3.4 | Analysis of molecular interactions between rice
AGPase subunits at different interfaces
To examine the residual interactions occurring at the interfaces of
homo- and hetero-dimeric complexes, we focused on the highest clustered
coordinate from the trajectory of the CII-S1 complex (Figure S4). The
PDBe-PISA web interface was utilized to perform a comprehensive analysis
of the intricate interactions involved. The interaction analysis
suggested multiple-interface interactions; (i) catalytic domain
interactions at the interfaces of the OsS1:OsS1’ and OsL1:OsL1’
homodimers, (ii) β-helix domain interactions at the interfaces of the
OsL1’:OsS1 and OsL1:OsS1’ heterodimers, and (iii) N-terminal loop –
catalytic domain loop interactions at the interfaces of the OsL1:OsS1
and OsL1’:OsS1’ heterodimers (Figure 4).
Interactions within the catalytic domains : Consistent
with the findings observed in the SS subunits of potato tuber AGPase29, our interaction analysis indicated the presence of
homodimeric (up-down) interactions at the interfaces of the catalytic
domains of OsS1:OsS1’ and OsL1:OsL1’ subunits (Figure 4A, B). A higher
number of interactions was observed at the interface of catalytic
domains between OsS1 and OsS1’ than between OsL1 and OsL1’. At the
interface of the OsS1 homodimer (S1’:S1), three H-bonds were noticed
(R132-E182 and Y145-R316) together with several electrostatic
(Q158-Q167/Q175, Y176/W178-Q158, G144-R136, and E152-N131) and
hydrophobic contacts (Figure 4A). However, at the OsL1 homodimeric
(L1:L1’) interface, we observed four H-bonds (R149-E168, E168-N149/H152,
and Q174-W195) and several electrostatic and hydrophobic interactions
(Figure 4B).
Interactions within the β-helix domains : The observed
interactions at the interfaces of the heterodimeric β-helix domains of
S1’:L1 and S1:L1’ are dominated by electrostatic as well as hydrophobic
components. We identified several intermolecular H-bonds
(L363/Q366-L371, Y373-P369, T389-I382, K390-T344/D379, S391-S380,
D392-D379, L393/C394-V377, R395-D374, I396-A375, D398-L378, A399-V272,
I401-S370, and H403-E384) together with electrostatic and hydrophobic
contacts (Figure 4C).
Interactions within N-terminal loop and catalytic domain
loop : Apart from the interactions observed within the catalytic and
β-helix domains, we also identified crucial heterodimeric interactions
at the N-terminal regions (Figure 4D). These interactions were similarly
observed in the interaction between OsL2 and OsS2b.27The interactions at the interfaces of the N-terminal loops are primarily
characterized by strong hydrogen bonding networks and electrostatic
contacts. However, unlike OsL2:OsS2b, we observed few interaction pairs
between the catalytic domain loop regions (highlighted in Figure 4D) are
largely hydrophobic. Overall, the key residues observed in the potato
tuber AGPase subunit (StLS:StSS) interactions11,12,29are conserved in the OsL1:OsS1.