title: Highly sampled tetranucleotide and tetraloop motifs enable evaluation of common RNA force fields.
abstract: Recent modifications and improvements to standard nucleic acid force fields have attempted to fix problems and issues that have been observed as longer timescale simulations have become routine. Although previous work has shown the ability to fold the UUCG stem-loop structure, until now no group has attempted to quantify the performance of current force fields using highly converged structural populations of the tetraloop conformational ensemble. In this study, we report the use of multiple independent sets of multidimensional replica exchange molecular dynamics (M-REMD) simulations with different initial conditions to generate well-converged conformational ensembles for the tetranucleotides r(GACC) and r(CCCC), as well as the larger UUCG tetraloop motif. By generating what is to our knowledge the most complete RNA structure ensembles reported to date for these systems, we remove the coupling between force field errors and errors due to incomplete sampling, providing a comprehensive comparison between current top-performing MD force fields for RNA. Of the RNA force fields tested in this study, none demonstrate the ability to correctly identify the most thermodynamically stable structure for all three systems. We discuss the deficiencies present in each potential function and suggest areas where improvements can be made. The results imply that although "short" (nsec-μsec timescale) simulations may stay close to their respective experimental structures and may well reproduce experimental observables, inevitably the current force fields will populate alternative incorrect structures that are more stable than those observed via experiment.
authors.affiliation: Department of Medicinal Chemistry, College of Pharmacy, L.S. Skaggs Pharmacy Research Institute, University of Utah, Salt Lake City, Utah 84112, USA.
authors.forename: Christina
authors.initials: C
authors.lastname: Bergonzo
authors.affiliation: Department of Medicinal Chemistry, College of Pharmacy, L.S. Skaggs Pharmacy Research Institute, University of Utah, Salt Lake City, Utah 84112, USA.
authors.forename: Niel M
authors.initials: NM
authors.lastname: Henriksen
authors.affiliation: Department of Medicinal Chemistry, College of Pharmacy, L.S. Skaggs Pharmacy Research Institute, University of Utah, Salt Lake City, Utah 84112, USA.
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Roe
authors.affiliation: Department of Medicinal Chemistry, College of Pharmacy, L.S. Skaggs Pharmacy Research Institute, University of Utah, Salt Lake City, Utah 84112, USA.
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Cheatham
mesh_terms: D019295:Computational Biology / Q000379:methods*; D009682:Magnetic Resonance Spectroscopy; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs; D012313:RNA / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D012313:RNA
keywords: AMBER; CHARMM; RNA; enhanced sampling; force fields; molecular dynamics; replica exchange