Enzymatic Mechanisms of Phosphate and Sulfate Transfer

Reactivity of metal-oxo clusters towards biomolecules: from discrete polyoxometalates to metal-organic frameworks

Metal-oxo clusters hold great potential in several fields such as catalysis, materials science, energy storage, medicine, and biotechnology. These nanoclusters of transition metals with oxygen-based ligands have also shown promising reactivity towards several classes of biomolecules, including proteins, nucleic acids, nucleotides, sugars, and lipids. This reactivity can be leveraged to address some of the most pressing challenges we face today, from fighting various diseases, such as cancer and viral infections, to the development of sustainable and environmentally friendly energy sources. For instance, metal-oxo clusters and related materials have been shown to be effective catalysts for biomass conversion into renewable fuels and platform chemicals. Furthermore, their reactivity towards biomolecules has also attracted interest in the development of inorganic drugs and bioanalytical tools. Additionally, the structural versatility of metal-oxo clusters allows for the efficiency and selectivity of the biomolecular reactions they promote to be readily tuned, thereby providing a pathway towards reaction optimization. The properties of the catalyst can also be improved through incorporation into solid supports or by linking metal-oxo clusters together to form Metal-Organic Frameworks (MOFs), which have been demonstrated to be powerful heterogeneous catalysts. Therefore, this review aims to provide a comprehensive and critical analysis of the state of the art on biomolecular transformations promoted by metal-oxo clusters and their applications, with a particular focus on structure-activity relationships.

Structural biology of MCR-1-mediated resistance to polymyxin antibiotics

Polymyxins, a last resort antibiotic, target the outer membrane of pathogens and are used to address the increasing prevalence of multidrug-resistant Gram-negative bacteria. The plasmid-encoded enzyme MCR-1 confers polymyxin resistance to bacteria by modifying the outer membrane. Transferable resistance to polymyxins is a major concern; therefore, MCR-1 is an important drug target. In this review, we discuss recent structural and mechanistic aspects of MCR-1 function, its variants and homologs, and how they are relevant to polymyxin resistance. Specifically, we discuss work on polymyxin-mediated disruption of the outer and inner membranes, computational studies on the catalytic mechanism of MCR-1, mutagenesis and structural analysis concerning residues important for substrate binding in MCR-1, and finally, advancements in inhibitors targeting MCR-1.

Biochemical Resistivity against Free Radicals and Microbes: Cooperative Action of Zn(II)/Imidazole in Phosphoesterase-Mediated Cell Death

This work delivers a targeted synthesis of four isostructural O-substituted imidazole-based zinc(II) complexes, namely, [Zn2(L1)2(I)2](DMF) (1), [Zn2(L2)2(I)2](DMF) (2), [Zn2(L1)2(Br)2] (3), and [Zn2(L2)2(Br)2] (4), derived from homologous Schiff-base ligands HL1 and HL2 to explore their impact on free radicals, microbes, and dephosphorylation of phosphoesters. The antioxidant activity of all complexes was checked by various radical scavenging assays (ABTS+•, DPPH•, and H2O2 radical quenching). Among them, complex 2 showed superior radical quenching activity, as indicated by its lowest EC50 value and thus maximum antioxidative capability. Again, antibacterial assays against several Gram-positive and Gram-negative bacteria were conducted to evaluate the zone of inhibition. The minimum bactericidal concentration and minimum inhibitory concentration values from the microdilution method for all complexes revealed complex 3 to have maximum potency against Gram-positive bacteria. The P-O bond hydrolysis in the phospholipid chain caused by the hydrolytic phosphoesterase activity of the Zn(II)-complexes plays a crucial role in cell membrane rupture. A model substrate 4-PNPP was used to explain the potency of monomeric Zn(II) complex (3) for cell penetration over dimeric one (2) with a proper mechanism. Furthermore, a heme model substrate, Fe(TPP)Cl, has been introduced with the most potent complex 3 and has spectrophotometric evidence for covalent interaction with imidazole and Fe(III) that can disrupt the nitric oxide dioxygenase function of flavohemoglobin, leading to bacterial cell death. To our knowledge, this is the first case to report a novel mechanism of antimicrobial action where both the metal and the ligand are cooperatively involved in bacterial cell death. The main goal of this work is to invent multifunctional therapeutics as well as the proper chemical rationalization of biological processes using mechanistic approaches, which includes investigating the roles of halides, imidazoles, and solution-phase structural variations of complexes..

Crystal structure of phosphate bound Acyl phosphatase mini-enzyme from Deinococcus radiodurans at 1Å resolution

Acylphosphatase (Acp) is a hydrolase which specifically cleaves carboxyl-phosphate bond of intermediates of metabolic pathways. It is a small cytosolic enzyme found in both prokaryotic and eukaryotic organisms. Previous crystal structures of acylphosphatase from different organisms have provided insights into the active site but the complete understanding of substrate binding and catalytic mechanisms in acylphosphatase remain elusive. Here we report the crystal structure of phosphate bound acylphosphatase from a mesothermic bacterium, Deinococcus radiodurans (drAcp) at resolution of 1.0 Å. Our structural analysis shows how the terminal phosphate group of substrates is bound to the active site, highlighting the importance of arginine in substrate recognition, role of asparagine in mode of catalysis and shedding light on the reaction mechanism. Additionally, the protein can refold after thermal melting by gradually lowering the temperature. To further explore the dynamics of drAcp, molecular dynamics simulation of drAcp and homologs from thermophilic organisms were carried out which revealed similar root mean square fluctuation profile but drAcp showed comparatively higher fluctuations.

