pK a of ubiquinone, menaquinone, phylloquinone, plastoquinone, and rhodoquinone in aqueous solution

Biomimetic Synthesis and Chemical Proteomics Reveal the Mechanism of Action and Functional Targets of Phloroglucinol Meroterpenoids

Natural products perennially serve as prolific sources of drug leads and chemical probes, fueling the development of numerous therapeutics. Despite their scarcity, natural products that modulate protein function through covalent interactions with lysine residues hold immense potential to unlock new therapeutic interventions and advance our understanding of the biological processes governed by these modifications. Phloroglucinol meroterpenoids constitute one of the most expansive classes of natural products, displaying a plethora of biological activities. However, their mechanism of action and cellular targets have, until now, remained elusive. In this study, we detail the concise biomimetic synthesis, computational mechanistic insights, physicochemical attributes, kinetic parameters, molecular mechanism of action, and functional cellular targets of several phloroglucinol meroterpenoids. We harness synthetic clickable analogues of natural products to probe their disparate proteome-wide reactivity and subcellular localization through in-gel fluorescence scanning and cell imaging. By implementing sample multiplexing and a redesigned lysine-targeting probe, we streamline a quantitative activity-based protein profiling, enabling the direct mapping of global reactivity and ligandability of proteinaceous lysines in human cells. Leveraging this framework, we identify numerous lysine-meroterpenoid interactions in breast cancer cells at tractable protein sites across diverse structural and functional classes, including those historically deemed undruggable. We validate that phloroglucinol meroterpenoids perturb biochemical functions through stereoselective and site-specific modification of lysines in proteins vital for breast cancer metabolism, including lipid signaling, mitochondrial respiration, and glycolysis. These findings underscore the broad potential of phloroglucinol meroterpenoids for targeting functional lysines in the human proteome.

Computational Modeling Analysis of Kinetics of Fumarate Reductase Activity and ROS Production during Reverse Electron Transfer in Mitochondrial Respiratory Complex II

Reverse electron transfer in mitochondrial complex II (CII) plays an important role in hypoxia/anoxia, in particular, in ischemia, when the blood supply to an organ is disrupted and oxygen is not available. A computational model of CII was developed in this work to facilitate the quantitative analysis of the kinetics of quinol-fumarate reduction as well as ROS production during reverse electron transfer in CII. The model consists of 20 ordinary differential equations and 7 moiety conservation equations. The parameter values were determined at which the kinetics of electron transfer in CII in both forward and reverse directions would be explained simultaneously. The possibility of the existence of the "tunnel diode" behavior in the reverse electron transfer in CII, where the driving force is QH₂, was tested. It was found that any high concentrations of QH₂ and fumarate are insufficient for the appearance of a tunnel effect. The results of computer modeling show that the maximum rate of succinate production cannot provide a high concentration of succinate in ischemia. Furthermore, computational modeling results predict a very low rate of ROS production, about 50 pmol/min/mg mitochondrial protein, which is considerably less than 1000 pmol/min/mg protein observed in CII in forward direction.

Single protonation of the reduced quinone in respiratory complex I drives four-proton pumping

Complex I is a key proton-pumping enzyme in bacterial and mitochondrial respiratory electron transport chains. Using quantum chemistry and electrostatic calculations, we have examined the pKa of the reduced quinone QH-/QH2 in the catalytic cavity of complex I. We find that pKa (QH-/QH2) is very high, above 20. This means that the energy of a single protonation reaction of the doubly reduced quinone (i.e. the reduced semiquinone QH-) is sufficient to drive four protons across the membrane with a potential of 180 mV. Based on these calculations, we propose a possible scheme of redox-linked proton pumping by complex I. The model explains how the energy of the protonation reaction can be divided equally among four pumping units of the pump, and how a single proton can drive translocation of four additional protons in multiple pumping blocks.

