The fluorinated organic solvents 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP) and hexafluoro-acetone trihydrate (HFA) have been successfully used to produce silk fibroin Fibers with high strength. To understand the reasons for the difference in strength between regenerated silk fibers prepared from these two solvents, we analyzed and compared properties of the native silk fibroin and (AGSGAG)(2), a model for the crystalline part of fibroin, in the two solvents. The C-13 and H-1 chemical shifts obtained from H-1-C-13 HSQC spectra of silk fibroin in HFIP, HFA, and water indicates that silk fibroin formed helix-like structure in the fluorinated alcohols. A similar tendency was observed for (AGSGAG)(2) although the chemical shift change is smaller. Intramolecular H-1-H-1 NOE data for (AGSGAG)(2) imply the presence of helical structures in the middle part of the peptide in HFIP and bill not in HFA, although all equilibrating collection of conformations likely are present in both solvents. For the peptide dissolved in HFIP, cross-relaxation parameters (sigma(HF)) arising from interactions between spins of the solvent and the solute are in good agreement for most protons of the peptide with those predicted from theory. In contrast, observed sigma(HF) for peptide in HFA are negative at all residues while positive sigma(HF) are expected. These results are interpreted to indicate that solute-solvent interactions in HFA persist longer than in HFIP.