Characterization of a Partially Structured Intermediate of Cardiotoxin VI from Naja naja atra at High Temperature

The unfolding kinetics of cardiotoxin analogue VI from Taiwan cobra (Naja naja atra) have been studied at 473 K, pH 7.0 in the presence of 0.1 M NaCl using molecular dynamics simulations for 50 ns. Trajectory structures stored at every 25 ps (2000 structures) were probed at molecular (RMSD and radius of gyration) and residue (RMSF, surface area accessibility and secondary structures) level resolutions by means of various computational strategies. Comprehensive analysis of the data suggested that the C-terminal tail of the protein, which is sandwiched in the cleft region, was first destabilized followed by double-stranded domain and strand IV of triplestranded domain of the protein. Strikingly, it was found that the protein assumed a partially structured state consisting of a sheet composed of stand III and V at around 16 ns and the intermediate was also found to be stable in the rest of the dynamic scales at 473 K. The structural features of the partially structured intermediate and its implications on understanding the stability and folding dynamics of the protein have been brought into fore in detail.