Lens alpha-crystallin subunits alphaA and alphaB are differentially expressed and have a 3-to-1 ratio in most mammalian lenses by intermolecular exchange. The biological significance of this composition and the mechanism of exchange are not clear. Preparations of human recombinant alphaA- and alphaB-crystallins provide a good system in which to study this phenomenon. Both recombinant alphaA- and alphaB-crystallins are folded and aggregated to the size of the native alpha-crystallin. During incubation together, they undergo an intermolecular exchange as shown by native isoelectric focusing. Circular dichroism measurements indicate that the protein with a 3-to-1 ratio of alphaA- and alphaB-crystallins has the same secondary structure but somewhat different tertiary structures after exchange: the near-UV CD increases after exchange. The resulting hybrid aggregate is more stable than the individual homogeneous aggregates: at 62 degrees C, alphaB-crystallin is more susceptible to aggregation and displays a greater light scattering than alphaA-crystallin. This heat-induced aggregation of alphaB-crystallin, however, was suppressed by intermolecular exchange with alphaA-crystallin. These phenomena are also observed by fast performance liquid chromatography gel filtration patterns. The protein structure of alphaB-crystallin is stabilized by intermolecular exchange with alphaA-crystallin.