Electrostatic layer-by-layer assembly (LBL) is a versatile method of fabricating ultrathin multilayer films, coatings, and microcapsules from materials in solution, notably, oppositely charged polyelectrolytes in water. Polypeptides, a special type of polyelectrolyte, have recently shown promise for a range of applications in biotechnology and medicine, for example, artificial cells, drug delivery systems, cell/tissue scaffolds, artificial viruses, and implantable device coatings. Poly(L-lysine) (PLL) and poly(L-glutamic acid) ( PLGA) at neutral pH are model oppositely charged polypeptides. Experimental studies have shown that PLL/PLGA multilayer films contain a substantial amount of beta-sheets. Here, we present findings of a molecular dynamics ( MD) study of the physical basis of interaction between PLL and PLGA in multilayer film models. Simulations have been carried out to study structural and dynamical properties of PLL/PLGA aggregates in beta-sheet conformation. The results suggest that hydrophobic interactions, in addition to electrostatics interactions, play a significant role in PLL/PLGA multilayers. The preferred orientation of peptides in the beta-sheet structures is antiparallel within sheets and parallel between sheets. Intersheet hydrogen-bond formation is more likely the result of peptide association than the cause. The approach provides a general means to understand better how various types of noncovalent interactions contribute to the structure and stability of polypeptide multilayer films.