title: Structural insight into RNA hairpin folding intermediates.
abstract: Hairpins are a ubiquitous secondary structure motif in RNA molecules. Despite their simple structure, there is some debate over whether they fold in a two-state or multi-state manner. We have studied the folding of a small tetraloop hairpin using a serial version of replica exchange molecular dynamics on a distributed computing environment. On the basis of these simulations, we have identified a number of intermediates that are consistent with experimental results. We also find that folding is not simply the reverse of high-temperature unfolding and suggest that this may be a general feature of biomolecular folding.
authors.affiliation: Biophysics Program, Stanford University, Stanford, California 94305, USA.
authors.forename: Gregory R
authors.initials: GR
authors.lastname: Bowman
authors.forename: Xuhui
authors.initials: X
authors.lastname: Huang
authors.forename: Yuan
authors.initials: Y
authors.lastname: Yao
authors.forename: Jian
authors.initials: J
authors.lastname: Sun
authors.forename: Gunnar
authors.initials: G
authors.lastname: Carlsson
authors.forename: Leonidas J
authors.initials: LJ
authors.lastname: Guibas
authors.forename: Vijay S
authors.initials: VS
authors.lastname: Pande
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D012313:RNA