alpha-Crystallin, a heteromultimeric protein made up of alpha A- and alpha B-crystallins, functions as a molecular chaperone in preventing the aggregation of proteins. We have shown earlier that structural perturbation of alpha-crystallin can enhance its chaperone-like activity severalfold. The two subunits of alpha-crystallin have extensive sequence homology and individually display chaperone-like activity. We have investigated the chaperone-like activity of alpha A- and alpha B-crystallin homoaggregates against thermal and nonthermal modes of aggregation. me find that, against a nonthermal mode of aggregation, alpha B-crystallin shows significant protective ability even at subphysiological temperatures, at which alpha A-crystallin or heteromultimeric alpha-crystallin exhibit very little chaperone-like activity. Interestingly, differences in the protective ability of these homoaggregates against the thermal aggregation of beta(L)-crystallin is negligible. To investigate this differential behavior, me have monitored the temperature-dependent structural changes in both the proteins using fluorescence and circular dichroism spectroscopy. Intrinsic tryptophan fluorescence quenching by acrylamide shows that the tryptophans in alpha B-crystallin are more accessible than the lone tryptophan in alpha A-crystallin even at 25 degrees C. Protein-bound 8-anilinon-aphthalene-1-sulfonate fluorescence demonstrates the higher solvent accessibility of hydrophobic surfaces on alpha B-crystallin. Circular dichroism studies show some tertiary structural changes in alpha A-crystallin above 50 degrees C, alpha B-crystallin, on the other hand, shows significant alteration of tertiary structure by 45 degrees C, Our study demonstrates that despite a high degree of sequence homology and their generally accepted structural similarity, alpha B-crystallin is much more sensitive to temperature-dependent structural perturbation than alpha A- or alpha-crystallin and shows differences in its chaperone-like properties. These differences appear to be relevant to temperature-dependent enhancement of chaperone-like activity of alpha-crystallin and indicate different roles for the two proteins both in alpha-crystallin heteroaggregate and as separate proteins under stress conditions.