Protein metabolism is known to be affected by dietary proteins, but the fundamental mechanisms that underlie the changes in protein metabolism are unclear. The aim of the present study was to test the effects of feeding growing rats with balanced diets containing soya protein isolate, zein and casein as the sole protein source on the expression of genes related to protein metabolism responses in skeletal muscle. The results showed that feeding a zein protein diet to the growing rats induced changes in protein anabolic and catabolic metabolism in their gastrocnemius muscles when compared with those fed either the reference protein casein diet or the soya protein isolate diet. The zein protein diet increased not only the mRNA levels and phosphorylation of mammalian target of rapamycin (mTOR), but also the mRNA expression of muscle atrophy F-box (MAFbx)/atrogin-1 and muscle ring finger 1 (MuRF1), as well as the forkhead box-O (FoxO) transcription factors involved in the induction of the E3 ligases. The amino acid profile of proteins seems to control signalling pathways leading to changes in protein synthesis and proteolysis.