The self-assembly process of stoichiometric complexes formed by poly (alpha-glutamate) and dodecyltrimethyl ammonium molecular cations has been studied at the atomistic by molecular dynamics simulations. The results presented in this work depict a time-dependent succession of events. Among them, the formation of the assembled complex is an extraordinarily fast event. On the other side, the surfactant units do not influence the kinetics of the polypeptide folding process, showing that the characteristic independent organization experimentally detected for the charged groups and aliphatic tails has its reflection during the assembly process. Through these results, it is possible to infer new strategies to engineer the final nano-organization that these stoichiometric complexes can adopt. The instantaneous assembly of the oppositely charged components allows a further kinetic control over the polypeptide folding process, which is expected to take place in time scales that are between 10 and 100 times larger than those explored in this work. (C) 2008 Wiley Periodicals, Inc.