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Szafran, K.

Publications and source records attributed to Szafran, K..

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LPOR and the membranes - evolutionary pathway towards prolamellar body formation

Light-dependent protochlorophyllide oxidoreductase (LPOR) has captivated the interest of the research community for decades. One reason is the photocatalytic nature of the reaction catalyzed by the enzyme, and the other is the involvement of LPOR in the formation of a paracrystalline lattice called a prolamellar body (PLB) that disintegrates upon illumination, initiating a process of photosynthetic membrane formation. In this paper, we have integrated three traditional methods previously employed to study the properties of the enzyme to investigate how LPOR evolved and how PLB forms. We found that in cyanobacteria, LPOR activity appears to be independent of lipids, with membrane interaction primarily affecting the enzyme post-reaction, with MGDG and PG having opposite effects on SynPOR. In contrast, plant isoforms exhibit sequence alterations, rendering the enzyme effective in substrate binding mainly in the presence of anionic lipids, depending on residues at positions 122, 312, and 318. Moreover, we demonstrated that the interaction with MGDG could initially serve as enhancement of the substrate specificity towards monovinyl-protochlorophyllide (Pchlide). We have shown that the second LPOR isoforms of eudicots and monocots accumulated mutations that made these variants less and more dependent on anionic lipids, respectively. Finally, we have shown that in the presence of Pchlide, NADP+, and the lipids, plant but not cyanobacterial LPOR homolog remodel membranes into the cubic phase. The cubic phase is preserved if samples supplemented with NADP+ are enriched with NADPH. The results are discussed in the evolutionary context, and the model of PLB formation is presented. SignificanceLPOR is a unique enzyme with photocatalytic properties, developed by cyanobacteria and inherited by algae and plants. In this study, we investigated the properties of the cyanobacterial homolog, revealing that two lipids, PG and MGDG, have opposite effects on enzyme activity. Additionally, we identified mutations in plant isoforms that render the enzyme dependent on anionic lipids. Moreover, we demonstrated that in the presence of NADP+, the plant homolog remodels lipids into a cubic phase, which appears to be the initial step of prolamellar body (PLB) formation. PLB is a unique paracrystalline arrangement of lipids and proteins found in immature chloroplasts, which disintegrates upon illumination, initiating photosynthetic membrane formation.

biochemistry↗

Pigment Binding in The Light-Dependent Protochlorophyllide Oxidoreductase

The Light-Dependent Protochlorophyllide Oxidoreductase (LPOR) is a key enzyme in chlorophyll biosynthesis and its photocatalytic mechanism has long intrigued researchers. However, the lack of structural data for the active complex has impeded understanding of its reaction mechanism. A recent high-resolution structure of enzyme in the active conformation has established a robust foundation for validating hypotheses concerning pigment binding, residue involvement, and consequently, the reaction mechanism. Surprisingly, this new structure challenges previously proposed mechanisms, especially concerning the orientation of the bound protochlorophyllide (Pchlide) pigment. In this study, we employ molecular dynamics and hybrid quantum-mechanics/molecular-mechanics (QM/MM) simulations along with site-directed mutagenesis to compare two Pchlide binding modes: one aligned with previous proposals (mode A), and the other consistent with the recent experimental data (mode B). Binding energy calculations reveal thermodynamic instability of binding mode A due to nonspecific interactions, while mode B exhibits distinct stabilizing interactions yielding favorable binding. QM/MM-based local energy decomposition analysis unravels a complex interaction network that reinforces pigment stabilization in this conformation. Notably, interactions involving Tyr177, His319, and the carboxyl group at C131 influence the pigments excited state energy and potentially contributing to the substrate specificity of the enzyme. Our results uniformly favor binding mode B as represented in the new cryo-EM structure, over the previously assumed mode A. These findings challenge established interpretations and underscore the need for a comprehensive re-evaluation of the reaction mechanism of LPOR that correctly considers pigment interactions and substrate orientation in the binding pocket. Significance StatementA crucial step in the biosynthesis of the all-important photosynthetic pigment chlorophyll is the reduction of a double C=C bond in its precursor protochlorophyllide (PChlide). This is catalyzed by the Light-Dependent Protochlorophyllide Oxidoreductase (LPOR) via an extremely rare example of a biological photocatalytic reaction. Understanding of the LPOR mechanism has been hindered by limited insight into the structure of its active complex. A recent high-resolution LPOR cryo-EM structure substantiates pigment binding, residue interactions, and the reaction mechanism, but contrasts markedly with all previous assumptions regarding the binding mode of the substrate PChlide. Using molecular dynamics simulations, quantum-mechanics/molecular-mechanics calculations, and mutagenesis, we compare and evaluate the two possible Pchlide binding modes, the one assumed previously (mode A) and the one supported by recent data (mode B). Our findings conclusively favor mode B, challenging prior assumptions and pointing toward novel mechanistic possibilities for this unique photocatalytic reaction.

biochemistry↗