Conformational Selection by the aIF2 GTPase: A Molecular Dynamics Study of Functional Pathways

Archaeal initiation factor 2 (aIF2) is a GTPase involved in protein biosynthesis. In its GTP-bound, “ON” conformation, it binds an initiator tRNA and carries it to the ribosome. In its GDP-bound, “OFF” conformation, it dissociates from tRNA. To improve our understanding of the role of each conformational state in the aIF2 “life cycle”, we start from the state immediately after GTP hydrolysis, ON:GDP:Pi (where Pi is inorganic phosphate), and consider the possible next steps on the pathway to the OFF:GDP product. The first possibility is Pi dissociation, leading to ON:GDP, which could then relax into OFF:GDP. We use molecular dynamics simulations to compute the Pi dissociation free energy and show that dissociation is highly favorable. The second possibility is conformational relaxation into the OFF state before Pi dissociation, to form OFF:GDP:Pi. We estimate the corresponding free energy approximately, 2 ± 3.5 kcal/mol, so that this is an uphill or weakly downhill process. A third possibility is relaxation into another conformation, neither ON nor OFF. Indeed, a third, “MIXED” conformation was seen recently in a crystal structure of the aIF2:GDP:Pi complex. For this conformational state, Pi dissociation is weakly unfavorable, in contrast to the ON and OFF states. From this, we will deduce that if the MIXED:GDP complex is not too unstable, the ON:GDP:Pi → MIXED:GDP:Pi transformation is a downhill process, which can occur spontaneously. This suggests that the MIXED state could be a functional intermediate.