Controlled Hydrolysis of Phosphate Esters: A Route to Calixarene-Supported Rare-Earth Clusters

Phosphate ester bonds are widely present in nature (e. g. DNA/RNA) and can be extremely stable against hydrolysis without the help of catalysts. Previously, we showed how the combination of phosphoryl and calix[4]arene moieties in the same organic framework (L_PO ) allows isolation of single lanthanide (Ln) metal ions as [Ln^III (L_PO )₂ ](O₃ SCF₃ )₃ . Here we report how by controlling the reaction conditions a new hydrolyzed phosphoryl-calix[4]arene ligand (H₃ L_HPO ) is formed as a result of Ln^III -mediated P-OEt bond cleavage in three out of the eight possible sites in L_PO . The chelating nature of H₃ L_HPO traps the Ln^III species in the form of [Ln^III (L_HPO )((EtO)₂ P(O)OH)]₂ dimers (Ln=La, Dy, Tb, Gd), where the Dy derivative shows slow magnetization relaxation. The strategy presented herein could be extended to access a broader library of hydrolyzed platforms (H_x L_HPO ; x=1-8) that may represent mimics of nuclease enzymes.

Mechanistic and evolutionary insights into alkaline phosphatase superfamily through structure-function studies on Sphingomonas alkaline phosphatase

Alkaline phosphatases (APs), represented by E. coli AP (ECAP), employ an arginine residue to stabilize the phosphoryl group in the active site; whereas, AP from Sphingomonas (SPAP) shows a unique combination of substrate-binding residues; Thr89, Asn110, Lys171, and Arg173. Although such combination has been observed only in SPAP, these residues are present separately in different members of the AP superfamily. Here, we establish the presence of two distinct classes of APs; ECAP-type and SPAP-type. Bioinformatic analyses show that SPAP-type of APs are widely distributed in the bacterial kingdom. The role of active site residues in the catalytic mechanism has been delineated through a set of crystal structures reported here. These structures, representing different stages of the reaction pathway provide wealth of information for the catalytic mechanism. Despite critical differences in the substrate binding residues, SPAP follows a mechanism similar to that of ECAP-type of APs. Structure-based phylogenetic analysis suggests that SPAP and ECAP may have diverged very early during the evolution from a common ancestor. Moreover, it is proposed that the SPAP-type of APs are fundamental members of the AP superfamily and are more closely related to other members of the superfamily as compared to the ECAP-type of APs.

Solvent and solvation effects on reactivities and mechanisms of phospho group transfers from phosphate and phosphinate esters to nucleophiles

Organophosphorus esters fulfil many industrial, agricultural, and household roles. Nature has deployed phosphates and their related anhydrides as energy carriers and reservoirs, as constituents of genetic materials in the form of DNA and RNA, and as intermediates in key biochemical conversions. The transfer of the phosphoryl (PO₃) group is thus a ubiquitous biological process that is involved in a variety of transformations at the cellular level such as bioenergy and signals transductions. Significant attention has been paid in the last seven decades to understanding the mechanisms of uncatalyzed (solution) chemistry of the phospho group transfer because of the notion that enzymes convert the dissociative transition state structures in the uncatalyzed reactions into associative ones in the biological processes. In this regard, it has also been proposed that the rate enhancements enacted by enzymes result from the desolvation of the ground state in the hydrophobic active site environments, although theoretical calculations seem to disagree with this position. As a result, some attention has been paid to the study of the effects of solvent change, from water to less polar solvents, in uncatalyzed phospho transfer reactions. Such changes have consequences on the stabilities of the ground and the transition states of reactions which affect reactivities and, sometimes, the mechanisms of reactions. This review seeks to collate and evaluate what is known about solvent effects in this domain, especially their effects on rates of reactions of different classes of organophosphorus esters. The outcome of this exercise shows that a systematized study of solvent effects needs to be undertaken to fully understand the physical organic chemistry of the transfer of phosphates and related molecules from aqueous to substantially hydrophobic environments, since significant knowledge gaps exist.

The Power of Biocatalysts for Highly Selective and Efficient Phosphorylation Reactions

Reactions involving the transfer of phosphorus-containing groups are of key importance for maintaining life, from biological cells, tissues and organs to plants, animals, humans, ecosystems and the whole planet earth. The sustainable utilization of the nonrenewable element phosphorus is of key importance for a balanced phosphorus cycle. Significant advances have been achieved in highly selective and efficient biocatalytic phosphorylation reactions, fundamental and applied aspects of phosphorylation biocatalysts, novel phosphorylation biocatalysts, discovery methodologies and tools, analytical and synthetic applications, useful phosphoryl donors and systems for their regeneration, reaction engineering, product recovery and purification. Biocatalytic phosphorylation reactions with complete conversion therefore provide an excellent reaction platform for valuable analytical and synthetic applications.

Phosphorylation and sulfation share a common biosynthetic pathway, but extend biochemical and evolutionary diversity of biological macromolecules in distinct ways

Phosphate and sulfate groups are integral to energy metabolism and introduce negative charges into biological macromolecules. One purpose of such modifications is to elicit precise binding/activation of protein partners. The physico-chemical properties of the two groups, while superficially similar, differ in one important respect—the valency of the central (phosphorus or sulfur) atom. This dictates the distinct properties of their respective esters, di-esters and hence their charges, interactions with metal ions and their solubility. These, in turn, determine the contrasting roles for which each group has evolved in biological systems. Biosynthetic links exist between the two modifications; the sulfate donor 3′-phosphoadenosine-5′-phosphosulfate being formed from adenosine triphosphate (ATP) and adenosine phosphosulfate, while the latter is generated from sulfate anions and ATP. Furthermore, phosphorylation, by a xylosyl kinase (Fam20B, glycosaminoglycan xylosylkinase) of the xylose residue of the tetrasaccharide linker region that connects nascent glycosaminoglycan (GAG) chains to their parent proteoglycans, substantially accelerates their biosynthesis. Following observations that GAG chains can enter the cell nucleus, it is hypothesized that sulfated GAGs could influence events in the nucleus, which would complete a feedback loop uniting the complementary anionic modifications of phosphorylation and sulfation through complex, inter-connected signalling networks and warrants further exploration.

