Acidic proteins are generally thought to control mineral formation and growth in biocalcification. Analysis of proteinaceous components in the soluble and insoluble matrix fractions of sclerites in Sinularia polydactyla indicates that aspartic acid composes about 60% of the insoluble and 29% of the soluble matrix fractions. We previously analyzed aspartic acids in the matrix fractions (insoluble = 17 mol%; soluble = 38 mol%) of sclerites from a different type of soft coral, Lobophytum crassum, which showed comparatively lower aspartic acid-rich proteins than S. polydactyla. Thus, characterization of highly acidic proteins in the organic matrix of present species is an important first step toward linking function to individual proteins in soft coral. Here, we show that aspartic-acid rich proteins can control the CaCO(3) polymorph in vitro. The CaCO(3) precipitates in vitro in the presence of aspartic acid-rich proteins and 50 mM Mg(2+) was verified by Raman microprobe analysis. The matrix proteins of sclerites demonstrated that the aspartic-acid rich domain is crucial for the calcite precipitation in soft corals. The crystalline form of CaCO(3) in the presence of aspartic acid-rich proteins in vitro was identified by X-ray diffraction and, revealed calcitic polymorphisms with a strong (104) reflection. The structure of soft coral organic matrices containing aspartate-rich proteins and polysaccharides was assessed by Fourier transform infrared spectroscopy. These results strongly suggest that the aspartic acid-rich proteins within the organic matrix of soft corals play a key role in biomineralization regulation.