Proton-mediated photoprotection mechanism in photosystem II

Photo-induced charge separation, which is terminated by electron transfer from the primary quinone Q_A to the secondary quinone Q_B, provides the driving force for O₂ evolution in photosystem II (PSII). However, the backward charge recombination using the same electron-transfer pathway leads to the triplet chlorophyll formation, generating harmful singlet-oxygen species. Here, we investigated the molecular mechanism of proton-mediated Q_A ^⋅- stabilization. Quantum mechanical/molecular mechanical (QM/MM) calculations show that in response to the loss of the bicarbonate ligand, a low-barrier H-bond forms between D2-His214 and Q_A ^⋅-. The migration of the proton from D2-His214 toward Q_A ^⋅- stabilizes Q_A ^⋅-. The release of the bicarbonate ligand from the binding Fe²⁺ site is an energetically uphill process, whereas the bidentate-to-monodentate reorientation is almost isoenergetic. These suggest that the bicarbonate protonation and decomposition may be a basis of the mechanism of photoprotection via Q_A ^⋅-/Q_AH^⋅ stabilization, increasing the Q_A redox potential and activating a charge-recombination pathway that does not generate the harmful singlet oxygen.

ROS production and signalling in chloroplasts: cornerstones and evolving concepts

Reactive oxygen species (ROS) such as singlet oxygen, superoxide (O₂^●- ) and hydrogen peroxide (H₂ O₂ ) are the markers of living cells. Oxygenic photosynthesis produces ROS in abundance, which act as a readout of a functional electron transport system and metabolism. The concept that photosynthetic ROS production is a major driving force in chloroplast to nucleus retrograde signalling is embedded in the literature, as is the role of chloroplasts as environmental sensors. The different complexes and components of the photosynthetic electron transport chain (PETC) regulate O₂^●- production in relation to light energy availability and the redox state of the stromal Cys-based redox systems. All of the ROS generated in chloroplasts have the potential to act as signals and there are many sulphhydryl-containing proteins and peptides in chloroplasts that have the potential to act as H₂ O₂ sensors and function in signal transduction. While ROS may directly move out of the chloroplasts to other cellular compartments, ROS signalling pathways can only be triggered if appropriate ROS-sensing proteins are present at or near the site of ROS production. Chloroplast antioxidant systems serve either to propagate these signals or to remove excess ROS that cannot effectively be harnessed in signalling. The key challenge is to understand how regulated ROS delivery from the PETC to the Cys-based redox machinery is organised to transmit redox signals from the environment to the nucleus. Redox changes associated with stromal carbohydrate metabolism also play a key role in chloroplast signalling pathways.

Design, synthesis, high algicidal potency, and putative mode of action of new 2-cyclopropyl-4-aminopyrimidine hydrazones

Control of cyanobacteria harmful algal blooms remains a global challenge. In the present study, a series of novel 2-cyclopropyl-4-aminopyrimidine hydrazones were designed and synthesized as potential algicides. Compounds 4a, 4b, 4h, 4j, 4k, 4l, and 4m showed potent inhibition against Synechocystis sp. PCC6803 (median effective concentration, EC₅₀ = 1.1 to 1.7 μM) and Microcystis aeruginosa FACHB905 (EC₅₀ = 1.2 to 2.0 μM), more potent than, or comparably with, copper sulfate (PCC6803, EC₅₀ = 1.8 μM; FACHB905, EC₅₀ = 2.2 μM) and prometryne (PCC6803, EC₅₀ = 12.3 μM; FACHB905, EC₅₀ = 7.2 μM). Compound 4k exhibited algicidal activity in an expanded culture system, and was less toxic than copper sulfate to zebrafish. Electron microscope analyses showed that 4k damaged cyanobacterial cells and decreased the number of thylakoid lamellae. Transcriptomic and qPCR analyses suggest that 4k interfered photosynthesis-related pathways. Treatment with 4k significantly decreased the maximum quantum yield of photosystem II and the photosynthetic electron transfer rate, and the resulting reactive oxygen species damaged thylakoid membranes and photosystem I. The results suggest that 4k is a potential lead for further development of effective and safe algicides.

