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Keywords:

  • Beta-hairpin;
  • Protein folding;
  • Site-dependent;
  • Probe-dependent;
  • MD simulations

Abstract

The b-hairpin is a building block in the β-sheet structure. Understanding the formation of the β-hairpin may provide insight into the formation of β-sheet structures in, for example, protein amyloids. In this study, we performed molecular dynamics (MD) simulations to investigate the temperature-dependent transition behaviors of the GB1 β-hairpin peptide. The simulated results are analysed in terms of distances between pairs of peptide bonds and site-dependent dihedral angles. Our results show that the properties of the hairpin can be site-dependent and that the dependency is primarily associated with the hairpin's geometrical shape and specific interactions, such as hydrophobic clustering. Thus our study provides a foundation for the interpretation of probe-dependent experimental results.