Conformational equilibrium in the alanine dipeptide in the gas phase and aqueous solution: a comparison of theoretical results

Abstract

The acetyl and methyl amide blocked alanine amino acid, commonly referred to as the alanine dipeptide, has often been used as a model in theoretical studies of backbone conformational equilibria in proteins. In order to evaluate the solvent effects on the conformational equilibrium of the dipeptide, we have used molecular dynamics simulations with holonomic backbone dihedral angle constraints and thermodynamic perturbation theory to calculate free energy profiles along paths connecting four important conformations of the dipeptide in the gas phase and in water. We found that the extended β conformation is the most stable both in the gas phase and in water