The RNA hairpin loops represent important RNA topologies with indispensable biological functions in RNA folding and tertiary interactions. 5'-UNCG-3' and 5'-GNRA-3' RNA tetraloops are the most important classes of RNA hairpin loops. Both tetraloops are highly structured with characteristic signature three-dimensional features and are recurrently seen in functional RNAs and ribonucleoprotein particles. Explicit solvent molecular dynamics (MD) simulation is a computational technique which can efficiently complement the experimental data and provide unique structural dynamics information on the atomic scale. Nevertheless, the outcome of simulations is often compromised by imperfections in the parametrization of simplified pairwise additive empirical potentials referred to also as force fields. We have pointed out in several recent studies that a force field description of single-stranded hairpin segments of nucleic acids may be particularly challenging for the force fields. In this paper, we report a critical assessment of a broad set of MD simulations of UUCG, GAGA, and GAAA tetraloops using various force fields. First, we utilized the three widely used variants of Cornell et al. (AMBER) force fields known as ff94, ff99, and ff99bsc0. Some simulations were also carried out with CHARMM27. The simulations reveal several problems which show that these force fields are not able to retain all characteristic structural features (structural signature) of the studied tetraloops. Then we tested four recent reparameterizations of glycosidic torsion of the Cornell et al. force field (two of them being currently parametrized in our laboratories). We show that at least some of the new versions show an improved description of the tetraloops, mainly in the syn glycosidic torsion region of the UNCG tetraloop. The best performance is achieved in combination with the bsc0 parametrization of the α/γ angles. Another critically important region to properly describe RNA molecules is the anti/high-anti region of the glycosidic torsion, where there are significant differences among the tested force fields. The tetraloop simulations are complemented by simulations of short A-RNA stems, which are especially sensitive to an appropriate description of the anti/high-anti region. While excessive accessibility of the high-anti region converts the A-RNA into a senseless "ladder-like" geometry, excessive penalization of the high-anti region shifts the simulated structures away from typical A-RNA geometry to structures with a visibly underestimated inclination of base pairs with respect to the helical axis.

Departments of Medicinal Chemistry Pharmaceutical Chemistry and Pharmaceutics and Bioengineering University of Utah Salt Lake City Utah 84112 United States

Institute of Biophysics Academy of Sciences of the Czech Republic KraloVopolska 135 612 65 Brno Czech Republic

Joint Research Program in Computational Biology Institut de Recerca Biomédica and Barcelona Superocomputing Center Baldiri i Reixac 10 Barcelona 08028 Spain Jordi Girona 31 Barcelona 08028 Spain and Departament de Bioquýmica i Biologýa Molecular Facultat de Biologýa AVga Diagonal 645 UniVersitat de Barcelona Barcelona 08028 Spain

Regional Centre of Advanced Technologies and Materials Department of Physical Chemistry Faculty of Science Palacky UniVersity Olomouc tr 17 listopadu 12 771 46 Olomouc Czech Republic

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Leontis NB; Westhof E Analysis of RNA motifs. Cur. Opin. Struct. Biol 2003, 13, 300–308. PubMed

Mathews DH; Turner DH Prediction of RNA secondary structure by free energy minimization. Cur. Opin. Struct. Biol 2006, 16, 270–278. PubMed

Tuerk C; Gauss P; Thermes C; Groebe DR; Gayle M; Guild N; Stormo G; Daubentoncarafa Y; Uhlenbeck OC; Tinoco I; Brody EN; Gold L CUUCGG Hairpins - Extraordinarily Stable RNA Secondary Structures Associated with Various Biochemical Processes. Proc. Natl. Acad. Sci 1988, 85, 1364–1368. PubMed PMC

Uhlenbeck OC Nucleic-Acid Structure - Tetraloops and RNA Folding. Nature 1990, 346, 613–614. PubMed

Woese CR; Winker S; Gutell RR Architecture of Ribosomal-RNA - Constraints on the Sequence of Tetra-Loops. Proc. Natl. Acad. Sci 1990, 87, 8467–8471. PubMed PMC

Wolters J The Nature of Preferred Hairpin Structures in 16s-Like Ribosomal-RNA Variable Regions. Nucleic Acids Res. 1992, 20, 1843–1850. PubMed PMC

Bevilacqua PC; Blose JM Structures, kinetics, thermo-dynamics, and biological functions of RNA hairpins. Annu. Rev. Phys. Chem 2008, 59, 79–103. PubMed

Hsiao C; Mohan S; Hershkovitz E; Tannenbaum A; Williams LD Single nucleotide RNA choreography. Nucleic Acids Res. 2006, 34, 1481–1491. PubMed PMC

