The effect of the protein environment surrounding chromophores (protein nanospaces) on the photoinduced ultrafast twisting of chromophores in photoactive yellow protein (PYP) was investigated by comparing the femtosecond-picosecond fluorescence dynamics of wild type PYP with those of the chromophore in aqueous solution as well as in protein nanospace modified by site-directed mutagenesis; The rate of the twisted state formation of the chromophore (the primary step of the trans --> cis photoisomerization) was demonstrated to be considerably enhanced in protein compared with the aqueous solution. Moreover, results of the measurements of fluorescence dynamics of the chromophore in the protein nanospace modified by site-directed mutagenesis implied that the twisted state formation by flipping the thioester Linkage of the chromophore was slowed by modifying the nanospace structure to a slightly looser one. Namely, the more restricted structure of the protein nanospace in the wild-type PYP seems to be best engineered for the twisting by the flipping mechanism.