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J Am Chem Soc. 2008 Jan 23;130(3):815-7. Epub 2007 Dec 23.

Simulation of the pressure and temperature folding/unfolding equilibrium of a small RNA hairpin.

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Department of Physics, Applied Physics and Astronomy, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, USA.


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.

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