The interactions of 2 different fusion constructs of a plant cysteine proteinase (CP)/cysteine protein ase inhibitor (CPI) pair designated as R1: H 2 N maltose binding protein CPI CP COOH and R2: H 2 N mal tose binding protein CP CPI COOH with 4 different D amino acids including D Ala, D Ser, D Asp and D Phe were analyzed using experimental methods and computational tools. The results showed that the relative activity of CP is increased in purified R2 product and test D amino acids tend to interact with CP/CPI pair. In contrast, the functionality of R1 product was not influenced by test D amino acids. Determination of the effects of D enantiomers of amino acids on the fusion forms of 2 functionally related proteins such as CP and CPI is the first research in this area. The results related to the binding abilities and the functional properties of 2 differ entially organized forms of CP/CPI pair are predicted to be used as biotechnological clues to make switchable expression systems of 2 functionally related proteins in the future.