Hydrolysis of nucleoside triphosphates other than ATP by nitrogenase

Highly Selective Potentiometric Sensing of Biologically Relevant Pyrophosphate and Lysophosphatidic Acid Using N-Alkyl/Aryl Ammonium Resorcinarenes/Extended-Resorcinarenes as Ionophores

The ionophore properties of four kinds of N-alkyl/aryl ammonium resorcinarenes and extended-resorcinarenes were inspected for the first time to fabricate polymeric membrane electrodes for determination of biologically relevant pyrophosphate (PPi) and lysophosphatidic acid (LPA). The proposed ion selective electrodes (ISEs) showed significant preference for PPi and LPA with significant selectivity pattern differences from the Hofmeister series. To gain further insight into the performances of the developed ISEs, the binding constants of ionophore-anion complexes in the plasticized membrane phase were investigated, along with the optimized geometries and calculated electrostatic potential. Nernstian potential responses with good reversibility to target anions can be observed when shifting the optimized membranes in aqueous solutions in the concentration range from 10^-6.5 to 10^-2.3/10^-2.2 M. Moreover, potentiometric sensings of PPi and LPA in mineral water and artificial serum were achieved in low μM concentration range, demonstrating their promising real-world applications. These results provide a promising avenue for the development of polymeric membrane electrodes for biological relevant anions and will broaden the scope of potentiometric sensing.

A novel AIE-active imidazolium macrocyclic ratiometric fluorescence sensor for pyrophosphate anion

An imidazolium bridged macrocyclophane was synthesized as a ratiometric fluorescence sensor with aggregation-induced emission (AIE) characteristic to detect pyrophosphate anion with high selectivity among various anions. In the presence of zinc ion, macrocyclophane can form aggregates through complexation with pyrophosphate anion and emit ratiometric fluorescence, resulting from an enhancement in its aggregate-state emission and a reduction in its monomer emission. This AIE-active macrocycle showed great potential as a ratiometric fluorescence receptor.

Selective sensing of ATP by hydroxide-bridged dizinc(ii) complexes offering a hydrogen bonding cavity

This work illustrates the highly selective fluorescence detection of ATP in the presence of other competing anions, such as AMP, ADP, PPi and other phosphates by using a set of hydroxide-bridged dizinc(ii) complexes offering a cavity lined with hydrogen bonds and other interactive forces. ATP, as a whole, was recognized by the synergic combination of Zn-phosphate bonding, ππ stacking between the adenine ring of ATP and the pyridine ring of the dizinc complex and hydrogen bonding interactions that modulate the cavity structure of the dizinc complexes.

Conformational Re-engineering of Porphyrins as Receptors with Switchable N-H⋅⋅⋅X-Type Binding Modes

The selectivity and functional variability of porphyrin cofactors are typically based on substrate binding of metalloporphyrins wherein the pyrrole nitrogen units only serve to chelate the metal ions. Yet, using the porphyrin inner core system for other functions is possible through conformational engineering. As a first step towards porphyrin “enzyme‐like” active centers, a structural and spectroscopic study of substrate binding to the inner core porphyrin system shows that a highly saddle‐distorted porphyrin with peripheral amino receptor groups (1, 2,3,7,8,12,13,17,18‐octaethyl‐5,10,15,20‐tetrakis(2‐aminophenyl)porphyrin) coordinates analytes in a switchable manner dependent on the acidity of the solution. The supramolecular ensemble exhibits exceptionally high affinity to and selectivity for the pyrophosphate anion (2.26±0.021)×10⁹  m⁻¹. ¹H NMR spectroscopic studies provided insight into the likely mode of binding and the characterization of atropisomers, all four of which were also studied by X‐ray crystallography.

High-affinity and selective detection of pyrophosphate in water by a resorcinarene salt receptor

Pyrophosphate (PPi) is a byproduct of DNA and RNA synthesis, and abnormal levels are indicative of disease. We report the high-affinity binding of PPi in water by N-alkyl ammonium resorcinarene chloride receptors. Experimental analysis using ¹H and ³¹P NMR, isothermal titration calorimetry, mass spectrometry, and UV-vis spectroscopy all support exceptional selectivity of these systems for PPi in water. The measured affinity of K₁ = 1.60 × 10⁷ M^-1 for PPi is three orders of magnitude larger than that observed for binding to another phosphate, ATP. This exceptional anion-binding affinity in water is explored through a detailed density functional theory computational study. These systems provide a promising avenue for the development of future innovative medical diagnostic tools.

Visualized discrimination of ATP from ADP and AMP through collapse of supramolecular gels

A supramolecular gel was fabricated through mixing of a cationic gelator with methyl orange. The addition of ATP into the gel caused a distinct gel-collapse, whereas ADP and AMP preserved the gel formation. This observation provided a simple visualized way to discriminate ATP from AMP and ADP.

