Structural insight into RNA hairpin folding intermediates.
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.
Bowman
Gregory R
GR
Biophysics Program, Stanford University, Stanford, California 94305, USA.
Huang
Xuhui
X
Yao
Yuan
Y
Sun
Jian
J
Carlsson
Gunnar
G
Guibas
Leonidas J
LJ
Pande
Vijay S
VS
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
D012313:RNA