Molecular dynamics insight into the diverse thermodynamic behavior of a beta-hairpin peptide
Journal
Journal of the Chinese Chemical Society
Journal Volume
60
Journal Issue
7
Pages
915-928
Date Issued
2013
Author(s)
Abstract
The �?hairpin is a building block in the �?sheet structure. Understanding the formation of the �?hairpin may provide insight into the formation of �?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 �?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. ? 2013 The Chemical Society Located in Taipei & Wiley-VCH Verlag GmbH & Co. KGaA.
Subjects
Beta-hairpin; MD simulations; Probe-dependent; Protein folding; Site-dependent
Type
journal article