Protein Motifs for Proton Transfers That Build the Transmembrane Proton Gradient

Biological membranes are barriers to polar molecules, so membrane embedded proteins control the transfers between cellular compartments. Protein controlled transport moves substrates and activates cellular signaling cascades. In addition, the electrochemical gradient across mitochondrial, bacterial and chloroplast membranes, is a key source of stored cellular energy. This is generated by electron, proton and ion transfers through proteins. The gradient is used to fuel ATP synthesis and to drive active transport. Here the mechanisms by which protons move into the buried active sites of Photosystem II (PSII), bacterial RCs (bRCs) and through the proton pumps, Bacteriorhodopsin (bR), Complex I and Cytochrome c oxidase (CcO), are reviewed. These proteins all use water filled proton transfer paths. The proton pumps, that move protons uphill from low to high concentration compartments, also utilize Proton Loading Sites (PLS), that transiently load and unload protons and gates, which block backflow of protons. PLS and gates should be synchronized so PLS proton affinity is high when the gate opens to the side with few protons and low when the path is open to the high concentration side. Proton transfer paths in the proteins we describe have different design features. Linear paths are seen with a unique entry and exit and a relatively straight path between them. Alternatively, paths can be complex with a tangle of possible routes. Likewise, PLS can be a single residue that changes protonation state or a cluster of residues with multiple charge and tautomer states.

Electron transport in Tradescantia leaves acclimated to high and low light: thermoluminescence, PAM-fluorometry, and EPR studies

Using thermoluminescence, PAM-fluorometry, and electron paramagnetic resonance (EPR) for assaying electron transport processes in chloroplasts in situ, we have compared photosynthetic characteristics in Tradescantia fluminensis leaves grown under low light (LL, 50-125 µmol photons m^-2 s^-1) or high light (HL, 875-1000 µmol photons m^-2 s^-1) condition. We found differences in the thermoluminescence (TL) spectra of LL- and HL-acclimated leaves. The LL and HL leaves show different proportions of the Q (~ 0 °C) and B (~ 25-30 °C) bands in their TL spectra; the ratios of the "light sums" of the Q and B bands being S_Q/S_B ≈ 1/1 (LL) and S_Q/S_B ≈ 1/3 (HL). This suggests the existence of different redox states of electron carriers on the acceptor side of PSII in LL and HL leaves, which may be affected, in particular, by different capacities of their photo-reducible PQ pools. Enhanced content of PQ in chloroplasts of LL leaves may be the reason for an efficient performance of photosynthesis at low irradiance. Kinetic studies of slow induction of Chl a fluorescence and measurements of P₇₀₀ photooxidation by EPR demonstrate that HL leaves have faster (about 2 times) response to switching on actinic light as compared to LL leaves grown at moderate irradiation. HL leaves also show higher non-photochemical quenching (NPQ) of Chl a fluorescence. These properties of HL leaves (faster response to light and generation of enhanced NPQ) reflect the flexibility of their photosynthetic apparatus, providing sustainability and rapid response to fluctuations of environmental light intensity and solar stress resistance. Analysis of time-courses of the EPR signals of [Formula: see text] induced by far-red (λ_max = 707 nm), exciting predominantly PSI, and white light, exciting both PSI and PSII, suggests that there is a contribution of cyclic electron flow around PSI to electron flow through PSI in HL leaves. The data obtained are discussed in terms of photosynthetic apparatus sustainability of HL and LL leaves under variable irradiation conditions.

Charge polarization imposed by the binding site facilitates enzymatic redox reactions of quinone

Quinone reduction site (Q_i) of cytochrome bc₁ represents one of the canonical sites used to explore the enzymatic redox reactions involving semiquinone (SQ) states. However, the mechanism by which Q_i allows the completion of quinone reduction during the sequential transfers of two electrons from the adjacent heme b_H and two protons to C1- and C4-carbonyl remains unclear. Here we established that the SQ coupled to an oxidized heme b_H is a dominant intermediate of catalytic forward reaction and, contrary to the long-standing assumption, represents a significant population of SQ detected across pH 5-9. The pH dependence of its redox midpoint potential implicated proton exchange with histidine. Complementary quantum mechanical calculations revealed that the SQ anion formed after the first electron transfer undergoes charge and spin polarization imposed by the electrostatic field generated by histidine and the aspartate/lysine pair interacting with the C4- and C1-carbonyl, respectively. This favors a barrierless proton exchange between histidine and the C4-carbonyl, which continues until the second electron reaches the SQ_i. Inversion of charge polarization facilitates the uptake of the second proton by the C1-carbonyl. Based on these findings we developed a comprehensive scheme for electron and proton transfers at Q_i featuring the equilibration between the anionic and neutral states of SQ_i as means for a leak-proof stabilization of the radical intermediate. The key catalytic role of the initial charge/spin polarization of the SQ anion at the active site, inherent to the proposed mechanism, may also be applicable to the other quinone oxidoreductases.

