Interactions of hydrophobic molecular domains determine many of the functional properties of food proteins and colloidal food aggregates, such as emulsification, gelation, and foaming ability. A molecular basis for macromolecular interactions and conformational stability is established through investigation of simple model systems. Molecular modeling and dynamics simulations have been used to study the role of hydrophobic interaction forces in driving the formation of model amphiphile aggregate systems. An approximation to hydrophobic attraction between hydrocarbon tails was required to achieve stable, dynamic aggregate models for Aerosol-OT (AOT)/water/oil microemulsions, micelles of AOT in water, and a stacked AOT/para-chlorophenol gel in either CCl4 or benzene. One- and two-dimensional NMR spectroscopic methods have been used to characterize the pH and temperature dependent conformational changes in the model poly-peptide poly(L-lysine). Changes in proton chemical shifts and line widths indicate that the backbone mobility of poly(L-lysine) is not greatly diminished by the coil-helix transition. ROESY and transverse-ROESY couplings, as well as T-1 and T-2 relaxation measurements, suggest that lysyl side chain mobility remains largely unrestricted upon formation of periodic secondary structure. Molecular dynamics simulations of poly(L-lysine) conformers substantiate the importance of hydrophobic side chain domains in stabilizing secondary structural features in aqueous solution.