Equilibrium properties and force-driven unfolding pathways of RNA molecules
arXiv:0910.5089 · doi:10.1103/PhysRevLett.103.188102
Abstract
The mechanical unfolding of a simple RNA hairpin and of a 236--bases portion of the Tetrahymena thermophila ribozyme is studied by means of an Ising--like model. Phase diagrams and free energy landscapes are computed exactly and suggest a simple two--state behaviour for the hairpin and the presence of intermediate states for the ribozyme. Nonequilibrium simulations give the possible unfolding pathways for the ribozyme, and the dominant pathway corresponds to the experimentally observed one.
Main text + appendix, to appear in Phys. Rev. Lett
References in corpus (11)
- Mechanical unfolding of RNA hairpins
- Exact Solution of the Munoz-Eaton Model for Protein Folding
- Mechanical unfolding of RNA: From hairpins to structures with internal multiloops
- Force Dependent Hopping Rates of RNA Hairpins can be Estimated from Accurate Measurement of the Folding Landscapes
- An Ising-Like model for protein mechanical unfolding
- Slow nucleic acid unzipping kinetics from sequence-defined barriers
- Mechanically probing the folding pathway of single RNA molecules
- Mechanical unfolding and refolding pathways of ubiquitin
- The secondary structure of RNA under tension
- Protein mechanical unfolding: a model with binary variables
- Kinetic barriers in RNA unzipping
Cited by in corpus (8)
- Molten globule-like transition state of protein barnase measured with calorimetric force spectroscopy
- Theory for RNA folding, stretching, and melting including loops and salt
- Analysis of the Equilibrium and Kinetics of the Ankyrin Repeat Protein Myotrophin
- Direction dependent mechanical unfolding and Green Fluorescent Protein as a force sensor
- Effects of confinement on thermal stability and folding kinetics in a simple Ising-like model
- Pathways of mechanical unfolding of FnIII_{10}: low force intermediates
- Nonequilibrium dynamics of an exactly solvable Ising-like model and protein translocation
- Transfer matrix solution of the Wako-Saitô-Muñoz-Eaton model augmented by arbitrary short range interactions