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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.

Author information

1
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

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.

PMID:
18154332
DOI:
10.1021/ja074191i
[Indexed for MEDLINE]

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