The alanine dipeptide free energy surface in solution

Abstract

Molecular dynamics (MD) simulations have been used to determine the two dimensional free energy surface of the alanine dipeptide in solution. The intramolecular dipeptide interactions were described by the CHARMM22 force field. Three models of solvation were considered; (i) a simple scaling of electrostatic interactions, (ii) solvation energies determined by finite difference Poisson–Boltzmann calculations, and (iii) inclusion of explicit TIP3P solvent molecules. All three solvation models produced qualitatively similar effects, but differed significantly in their quantitative values. In particular, the continuum based models predicted the β (extended) conformation to be most stable, whereas the explicit solvent model favored the αR (folded) conformation. Comparison with experimental data for the H–N–Cα-Hα coupling constant, helix–coil transition thermodynamics, and polypeptide infinite chain length characteristic ratios was performed. The explicit solvent surface produced the strongest agreement with experiment, although there is no unambiguous data to support any of the solvent models.