[[alternative]]Molecular Dynamics Simulation of Cardiotoxins

[[abstract]]Cardiotoxins from venom of Taiwan Cobra, Naja naja atra, are small 5-β strand and 3-loop basic proteins of 60~62 residues cross-linked by four disulfide bridges. Molecular dynamics simulation was carried out to examine backbone mobility of CTX II in solution and aid in interpretation of order parameters of Cα-H bonds obtained from NMR experiments based on Lipari-Szabo theory. The Calculated order parameters of C□-H bonds and B-factors of CTX II in solution were compared with NMR-derived backbone order parameters and crystal structure data, respectively. Overall qualitative agreement was obtained whereas the calculated values and experimental results of many residues are in good agreement quantitatively. The discrepancies between the present computed results and experiments values, physical basis, and plausible biological function are discussed. Derivation in structure of CTX II in MD simulation from NMR structure occurs at loops, particularly at loop1. From the present subnano second molecular dynamics trajectories of CTX II and CTX III, the calculated order parameters show that, at loop1 and loop3 segments, the structural fluctuation of CTX II is smaller than CTX III but larger than CTX III at loop2.