Differential scanning calorimetry, circular dichroism, and visible absorption spectrophotometry were employed to elucidate the structural stability of thermophilic phycocyanin derived from Cyanidium caldarium, a eucaryotic organism which contains a nucleus, grown in acidic conditions (pH 3.4) at 54 degrees C. The obtained results were compared with those previously reported for thermophilic phycocyanin derived from Synechococcus lividus, a procaryote containing no organized nucleus, grown in alkaline conditions (pH 8.5) at 52 degrees C. The temperature of thermal unfolding (t(d)) was found to be comparable between C. caldarium (73 degrees C) and S. lividus (74 degrees C) phycocyanins. The apparent free energy of unfolding (DeltaG([urea]=0)) at zero denaturant (urea) concentration was also comparable: 9.1 and 8.7 kcal/mole for unfolding the chromophore part of the protein, and 5.0 and 4.3 kcal/mole for unfolding the apoprotein part of the protein, respectively. These values of t(d) and DeltaG([urea]=0) were significantly higher than those previously reported for mesophilic Phormidium luridum phycocyanin (grown at 25 degrees C). These findings revealed that relatively higher values of t(d) and DeltaG([urea]=0) were characteristics of thermophilic proteins. In contrast, the enthalpies of completed unfolding (DeltaH(d)) and the half-completed unfolding (DeltaH(d)) 1 2 for C. caldarium phycocyanin were much lower than those for S. lividus protein (89 versus 180 kcal/mole and 62 versus 115 kcal/mole, respectively). Factors contributing to a lower DeltaH(d) in C. caldarium protein and the role of charged groups in enhancing the stability of thermophilic proteins were discussed.