Paper Citing NAMD - Abstract
Tsai, Min-Yeh; Yuan, Jian-Min; Yamaki, Masahiro; Lin, Chih-Kai; Lin, Sheng Hsien
Molecular Dynamics Insight into the Diverse Thermodynamic Behavior of a Beta-Hairpin Peptide
JOURNAL OF THE CHINESE CHEMICAL SOCIETY, 60:915-928, JUL 2013
The b-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.
