The multi-component fluorescence intensity decay of variant-3 scorpion neurotoxin is measured with time-correlated single photon counting as a function of guanidine hydrochloride (GuHCl) concentration. Available evidence suggests that while the NH2-terminal β- sheet strand may be denatured in GuHCl, the remaining core neurotoxin structure remains intact. We investigate this hypothesis with computer simulations of variant-3 scorpion neurotoxin with lysine-1 to tyrosine-4 deleted. Previous combination thermodynamic perturbation and umbrella sampling, adiabatic mapping and minimum perturbation mapping computer simulations of tryptophan-47 in the native neurotoxin exhibited multiple rotational isomers that might correspond to the observed fluorescence intensity decay components. The new simulations allow us to compare the number of rotational isomers, the isomer populations, the order parameters, and the transition state theory isomer interconversion rates in the native and denatured states.