Enzyme-assisted metal nanoparticles etching based plasmonic ELISA: Progress and insights

The unique size and shape tunable localized surface plasmon resonance (LSPR) properties of the noble metal nanoparticle have been extensively exploited to realize a variety of enzyme-based optical biosensors. Although approaches like metal film deposition, nanoparticle aggregation, and synthesis & growth of metal nanoparticles are quite useful, metal nanoparticle etching-based biosensors offer greater sensitivity, selectivity, and stability against various environmental factors which makes this strategy easy to use for field applications. This review discusses the current state-of-art of plasmonic nanoparticle etching-based enzyme-linked immunosorbent assay (ELISA) realized for visual detection of various analytes. The naked eye detection, i.e. without any optical readout device, is the additional advantage of this sensing approach that reduces the analysis cost significantly making it feasible under resource-constrained settings. This review paper provides deeper insights into biocatalytic etching mechanisms of various plasmonic nanoparticles resulting in vivid color change as a function of analyte concentration. Although nanoparticle etching-based ELISA has huge potential, steps need to be taken to realize a point-of-care (POC) nanodiagnostic before its translation to a commercial technique or product that can be achieved in near future by integrating it with microfluidics technology and other technological avenues.

A Kinetic Isotope Effect in the Formation of Lanthanide Phosphate Nanocrystals

Mechanisms of nucleation and growth of crystals are still attracting a great deal of interest, in particular with recent advances in experimental techniques aimed at studying such phenomena. Studies of kinetic isotope effects in various reactions have been useful for elucidating reaction mechanisms, and it is believed that the same may apply for crystal formation kinetics. In this work, we present a kinetic study of the formation of europium-doped terbium phosphate nanocrystals under acidic conditions, including a strong H/D isotope effect. The nanocrystal growth process could be quantitatively followed through monitoring of the europium luminescence intensity. Hence, such lanthanide-based nanocrystals may serve as unique model systems for studying crystal nucleation and growth mechanisms. By combining the luminescence and NMR kinetics data, we conclude that the observed delayed nucleation occurs due to initial formation of pre-nucleation clusters or polymers of the lanthanide and phosphate ions, which undergo a phase transformation to crystal nuclei and further grow by cluster attachment. A scaling behavior observed on comparison of the H₂O and D₂O-based pre-nucleation and nanocrystal growth kinetics led us to conclude that both pre-nucleation and nanocrystal growth processes are of similar chemical nature.

Essential Functional Interplay of the Catalytic Groups in Acid Phosphatase

The cooperative interplay between the functional devices of a preorganized active site is fundamental to enzyme catalysis. An in-depth understanding of this phenomenon is central to elucidating the remarkable efficiency of natural enzymes and provides an essential benchmark for enzyme design and engineering. Here, we study the functional interconnectedness of the catalytic nucleophile (His18) in an acid phosphatase by analyzing the consequences of its replacement with aspartate. We present crystallographic, biochemical, and computational evidence for a conserved mechanistic pathway via a phospho-enzyme intermediate on Asp18. Linear free-energy relationships for phosphoryl transfer from phosphomonoester substrates to His18/Asp18 provide evidence for the cooperative interplay between the nucleophilic and general-acid catalytic groups in the wild-type enzyme, and its substantial loss in the H18D variant. As an isolated factor of phosphatase efficiency, the advantage of a histidine compared to an aspartate nucleophile is ∼10⁴-fold. Cooperativity with the catalytic acid adds ≥10²-fold to that advantage. Empirical valence bond simulations of phosphoryl transfer from glucose 1-phosphate to His and Asp in the enzyme explain the loss of activity of the Asp18 enzyme through a combination of impaired substrate positioning in the Michaelis complex, as well as a shift from early to late protonation of the leaving group in the H18D variant. The evidence presented furthermore suggests that the cooperative nature of catalysis distinguishes the enzymatic reaction from the corresponding reaction in solution and is enabled by the electrostatic preorganization of the active site. Our results reveal sophisticated discrimination in multifunctional catalysis of a highly proficient phosphatase active site.

Degradation of pesticides diazinon and diazoxon by phosphotriesterase: insight into divergent mechanisms from QM/MM and MD simulations

Enzymatic hydrolysis by phosphotriesterase (PTE) is one of the most effective ways of degrading organophosphorus pesticides, but the catalytic efficiency depends on the structural features of substrates. Here the enzymatic degradation of diazinon (DIN) and diazoxon (DON), characterized by PS and PO, respectively, have been investigated by QM/MM calculations and MM MD simulations. Our calculations demonstrate that the hydrolysis of DON (with PO) is inevitably initiated by the nucleophilic attack of the bridging-OH^- on the phosphorus center, while for DIN (with PS), we proposed a new degradation mechanism, initiated by the nucleophilic attack of the Zn_α-bound water molecule, for its low-energy pathway. For both DIN and DON, the hydrolytic reaction is predicted to be the rate-limiting step, with energy barriers of 18.5 and 17.7 kcal mol^-1, respectively. The transportation of substrates to the active site, the release of the leaving group and the degraded product are generally verified to be favorable by MD simulations via umbrella sampling, both thermodynamically and dynamically. The side-chain residues Phe132, Leu271 and Tyr309 play the gate-switching role to manipulate substrate delivery and product release. In comparison with the DON-enzyme system, the degraded product of DIN is more easily released from the active site. These new findings will contribute to the comprehensive understanding of the enzymatic degradation of toxic organophosphorus compounds by PTE.

Mono- and dinuclear zinc complexes bearing identical bis(thiosemicarbazone) ligand that exhibit alkaline phosphatase-like catalytic reactivity

Mono- and dinuclear zinc(II) complexes bearing bis(thiosemicarbazone) (bTSC) ligand were employed in the cleavage of phosphoester bonds. Comparative kinetic studies combined with theory suggested that the P-O bond cleavage is much accelerated by dinuclear zinc(II) complex in the presence of base. Based on the DFT-optimized structures of the proposed intermediates, it is plausible that (1) the removal of sulfur atoms of bTSC ligand from the zinc center provides two vacant sites for the binding of water (or hydroxide ion) and phosphoester and (2) the H-bonding between water (or hydroxide ion) and phosphoester, through several water molecules, may also assist the P-O bond cleavage and facilitate the nucleophilic attack. The kinetic and catalytic studies on the hydrolysis of phosphoester by dinuclear zinc complex showed a much-enhanced reactivity under basic reaction conditions, reaching over 95% conversion yield within 4 h. The currently presented compounds are arguably one of the faster synthetic Zn-based model performing phosphatase-like activity presented so far.

