Peptide folding simulations: no solvent required?

Abstract

Several simulation methods are currently in use to study peptide and protein folding. They can be classified in three groups depending on how the solvent is treated. At the simplest level, the solvent is ignored. At a second level, solvent effects are implicitly represented in the atomic interaction function. At the third level, solvent degrees of freedom are treated explicitly. We have performed molecular dynamics simulations in vacuum, stochastic dynamics simulations, and molecular dynamics simulations in methanol of the folding of a β-heptapeptide to test these different levels of approximation. The results clearly show that the solvent cannot be ignored in folding simulations, and highlight the difficulties of implicitly modelling solvent effects in an atomic interaction function for a solute.