Structural insights into signal transduction in photoactivated adenylyl cyclase through molecular dynamics simulations

OaPAC, from Oscillatoria acuminata, is a homodimer protein consisting of the blue-light using flavin domain and the adenylyl cyclase (AC) domain, linked by long coiled-coil α3-helices. Upon blue-light absorption, a rearrangement of the hydrogen-bonding network involving the flavin chromophore, Y6, and Q48 triggers signal propagation through the α3-helices to the AC domain. While the recent crystallographic structure of the W90-M92-switched conformation in the light state provided significant structural information, the underlying atomistic mechanism of signal transduction remains unclear. In this study, we performed molecular dynamics simulations of OaPAC for four models: wild-type (WT) dark state, W90-M92 unswitched WT light state, W90-M92 switched WT light state, and W90-M92 unswitched L111A/L115A light state. Our results show that the switched WT light-state model exhibits structural fluctuation approximately twice as large as that in the unswitched WT light state. Furthermore, we identified a pronounced transition between two distinct conformational states in the switched WT light-"open" and "closed" -characterized by the angle between the α3-helices and the "handle" region. Notably, the occupancy of the closed conformation was highest in the switched WT light state. In contrast, the non-functional L111A/L115A mutant remained trapped in a rigid open conformation, reflecting its loss of activity and linking structural flexibility to enzymatic competence. These findings suggest that the W90-M92 conformational switch is a critical, multi-step trigger of OaPAC signal transduction, inducing a transient asymmetric (open-closed) conformation and a flexion motion that may facilitate enzymatic activation. This study would provide key atomistic insights for the rational design of advanced optogenetic actuators.