Theoretical Study on Storage and Release of Firefly Luciferin

Among numerous bioluminescent organisms, firefly is the most studied one. Recent experiment proposed that sulfoluciferin (SLH₂ ) may serve as a storage form of luciferin (LH₂ ). In the present article, we employed density functional theory calculation to uncover the mechanism and detailed process of the storage and release reactions. Due to lack of available crystallographic structure of the related enzyme, the calculation was performed on a model system. For the storage reaction, possible amino acid residues were used for imitating the protein environment. For the release reaction, the dielectric constant of 3.0 was employed to simulate the polarity of the protein cavity. The computational results indicated that the reactions from LH₂ to SLH₂ and from SLH₂ to LH₂ are both exergonic, which favor the storage and release processes and coincide with the experimental observation. Basing on experimental and current theoretical study, we supplemented the stages of LH₂ storage and release in the entire bioluminescent cycle of firefly. The current theoretical calculation could inspire the study on LH₂ storage and release of other bioluminescent organisms.

Mechanistic Insights into Promoted Hydrolysis of Phosphoester Bonds by MoO2Cl2(DMF)2

A phosphoester bond is a crucial structural block in biological systems, whose occurrence is regulated by phosphatases. Molybdenum compounds have been reported to be active in phosphate ester hydrolysis of model phosphates. Specifically, MoO₂Cl₂(DMF)₂ is active in the hydrolysis of para-nitrophenyl phosphate (pNPP), leading to heteropolyoxometalate structures. We use density functional theory (DFT) to clarify the mechanism by which these species promote the hydrolysis of the phosphoester bond. The present calculations give insight into several key aspects of this reaction: (i) the speciation of this complex prior to interaction with the phosphate (DMF release, Mo-Cl hydrolysis, and pH influence on the speciation), (ii) the competition between phosphate addition and the molybdate nucleation process, (iii) and the mechanisms by which some plausible active species promote this hydrolysis in different conditions. We described thoroughly two different pathways depending on the nucleation possibilities of the molybdenum complex: one mononuclear mechanism, which is preferred in conditions in which very low complex concentrations are used, and another dinuclear mechanism, which is preferred at higher concentrations.

Nucleophilic Neutralization of Organophosphates: Lack of Selectivity or Plenty of Versatility?

Neutralization of organophosphates is an issue of public health and safety, involving agrochemicals and chemical warfare. A promising approach is the nucleophilic neutralization, scope of this review, which focuses on the molecular nucleophiles: hydroxide, imidazole derivatives, alpha nucleophiles, amines and other nucleophiles. A reactivity mapping is given correlating the pathways and reaction efficiency with structural dependence of the nucleophile (basicity) and the organophosphate (electrophilic centers, P=O/P=S shift, leaving and non-leaving group). Reactions extremely unfavorable (>20 years) can be reduced to seconds with various nucleophiles, some which are catalytic. Although there is no universal nucleophile, a lack of selectivity in some cases accounts for plenty of versatility in other reactions. The ideal neutralization requires a solid mechanistic understanding, together with balancing factors such as milder conditions, fast process, selectivity and less toxic products.

A colorimetric indicator-displacement assay based on stable Cu2+ selective carbon dots for fluorescence turn-on detection of pyrophosphate anions in urine

Determination of PPi levels in urine represents a measurable factor for diagnostic, treatment, and monitoring of urolithiasis. Owing to the quenching ability of Cu²⁺ on fluorescent carbon dots (CDs) and strong binding affinity between Cu²⁺ and PPi, we develop a new off-on assay for PPi detection using newly BPHA CDs (BPHA: N,N-bis(pyridin-2-ylmethyl)hexan-1-amine). The fluorescence intensity of BPHA CDs was significantly quenched by Cu²⁺ ("off") through forming BPHA CDs/Cu²⁺ complexes and the fluorescence intensity of BPHA CDs /Cu²⁺ system was completely resumed by PPi ("on") owing to the release of free Cu²⁺. The fluorescence turn-off/on approach showed a highly selective response to PPi over the large family of other anions. The detection limits were 0.094 μM for Cu²⁺ and 0.025 μM for PPi, respectively. A wide linear range for PPi was up to 4400 μM. The indicator displacement assay (IDAs) using pyrocatechol violet (PV) as a colorimetric indicator was carried out to detect PPi with the naked eyes. The "off-on" fluorescent sensor based on BPHA CDs shows many merits, including convenient operation, cost-saving, high sensitivity, selectivity, stability and wide detecting range, which is applied to PPi detection in human urine sample.

Toward Catalytic Antibiotics: Redesign of Fluoroquinolones to Catalytically Fragment Chromosomal DNA

A library of ciprofloxacin-nuclease conjugates was designed and synthesized to investigate their potential as catalytic antibiotics. The Cu(II) complexes of the new designer compounds (i) showed excellent in vitro hydrolytic and oxidative DNase activity, (ii) showed good antibacterial activity against both Gram-negative and Gram-positive bacteria, and (iii) proved to be highly potent bacterial DNA gyrase inhibitors via a mechanism that involves stabilization of the fluoroquinolone-topoisomerase-DNA ternary complex. Furthermore, the Cu(II) complexes of two of the new designer compounds were shown to fragment supercoiled plasmid DNA into linear DNA in the presence of DNA gyrase, demonstrating a "proof of concept" in vitro. These ciprofloxacin-nuclease conjugates can therefore serve as models with which to develop next-generation, in vivo functioning catalytic antimicrobials.

