A 500-ps Molecular Dynamics Simulation Trajectory of Cardiotoxin II from Taiwan Cobra Venom in solution: Correlation with NMR and X-Ray Crystallography Data

摘要

Molecular dynamics simulation of a small, basic, all #beta#-sheet cardiotoxin, CTX II, from Taiwan cobra venom, with proper treatment of long-range electrostatic interactions, was carried out to examine the backbone mobility of CTX II in solution and aid in interpretation of order parameters of C_#alpha#-H bonds obtained from NMR experiments based on the Lipari-Szabo theory. The calculated order parameters of C_#alpha#-H bonds and B-factors of CTX II in solution were compared with NMR-derived backbone order parameters and the crystal structure data, respectively. An overall qualitative agreement was obtained and, quantitatively, the calculated values and experimental results of many residues were also in good agreement. The discrepancies between the results computed herein and the experimental values, physical bases, and plausible biological functions are discussed.