Examination of two-strand β-sheet conformations of peptides using molecular dynamics simulation with local enhanced sampling method.

 

Tzu-Hsien Wu and Ying-Chieh Sun*

Department of Chemistry, National Taiwan Normal University 88 Sec. 4, Tingchow Road, Taipei, Taiwan.

 

The two-strand β-sheet conformations of peptides of 20 residues, which are located at the initial folding site, obtained from NMR structure of cardiotoxins (CTX) from venom of Taiwan cobra, were examined using molecular dynamics simulation with the locally enhanced sampling (LES) method. The trajectories showed that the peptide of CTX3 (CTX2), starting from CTX2 (CTX3) β conformation, is able to transit and move close to CTX3 (CTX2) β conformation with LES at <300 ps while the conformation transition was not seen up to 1 ns without LES. The effects of number of copies and copy region of LES method in the simulation results were examined. Molecular interactions at the site of conformation transition were analyzed and discussed.