Reactions of aryl dimethylphosphinothioate esters with anionic oxygen nucleophiles: transition state structure in 70% water-30% ethanol

Aryl dimethylphosphinates, 2, react with anionic oxygen nucleophiles in water via a concerted (ANDN) mechanism. With EtO- in anhydrous ethanol, the mechanism is associative (AN + DN), with rate-limiting pentacoordinate intermediate formation. This change in mechanism with solvent change has been ascribed to changes in the nucleophile and leaving group basicities accompanying solvent change. This paper reports on a kinetic analysis of the reactions of the aryl dimethylphosphinothioates, 3a-g, with oxygen nucleophiles in 70% water-30% ethanol (v/v) solvent at 25 °C, reactions known to proceed by a concerted mechanism in water, to test the rationalization stated above, since the nucleophiles and LGs of interest are more basic in aqueous ethanol than in water. The change in solvent causes an ca. 14 to 320-fold decrease in rate. Hammett and Brønsted-type correlations characterize a concerted TS with less P-LG bonding in aqueous ethanol than in water. Two opposing consequences are associated with the solvent change: (a) increased basicity of nucleophiles and LGs, which lead to a modest tightening of the TS; and (b) better stabilization of the IS relative to the TS in aqueous ethanol, which results in a slower reaction with a more product-like TS. Hammond and anti-Hammond effects on the TS arising from better stabilization of the IS over the TS dominate over the effects of increased nucleophile and LG basicity in determining the looser TS structure in aqueous ethanol. An altered TS structure is consistent with an altered reaction potential energy surface, in this case caused by a change in solvent polarity.

The oxygen isotopic signature of soil- and plant-derived sulphate is controlled by fertilizer type and water source

The oxygen isotope signature of sulphate (δ¹⁸ O_sulphate ) is increasingly used to study nutritional fluxes and sulphur transformation processes in a variety of natural environments. However, mechanisms controlling the δ¹⁸ O_sulphate signature in soil-plant systems are largely unknown. The objective of this study was to determine key factors, which affect δ¹⁸ O_sulphate values in soil and plants. The impact of an ¹⁸ O-water isotopic gradient and different types of fertilizers was investigated in a soil incubation study and a radish (Raphanus sativus L.) greenhouse growth experiment. Water provided 31-64% of oxygen atoms in soil sulphate formed via mineralization of organic residues (green and chicken manures) while 49% of oxygen atoms were derived from water during oxidation of elemental sulphur. In contrast, δ¹⁸ O_sulphate values of synthetic fertilizer were not affected by soil water. Correlations between soil and plant δ¹⁸ O_sulphate values were controlled by water δ¹⁸ O values and fertilizer treatments. Additionally, plant δ³⁴ S data showed that the sulphate isotopic composition of plants is a function of S assimilation. This study documents the potential of using compound-specific isotope ratio analysis for investigating and tracing fertilization strategies in agricultural and environmental studies.

Differences in the Nature of the Phosphoryl Transfer Transition State in Protein Phosphatase 1 and Alkaline Phosphatase: Insights from QM Cluster Models

Quantum mechanical (QM) cluster models are used to probe effects on the catalytic properties of protein phosphatase 1 (PP1) and alkaline phosphatase (AP) due to metal ions and active site residues. The calculations suggest that the phosphoryl transfer transition states in PP1 are synchronous in nature with a significant degree of P-Olg cleavage, while those in AP are tighter with a modest degree of P-Olg cleavage and a range of P-Onuc formation. Similar to observations made in our recent work, a significant degree of cross talk between the forming and breaking P-O bonds complicates the interpretation of the Brønsted relation, especially in regard to AP for which the computed βlg/βEQ,lg value does not correlate with the degree of P-Olg cleavage regardless of the metal ions in the active site. By comparison, the correlation between βlg/βEQ,lg and the P-Olg bond order is more applicable to PP1, which generally exhibits less variation in the transition state than AP. Results for computational models with swapped metal ions between PP1 and AP suggest that the metal ions modulate both the nature of the transition state and the degrees of sensitivity of the transition state to the leaving group. In the reactant state, the degree of the scissile bond polarization is also different in the two enzymes, although this difference appears to be largely determined by the active site residues rather than the metal ions. Therefore, both the identity of the metal ion and the positioning of polar or charged residues in the active site contribute to the distinct catalytic characteristics of these enzymes. Several discrepancies observed between the QM cluster results and the available experimental data highlight the need for further QM/MM method developments for the quantitative analysis of metalloenzymes that contain open-shell transition metal ions.

Editing Domain Motions Preorganize the Synthetic Active Site of Prolyl-tRNA Synthetase

Prolyl-tRNA synthetases (ProRSs) catalyze the covalent attachment of proline onto cognate tRNAs, an indispensable step for protein synthesis in all living organisms. ProRSs are modular enzymes and the "prokaryotic-like" ProRSs are distinguished from "eukaryotic-like" ProRSs by the presence of an editing domain (INS) inserted between motifs 2 and 3 of the main catalytic domain. Earlier studies suggested the presence of coupled-domain dynamics could contribute to catalysis; however, the role that the distal, highly mobile INS domain plays in catalysis at the synthetic active site is not completely understood. In the present study, a combination of theoretical and experimental approaches has been used to elucidate the precise role of INS domain dynamics. Quantum mechanical/molecular mechanical simulations were carried out to model catalytic Pro-AMP formation by Enterococcus faecalis ProRS. The energetics of the adenylate formation by the wild-type enzyme was computed and contrasted with variants containing active site mutations, as well as a deletion mutant lacking the INS domain. The combined results revealed that two distinct types of dynamics contribute to the enzyme's catalytic power. One set of motions is intrinsic to the INS domain and leads to conformational preorganization that is essential for catalysis. A second type of motion, stemming from the electrostatic reorganization of active site residues, impacts the height and width of the energy profile and has a critical role in fine tuning the substrate orientation to facilitate reactive collisions. Thus, motions in a distal domain can preorganize the active site of an enzyme to optimize catalysis.

