Mercedes Benz model of neutral amino-acid side chains

We present a 2-d coarse-grain model of polar and non-polar amino-acid side chains, and investigate their thermodynamic and structural properties in solution. The molecules interact via a Lennard-Jones potential and a local treatment of the hydrogen bond energy. Such a form allows very fast highly converged calculations. Estimates of the Gibbs free energy of hydration (GFEH) of the solutes show good qualitative agreement with experiments. We find moreover that contributions to the GFEH are linked to the perturbations of the solvent hydration shell structure. For large hydrophobic solutes, unfavorable GFEH results mainly from an increase of the water water energy contribution, while for hydrophilic solutes the increase in solvent energy is compensated by the solute-solvent energy. The model appears therefore to capture the main features of non-charged amino-acids hydration. (c) 2006 Elsevier B.V. All rights reserved.