title: Ensemble simulations: folding, unfolding and misfolding of a high-efficiency frameshifting RNA pseudoknot.
abstract: Massive all-atom molecular dynamics simulations were conducted across a distributed computing network to study the folding, unfolding, misfolding and conformational plasticity of the high-efficiency frameshifting double mutant of the 26 nt potato leaf roll virus RNA pseudoknot. Our robust sampling, which included over 40 starting structures spanning the spectrum from the extended unfolded state to the native fold, yielded nearly 120 μs of cumulative sampling time. Conformational microstate transitions on the 1.0 ns to 10.0 μs timescales were observed, with post-equilibration sampling providing detailed representations of the conformational free energy landscape and the complex folding mechanism inherent to the pseudoknot motif. Herein, we identify and characterize two alternative native structures, three intermediate states, and numerous misfolded states, the latter of which have not previously been characterized via atomistic simulation techniques. While in line with previous thermodynamics-based models of a general RNA folding mechanism, our observations indicate that stem-strand-sequence-separation may serve as an alternative predictor of the order of stem formation during pseudoknot folding. Our results contradict a model of frameshifting based on structural rigidity and resistance to mechanical unfolding, and instead strongly support more recent studies in which conformational plasticity is identified as a determining factor in frameshifting efficiency.
authors.affiliation: Department of Chemistry & Biochemistry, California State University Long Beach, Long Beach, CA 90840, USA.|Department of Computer Engineering & Computer Science, California State University Long Beach, Long Beach, CA 90840, USA.
authors.forename: Khai K
authors.initials: KK
authors.lastname: Q Nguyen
authors.affiliation: Department of Chemistry & Biochemistry, California State University Long Beach, Long Beach, CA 90840, USA.|Department of Physics & Astronomy, California State University Long Beach, Long Beach, CA 90840, USA.
authors.forename: Yessica K
authors.initials: YK
authors.lastname: Gomez
authors.affiliation: Department of Chemistry & Biochemistry, California State University Long Beach, Long Beach, CA 90840, USA.
authors.forename: Mona
authors.initials: M
authors.lastname: Bakhom
authors.affiliation: Department of Physics & Astronomy, California State University Long Beach, Long Beach, CA 90840, USA.
authors.forename: Amethyst
authors.initials: A
authors.lastname: Radcliffe
authors.affiliation: Department of Chemistry & Biochemistry, California State University Long Beach, Long Beach, CA 90840, USA.
authors.forename: Phuc
authors.initials: P
authors.lastname: La
authors.affiliation: Department of Chemistry & Biochemistry, California State University Long Beach, Long Beach, CA 90840, USA.
authors.forename: Dakota
authors.initials: D
authors.lastname: Rochelle
authors.affiliation: Department of Chemistry & Biochemistry, California State University Long Beach, Long Beach, CA 90840, USA.
authors.forename: Ji Won
authors.initials: JW
authors.lastname: Lee
authors.affiliation: Department of Chemistry & Biochemistry, California State University Long Beach, Long Beach, CA 90840, USA.
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Sorin
mesh_terms: D018965:Frameshifting, Ribosomal / Q000235:genetics*; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D018515:Plant Leaves / Q000821:virology; D010942:Plant Viruses / Q000737:chemistry / Q000235:genetics; D059370:RNA Folding / Q000235:genetics*; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics*; D011198:Solanum tuberosum / Q000821:virology; D013816:Thermodynamics
chemical_list: D012367:RNA, Viral