Swine pepsinogen folding intermediates are highly structured, motile molecules.

Refolding of urea- or alkali-unfolded swine pepsinogen occurs by rapid formation of partially folded intermediates (Is) which are slowly converted into the native protein (N). This slow reaction involves isomerization of proline residues in the protein to the configurations occurring in N. Kinetic studies on changes in absorbance or circular dichroism indicate Is to be close to the native structure, which fluorescence and hydrogen exchange measurements show Is to be much more open to solvent than N. Fluorescent probe binding suggests that Is has a more hydrophobic surface than N. These contrasting results are interpreted to show that the presence of wrong proline residues does not greatly inhibit the overall folding of pepsinogen but prevents close packing of structural elements into the highly cooperative, stable, native form. Is may be very similar to N in average structure, but is a much more fluctuating species.