Role of Thylakoid Lipids in Protochlorophyllide Oxidoreductase Activation: Allosteric Mechanism Elucidated by a Computational Study

Light-dependent protochlorophyllide oxidoreductase (LPOR) is a chlorophyll synthetase that catalyzes the reduction of protochlorophyllide (Pchlide) to chlorophyllide (Chlide) with indispensable roles in regulating photosynthesis processes. A recent study confirmed that thylakoid lipids (TL) were able to allosterically enhance modulator-induced LPOR activation. However, the allosteric modulation mechanism of LPOR by these compounds remains unclear. Herein, we integrated multiple computational approaches to explore the potential cavities in the Arabidopsis thaliana LPOR and an allosteric site around the helix-G region where high affinity for phosphatidyl glycerol (PG) was identified. Adopting accelerated molecular dynamics simulation for different LPOR states, we rigorously analyzed binary LPOR/PG and ternary LPOR/NADPH/PG complexes in terms of their dynamics, energetics, and attainable allosteric regulation. Our findings clarify the experimental observation of increased NADPH binding affinity for LPOR with PGs. Moreover, the simulations indicated that allosteric regulators targeting LPOR favor a mechanism involving lid opening upon binding to an allosteric hinge pocket mechanism. This understanding paves the way for designing novel LPOR activators and expanding the applications of LPOR.

Automated summary

A recent study confirmed that thylakoid lipids (TL) can activate LPOR. However, the allosteric modulation mechanism of LPOR by these compounds remains unclear. In this study, we used multiple computational approaches to explore potential cavities in Arabidopsis thaliana LPOR and identified a high-affinity binding site for phosphatidyl glycerol (PG) around the helix-G region. Through molecular dynamics simulations, we analyzed LPOR/PG and LPOR/NADPH/PG complexes and gained insights into their dynamics, energetics, and potential allosteric regulation. Our findings clarify the NADPH binding affinity for LPOR in the presence of PGs and suggest a mechanism involving lid opening upon binding of allosteric regulators to an allosteric hinge pocket.