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Conclusion

The dynamical simulation of folding equilibria of a variety of foldamers at the atomic level including explicit treatment of solvent degrees of freedom offers the possibility of analyzing the factors that drive the conformational distribution towards a particular fold. A necessary condition to predict the various stable folds under different thermodynamic and solvation conditions in agreement with experimental data seems to be the use of a biomolecular force field that is calibrated using thermodynamic data of the condensed phase. Currently available computing power only allows adequate sampling of the conformational ensemble and the (un)folding transitions for not too large polypeptide analogs. However, the relatively small size of the denatured or unfolded state of polypeptides and the continuing rapid growth of computing power offer the perspective to simulate the folding equilibrium of a small protein within the next decade.

Acknowledgment

We thank Riccardo Baron, Xavier Daura, Peter Gee, Alice Glattli, Chris Oosten-brink, Daniel Trzesniak and Nico van der Vegt for making available material for this article. Financial support of the National Center of Competence in Research (NCCR) in Structural Biology of the Swiss National Science Foundation (SNSF) is gratefully acknowledged.

References

1 H.J.C. Berendsen, Science 2001, 294,

5 D.J. Hill, M.J. Mio, R.B. Prince, T.S. Hughes, J.S. Moore, Chem. Rev. 2001,

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