Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
J Pept Sci. 2013 Aug;19(8):516-27. doi: 10.1002/psc.2530. Epub 2013 Jun 21.
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.
在枯草溶菌素折叠过程中，一个重要的成核事件涉及到由序列（21）DTVKLMYKGQPMTFR（35）形成β发夹。早期研究表明，转角序列'YKGQP'在该β发夹折叠中起着重要作用。为了了解上述β发夹序列中转角序列'YKGQP'的主动或被动性质，我们通过分子动力学模拟研究了甘氨酸突变肽 Ac-(2) DTVKLMYGGQPMTFR(16)-NMe（K9G:15）、Ac-(2) DTVKLMYKGGPMTFR(16)-NMe（Q11G:15）、Ac-(2) DTVKLMYGGGPMTFR(16)-NMe（K9G/Q11G:15）和 Ac-(2) DTVKLMGGGGGMTFR(16)-NMe（penta-G:15），使用两种不同的未折叠状态，即聚脯氨酸 II 和伸展构象形式作为起始状态。此外，还分别研究了 5 肽突变转角肽 Ac-(2) YGGQP(6)-NMe（K3G:5）、Ac-(2) YKGGP(6)-NMe（Q5G:5）、Ac-(2) YGGGP(6)-NMe（K3G/Q5G:5）和 Ac-(2) GGGGG(6)-NMe（penta-G:5）。我们的结果表明，所有 15 肽突变体都发生了初始疏水塌陷和环闭合，但只有 K9G:15 突变体形成了稳定的类似天然的β发夹。在其他 15 肽突变体中，疏水塌陷状态不会进一步形成β发夹。在对 penta-G:15 突变体进行的不同模拟中，只有一种模拟中采样到了具有高度柔性环区（(8) GGGGG(12)）的非天然β发夹构象，该环区没有作为 5 肽的特定构象偏好。虽然 K3G:5 模拟中的序列'YGGQP'显示出相对较高的β转角倾向，但在 K9G:15 肽中存在该序列似乎驱动了β发夹的形成。因此，这些结果似乎表明，对于稳定β发夹的形成，初始疏水塌陷需要转角倾向的辅助。仅仅初始疏水塌陷不足以指导β发夹的形成。
