Proteins comprising each of the two plant nonspecific lipid transfer protein (LTP) families, LTP1s and LTP2s, share similar folds and biological functions and are stabilized by four native disulfide bonds. Disulfide-scrambling experiments suggested that rice LTP2 is more thermostable than rice LTP1 and identified multiple disulfide-scrambled isomers for LTP1 but only one for LTP2. According to the potential energy evaluated in two GROMOS force fields, however, rice LTP1 is more stable than either rice or wheat LTP2. Moreover, the published rice LTP2 NMR model structure is found to be highly unfavorable. The reasons for this are investigated, and it is found that the rice LTP2 sequence is in fact more compatible with the more ordered X-ray structure of wheat LTP2 than with the published rice LTP2 NMR model structure. The proposed disulfide bond shuffling of rice LTP1, rice LTP2, and, for comparative purposes, wheat LTP2 and a homology model combining the rice LTP2 sequence with the wheat LTP2 structure is then investigated with a computational disulfide-scrambling technique.