Exploring the structural assembly of rice ADP-glucose pyrophosphorylase subunits using MD simulation

ADP-glucose pyrophosphorylase plays a pivotal role as an allosteric enzyme essential for starch biosynthesis in plants. The higher plant AGPase comparises of a pair of large and a pair of small subunits to form a heterotetrameric complex. Growing evidence indicates that each subunit plays a distinct role in regulating the underlying mechanism of starch biosynthesis. In the rice genome, there are four large subunit genes (OsL1-L4) and three small subunit genes (OsS1, OsS2a, and OsS2b). While the structural assembly of cytosolic rice AGPase subunits (OsL2:OsS2b) is known, no such study has been thus far reported for plastidial rice AGPase (OsL1:OsS1). In this study, we employed protein modeling and MD simulation approaches to gain insights into the structural association of plastidial AGPase subunits. The results demonstrate that the heterotetramic association of OsL1:OsS1 is very similar to that of cytosolic OsL2:OsS2b and potato plastidial AGPase heterotetramers. Moreover, the yeast-two-hybrid results, which resemble potato AGPase L1:S1, suggest a difference in protein conformation between OsL1:OsS1 and OsL2:OsS2b. Thus, the regulatory and catalytic mechanisms for plastidial AGPase (OsL1:OsS1) could be different in rice culm and developing endosperm compared to those of OsL2:OsS2b, which is found predominantly in rice endosperm.