Biothiols as chelators for preparation of N-(aminobutyl)-N-(ethylisoluminol)/Cu(2+) complexes bifunctionalized gold nanoparticles and sensitive sensing of pyrophosphate ion

In this work, chemiluminescence (CL) reagent and catalyst metal ion complexes bifunctionalized gold nanoparticles (BF-AuNPs) with high CL efficiency were synthesized via an improved synthesis strategy. Biothiols, such as cysteine (Cys), cysteinyl-glycine (Cys-Gly), homocysteine (Hcy), and glutathione (GSH), instead of 2-[bis[2-[carboxymethyl-[2-oxo-2-(2-sulfanylethylamino)ethyl]amino]ethyl]amino]acetic acid (DTDTPA), were used as new chelators. N-(aminobutyl)-N-(ethylisoluminol) (ABEI) was used as a model of CL reagents and Cu(2+) as a model of metal ion. In this strategy, biothiols were first grafted on the surface of ABEI-AuNPs by Au-S bond. Then, Cu(2+) was captured onto the surface of ABEI-AuNPs by the coordination reaction to form BF-AuNPs. The CL intensity of Cu(2+)-Cys/ABEI-AuNPs was 1 order of magnitude higher than that of DTDTPA/Cu(2+)-ABEI-AuNPs synthesized by the previous work. Moreover, strong CL emission of Cu(2+)-Cys/ABEI-AuNPs was also observed in neutral pH conditions. In addition, the present BF-AuNPs synthesis method exhibited advantages over the previous method in CL efficiency, simplicity, and synthetic rate. Finally, by virtue of Cu(2+)-Cys/ABEI-AuNPs as a platform, a simple CL chemosensor for the sensitive and selective detection of pyrophosphate ion (PPi) was established based on the competitive coordination interactions of Cu(2+) between Cys and PPi. The method exhibited a wide detection range from 10 nM to 100 μM, with a low detection limit of 3.6 nM. The chemosensor was successfully applied to the detection of PPi in human plasma samples. It is of great application potential in clinical analysis. This work reveals that BF-AuNPs could be used as ideal nanointerface for the development of novel analytical methods.

Electron transfer precedes ATP hydrolysis during nitrogenase catalysis

The biological reduction of N2 to NH3 catalyzed by Mo-dependent nitrogenase requires at least eight rounds of a complex cycle of events associated with ATP-driven electron transfer (ET) from the Fe protein to the catalytic MoFe protein, with each ET coupled to the hydrolysis of two ATP molecules. Although steps within this cycle have been studied for decades, the nature of the coupling between ATP hydrolysis and ET, in particular the order of ET and ATP hydrolysis, has been elusive. Here, we have measured first-order rate constants for each key step in the reaction sequence, including direct measurement of the ATP hydrolysis rate constant: kATP = 70 s(-1), 25 °C. Comparison of the rate constants establishes that the reaction sequence involves four sequential steps: (i) conformationally gated ET (kET = 140 s(-1), 25 °C), (ii) ATP hydrolysis (kATP = 70 s(-1), 25 °C), (iii) Phosphate release (kPi = 16 s(-1), 25 °C), and (iv) Fe protein dissociation from the MoFe protein (kdiss = 6 s(-1), 25 °C). These findings allow completion of the thermodynamic cycle undergone by the Fe protein, showing that the energy of ATP binding and protein-protein association drive ET, with subsequent ATP hydrolysis and Pi release causing dissociation of the complex between the Fe(ox)(ADP)2 protein and the reduced MoFe protein.

Studies on acedan-based mononuclear zinc complexes toward selective fluorescent probes for pyrophosphate

We have demonstrated that mononuclear Zn(II)-dipicolylamine (DPA) complexes with an auxiliary ligand can fluorescently discriminate pyrophosphate over ATP with as high selectivity as the known fast responding dinuclear bis(ZnDPA) complexes.

Mechanism of Mo-dependent nitrogenase

Nitrogenase is the enzyme responsible for biological reduction of dinitrogen (N(2)) to ammonia, a form usable for life. Playing a central role in the global biogeochemical nitrogen cycle, this enzyme has been the focus of intensive research for over 60 years. This chapter provides an overview of the features of nitrogenase as a background to the subsequent chapters of this volume that detail the many methods that have been applied in an attempt to gain a deeper understanding of this complex enzyme.

