title: Simulation of the pressure and temperature folding/unfolding equilibrium of a small RNA hairpin.
abstract: We report molecular dynamics simulations of the equilibrium folding/unfolding thermodynamics of the RNA tetraloop in explicit solvent. A replica exchange molecular dynamics study of the r(CGUUGCCG) oligomer that forms a hairpin is performed for 226 ns per replica, using 52 replicas. We are able to show the unbiased folding of all replicas starting from extended conformations. The equilibrium pressure-temperature free energy of folding, DeltaG(P,T), is calculated from the averaged energy, pressure, and specific volume change upon folding of the oligomer as a function of T at constant volume. We find that this oligomer is destabilized by increasing hydrostatic pressure, similar to the behavior of globular proteins.
authors.affiliation: Department of Physics, Applied Physics and Astronomy, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, USA. angel@rpi.edu
authors.forename: Angel E
authors.initials: AE
authors.lastname: Garcia
authors.forename: Dietmar
authors.initials: D
authors.lastname: Paschek
mesh_terms: D003198:Computer Simulation; D008956:Models, Chemical; D009690:Nucleic Acid Conformation; D009843:Oligoribonucleotides; D011312:Pressure; D012313:RNA / Q000737:chemistry*; D013696:Temperature; D013816:Thermodynamics
chemical_list: D009843:Oligoribonucleotides; C526605:r(GCUUCGGC) RNA tetraloop; D012313:RNA