title: Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies.
abstract: The computer-aided folding of biomolecules, particularly RNAs, is one of the most difficult challenges in computational structural biology. RNA tetraloops are fundamental RNA motifs playing key roles in RNA folding and RNA-RNA and RNA-protein interactions. Although state-of-the-art Molecular Dynamics (MD) force fields correctly describe the native state of these tetraloops as a stable free-energy basin on the microsecond time scale, enhanced sampling techniques reveal that the native state is not the global free energy minimum, suggesting yet unidentified significant imbalances in the force fields. Here, we tested our ability to fold the RNA tetraloops in various force fields and simulation settings. We employed three different enhanced sampling techniques, namely, temperature replica exchange MD (T-REMD), replica exchange with solute tempering (REST2), and well-tempered metadynamics (WT-MetaD). We aimed to separate problems caused by limited sampling from those due to force-field inaccuracies. We found that none of the contemporary force fields is able to correctly describe folding of the 5'-GAGA-3' tetraloop over a range of simulation conditions. We thus aimed to identify which terms of the force field are responsible for this poor description of TL folding. We showed that at least two different imbalances contribute to this behavior, namely, overstabilization of base-phosphate and/or sugar-phosphate interactions and underestimated stability of the hydrogen bonding interaction in base pairing. The first artifact stabilizes the unfolded ensemble, while the second one destabilizes the folded state. The former problem might be partially alleviated by reparametrization of the van der Waals parameters of the phosphate oxygens suggested by Case et al., while in order to overcome the latter effect we suggest local potentials to better capture hydrogen bonding interactions.
authors.affiliation: Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc , 17. listopadu 12, 771 46 Olomouc, Czech Republic.
authors.forename: Petra
authors.initials: P
authors.lastname: Kührová
authors.affiliation: Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0520, United States.
authors.forename: Robert B
authors.initials: RB
authors.lastname: Best
authors.affiliation: Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265, 34136 Trieste, Italy.
authors.forename: Sandro
authors.initials: S
authors.lastname: Bottaro
authors.affiliation: Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265, 34136 Trieste, Italy.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Bussi
authors.affiliation: Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc , 17. listopadu 12, 771 46 Olomouc, Czech Republic.|Institute of Biophysics, Academy of Sciences of the Czech Republic , Kralovopolska 135, 612 65 Brno, Czech Republic.
authors.forename: Jiří
authors.initials: J
authors.lastname: Šponer
authors.affiliation: Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc , 17. listopadu 12, 771 46 Olomouc, Czech Republic.|Institute of Biophysics, Academy of Sciences of the Czech Republic , Kralovopolska 135, 612 65 Brno, Czech Republic.
authors.forename: Michal
authors.initials: M
authors.lastname: Otyepka
authors.affiliation: Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc , 17. listopadu 12, 771 46 Olomouc, Czech Republic.|Institute of Biophysics, Academy of Sciences of the Czech Republic , Kralovopolska 135, 612 65 Brno, Czech Republic.
authors.forename: Pavel
authors.initials: P
authors.lastname: Banáš
mesh_terms: D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D059370:RNA Folding; D020871:RNA Stability; D055672:Static Electricity; D013696:Temperature
chemical_list: D012313:RNA