PEDS Advance Access originally published online on June 25, 2009
Protein Engineering Design and Selection 2009 22(9):547-552; doi:10.1093/protein/gzp028
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This article appears in the following Protein Engineering issue: Computational Methods Special Issue [View the issue table of contents]
Towards temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. I: Molecular dynamics study of a pair of methane molecules in water at various temperatures
aw Odziej1,3
1Laboratory of Biopolymer Structure, Intercollegiate Faculty of Biotechnology, University of Gda
sk, Medical University of Gdask, Kadki 24, 80-822 Gdask
2Faculty of Chemistry, University of Gdask, ul. Sobieskiego 18, 80-952 Gdask, Poland
3Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA
4 To whom correspondence should be addressed. E-mail: has5{at}cornell.edu
By means of molecular dynamics simulations of a pair of methane molecules in a TIP3P periodic water box with the NVT scheme at six temperatures and, additionally, the NPT scheme at three temperatures ranging from T = 283 to 373 K, we determined the potential of mean force (PMF) of pairs of interacting methane molecules in water as functions of distance between the methane molecules. The PMFs converge to a single baseline only for r> 11 Å at all temperatures. The curves of the dimensionless PMF obtained at different temperatures with the NVT scheme overlap almost perfectly in the region of the contact minimum and still very well in the regions of the desolvation maximum and the solvent-separated minimum, which suggests that the temperature-dependent hydrophobic interaction potentials at constant volume in united-residue force fields can be obtained by scaling the respective dimensionless potentials by RT, R being the universal gas constant. For the dimensionless potentials of mean force obtained with the NPT scheme, the depth of the contact minimum increases, whereas the height of the desolvation maximum and the depth of the solvent-separated minimum decrease with temperature, in agreement with results reported in the literature.
Keywords: hydrophobic interactions/molecular dynamics/potential of mean force/temperature dependence
Received May 28, 2009; revised May 28, 2009; accepted June 3, 2009.