3.2 | Dynamic insights into interaction between rice
AGPase-L1/S1 and ATP
To access the critical residues of OsL1 and OsS1 participating in
ATP-binding, MD simulations of the ATP-docked complexes (OsL1-ATP and
OsS1-ATP) were carried out. As shown in Figure 2A, the AGPase subunits
were found to be conversed (with backbone RMSD of
~3.5-3.7Å) just after the production run. The computed
RMSD profiles of ATP (Figure 2A) and conformational ensembles of the
ATP-bound complexes (Figure 2B) suggested a stable ATP-AGPase
interaction during the course of simulation time. Furthermore, the
nature of ATP-AGPase interaction was evaluated by computing
intermolecular H-bonds and in-detail interaction analysis. The H-bond
analysis revealed a higher number of H-bonds (7.42) in the trajectory of
OsS1-ATP compared to OsL1-ATP (4.94) (Figure 2C), suggesting a stronger
binding of ATP to OsS1 than OsL1. This observation indicates a more
stable interaction between OsS1 and ATP. To identify the residues
essential for ATP-binding, we carried out RMSD-based cluster analysis
and used best-clustered OsL1/S1-ATP coordinates for interaction
analysis. As shown in Figure 2D, both models showed 9-10 intermolecular
polar contacts with several hydrophobic/electrostatic contacts. In
particular, one aspartic acid residue in both subunits (D215; OsL1 and
D194; OsS1) was found to form strong polar contacts with the sugar
backbone; where the adenine moiety surrounded by several conserved
residues (Figure 2D). To assess the precision of ATP binding, we
compared our findings with the ATP-binding residues of potato AGPase
subunits (Figure 2E). The comparison revealed a high degree of
conservation between the predicted ATP-binding residues of OsL1/OsS1 and
their counterparts in potato,18 indicating the
reliability and accuracy of our predictions.