Sarcoplasmic reticulum Ca2+-ATF'ase structure and organization in the membrane has been studied by infrared spectroscopy by decomposition of the amide I band. Besides the component bands assignable to secondary structure elements such as a-helix, P-sheet, etc. . . . , two unusual bands, one at 1,645 cm" in H 2 0 buffer and the other at 1,625 cm" in D 2 0 buffer are present. By perturbing the protein using temperature and limited proteolysis, the band at 1,645 cm" is tentatively assigned to a-helical segments located in the cytoplasmic domain and coupled to /?-sheet structure, whereas the band at 1,625 cm" arises probably from monomer-monomer contacts in the native oligomeric protein. The secondary structure obtained is 33% a-helical segments in the transmembrane plus stalk domain; 20% a-helix and 22% @sheet in the cytoplasmic domain plus 19% turns and 6% unordered structure. Thermal unfolding of Ca*+-ATPase is a complex process that cannot be described as a two-state denaturation. The results obtained are compatible with the idea that the protein is an oligomer at room temperature. The loss of the 1,625 cm" band upon heating would be consistent with a disruption of the oligomers in a process that later gives rise to aggregates (appearance of the 1,618 cm" band). This picture would also be compatible with early results suggesting that processes governing Ca2+ accumulation and ATPase activity are uncoupled at temperatures above 37"C, so that while ATPase activity proceeds at high rates, Ca2+ accumulation is inhibited.Keywords: Ca2+-ATPase; infrared spectroscopy; protein structure; proteolysis; sarcoplasmic reticulum; thermal analysis Knowledge of the structure-function relationship is essential in understanding the molecular mechanisms underlying the membranecontrolled biological processes. The X-ray three-dimensional structure of membrane proteins is still not well known, except for a few cases. Therefore, other lower resolution spectroscopic methods have to be used to gain insight of the structure and function of membrane proteins. Sarcoplasmic reticulum Ca2+-ATPase is an integral membrane protein that pumps calcium out of the cytoplasm during striated muscle relaxation (Martonosi, 1996). This ATPase is part of a family of P-type ion pumps that includes several cation-activated ATPases having in common ten predicted transmembrane helical segments (Stokes et al., 1994).The structure of sarcoplasmic reticulum Ca2+-ATPase has been predicted from the amino acid sequence (MacLennan et al., 1985) and from electron microscopy observations (Toyoshima et al., 1993). The protein appears to consist of an extensive beak-shaped cytoplasmic domain containing interconnected a-helical and P-strand segments, a stalk connecting the beak with the membrane, and the ten transmembrane segments characteristic of P-type ion pumps (Stokes et al., 1994). The cytoplasmic domain contains the active sites of ATP hydrolysis and phosphorylation while the Ca2+ channel is expected to be associated to the transmembrane domain. Some Ca2+-...