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RNA 3D Structure Analysis and Prediction pp 299–318Cite as

Ions in Molecular Dynamics Simulations of RNA Systems

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Part of the book series: Nucleic Acids and Molecular Biology ((NUCLEIC,volume 27))

Abstract

Ions and water molecules are intricately associated with biomolecular systems and play important structural and functional roles that are still not well understood. For RNA systems, the functions of these ions are not limited to the neutralization of the charges carried by the polyanionic backbone, since they also bind to very specific locations of the RNA 3D fold. Hence, it is essential to include them with the greatest possible accuracy in 3D structural models and especially in molecular dynamics (MD) simulations. This review aims at describing some of the successes achieved in the modeling of monovalent and divalent ions in RNA systems, as well as to highlight important deficiencies of current force fields and MD techniques that represent important challenges for future development.

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References

  • Auffinger P (2006) Molecular dynamics simulations of RNA systems: importance of the initial conditions. In: Sponer J, Lankas F (eds) Computational studies of DNA and RNA, vol II. Springer, Berlin, pp 283–300

    Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Auffinger P, Westhof E (2000) Water and ion binding around RNA and DNA (C, G)-oligomers. J Mol Biol 300:1113–1131

    PubMed  CAS  Google Scholar 

  • Auffinger P, Westhof E (2001) Water and ion binding around r(UpA)12 and d(TpA)12 oligomers – comparison with RNA and DNA (CpG)12 duplexes. J Mol Biol 305:1057–1072

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Auffinger P, Bielecki L, Westhof E (2004b) Anion binding to nucleic acids. Structure 12:379–388

    PubMed  CAS  Google Scholar 

  • Auffinger P, Cheatham TE, Vaiana AC (2007) Spontaneous formation of KCl aggregates in biomolecular simulations: a force field issue? J Chem Theor Comput 3:1851–1859

    CAS  Google Scholar 

  • Auffinger P, Grover N, Westhof E (2011) Metal ion binding to RNA. In: Sigel A, Sigel H, Sigel RKO (eds) Structural and catalytic roles of metal ions in RNA, vol 9. The Royal Society of Chemistry, Cambridge, pp 1–35

    Google Scholar 

  • Banas P, Rulisek L, Hanosova V, Svozil D, Walter NG, Sponer J, Otyepka M (2008) General base catalysis for cleavage by the active-site cytosine of the hepatitis delta virus ribozyme: QM/MM calculations establish chemical feasibility. J Phys Chem B 112:11177–11187

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Banas P, Walter NG, Sponer J, Otyepka M (2010) Protonation states of the key active site residues and structural dynamics of the glmS riboswitch as revealed by molecular dynamics. J Phys Chem B 114:8701–8712

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Besseova I, Reblova K, Leontis NB, Sponer J (2010) Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosome. Nucleic Acids Res 18:6247–6264

    Google Scholar 

  • Black Pyrkosz A, Eargle J, Sethi A, Luthey-Schulten Z (2010) Exit strategies for charged tRNA from GluRS. J Mol Biol 397:1350–1371

    PubMed  CAS  Google Scholar 

  • Bock CW, Katz AK, Markham GD, Glusker JP (1999) Manganese as a replacement for magnesium and zinc: functional comparison of the divalent ions. J Am Chem Soc 121:7360–7372

    CAS  Google Scholar 

  • Bock CW, Markham GD, Katz AK, Glusker JP (2006) The arrangement of first- and second-shell water molecules around metal ions: effect of charge and size. Theor Chem Acc 115:100–112

    CAS  Google Scholar 

  • Callahan KM, Casillas-Ituarte NN, Roeselova M, Allen HC, Tobias DJ (2010) Solvation of magnesium dication: molecular dynamics simulation and vibrational spectroscopic study of magnesium chloride in aqueous solutions. J Phys Chem A 114:5141–5148

