Molecular dynamics simulations of certain mutant peptide models from staphylococcal nuclease reveal that initial hydrophobic collapse associated with turn propensity drives β‐hairpin folding

Abstract

An important nucleation event during the folding of staphylococcal nuclease involves the formation of a β-hairpin by the sequence (21) DTVKLMYKGQPMTFR(35) . Earlier studies show that the turn sequence 'YKGQP' has an important role in the folding of this β-hairpin. To understand the active or passive nature of the turn sequence 'YKGQP' in the folding of the aforementioned β-hairpin sequence, we studied glycine mutant peptides Ac-(2) DTVKLMYGGQPMTFR(16) -NMe (K9G:15), Ac-(2) DTVKLMYKGGPMTFR(16) -NMe (Q11G:15), Ac-(2) DTVKLMYGGGPMTFR(16) -NMe (K9G/Q11G:15), and Ac-(2) DTVKLMGGGGGMTFR(16) -NMe (penta-G:15) by using molecular dynamics simulations, starting with two different unfolded states, polyproline II and extended conformational forms. Further, 5mer mutant turn peptides Ac-(2) YGGQP(6) -NMe (K3G:5), Ac-(2) YKGGP(6) -NMe (Q5G:5), Ac-(2) YGGGP(6) -NMe (K3G/Q5G:5), and Ac-(2) GGGGG(6) -NMe (penta-G:5) were also studied individually. Our results show that an initial hydrophobic collapse and loop closure occurs in all 15mer mutants, but only K9G:15 mutant forms a stable native-like β-hairpin. In the other 15mer mutants, the hydrophobic collapsed state would not proceed to β-hairpin formation. Of the different simulations performed for the penta-G:15 mutant, in only one simulation a nonnative β-hairpin conformation is sampled with highly flexible loop region ((8) GGGGG(12) ), which has no specific conformational preference as a 5mer. While the sequence 'YGGQP' in the K3G:5 simulation shows relatively higher β-turn propensity, the presence of this sequence in K9G:15 peptide seems to be driving the β-hairpin formation. Thus, these results seem to suggest that for the formation of a stable β-hairpin, the initial hydrophobic collapse is to be assisted by a turn propensity. Initial hydrophobic collapse alone is not sufficient to guide β-hairpin formation.