Molecular dynamics simulations of certain mutant peptide models from stapylococcal nuclease reveal that initial hydrophobic collapse associated with turn propensity drive β-hairpin folding

Rashmi Tambe Shukla, Naveen Kumar, Yellamraju Sasidhar

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

An important nucleation event during the folding of staphylococcal nuclease involves the formation of a β-hairpin by the sequence 21DTVKLMYKGQPMTFR35. 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-2DTVKLMYGGQPMTFR16-NMe (K9G:15), Ac-2DTVKLMYKGGPMTFR16-NMe (Q11G:15), Ac-2DTVKLMYGGGPMTFR16-NMe (K9G/Q11G:15), and Ac-2DTVKLMGGGGGMTFR16-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-2YGGQP6-NMe (K3G:5), Ac-2YKGGP6-NMe (Q5G:5), Ac-2YGGGP6-NMe (K3G/Q5G:5), and Ac-2GGGGG6-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 (8GGGGG12), 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
Original languageEnglish
Pages (from-to)516-527
Number of pages11
JournalJournal of peptide science
Volume19
Issue number8
DOIs
Publication statusPublished - 2013

Keywords

  • METIS-302176
  • IR-89250

Fingerprint Dive into the research topics of 'Molecular dynamics simulations of certain mutant peptide models from stapylococcal nuclease reveal that initial hydrophobic collapse associated with turn propensity drive β-hairpin folding'. Together they form a unique fingerprint.

Cite this