Tris(2,4-di-tert-butylphenyl)phosphate: An Unexpected Abundant Toxic Pollutant Found in PM2.5

A novel pollutant, tris(2,4-di-tert-butylphenyl)phosphate (I168O), was identified in urban fine particulate matter (PM_2.5) samples in a nontargeted screening based on mass spectrometry for the first time. I168O was detected in all samples collected from two typical cities far away from each other in China. The concentrations of I168O reached up to 851 (median: 153) ng/m³, indicating that it was a widespread and abundant pollutant in the air. The antioxidant Irgafos 168 [I168, tris(2,4-di-tert-butylphenyl)phosphite] popularly added in plastics was the most suspected source for the detected I168O. Simulation studies indicated that heating, UV radiation, and water contact might significantly (p < 0.05) transform I168 to I168O. In particular, I168O might be magnificently evaporated into the air at high temperatures. The outdoor inhalation exposure of I168O may exert substantial health risks.

Self-Assembled Quaternary Ammonium-Containing Comb-Like Polyelectrolytes for the Hydrolysis of Organophosphorous Esters: Effect of Head Groups and Counter-Ions

The aim of this work was to increase the efficiency of catalytic systems for the hydrolytic cleavage of 4-nitrophenyl esters of phosphonic acids. Quaternary ammonium-containing comb-like polyelectrolytes («polymerized micelles») with ester cleavable fragments and a low aggregation threshold were used as catalysts. The synthesis of poly(11-acryloyloxyundecylammonium) surfactants with different counterions (Br^- , NO₃ ^- , CH₃ C₆ H₄ SO₃ ^- ) and head groups was realized by micellar free-radical polymerization. Molecular weight, critical association concentration, particle sizes and solubilization properties toward Orange OT were determined. Self-assemblies organized by poly(11-acryloyloxyundecyltrimethyl ammonium) bromide successfully catalyze the hydrolysis of 4-nitrophenyl butylchloromethylphosphonate up to two orders of magnitude compared to aqueous alkaline hydrolysis. The development of these catalysts is promising for industrial applications and organophosphorus compound detoxification.

Executing a Series of Zinc(II) Complexes of Homologous Schiff Base Ligands for a Comparative Analysis on Hydrolytic, Antioxidant, and Antibacterial Activities

Six zinc(II) complexes, namely, [Zn(HL¹H)Cl₂] (1), [Zn(HL¹H)Br₂] (2), [Zn₂(HL¹H)₂(OH)I₂]·I (3), [Zn(HL²)Cl] (4), [Zn₂(HL²)Br₃] (5), and [Zn(HL²)I] (6) have been manufactured by using two homologous Schiff base ligands H₂L¹ and H₂L² for the purpose of perlustrating their phosphatase-like activity, antioxidant activity, and antibacterial activity. Complexes 1, 2, 4, and 5 have been reported earlier by us, whereas complexes 3 and 6 have been synthesized and structurally characterized by regular physicochemical methods The hydrolytic property of the six complexes has been evaluated by checking the hydrolysis of the P-O bond of a widely used substrate, namely, disodium salt of (para-nitrophenyl)phosphate (PNPP) in 97.5% (v/v) mixture of N,N-dimethylformamide and water (DMF-water). Complexes 2-5 have profound efficiency toward hydrolysis of phosphate ester bonds, and complexes 1 and 6 were noted to be inactive toward hydrolysis. Complex 3 displayed the highest efficacy among the six complexes. Additionally, antioxidant and antibacterial activities of the complexes were studied thoroughly. A detailed study of their antioxidant property revealed that complex 3 manifested superior radical scavenging activity, thus exhibiting the highest antioxidant property. The antibacterial activity was tested using four investigating bacteria, specifically Listeria monocytogenes ATCC19111, Staphylococcus aureus ATCC 700699, Salmonella typhimurium ATCC 23564, and Escherichia coli ATCC 25922 by determining minimum inhibitory concentration (MIC) values using the microdilution method. Here as well, complex 3 exhibited the highest activity to both Gram positive and Gram negative bacteria. The chemistry behind these experimental findings has been manifested by shedding light upon the structural features of the complexes. The suitable choice of ligand H₂L¹ where one methylene group is less than its homologous ligand and metal precursor (ZnI₂) imparts a unique hydroxo-bridged molecular geometry and 2D hydrogen bonding network which in turn probably enhances the hydrolytic and biological activities of complex 3.

Catalytic Foldamers: When the Structure Guides the Function

Enzymes are predominantly proteins able to effectively and selectively catalyze highly complex biochemical reactions in mild reaction conditions. Nevertheless, they are limited to the arsenal of reactions that have emerged during natural evolution in compliance with their intrinsic nature, three-dimensional structures and dynamics. They optimally work in physiological conditions for a limited range of reactions, and thus exhibit a low tolerance for solvent and temperature conditions. The de novo design of synthetic highly stable enzymes able to catalyze a broad range of chemical reactions in variable conditions is a great challenge, which requires the development of programmable and finely tunable artificial tools. Interestingly, over the last two decades, chemists developed protein secondary structure mimics to achieve some desirable features of proteins, which are able to interfere with the biological processes. Such non-natural oligomers, so called foldamers, can adopt highly stable and predictable architectures and have extensively demonstrated their attractiveness for widespread applications in fields from biomedical to material science. Foldamer science was more recently considered to provide original solutions to the de novo design of artificial enzymes. This review covers recent developments related to peptidomimetic foldamers with catalytic properties and the principles that have guided their design.

