posted on 2023-12-20, 14:34authored byKwangho Nam, Abdul Raafik Arattu Thodika, Christin Grundström, Uwe H. Sauer, Magnus Wolf-Watz
This study explores
ligand-driven conformational changes in adenylate
kinase (AK), which is known for its open-to-close conformational transitions
upon ligand binding and release. By utilizing string free energy simulations,
we determine the free energy profiles for both enzyme opening and
ligand release and compare them with profiles from the apoenzyme.
Results reveal a three-step ligand release process, which initiates
with the opening of the adenosine triphosphate-binding subdomain (ATP
lid), followed by ligand release and concomitant opening of the adenosine
monophosphate-binding subdomain (AMP lid). The ligands then transition
to nonspecific positions before complete dissociation. In these processes,
the first step is energetically driven by ATP lid opening, whereas
the second step is driven by ATP release. In contrast, the AMP lid
opening and its ligand release make minor contributions to the total
free energy for enzyme opening. Regarding the ligand binding mechanism,
our results suggest that AMP lid closure occurs via an induced-fit
mechanism triggered by AMP binding, whereas ATP lid closure follows
conformational selection. This difference in the closure mechanisms
provides an explanation with implications for the debate on ligand-driven
conformational changes of AK. Additionally, we determine an X-ray
structure of an AK variant that exhibits significant rearrangements
in the stacking of catalytic arginines, explaining its reduced catalytic
activity. In the context of apoenzyme opening, the sequence of events
is different. Here, the AMP lid opens first while the ATP lid remains
closed, and the free energy associated with ATP lid opening varies
with orientation, aligning with the reported AK opening and closing
rate heterogeneity. Finally, this study, in conjunction with our previous
research, provides a comprehensive view of the intricate interplay
between various structural elements, ligands, and catalytic residues
that collectively contribute to the robust catalytic power of the
enzyme.