Antibodies reactive with distinct regions of the staphylococcal nuclease molecule were prepared both by immunization with polypeptide fragments of nuclease and by immunization with intact nuclease followed by fractionation of the antiserum on immunoabsorbent columns bearing the corresponding fragments.Comparisons of the interactions of these antibody preparations with nuclease, by quantitative precipitin assays and enzyme inhibition studies, showed marked differences attributable to the conformation of the immunizing antigens. An interpretive model is proposed in which antibodies fractionated from anti-nuclease serum react effectively only with the "native format determinants" of polypeptide fragments of nuclease. It is postulated that such determinants are generated in polypeptide fragments by spontaneous and reversible folding of the polypeptide chain. The model permits experimental determination of parameters, Keonf, for the proposed confornmational equilibria.Fragment (99-149) * is an enzymatically inactive polypeptide produced by cyanogen bromide digestion of staphylococcal nuclease (1). Although more than half of the sequence of this fragment is folded as a-helix in the native nuclease molecule (2), the fragment has been shown by circular dichroism studies to contain less than 5% a-helix, and has been considered to be devoid of ordered structure (3). When fragment (99-149) is mixed in solution with another inactive fragment of nuclease, fragment (1-126), the two fragments combine to regenerate enzymatic activity and ordered secondary structure (3). It has been postulated that in the folding of polypeptide chains that must occur during this combination, and in the folding of nuclease itself, regions of ordered secondary structure, such as the helices of fragment (99-149), may act as "nucleation" sites (4). We have, therefore, chosen to study conformational equilibria of this region of the nuclease polypeptide chain.We have recently described the preparation of antibodies specific for an antigenic determinant in region (99-126) of nuclease by sequential immunoabsorption of a goat antinuclease serum on columns of Sepharose to which selected polypeptide fragments of nuclease had been covalently attached (5). These antibodies, called anti-(99-126)., combine with nuclease to produce an enzymatically inactive, soluble complex (6). It was noted that the ability of these antibodies to bind to the polypeptide fragment (99-149) might be interpreted as indicating either that the antibodies recognized a determinant present in the unfolded form of the polypeptide or, alternatively, that fragment (99-149) can spontaneously and reversibly fold to form the same conformation that is present in the intact, native protein. This paper presents a comparison of the reactions of antibodies prepared against nuclease fragments with the reactions of corresponding antibodies prepared by fractionation of anti-nuclease serum. The results obtained indicate the importance of antigen conformation in the binding of anti-nuclease an...