome at 3.5 angstrom resolution. Science. 2005;310:827–834. PubMed

Zacharias M. Comparison of molecular dynamics and harmonic mode calculations on RNA. Biopolymers. 2000;54:547–560. PubMed

Tama F, Wriggers W, Brooks CL. Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory. J. Mol. Biol. 2002;321:297–305. PubMed

Tama F, Valle M, Frank J, Brooks CL. Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy. Proc. Natl Acad. Sci. USA. 2003;100:9319–9323. PubMed PMC

Fulle S, Gohlke H. Molecular recognition of RNA: challenges for modelling interactions and plasticity. J. Mol. Recognit. 2010;23:220–231. PubMed

Van Wynsberghe AW, Cui Q. Comparison of mode analyses at different resolutions applied to nucleic acid systems. Biophys. J. 2005;89:2939–2949. PubMed PMC

Kramer MA. Nonlinear principal component analysis autoassociative neural networks. AIChE J. 1991;37:233–243.

Cheatham TE, Young MA. Molecular dynamics simulation of nucleic acids: successes, limitations, and promise. Biopolymers. 2000;56:232–256. PubMed

Fadrna E, Spackova N, Stefl R, Koca J, Cheatham TE, Sponer J. Molecular dynamics simulations of guanine quadruplex loops: advances and force field limitations. Biophys. J. 2004;87:227–242. PubMed PMC

Zacharias M. Simulation of the structure and dynamics of nonhelical RNA motifs. Curr. Opin. Struct. Biol. 2000;10:311–317. PubMed

Lankas F, Sponer J, Hobza P, Langowski J. Sequence-dependent elastic properties of DNA. J. Mol. Biol. 2000;299:695–709. PubMed

Sanbonmatsu KY, Joseph S, Tung CS. Simulating movement of tRNA into the ribosome during decoding. Proc. Natl Acad. Sci. USA. 2005;102:15854–15859. PubMed PMC

Gao HX, Sengupta J, Valle M, Korostelev A, Eswar N, Stagg SM, Van Roey P, Agrawal RK, Harvey SC, Sali A, et al. Study of the structural dynamics of the E-coli 70S ribosome using real-space refinement. Cell. 2003;113:789–801. PubMed

Sergiev PV, Lesnyak DV, Burakovsky DE, Kiparisov SV, Leonov AA, Bogdanov AA, Brimacombe R, Dontsova OA. Alteration in location of a conserved GTPase-associated center of the ribosome induced by mutagenesis influences the structure of peptidyltransferase center and activity of elongation factor G. J. Biol. Chem. 2005;280:31882–31889. PubMed

Mokdad A, Leontis NB. Ribostral: an RNA 3D alignment analyzer and viewer based on basepair isostericities. Bioinformatics. 2006;22:2168–2170. PubMed PMC

Miyoshi T, Uchiumi T. Functional interaction between bases C1049 in domain II and G2751 in domain VI of 23S rRNA in Escherichia coli ribosomes. Nucleic Acids Res. 2008;36:1783–1791. PubMed PMC

Sanbonmatsu KY. Alignment/misalignment hypothesis for tRNA selection by the ribosome. Biochimie. 2006;88:1075–1089. PubMed

Diaconu M, Kothe U, Schlunzen F, Fischer N, Harms JM, Tonevitsky AG, Stark H, Rodnina MV, Wahl MC. Structural basis for the function of the ribosomal L7/12 stalk in factor binding and GTPase activation. Cell. 2005;121:991–1004. PubMed

Gao YG, Selmer M, Dunham CM, Weixlbaumer A, Kelley AC, Ramakrishnan V. The structure of the ribosome with elongation factor G trapped in the posttranslocational state. Science. 2009;326:694–699. PubMed PMC

Kavran JM, Steitz TA. Structure of the base of the L7/L12 stalk of the Haloarcula marismortui large ribosomal subunit: analysis of L11 movements. J. Mol. Biol. 2007;371:1047–1059. PubMed

Kiparisov S, Petrov A, Meskauskas A, Sergiev PV, Dontsova OA, Dinman JD. Structural and functional analysis of 5S rRNA in Saccharomyces cerevisiae. Mol. Genet. Genomics. 2005;274:235–247. PubMed PMC

Rakauskaite R, Dinman JD. An arc of unpaired “hinge bases” facilitates information exchange among functional centers of the ribosome. Mol. Cell. Biol. 2006;26:8992–9002. PubMed PMC

Sergiev PV, Kiparisov SV, Burakovsky DE, Lesnyak DV, Leonov AA, Bogdanov AA, Dontsova OA. The conserved A-site finger of the 23 S rRNA: just one of the intersubunit bridges or a part of the allosteric communication pathway? J. Mol. Biol. 2005;353:116–123. PubMed

Gao N, Frank J. A library of RNA bridges. Nat. Chem. Biol. 2006;2:231–232. PubMed

Komoda T, Sato NS, Phelps SS, Namba N, Joseph S, Suzuki T. The a-site finger in 23 S rRNA acts as a functional attenuator for translocation. J. Biol. Chem. 2006;281:32303–32309. PubMed

Piekna-Przybylska D, Przybylski P, Baudin-Baillieu AS, Rousset JP, Fournier MJ. Ribosome performance is enhanced by a rich cluster of pseudouridines in the A-site finger region of the large subunit. J. Biol. Chem. 2008;283:26026–26036. PubMed PMC

Agirrezabala X, Lei JL, Brunelle JL, Ortiz-Meoz RF, Green R, Frank J. Visualization of the hybrid state of tRNA binding promoted by spontaneous ratcheting of the ribosome. Mol. Cell. 2008;32:190–197. PubMed PMC

Yusupov MM, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, Cate JHD, Noller HF. Crystal structure of the ribosome at 5.5 angstrom resolution. Science. 2001;292:883–896. PubMed

Reblova K, Razga F, Li W, Gao H, Frank J, Sponer J. Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and cryo-EM. Nucleic Acids Res. 2009;38:1325–1340. PubMed PMC

Klein DJ, Moore PB, Steitz TA. The roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit. J. Mol. Biol. 2004;340:141–177. PubMed

Zirbel CL, Sponer JE, Sponer J, Stombaugh J, Leontis NB. Classification and energetics of the base-phosphate interactions in RNA. Nucleic Acids Res. 2009;37:4898–4918. PubMed PMC

Harms J, Schluenzen F, Zarivach R, Bashan A, Gat S, Agmon I, Bartels H, Franceschi F, Yonath A. High resolution structure of the large ribosomal subunit from a mesophilic eubacterium. Cell. 2001;107:679–688. PubMed

Laurberg M, Asahara H, Korostelev A, Zhu JY, Trakhanov S, Noller HF. Structural basis for translation termination on the 70S ribosome. Nature. 2008;454:852–857. PubMed

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