    PubMed  CAS  Google Scholar 

  • Case DA, Darden TA, Cheatham TE I, Simmerling CL, Wang J, Duke RE, Luo R, Walker RC, Zhang W, Merz KM, Roberts B, Wang B, Hayik S, Roitberg A, Seabra G, Kolossváry I, Wong KF, Paesani F, Vanicek J, Liu L, Wu X, Brozell SR, Steinbrecher T, Gohlke H, Cai Q, Ye X, Wang J, Hsieh M-J, Cui G, Roe DR, Mathews DH, Seetin MG, Sagui C, Babin V, Luchko T, Gusarov S, Kovalenko A, Kollman PA (2010) AMBER 11. University of California, San Francisco, CA

    Google Scholar 

  • Cheatham TE, Kollman PA (1997) Insight into the stabilization of A-DNA by specific ion association: spontaneous B-DNA to A-DNA transitions observed in molecular dynamics simulations of d(ACCCGCGGGT)2 in the presence of hexaamminecobalt(III). Structure 15:1297–1311

    Google Scholar 

  • Cheatham TE, Kollman PA (2000) Molecular dynamics simulation of nucleic acids. Annu Rev Phys Chem 51:435–471

    PubMed  CAS  Google Scholar 

  • Chen AA, Pappu RV (2007a) Quantitative characterization of ion pairing and cluster formation in strong 1:1 electrolytes. J Phys Chem B 111:6469–6478

    PubMed  CAS  Google Scholar 

  • Chen AA, Pappu RV (2007b) Parameters of monovalent ions in the AMBER-99 forcefield: assessment of inaccuracies and proposed improvements. J Phys Chem B 111:11884–11887

    PubMed  CAS  Google Scholar 

  • Chen AA, Draper DE, Pappu RV (2009a) Molecular simulation studies of monovalent counterion-mediated interactions in a model RNA kissing loop. J Mol Biol 390:805–819

    PubMed  CAS  Google Scholar 

  • Chen AA, Marucho M, Baker NA, Pappu RV (2009b) Simulations of RNA interactions with monovalent cations. Methods Enzymol 469:411–432

    PubMed  CAS  Google Scholar 

  • Correll CC, Freeborn B, Moore PB, Steitz TA (1997) Metals, motifs and recognition in the crystal structure of a 5S rRNA domain. Cell 91:705–712

    PubMed  CAS  Google Scholar 

  • Csaszar K, Spackova N, Stefl R, Sponer J, Leontis NB (2001) Molecular dynamics of the frame-shifting pseudoknot from beet western yellow virus: the role of non-Watson-Crick base-pairing, ordered hydration, cation binding and base mutations on stability and unfolding. J Mol Biol 313:1073–1091

    PubMed  CAS  Google Scholar 

  • Das U, Chen S, Fuxreiter M, Vaguine AA, Richelle J, Berman HM, Wodak SJ (2001) Checking nucleic acid crystal structures. Acta Crystallogr D57:813–828

    CAS  Google Scholar 

  • Ditzler MA, Sponer J, Walter NG (2009) Molecular dynamics suggest multifunctionality of an adenine imino group in acid-base catalysis of the hairpin ribozyme. RNA 15:560–575

    PubMed  CAS  Google Scholar 

  • Draper DE, Grilley D, Soto AM (2005) Ions and RNA folding. Annu Rev Biophys Biomol Struct 34:221–243

    PubMed  CAS  Google Scholar 

  • Eargle J, Black AA, Sethi A, Trabuco LG, Luthey-Schulten Z (2008) Dynamics of recognition between tRNA and elongation factor Tu. J Mol Biol 377:1382–1405

    PubMed  CAS  Google Scholar 

  • Feig M, Pettitt BM (1999) Sodium and chlorine ions as part of the DNA solvation shell. Biophys J 77:1769–1781

    PubMed  CAS  Google Scholar 

  • Giambasu GM, Lee TS, Sosa CP, Robertson MP, Scott WG, York DM (2010) Identification of dynamical hinge points of the L1 ligase molecular switch. RNA 16:769–780