Modeling the Alkaline Hydrolysis of Diaryl Sulfate Diesters: A Mechanistic Study

Phosphate and sulfate esters have important roles in regulating cellular processes. However, while there has been substantial experimental and computational investigation of the mechanisms and the transition states involved in phosphate ester hydrolysis, there is far less work on sulfate ester hydrolysis. Here, we report a detailed computational study of the alkaline hydrolysis of diaryl sulfate diesters, using different DFT functionals as well as mixed implicit/explicit solvation with varying numbers of explicit water molecules. We consider the impact of the computational model on computed linear free-energy relationships (LFER) and the nature of the transition states (TS) involved. We obtain good qualitative agreement with experimental LFER data when using a pure implicit solvent model and excellent agreement with experimental kinetic isotope effects for all models used. Our calculations suggest that sulfate diester hydrolysis proceeds through loose transition states, with minimal bond formation to the nucleophile and bond cleavage to the leaving group already initiated. Comparison to prior work indicates that these TS are similar in nature to those for the alkaline hydrolysis of neutral arylsulfonate monoesters or charged phosphate diesters and fluorophosphates. Obtaining more detailed insights into the transition states involved assists in understanding the selectivity of enzymes that hydrolyze these reactions.

Insights into Catalytic Gas-Phase Hydrolysis of Organophosphate Chemical Warfare Agents by MOF-Supported Bimetallic Metal-Oxo Clusters

Zirconium-based metal-organic frameworks (Zr-MOFs) have been reported to be efficient catalysts for the hydrolysis of organophosphate chemical warfare agents (CWAs) in buffered solutions. However, for the gas-phase reaction, which is more relevant to the situation in a battlefield gas mask application, the kinetics of Zr-MOF catalysts may be severely hindered by strong product inhibition. To improve the catalytic performance, we computationally screened a series of synthetically accessible Zr-MOF-supported bimetallic metal-oxo clusters in which the metal-oxygen-metal active motif is preserved, aiming to find catalysts that have lower binding affinities to the hydrolysis product. For the promising catalyst Al₂O₂(OH)₂@NU-1000 identified from the screening using density functional theory, we mapped out the full reaction pathway of gas-phase dimethyl p-nitrophenolphosphate (DMNP) hydrolysis and analyzed the free energy profile as well as the turnover frequency (TOF). We found that the catalytic mechanism on the new catalyst is slightly different from the one on NU-1000, which also led to a different TOF-limiting step. Additional factors that can affect the overall catalytic performance in practical application, such as the amount of ambient moisture and the existence of acid gases that may poison the catalyst, have also been evaluated.

Correlations between the structure and the vibrational spectrum of the phosphate group. Implications for the analysis of an important functional group in phosphoproteins

Density functional theory calculations were used to establish correlations between the structure and the vibrational spectrum of the phosphate group in model compounds for phosphorylated amino acids. The model compounds were acetyl phosphate, methyl phosphate, and p-tolyl phosphate, which represented the phosphorylated amino acids aspartyl phosphate, serine or threonine phosphate, and tyrosine phosphate, respectively. The compounds were placed in different environments consisting of one or several HF or H₂O molecules, which modeled interactions of phosphorylated amino acids in the protein environment. The calculations were performed with the B3LYP functional and the 6-311++G(3df, 3pd) basis set. In general, the wavenumbers (or frequencies) of the stretching vibrations of the terminal P–O bonds correlated better with bond lengths of the phosphate group than with its bond angles. The best correlations were obtained with the shortest and the mean terminal P–O bond lengths with standard deviations from the trend line of only 0.2 pm. Other useful correlations were observed with the bond length difference between the shortest and longest terminal P–O bond and with the bond length of the bridging P–O bond.

Vibrational frequencies of phosphate are sensitive to bond length changes on the sub-picometer scale.

Unraveling mechanisms of the uncoordinated nucleophiles: theoretical elucidations of the cleavage of bis(p-nitrophenyl) phosphate mediated by zinc-complexes with apical nucleophiles

A theoretical approach was used to investigate the hydrolytic cleavage mechanisms of the bis(p-nitrophenyl) phosphate (BNPP⁻) catalyzed by Zn(ii)-complexes featuring uncoordinated nucleophiles. Ligand-based and alternative solvent-based nucleophilic attack reaction models are proposed. The pK_a values of the Zn(ii)-bound water molecules or ligands in the [Zn(LⁿH)(η-H₂O)(H₂O)]²⁺ (n = 1, 2 and 3) complexes, as well as the dimerization tendency of the mononuclear Zn(ii)-complexes, were found to significantly influence the reaction mechanisms. The Zn(ii)-L³ complexes were found to be more favorable for the hydrolytic cleavage of the BNPP⁻via a ligand-based nucleophilic attack pathway. This was due to the lower pK_a value for the deprotonation of the oxime ligand, the hard dimerization of the mononuclear Zn(ii)-L³ species, and the presence of an uncoordinated nucleophile. The origins of the uncoordinated reactions were systematically elucidated. The theoretical results reported here are in good agreement with experimental observations and more importantly, help to elucidate the factors that influence intermolecular nucleophilic attack reactions with coordinated/uncoordinated nucleophiles.

A theoretical approach was used to investigate the hydrolytic cleavage mechanisms of the bis(p-nitrophenyl) phosphate (BNPP⁻) catalyzed by Zn(ii)-complexes featuring uncoordinated nucleophiles.

Identification of a Specific Inhibitor of Human Scp1 Phosphatase Using the Phosphorylation Mimic Phage Display Method

Protein phosphatases are divided into tyrosine (Tyr) phosphatases and serine/threonine (Ser/Thr) phosphatases. While substrate trapping mutants are frequently used to identify substrates of Tyr phosphatases, a rapid and simple method to identify Ser/Thr phosphatase substrates is yet to be developed. The TFIIF-associating component of RNA polymerase II C-terminal domain (CTD) phosphatase/small CTD phosphatase (FCP/SCP) phosphatase family is one of the three types of Ser/Thr protein phosphatases. Defects in these phosphatases are correlated with the occurrence of various diseases such as cancer and neuropathy. Recently, we developed phosphorylation mimic phage display (PMPD) method with AlF4−, a methodology to identify substrates for FCP/SCP type Ser/Thr phosphatase Scp1. Here, we report a PMPD method using BeF3− to identify novel substrate peptides bound to Scp1. After screening peptide phages, we identified peptides that bound to Scp1 in a BeF3−-dependent manner. Synthetic phosphopeptide BeM12-1, the sequence of which was isolated at the highest frequency, directly bound to Scp1. The binding was inhibited by adding BeF3−, indicating that the peptide binds to the active center of catalytic site in Scp1. The phosphorylated BeM12-1 worked as a competitive inhibitor of Scp1. Thus, PMPD method may be applicable for the identification of novel substrates and inhibitors of the FCP/SCP phosphatase family.

