A series of molecular dynamics simulations have been performed to study the supramolecular structure of self-assembled complexes formed by N-dodecyltrimethylammonium cations and the synthetic polypeptide poly(alpha,L-glutamate). The influence of the type of solvent has been investigated, considering explicit environments of chloroform, water, and methanol on a stoichiometric complex containing 15 residues. In chloroform, the complex stabilizes in a regular structure: the polypeptide adopts an alpha-helix conformation that is regularly surrounded by surfactant molecules to form electrostatic interactions through a multiple interaction pattern. However, this structure destabilizes in methanol and water: (a) the alpha-helix unfolds in the two solvents and (b) the electrostatic links between the surfactant molecules and the polyanion are disrupted in aqueous solution, although these interactions are still preserved in methanol. The role of the solvent environment in stabilizing or destabilizing the polypeptide secondary structure, the organization of the surfactant molecules, and predominantly the surfactant-polypeptide supramolecular organization is discussed in detail. (c) 2006 Wiley Periodicals, Inc.