    PubMed  CAS  Google Scholar 

  • Gluick TC, Gerstner RB, Draper DE (1997) Effects of Mg2+, K+, and H+ on an equilibrium between alternative conformations of an RNA pseudoknot. J Mol Biol 270:451–463

    PubMed  CAS  Google Scholar 

  • Golebiowski J, Antonczak S, Di-Giorgio A, Condom R, Cabrol-Bass D (2004) Molecular dynamics simulation of hepatitis C virus IRES IIId domain: structural behavior, electrostatic and energetic analysis. J Mol Model 10:60–68

    PubMed  CAS  Google Scholar 

  • Harding MH (2006) Small revisions to predicted distances around metal sites in proteins. Acta Crystallogr D62:678–682

    CAS  Google Scholar 

  • Hashem Y, Auffinger P (2009) A short guide to molecular dynamics simulations of RNA systems. Methods 47:187–197

    PubMed  CAS  Google Scholar 

  • Hashem Y, Westhof E, Auffinger P (2008) Milestones in molecular dynamics simulations of RNA systems. In: Schwede T, Peitsch MC (eds) Computational structural biology, vol 13. World Scientific, London, pp 363–399

    Google Scholar 

  • Heddi B, Foloppe N, Hantz E, Hartmann B (2007) The DNA structure responds differently to physiological concentrations of K(+) or Na(+). J Mol Biol 368:1403–1411

    PubMed  CAS  Google Scholar 

  • Hermann T, Auffinger P, Scott WG, Westhof E (1997) Evidence for a hydroxide ion bridging two magnesium ions at the active site of the hammerhead ribozyme. Nucleic Acids Res 25:3421–3427

    PubMed  CAS  Google Scholar 

  • Hermann T, Auffinger P, Westhof E (1998) Molecular dynamics investigations of the hammerhead ribozyme RNA. Eur J Biophys 27:153–165

    CAS  Google Scholar 

  • Huang W, Kim J, Jha S, Aboul-ela F (2009) A mechanism for S-adenosyl methionine assisted formation of a riboswitch conformation: a small molecule with a strong arm. Nucleic Acids Res 37:6528–6539

    PubMed  CAS  Google Scholar 

  • Ikeda T, Boero M, Terakura K (2007) Hydration properties of magnesium and calcium ions from constrained first principles molecular dynamics. J Chem Phys 127:074503

    PubMed  Google Scholar 

  • Jiao D, King C, Grossfield A, Darden TA, Ren P (2006) Simulation of Ca2+ and Mg2+ solvation using polarizable atomic multipole potential. J Phys Chem B 110:18553–18559

    PubMed  CAS  Google Scholar 

  • Joung IS, Cheatham TE III (2008) Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations. J Phys Chem B 112:9020–9041

    PubMed  CAS  Google Scholar 

  • Joung IS, Cheatham TE III (2009) Molecular dynamics simulations of the dynamic and energetic properties of alkali and halide ions using water-model-specific ion parameters. J Phys Chem B 113:13279–13290

    PubMed  CAS  Google Scholar 

  • Kieft JS, Chase E, Costantino DA, Golden BL (2010) Identification and characterization of anion binding sites in RNA. RNA 16:1118–1123

    PubMed  CAS  Google Scholar 

  • Kirmizialtin S, Elber R (2010) Computational exploration of mobile ion distributions around RNA duplex. J Phys Chem B 114:8207–8220

    PubMed  CAS  Google Scholar 

  • Korolev N, Lyubartsev AP, Nordenskiold L, Laaksonen A (2001) Spermine: an “invisible” component in the crystals of B-DNA. A grand canonical Monte Carlo and molecular dynamics simulation study. J Mol Biol 308:907–917

    PubMed  CAS  Google Scholar 

  • Korolev N, Lyubartsev AP, Laaksonen A, Nordenskiold L (2002) On the competition between water, sodium ions, and spermine ion binding to DNA: a molecular dynamics computer simulation study. Biophys J 82:2860–2875

