Evaluation of the hydrophilic behaviour of a β-casein peptide by molecular dynamics simulation

Abstract

Abstract Molecular dynamics simulations of a β-casein peptide in the α-helix conformation in vacuum and aqueous solution have been performed to study the hydrophilic (and conversely hydrophobic) and hydration behaviour of this peptide. Both simulations were performed for a duration of 150 ps at 300 K using the GROMOS force field, with apolar hydrogen atoms treated as united atoms, and the SPC water model. A general conclusion is that the β-casein peptide hydrophilic behaviour can be characterized by comparison of (solvent) accessible surface area (SASA) and of the radius of gyration (Rg) in vacuum and in aqueous solution. These two criterion values increase when the peptide is moved from vacuum to water. For each amino-acid, the SASA difference gives a picture of their hydrophobicity which compares favorably with the standard scale used to predict the hydrophobicity profile of the polypeptide. The hydrogen bonding analysis has been carried out and the result of peptide-water hydrogen bonding has been satisfactory compared with previous simulation and NMR experiment. From calculations of the diffusion coefficient of water around the different atom types of peptide, it is found that the diffusion coefficient of water near polar atom is the smallest one, which is consistent with the recent experimental and simulation data.