Searching for folding initiation sites of staphylococcal nuclease: A study of N-terminal short fragments

The N‐terminal short fragments of staphylococcal nuclease (SNase), SNase20, SNase28, and SNase36, corresponding to the sequence regions, Ala1–Gly20, Ala1–Lys28, and Ala1–Leu36, respectively, as well as an 8‐residue peptide (Ala17–Ile18–Asp19–Gly20–Asp21–Thr22–Val23–Lys24) have been synthesized. The conformational states of these fragments were investigated using CD and NMR spectroscopy in aqueous solution and in trifluoroethanol (TFE)–H2O mixture. SNase20 containing a sequence corresponding to a bent peptide in native SNase shows a transient population of bend‐like conformation around Ala12–Thr13–Leu14 in TFE–H2O mixture. The sequence region of Ala17–Thr22 of SNase28 displays a localized propensity for turn‐like conformation in both aqueous solution and TFE—H2O mixture. The conformational ensemble of SNase36 in aqueous solution includes populated turn‐like conformations localized in sequence regions Ala17–Thr22 and Tyr27–Gln30. The analysis suggests that these sequence regions, which form the regular secondary structures in native protein, may serve as the folding nucleation sites of SNase fragments of different chain lengths starting from the N‐terminal end. Thus, the formation of bend‐ and turn‐like conformations of these sequence regions may be involved in the early folding events of the SNase polypeptide chain in vitro. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004