Blose JM; Proctor DJ; Veeraraghavan N; Misra VK; Bevilacqua PC Contribution of the Closing Base Pair to Exceptional Stability in RNA Tetraloops: Roles for Molecular Mimicry and Electrostatic Factors. J. Am. Chem. Soc 2009, 131, 8474–8484. PubMed

Varani G Exceptionally Stable Nucleic-Acid Hairpins. Annu. Rev. Biophys. Biomed 1995, 24, 379–404. PubMed

Marino JP; Gregorian RS; Csankovszki G; Crothers DM Bent Helix Formation between RNA Hairpins with Complementary Loops. Science 1995, 268, 1448–1454. PubMed

Chauhan S; Woodson SA Tertiary interactions determine the accuracy of RNA folding. J. Am. Chem. Soc 2008, 130, 1296–1303. PubMed PMC

Jaeger L; Michel F; Westhof E Involvement of a GNRA Tetraloop in Long-Range Tertiary Interactions. J. Mol. Biol 1994, 236, 1271–1276. PubMed

Ennifar E; Nikulin A; Tishchenko S; Serganov A; Nevskaya N; Garber M; Ehresmann B; Ehresmann C; Nikonov S; Dumas P The crystal structure of UUCG tetraloop. J. Mol. Biol 2000, 304, 35–42. PubMed

Tishchenko S; Nikulin A; Fomenkova N; Nevskaya N; Nikonov O; Dumas P; Moine H; Ehresmann B; Ehresmann C; Piendl W; Lamzin V; Garber M; Nikonov S Detailed analysis of RNA-protein interactions within the ribosomal protein S8-rRNA complex from the archaeon Methanococcus jannaschii. J. Mol. Biol 2001, 311, 311–324. PubMed

Carter AP; Clemons WM; Brodersen DE; Morgan-Warren RJ; Wimberly BT; Ramakrishnan V Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature 2000, 407, 340–348. PubMed

Nozinovic S; Furtig B; Jonker HRA; Richter C; Schwalbe H High-resolution NMR structure of an RNA model system: the 14-mer cUUCGg tetraloop hairpin RNA. Nucleic Acids Res. 2010, 38, 683–694. PubMed PMC

Sakata T; Hiroaki H; Oda Y; Tanaka T; Ikehara M; Uesugi S Studies on the Structure and Stabilizing Factor of the CUUCGG Hairpin Rna Using Chemically Synthesized Oligonucleotides. Nucleic Acids Res. 1990, 18, 3831–3839. PubMed PMC

Williams DJ; Hall KB Unrestrained stochastic dynamics simulations of the UUCG tetraloop using an implicit solvation model. Biophys. J 1999, 76, 3192–3205. PubMed PMC

Williams DJ; Boots JL; Hall KB Thermodynamics of 2′-ribose substitutions in UUCG tetraloops. RNA 2001, 7, 44–53. PubMed PMC

Leontis NB; Westhof E Geometric nomenclature and classification of RNA base pairs. RNA 2001, 7, 499–512. PubMed PMC

Allain FHT; Varani G Structure of the P1 Helix from Group-I Self-Splicing Introns. J. Mol. Biol 1995, 250, 333–353. 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

Miller JL; Kollman PA Theoretical studies of an exceptionally stable RNA tetraloop: Observation of convergence from an incorrect NMR structure to the correct one using unrestrained molecular dynamics. J. Mol. Biol 1997, 270, 436–450. PubMed

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.

Villa A; Widjajakusuma E; Stock G Molecular dynamics simulation of the structure, dynamics, and thermostability of the RNA hairpins uCACGg and cUUCGg. J. Phys. Chem. B 2008, 112, 134–142. PubMed

Riccardi L; Nguyen PH; Stock G Free-Energy Landscape of RNA Hairpins Constructed via Dihedral Angle Principal Component Analysis. J. Phys. Chem. B 2009, 113, 16660–16668. PubMed

Deng NJ; Cieplak P Free Energy Profile of RNA Hairpins: A Molecular Dynamics Simulation Study. Biophys. J 2010, 98, 627–636. PubMed PMC

Garcia AE; Paschek D Simulation of the pressure and temperature folding/unfolding equilibrium of a small RNA hairpin. J. Am. Chem. Soc 2008, 130, 815–817. PubMed

Zuo GH; Li WF; Zhang J; Wang J; Wang W Folding of a Small RNA Hairpin Based on Simulation with Replica Exchange Molecular Dynamics. J. Phys. Chem. B 2010, 114, 5835–5839. PubMed

Qin PZ; Feigon J; Hubbell WL Site-directed spin labeling studies reveal solution conformational changes in a GAAA tetraloop receptor upon Mg2+-dependent docking of a GAAA tetraloop. J. Mol. Biol 2005, 351, 1–8. PubMed

