Ternary Complex Formation and Photoactivation of a Photoenzyme Results in Altered Protein Dynamics

Theoretical and Experimental Studies on Plant Light-Dependent Protochlorophyllide Oxidoreductase as a Novel Target for Searching Potential Herbicides

Herbicide resistance is a prevalent problem that has posed a foremost challenge to crop production worldwide. Light-dependent enzyme NADPH: protochlorophyllide oxidoreductase (LPOR) in plants is a metabolic target that could satisfy this unmet demand. Herein, for the first time, we embarked on proposing a new mode of action of herbicides by performing structure-based virtual screening targeting multiple LPOR binding sites, with the determination of further bioactivity on the lead series. The feasibility of exploiting high selectivity and safety herbicides targeting LPOR was discussed from the perspective of the origin and phylogeny. Besides, we revealed the structural rearrangement and the selection key for NADPH cofactor binding to LPOR. Based on these, multitarget virtual screening was performed and the result identified compounds 2 affording micromolar inhibition, in which the IC₅₀ reached 4.74 μM. Transcriptome analysis revealed that compound 2 induced more genes related to chlorophyll synthesis in Arabidopsis thaliana, especially the LPOR genes. Additionally, we clarified that these compounds binding to the site enhanced the overall stability and local rigidity of the complex systems from molecular dynamics simulation. This study delivers a guideline on how to assess activity-determining features of inhibitors to LPOR and how to translate this knowledge into the design of novel and effective inhibitors against malignant weed that act by targeting LPOR.

Temperature and salt controlled tuning of protein clusters

The formation of molecular assemblies in protein solutions is of strong interest both from a fundamental viewpoint and for biomedical applications. While ordered and desired protein assemblies are indispensable for some biological functions, undesired protein condensation can induce serious diseases. As a common cofactor, the presence of salt ions is essential for some biological processes involving proteins, and in aqueous suspensions of proteins can also give rise to complex phase diagrams including homogeneous solutions, large aggregates, and dissolution regimes. Here, we systematically study the cluster formation approaching the phase separation in aqueous solutions of the globular protein BSA as a function of temperature (T), the protein concentration (c_p) and the concentrations of the trivalent salts YCl₃ and LaCl₃ (c_s). As an important complement to structural, i.e. time-averaged, techniques we employ a dynamical technique that can detect clusters even when they are transient on the order of a few nanoseconds. By employing incoherent neutron spectroscopy, we unambiguously determine the short-time self-diffusion of the protein clusters depending on c_p, c_s and T. We determine the cluster size in terms of effective hydrodynamic radii as manifested by the cluster center-of-mass diffusion coefficients D. For both salts, we find a simple functional form D(c_p, c_s, T) in the parameter range explored. The calculated inter-particle attraction strength, determined from the microscopic and short-time diffusive properties of the samples, increases with salt concentration and temperature in the regime investigated and can be linked to the macroscopic behavior of the samples.

Photocatalysis as the 'master switch' of photomorphogenesis in early plant development

Enzymatic photocatalysis is seldom used in biology. Photocatalysis by light-dependent protochlorophyllide oxidoreductase (LPOR)-one of only a few natural light-dependent enzymes-is an exception, and is responsible for the conversion of protochlorophyllide to chlorophyllide in chlorophyll biosynthesis. Photocatalysis by LPOR not only regulates the biosynthesis of the most abundant pigment on Earth but it is also a 'master switch' in photomorphogenesis in early plant development. Following illumination, LPOR promotes chlorophyll production, plastid membranes are transformed and the photosynthetic apparatus is established. Given these remarkable, light-induced pigment and morphological changes, the LPOR-catalysed reaction has been extensively studied from catalytic, physiological and plant development perspectives, highlighting vital, and multiple, cellular roles of this intriguing enzyme. Here, we offer a perspective in which the link between LPOR photocatalysis and plant photomorphogenesis is explored. Notable breakthroughs in LPOR structural biology have uncovered the structural-mechanistic basis of photocatalysis. These studies have clarified how photon absorption by the pigment protochlorophyllide-bound in a ternary LPOR-protochlorophyllide-NADPH complex-triggers photocatalysis and a cascade of complex molecular and cellular events that lead to plant morphological changes. Photocatalysis is therefore the master switch responsible for early-stage plant development and ultimately life on Earth.