Catalytic Hydrolysis of Phosphate Monoester by Supramolecular Complexes Formed by the Self-Assembly of a Hydrophobic Bis(Zn2+-cyclen) Complex, Copper, and Barbital Units That Are Functionalized with Amino Acids in a Two-Phase Solvent System

We previously reported on the preparation of supramolecular complexes by the 2:2:2 assembly of a dinuclear Zn²⁺-cyclen (cyclen = 1,4,7,10-tetraazacyclododecane) complex having a 2,2′-bipyridyl linker equipped with 0~2 long alkyl chains (Zn₂L¹~Zn₂L³), 5,5-diethylbarbituric acid (Bar) derivatives, and a copper(II) ion (Cu²⁺) in aqueous solution and two-phase solvent systems and their phosphatase activities for the hydrolysis of mono(4-nitrophenyl) phosphate (MNP). These supermolecules contain Cu₂(μ-OH)₂ core that mimics the active site of alkaline phosphatase (AP), and one of the ethyl groups of the barbital moiety is located in close proximity to the Cu₂(μ-OH)₂ core. The generally accepted knowledge that the amino acids around the metal center in the active site of AP play important roles in its hydrolytic activity inspired us to modify the side chain of Bar with various functional groups in an attempt to mimic the active site of AP in the artificial system, especially in two-phase solvent system. In this paper, we report on the design and synthesis of new supramolecular complexes that are prepared by the combined use of bis(Zn²⁺-cyclen) complexes (Zn₂L¹, Zn₂L², and Zn₂L³), Cu²⁺, and Bar derivatives containing amino acid residues. We present successful formation of these artificial AP mimics with respect to the kinetics of the MNP hydrolysis obeying Michaelis–Menten scheme in aqueous solution and a two-phase solvent system and to the mode of the product inhibition by inorganic phosphate.

GTP Hydrolysis Without an Active Site Base: A Unifying Mechanism for Ras and Related GTPases

GTP hydrolysis is a biologically crucial reaction, being involved in regulating almost all cellular processes. As a result, the enzymes that catalyze this reaction are among the most important drug targets. Despite their vital importance and decades of substantial research effort, the fundamental mechanism of enzyme-catalyzed GTP hydrolysis by GTPases remains highly controversial. Specifically, how do these regulatory proteins hydrolyze GTP without an obvious general base in the active site to activate the water molecule for nucleophilic attack? To answer this question, we perform empirical valence bond simulations of GTPase-catalyzed GTP hydrolysis, comparing solvent- and substrate-assisted pathways in three distinct GTPases, Ras, Rab, and the G_αi subunit of a heterotrimeric G-protein, both in the presence and in the absence of the corresponding GTPase activating proteins. Our results demonstrate that a general base is not needed in the active site, as the preferred mechanism for GTP hydrolysis is a conserved solvent-assisted pathway. This pathway involves the rate-limiting nucleophilic attack of a water molecule, leading to a short-lived intermediate that tautomerizes to form H₂PO₄^- and GDP as the final products. Our fundamental biochemical insight into the enzymatic regulation of GTP hydrolysis not only resolves a decades-old mechanistic controversy but also has high relevance for drug discovery efforts. That is, revisiting the role of oncogenic mutants with respect to our mechanistic findings would pave the way for a new starting point to discover drugs for (so far) "undruggable" GTPases like Ras.

Two-Component Sensing and Regulation: How Do Histidine Kinases Talk with Response Regulators at the Molecular Level?

Perceiving environmental and internal information and reacting in adaptive ways are essential attributes of living organisms. Two-component systems are relevant protein machineries from prokaryotes and lower eukaryotes that enable cells to sense and process signals. Implicating sensory histidine kinases and response regulator proteins, both components take advantage of protein phosphorylation and flexibility to switch conformations in a signal-dependent way. Dozens of two-component systems act simultaneously in any given cell, challenging our understanding about the means that ensure proper connectivity. This review dives into the molecular level, attempting to summarize an emerging picture of how histidine kinases and cognate response regulators achieve required efficiency, specificity, and directionality of signaling pathways, properties that rely on protein:protein interactions. α helices that carry information through long distances, the fine combination of loose and specific kinase/regulator interactions, and malleable reaction centers built when the two components meet emerge as relevant universal principles.

Catalytic Hydrolysis of Phosphate Monoester by Supramolecular Phosphatases Formed from a Monoalkylated Dizinc(II) Complex, Cyclic Diimide Units, and Copper(II) in Two-Phase Solvent System

Design and synthesis of enzyme mimic with programmed molecular interaction among several building blocks including metal complexes and metal chelators is of intellectual and practical significance. The preparation of artificial enzymes that mimic the natural enzymes such as hydrolases, phosphatases, etc. remains a great challenge in the field of supramolecular chemistry. Herein we report on the design and synthesis of asymmetric (nonsymmetric) supermolecules by the 2:2:2 self-assembly of an amphiphilic zinc(II)-cyclen complex containing a 2,2'-bipyridyl linker and one long alkyl chain (Zn₂L³), barbital analogues, and Cu²⁺ as model compounds of an enzyme alkaline phosphatase that catalyzes the hydrolysis of phosphate monoesters such as mono(4-nitrophenyl)phosphate at neutral pH in two-phase solvent system (H₂O/CHCl₃) in pH 7.4 and 37 °C. Hydrolytic activity of these complexes was found to be catalytic, and their catalytic turnover numbers are 3-4. The mechanistic studies based on the UV/vis and emission spectra of the H₂O and CHCl₃ phases of the reaction mixtures suggest that the hydrophilicity/hydrophobicity balance of the supramolecular catalysts is an important factor for catalytic activity.