Redox potentials along the redox-active low-barrier H-bonds in electron transfer pathways

Local proton transfer along redox-active low-barrier H-bonds can alter the driving force or electronic coupling for electron transfer, as the redox potential values depend on the H⁺ position in low-barrier H-bonds.

Minimizing an Electron Flow to Molecular Oxygen in Photosynthetic Electron Transfer Chain: An Evolutionary View

Recruitment of H₂O as the final donor of electrons for light-governed reactions in photosynthesis has been an utmost breakthrough, bursting the evolution of life and leading to the accumulation of O₂ molecules in the atmosphere. O₂ molecule has a great potential to accept electrons from the components of the photosynthetic electron transfer chain (PETC) (so-called the Mehler reaction). Here we overview the Mehler reaction mechanisms, specifying the changes in the structure of the PETC of oxygenic phototrophs that probably had occurred as the result of evolutionary pressure to minimize the electron flow to O₂. These changes are warranted by the fact that the efficient electron flow to O₂ would decrease the quantum yield of photosynthesis. Moreover, the reduction of O₂ leads to the formation of reactive oxygen species (ROS), namely, the superoxide anion radical and hydrogen peroxide, which cause oxidative stress to plant cells if they are accumulated at a significant amount. From another side, hydrogen peroxide acts as a signaling molecule. We particularly zoom in into the role of photosystem I (PSI) and the plastoquinone (PQ) pool in the Mehler reaction.

Redox potentials of ubiquinone, menaquinone, phylloquinone, and plastoquinone in aqueous solution

Quinones serve as redox active cofactors in bacterial photosynthetic reaction centers: photosystem I, photosystem II, cytochrome bc ₁, and cytochrome b ₆ f. In particular, ubiquinone is ubiquitous in animals and most bacteria and plays a key role in several cellular processes, e.g., mitochondrial electron transport. Their experimentally measured redox potential values for one-electron reduction E _m(Q/Q^·-) were already reported in dimethylformamide (DMF) versus saturated calomel electrode but not in water versus normal hydrogen electrode (NHE). We calculated E _m(Q/Q^·-) of 1,4-quinones using a quantum chemical approach. The calculated energy differences of reduction of Q to Q^·- in DMF and water for 1,4-quinone derivatives correlated highly with the experimentally measured E _m(Q/Q^·-) in DMF and water, respectively. E _m(Q/Q^·-) were calculated to be -163 mV for ubiquinone, -260 mV for menaquinone and phylloquinone, and -154 mV for plastoquinone in water versus NHE.

Small Dense Low-Density Lipoprotein as Biomarker for Atherosclerotic Diseases

Low-density lipoprotein (LDL) plays a key role in the development and progression of atherosclerosis and cardiovascular disease. LDL consists of several subclasses of particles with different sizes and densities, including large buoyant (lb) and intermediate and small dense (sd) LDLs. It has been well documented that sdLDL has a greater atherogenic potential than that of other LDL subfractions and that sdLDL cholesterol (sdLDL-C) proportion is a better marker for prediction of cardiovascular disease than that of total LDL-C. Circulating sdLDL readily undergoes multiple atherogenic modifications in blood plasma, such as desialylation, glycation, and oxidation, that further increase its atherogenicity. Modified sdLDL is a potent inductor of inflammatory processes associated with cardiovascular disease. Several laboratory methods have been developed for separation of LDL subclasses, and the results obtained by different methods can not be directly compared in most cases. Recently, the development of homogeneous assays facilitated the LDL subfraction analysis making possible large clinical studies evaluating the significance of sdLDL in the development of cardiovascular disease. Further studies are needed to establish guidelines for sdLDL evaluation and correction in clinical practice.