    PubMed  CAS  Google Scholar 

  • Korolev N, Lyubartsev AP, Laaksonen A, Nordenskiold L (2003) A molecular dynamics simulation study of oriented DNA with polyamine and sodium counterions: diffusion and averaged binding of water and cations. Nucleic Acids Res 31:5971–5981

    PubMed  CAS  Google Scholar 

  • Korolev N, Lyubartsev AP, Laaksonen A, Nordenskiold L (2004) Molecular dynamics simulation study of oriented polyamine- and Na-DNA: sequence specific interactions and effects on DNA structure. Biopolymers 73:542–555

    PubMed  CAS  Google Scholar 

  • Krasovska MV, Sefcikova J, Spackova N, Sponer J, Walter NG (2005) Structural dynamics of precursor and product of the RNA enzyme from the hepatitis delta virus as revealed by molecular dynamics simulations. J Mol Biol 351:731–748

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Lambert D, Leipply D, Shiman R, Draper DE (2009) The influence of monovalent cation size on the stability of RNA tertiary structures. J Mol Biol 390:791–804

    PubMed  CAS  Google Scholar 

  • Leclerc F (2010) Hammerhead ribozymes: true metal or nucleobase catalysis? Where is the catalytic power from? Molecules 15:5389–5407

    PubMed  CAS  Google Scholar 

  • Lee TS, York DM (2008) Origin of mutational effects at the C3 and G8 positions on hammerhead ribozyme catalysis from molecular dynamics simulations. J Am Chem Soc 130:7168–7169

    PubMed  CAS  Google Scholar 

  • Lee TS, Silva-Lopez C, Martick M, Scott WG, York DM (2007) Insight into the role of Mg2+ in hammerhead ribozyme catalysis from X-ray crystallography and molecular dynamics simulation. J Chem Theor Comput 3:325–327

    CAS  Google Scholar 

  • Lee TS, Giambasu GM, Sosa CP, Martick M, Scott WG, York DM (2009) Threshold occupancy and specific cation binding modes in the hammerhead ribozyme active site are required for active conformation. J Mol Biol 388:195–206

    PubMed  CAS  Google Scholar 

  • Lopes PE, Roux B, Mackerell AD (2009) Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability. Theory and applications. Theor Chem Acc 124:11–28

    PubMed  CAS  Google Scholar 

  • Makarov VA, Feig M, Andrews BK, Pettitt MM (1998) Diffusion of solvent around biomolecular solutes: a molecular dynamics simulation study. Biophys J 75:150–158

    PubMed  CAS  Google Scholar 

  • Manning GS (1978) The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides. Q Rev Biophys 11:179–246

    PubMed  CAS  Google Scholar 

  • Markham GD, Glusker JP, Bock CW (2002) The arrangement of first and second-sphere water molecules in divalent magnesium complexes: results from molecular orbital and density functional theory and from structural crystallography. J Phys Chem B 106:5118–5134

    CAS  Google Scholar 

  • Martick M, Lee TS, York DM, Scott WG (2008) Solvent structure and hammerhead ribozyme catalysis. Chem Biol 15:332–342

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Mlynsky V, Banas P, Hollas D, Reblova K, Walter NG, Sponer J, Otyepka M (2010) Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme. J Phys Chem B 114:6642–6652

    PubMed  CAS  Google Scholar 

  • Muller T, Walter B, Wirtz A, Burkovski A (2006) Ammonium toxicity in bacteria. Curr Microbiol 52:400–406

    PubMed  Google Scholar 

  • Noy A, Soteras I, Luque FJ, Orozco M (2009) The impact of monovalent ion force field model in nucleic acids simulations. Phys Chem Chem Phys 11:10596–10607

    PubMed  CAS  Google Scholar 

  • Ohtaki H (2001) Ionic solvation in aqueous and nonaqueous solutions. Monatshefte für Chemie 132:1237–1268

    CAS  Google Scholar 

  • Oliva R, Cavallo L (2009) Frequency and effect of the binding of Mg2+, Mn2+, and Co2+ ions on the guanine base in Watson-Crick and reverse Watson-Crick base pairs. J Phys Chem B 113:15670–15678