CooC1 from Carboxydothermus hydrogenoformans is a nickel-binding ATPase

The maturation of nickel-dependent enzymes requires the participation of several accessory proteins. Typically the hydrolysis of nucleotides is necessary for the final metal transfer steps. The ATPase CooC has been implicated in the insertion of nickel into the Ni,Fe cluster (C cluster) of the carbon monoxide dehydrogenase from Rhodospirillum rubrum. Analysis of the amino acid sequence of CooC suggests the presence of motifs typical for the MinD family of SIMIBI class NTPases, which contain a deviant Walker A motif. The genome of the carboxidotrophic hydrogenogenic bacterium Carboxydothermus hydrogenoformans contains three open reading frames with distinct sequence homology to CooC from R. rubrum. We overproduced, isolated, and studied CooC1 from C. hydrogenoformans. As-isolated CooC1 is monomeric in the absence of ligands but dimerizes in the presence of either nickel, ADP, or ATP. CooC1 shows ATPase activity, and the ADP- and ATP-bound dimeric states are distinguished by their stability. The K8A mutant of CooC1, in which alanine replaces the signature lysine typical for the deviant Walker A motif in the MinD family, is incapable of both ATP hydrolysis and ATP-dependent dimerization. This corroborates that CooC1 is indeed a member of the MinD family and suggests an analogous dynamic equilibrium between monomeric and dimeric states. CooC proteins are involved in the insertion of nickel into carbon monoxide dehydrogenases, and we found that one CooC1 dimer binds one Ni(II) ion with nanomolar affinity. Ni-induced dimerization and the Ni(II)-CooC1 stoichiometry suggest that the Ni-binding site of CooC1 occurs in the dimer interface.

Evidence for a synergistic salt-protein interaction -- complex patterns of activation vs. inhibition of nitrogenase by salt

The molybdenum nitrogenase enzyme system, comprised of the MoFe protein and the Fe protein, catalyzes the reduction of atmospheric N(2) to NH(3). Interactions between these two proteins and between Fe protein and nucleotides (MgADP and MgATP) are crucial to catalysis. It is well established that salts are inhibitors of nitrogenase catalysis that target these interactions. However, the implications of salt effects are often overlooked. We have reexamined salt effects in light of a comprehensive framework for nitrogenase interactions to offer an in-depth analysis of the sources of salt inhibition and underlying apparent cooperativity. More importantly, we have identified patterns of salt activation of nitrogenase that correspond to at least two mechanisms. One of these mechanisms is that charge screening of MoFe protein-Fe protein interactions in the nitrogenase complex accelerates the rate of nitrogenase complex dissociation, which is the rate-limiting step of catalysis. This kind of salt activation operates under conditions of high catalytic activity and low salt concentrations that may resemble those found in vivo. While simple kinetic arguments are strong evidence for this kind of salt activation, further confirmation was sought by demonstrating that tight complexes that have previously displayed little or no activity due to the inability of Fe protein to dissociate from the complex are activated by the presence of salt. This occurs for the combination Azotobacter vinelandii MoFe protein with: (a) the L127Delta Fe protein; and (b) Clostridium pasteurianum Fe protein. The curvature of activation vs. salt implies a synergistic salt-protein interaction.

Purification and characterization of membrane-associated CooC protein and its functional role in the insertion of nickel into carbon monoxide dehydrogenase from Rhodospirillum rubrum

The accessory protein CooC, which contains a nucleotide-binding domain (P-loop) near the N terminus, participates in the maturation of the nickel center of carbon monoxide dehydrogenase (CODH). In this study, CooC was purified from the chromatophore membranes of Rhodospirillum rubrum with a 3,464-fold purification and a 0.8% recovery, and its biochemical properties were characterized. CooC is a homodimer with a molecular mass of 61-63 kDa, contains less than 0.1 atom of Ni(2+) or Fe(2+) per dimer, and has a lambda(max) at 277.5 nm (epsilon(277.5) 32.1 mm(-1) cm(-1)) with no absorption peaks at the visible region. CooC catalyzes the hydrolysis of ATP and GTP with K(m) values of 24.4 and 26.0 microm and V(max) values of 58.7 and 3.7 nmol/min/mg protein for ATP and GTP hydrolysis, respectively. The P-loop mutated form of K13Q CooC was generated by site-specific replacement of lysine by glutamine and was purified according to the protocol for wild-type CooC purification. The K13Q CooC was inactive both in ATP hydrolysis and in vivo nickel insertion. In vitro nickel activation of apoCODH in the cell extracts from UR2 (wild type) and UR871 (K13Q CooC) showed that activation of nickel-deficient CODH was enhanced by CooC and dependent upon ATP hydrolysis. The overall results suggest that CooC couples ATP hydrolysis with nickel insertion into apoCODH. On the basis of our results and models for analogous systems, the functional roles of CooC in nickel processing into the active site of CODH are presented.