Comparative studies of the conformation of the N-terminal fragments of staphylococcal nuclease R in solution.

In order to elucidate the folding of nascent peptide, five peptide fragments of staphylococcal nuclease R starting from N-terminal end and of different chain lengths are made by deletion of 47, 39, 28, 14 and 8 amino-acid residues from its C-terminal end, respectively. Changes in conformation of the N-terminal fragments have been compared by using Fourier-transform infrared spectra, far-ultraviolet circular dichroism spectra and analysis of surface hydrophobicity. The experiments indicate that all the five fragments have certain amounts of residual structure; in general, with increasing the peptide chain, the contents of secondary structure and the enzyme's activity of the peptide increase, and the exposed hydrophobic side chains brought about by the deletion of C-terminal residues are gradually buried in the interior of the nuclease. However, the ordered secondary structures do not always increase with increasing the peptide chain. Further growth of the length of the peptide chain could have an important effect on the conformation of the peptide fragment already synthesized, suggesting some structural adjustments should be necessary in order for the newly synthesized polypeptide to attain its final native conformation. These results support Tsou's nascent peptide folding hypothesis (Tsou, C.-L. (1988) Biochemistry 27, 1809-1812).