    PubMed  CAS  Google Scholar 

  • Park JM, Boero M (2010) Protonation of a hydroxide anion bridging two divalent magnesium cations in water probed by first-principles metadynamics simulation. J Phys Chem B 114:11102–11109

    PubMed  CAS  Google Scholar 

  • Petrov AS, Lamm G, Pack GR (2002) Water-mediated magnesium-guanine interactions. J Phys Chem B 106:3294–3300

    CAS  Google Scholar 

  • Petrov AS, Lamm G, Pack GR (2005) Calculation of the binding free energy for magnesium-RNA interactions. Biopolymers 77:137–154

    PubMed  CAS  Google Scholar 

  • Priyakumar UD (2010) Atomistic details of the ligand discrimination mechanism of S(MK)/SAM-III riboswitch. J Phys Chem B 114:9920–9925

    PubMed  CAS  Google Scholar 

  • Rao JS, Dinadayalane TC, Leszczynski J, Sastry GN (2008) Comprehensive study on the solvation of mono- and divalent metal cations: Li+, Na+, K+, Be2+, Mg2+ and Ca2+. J Phys Chem A 112:12944–12953

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Reblova K, Spackova N, Sponer JE, Koca J, Sponer J (2003a) Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets. Nucleic Acids Res 31:6942–6952

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Reblova K, Spackova N, Koca J, Leontis NB, Sponer J (2004) Long-residency hydration, cation binding, and dynamics of loop E/helix IV rRNA-L25 protein complex. Biophys J 87:3397–3412

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Reblova K, Fadrna E, Sarzynska J, Kulinski T, Kulhanek P, Ennifar E, Koca J, Sponer J (2007) Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by molecular dynamics. Biophys J 93:3932–3949

    PubMed  CAS  Google Scholar 

  • Reblova K, Razga F, Li W, Gao H, Frank J, Sponer J (2010a) Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM. Nucleic Acids Res 38:1325–1340

    PubMed  CAS  Google Scholar 

  • Reblova K, Strelcova Z, Kulhanek P, Besseova I, Mathews DH, van Nostrand K, Yildirim I, Turner DH, Sponer J (2010b) An RNA molecular switch: intrinsic flexibility of 23S rRNA helices 40 and 68 5′-UAA/5′-GAN internal loops studied by molecular dynamics methods. J Chem Theor Comput 6:910–929

    CAS  Google Scholar 

  • Rhodes MM, Reblova K, Sponer J, Walter NG (2006) Trapped water molecules are essential to structural dynamics and function of a ribozyme. Proc Natl Acad Sci USA 103:13380–13385

    PubMed  CAS  Google Scholar 

  • Romanowska J, Setny P, Trylska J (2008) Molecular dynamics study of the ribosomal A-site. J Phys Chem B 112:15227–15243

    PubMed  CAS  Google Scholar 

  • Sanbonmatsu KY, Tung CS (2006) High performance computing in biology: multimillion atom simulations of nanoscale systems. J Struct Biol 157:470–480

    PubMed  Google Scholar 

  • Sefcikova J, Krasovska MV, Spackova N, Sponer J, Walter NG (2007) Impact of an extruded nucleotide on cleavage activity and dynamic catalytic core conformation of the hepatitis delta virus ribozyme. Biopolymers 85:392–406

    PubMed  CAS  Google Scholar 

  • Sharma M, Bulusu G, Mitra A (2009) MD simulations of ligand-bound and ligand-free aptamer: molecular level insights into the binding and switching mechanism of the add A-riboswitch. RNA 15:1673–1692

    PubMed  CAS  Google Scholar 

  • Sorin EJ, Rhee YM, Pande VS (2005) Does water play a structural role in the folding of small nucleic acids? Biophys J 88:2516–2524

    PubMed  CAS  Google Scholar 

  • Spackova N, Reblova K, Sponer J (2010) Structural dynamics of the box C/D RNA kink-turn and its complex with proteins: the role of the A-minor 0 interaction, long-residency water bridges, and structural ion-binding sites revealed by molecular simulations. J Phys Chem B 114:10581–10593