Reblova K; Razga F; Li W; Gao HX; Frank J; Sponer J Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM. Nucleic Acids Res. 2010, 38, 1325–1340. PubMed PMC

Stombaugh J; Zirbel CL; Westhof E; Leontis NB Frequency and isostericity of RNA base pairs. Nucleic Acids Res. 2009, 37, 2294–2312. PubMed PMC

Heus HA; Pardi A Structural Features That Give Rise to the Unusual Stability of RNA Hairpins Containing GNRA Loops. Science 1991, 253, 191–194. PubMed

Pley HW; Flaherty KM; Mckay DB 3-Dimensional Structure of a Hammerhead Ribozyme. Nature 1994, 372, 68–74. PubMed

Scott WG; Finch JT; Klug A The Crystal-Structure of an all-RNA Hammerhead Ribozyme - a Proposed Mechanism for RNA Catalytic Cleavage. Cell 1995, 81, 991–1002. PubMed

Correll CC; Swinger K Common and distinctive features of GNRA tetraloops based on a GUAA tetraloop structure at 1.4 angstrom resolution. RNA 2003, 9, 355–363. PubMed PMC

Correll CC; Wool IG; Munishkin A The two faces of the Escherichia coli 23 S rRNA sarcin/ricin domain: The structure at 1.11 angstrom resolution. J. Mol. Biol 1999, 292, 275–287. PubMed

Correll CC; Beneken J; Plantinga MJ; Lubbers M; Chan YL The common and the distinctive features of the bulged-G motif based on a 1.04 angstrom resolution RNA structure. Nucleic Acids Res. 2003, 31, 6806–6818. PubMed PMC

Correll CC; Munishkin A; Chan YL; Ren Z; Wool IG; Steitz TA Crystal structure of the ribosomal RNA domain essential for binding elongation factors. Proc. Natl. Acad. Sci 1998, 95, 13436–13441. PubMed PMC

Ban N; Nissen P; Hansen J; Moore PB; Steitz TA The complete atomic structure of the large ribosomal subunit at 2.4 angstrom resolution. Science 2000, 289, 905–920. PubMed

Szewczak AA; Moore PB; Chan YL; Wool IG The Conformation of the Sarcin Ricin Loop from 28s Ribosomal-RNA. Proc. Natl. Acad. Sci 1993, 90, 9581–9585. PubMed PMC

Szewczak AA; Moore PB The Sarcin Ricin Loop, a Modular RNA. J. Mol. Biol 1995, 247, 81–98. PubMed

Yang XJ; Gerczei T; Glover L; Correll CC Crystal structures of restrictocin-inhibitor complexes with implications for RNA recognition and base flipping. Nat. Struct. Biol 2001, 8, 968–973. PubMed

Jucker FM; Heus HA; Yip PF; Moors EHM; Pardi A A network of heterogeneous hydrogen bonds in GNRA tetraloops. J. Mol. Biol 1996, 264, 968–980. PubMed

Menger M; Eckstein F; Porschke D Dynamics of the RNA hairpin GNRA tetraloop. Biochemistry 2000, 39, 4500–4507. PubMed

Xia TB Taking femtosecond snapshots of RNA conformational dynamics and complexity. Curr. Opin. Chem. Biol 2008, 12, 604–611. PubMed

Johnson JE; Hoogstraten CG Extensive Backbone Dynamics in the GCAA RNA Tetraloop Analyzed Using C-13 NMR Spin Relaxation and Specific Isotope Labeling. J. Am. Chem. Soc 2008, 130, 16757–16769. PubMed PMC

Zhao L; Xia TB Direct revelation of multiple conformations in RNA by femtosecond dynamics. J. Am. Chem. Soc 2007, 129, 4118–4119. PubMed

Sorin EJ; Engelhardt MA; Herschlag D; Pande VS RNA simulations: Probing hairpin unfolding and the dynamics of a GNRA tetraloop. J. Mol. Biol 2002, 317, 493–506. PubMed

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

Depaul AJ; Thompson EJ; Patel SS; Haldeman K; Sorin EJ Equilibrium conformational dynamics in an RNA tetraloop from massively parallel molecular dynamics. Nucleic Acids Res. 2010, 38, 4856–4867. PubMed PMC

Bowman GR; Huang XH; Yao Y; Sun J; Carlsson G; Guibas LJ; Pande VS Structural insight into RNA hairpin folding intermediates. J. Am. Chem. Soc 2008, 130, 9676–9678. PubMed PMC

Ferner J; Villa A; Duchardt E; Widjajakusuma E; Wohnert J; Stock G; Schwalbe H NMR and MD studies of the temperature-dependent dynamics of RNA YNMG-tetraloops. Nucleic Acids Res. 2008, 36, 1928–1940. PubMed PMC

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

Fadrna E; Spackova N; Sarzynska J; Koca J; Orozco M; Cheatham TE; Kulinski T; Sponer J Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields. J. Chem. Theory Comput 2009, 5, 2514–2530. PubMed

Ditzler MA; Otyepka M; Sponer 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

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

MacKerell AD; Banavali NK All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution. J. Comput. Chem 2000, 21, 105–120.

