title: Simultaneous NMR characterisation of multiple minima in the free energy landscape of an RNA UUCG tetraloop.
abstract: RNA molecules in solution tend to undergo structural fluctuations of relatively large amplitude and to populate a range of different conformations some of which with low populations. It is still very challenging, however, to characterise the structures of these low populated states and to understand their functional roles. In the present study, we address this problem by using NMR residual dipolar couplings (RDCs) as structural restraints in replica-averaged metadynamics (RAM) simulations. By applying this approach to a 14-mer RNA hairpin containing the prototypical UUCG tetraloop motif, we show that it is possible to construct the free energy landscape of this RNA molecule. This free energy landscapes reveals the surprisingly rich dynamics of the UUCG tetraloop and identifies the multiple substates that exist in equilibrium owing to thermal fluctuations. The approach that we present is general and can be applied to the study of the free energy landscapes of other RNA or RNA-protein systems.
authors.affiliation: Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK. mv245@cam.ac.uk.
authors.forename: Aditi N
authors.identifier: http://orcid.org/0000-0003-4361-6561
authors.initials: AN
authors.lastname: Borkar
authors.affiliation: Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Canada M5S 1A8.
authors.forename: Pramodh
authors.initials: P
authors.lastname: Vallurupalli
authors.affiliation: Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK. mv245@cam.ac.uk.
authors.forename: Carlo
authors.initials: C
authors.lastname: Camilloni
authors.affiliation: Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Canada M5S 1A8.
authors.forename: Lewis E
authors.initials: LE
authors.lastname: Kay
authors.affiliation: Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK. mv245@cam.ac.uk.
authors.forename: Michele
authors.initials: M
authors.lastname: Vendruscolo
mesh_terms: 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