    PubMed  CAS  Google Scholar 

  • Takamoto K, He Q, Morris S, Chance MR, Brenowitz M (2002) Monovalent cations mediate formation of native tertiary structure of the Tetrahymena thermophila ribozyme. Nat Struct Biol 9:928–933

    PubMed  CAS  Google Scholar 

  • Torres RA, Bruice TC (2000) The mechanism of phosphodiester hydrolysis – near in-line attack conformations in the hammerhead ribozyme. J Am Chem Soc 122:781–791

    CAS  Google Scholar 

  • Torres RA, Himo F, Bruice TC, Noodleman L, Lovell T (2003) Theoretical examination of Mg(2+)-mediated hydrolysis of a phosphodiester linkage as proposed for the hammerhead ribozyme. J Am Chem Soc 125:9861–9867

    PubMed  CAS  Google Scholar 

  • Trabuco LG, Schreiner E, Eargle J, Cornish P, Ha T, Luthey-Schulten Z, Schulten K (2010) The role of L1 stalk-tRNA interaction in the ribosome elongation cycle. J Mol Biol 402:741–760

    PubMed  CAS  Google Scholar 

  • Vaiana AC, Westhof E, Auffinger P (2006) A molecular dynamics simulation study of an aminoglycoside/A-site RNA complex: conformational and hydration patterns. Biochimie 88:1061–1073

    PubMed  CAS  Google Scholar 

  • Veeraraghavan N, Bevilacqua PC, Hammes-Schiffer S (2010) Long-distance communication in the HDV ribozyme: insights from molecular dynamics and experiments. J Mol Biol 402:278–291

    PubMed  CAS  Google Scholar 

  • Vieregg J, Cheng W, Bustamante C, Tinoco I Jr (2007) Measurement of the effect of monovalent cations on RNA hairpin stability. J Am Chem Soc 129:14966–14973

    PubMed  CAS  Google Scholar 

  • Villa A, Wohnert J, Stock G (2009) Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch. Nucleic Acids Res 37:4774–4786

    PubMed  CAS  Google Scholar 

  • Woodson SA (2005) Metal ions and RNA folding: a highly charged topic with a dynamic future. Curr Opin Chem Biol 9:104–109

    PubMed  CAS  Google Scholar 

  • Young MA, Jayaram B, Beveridge DL (1997) Intrusion of counterions into the spine of hydration in the minor groove of B-DNA: fractional occupancy of electronegative pockets. J Am Chem Soc 119:59–69

    CAS  Google Scholar 

  • Yu H, Whitfield TW, Harder E, Lamoureux G, Vorobyov I, Anisimov VM, MacKerell AD, Roux B (2010) Simulating monovalent and divalent ions in aqueous solution using a Drude polarizable force field. J Chem Theor Comput 6:774–786

    CAS  Google Scholar 

  • Zhang C, Raugei S, Eisenberg B, Carloni P (2010) Molecular dynamics in physiological solutions: force fields, alkali metal ions, and ionic strength. J Chem Theor Comput 6:2167–2175

    CAS  Google Scholar 

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Acknowledgments

The author wishes to thank Prof. Eric Westhof for ongoing support and Prof. Neocles Leontis for useful comments and discussions.

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  1. Architecture et réactivité de l’ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, 67084, Strasbourg, France

    Pascal Auffinger

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  1. Dept. Chemistry, Bowling Green State University, Bowling Green, 43403, Ohio, USA

    Neocles Leontis

  2. Inst. Biologie Moleculaire, et Cellulaire, CNRS, rue Rene Descartes 15, Strasbourg CX, 67084, France

    Eric Westhof

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Auffinger, P. (2012). Ions in Molecular Dynamics Simulations of RNA Systems. In: Leontis, N., Westhof, E. (eds) RNA 3D Structure Analysis and Prediction. Nucleic Acids and Molecular Biology, vol 27. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-25740-7_14

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