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

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

Case DA; Darden TA; Cheatham TE III; Simmerling CL; Wang J; Duke RE; Luo R; Walker RC; Zhang W; Merz KM; Roberts BP; Wang B; Hayik S; Roitberg A; Seabra G; Kolossváry I; Wong KF; Paesani F; Vanicek J; 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 AMBER 10; University of California: San Francisco, 2009.

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

Jorgensen WL; Chandrasekhar J; Madura JD; Impey RW; Klein ML Comparison of Simple Potential Functions for Simulating Liquid Water. J. Chem. Phys 1983, 79, 926–935.

Berendsen HJC; Postma JPM; Vangunsteren WF; Dinola A; Haak JR Molecular-Dynamics with Coupling to an External Bath. J. Chem. Phys 1984, 81, 3684–3690.

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.

Essmann U; Perera L; Berkowitz ML; Darden T; Lee H; Pedersen LG A Smooth Particle Mesh Ewald Method. J. Chem. Phys 1995, 103, 8577–8593.

Ode H; Matsuo Y; Neya S; Hoshino T Force Field Parameters for Rotation Around chi Torsion Axis in Nucleic Acids. J. Comput. Chem 2008, 29, 2531–2542. PubMed

Yildirim I; Stern HA; Kennedy SD; Tubbs JD; Turner DH Reparameterization of RNA chi Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine. J. Chem. Theory Comput 2010, 6, 1520–1531. PubMed PMC

Riley KM; Pitonak M; Jurecka P; Hobza P, Stabilization and Structure Calculations for Noncovalent Interactions in Extended Molecular Systems Based on Wave Function and Density Functional Theories. Chem. Rev 2010, in press. PubMed

Berendsen HJC; Grigera JR; Straatsma TP The Missing Term in Effective Pair Potentials. J. Phys. Chem 1987, 91, 6269–6271.

Joung IS; Cheatham TE Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations. J. Phys. Chem. B 2008, 112, 9020–9041. PubMed PMC

Phillips JC; Braun R; Wang W; Gumbart J; Tajkhorshid E; Villa E; Chipot C; Skeel RD; Kale L; Schulten K Scalable molecular dynamics with NAMD. J. Comput. Chem 2005, 26, 1781–1802. PubMed PMC

Brooks BR; Bruccoleri RE; Olafson DJ; States DJ; Swaminathan S; Karplus M CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations. J. Comput. Chem 1983, 4, 187–217.

Martyna GJ; Tobias DJ; Klein ML Constant-Pressure Molecular-Dynamics Algorithms. J. Chem. Phys 1994, 101, 4177–4189.

Feller SE; Zhang YH; Pastor RW; Brooks BR Constant-Pressure Molecular-Dynamics Simulation - the Langevin Piston Method. J. Chem. Phys 1995, 103, 4613–4621.

Perez A; Lankas F; Luque FJ; Orozco M Towards a molecular dynamics consensus view of B-DNA flexibility. Nucleic Acids Res. 2008, 36, 2379–2394. PubMed PMC

Lu XJ; Olson WK 3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures. Nat. Protoc 2008, 3, 1213–1227. PubMed PMC

Mlynsky V; Banas P; Hollas D; Reblova K; Walter NG; Sponer J; Otyepka M 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 2010, 114, 6642–6652. PubMed PMC

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

Sarzynska J; Reblova K; Sponer J; Kulinski T Conformational transitions of flanking purines in HIV-1 RNA dimerization initiation site kissing complexes studied by Charmm explicit solvent molecular dynamics. Biopolymers 2008, 89, 732–746. PubMed

Sponer J; Kypr J Different Intrastrand and Interstrand Contributions to Stacking Account for Roll Variations at the Alternating Purine-Pyrimidine Sequences in a-DNA and a-Rna. J. Mol. Biol 1991, 221, 761–764. PubMed

Bhattacharyya D; Bansal M A Self-Consistent Formulation for Analysis and Generation of Non-Uniform DNA Structures. J. Biomol. Struct. Dyn 1989, 6, 635–653. PubMed

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