A homogeneous quenching resonance energy transfer assay for the kinetic analysis of the GTPase nucleotide exchange reaction

A quenching resonance energy transfer (QRET) assay for small GTPase nucleotide exchange kinetic monitoring is demonstrated using nanomolar protein concentrations. Small GTPases are central signaling proteins in all eukaryotic cells acting as a “molecular switches” that are active in the GTP-state and inactive in the GDP-state. GTP-loading is highly regulated by guanine nucleotide exchange factors (GEFs). In several diseases, most prominently cancer, this process in misregulated. The kinetics of the nucleotide exchange reaction reports on the enzymatic activity of the GEF reaction system and is, therefore, of special interest. We determined the nucleotide exchange kinetics using europium-labeled GTP (Eu-GTP) in the QRET assay for small GTPases. After GEF catalyzed GTP-loading of a GTPase, a high time-resolved luminescence signal was found to be associated with GTPase bound Eu-GTP, whereas the non-bound Eu-GTP fraction was quenched by soluble quencher. The association kinetics of the Eu-GTP was measured after GEF addition, whereas the dissociation kinetics could be determined after addition of unlabeled GTP. The resulting association and dissociation rates were in agreement with previously published values for H-Ras^Wt, H-Ras^Q61G, and K-Ras^Wt, respectively. The broader applicability of the QRET assay for small GTPases was demonstrated by determining the kinetics of the Ect2 catalyzed RhoA^Wt GTP-loading. The QRET assay allows the use of nanomolar protein concentrations, as more than 3-fold signal-to-background ratio was achieved with 50 nM GTPase and GEF proteins. Thus, small GTPase exchange kinetics can be efficiently determined in a HTS compatible 384-well plate format.

Adducts of Niobium (V) and Tantalum (V) Halides. XV. Ligand Exchange of the Adducts with Some Phosphoryl Compounds

The ligand exchange MX₅·L + *L?MX₅·*L + L for the octahedral adducts MX₅·L, in an inert solvent (CH₂Cl₂ or CHCl₃) with neutral ligands, proceeds via a dissociative D mechanism when M = Nb, X = Cl and L = phosphoryl compound. A dissociative interchange I_d mechanism is suggested when M = Nb or Ta, and X = F. A first order rate law and positive values for ΔS* (+4 to +14 cal K^?1 mol^?1) are observed for the exchanges on the pentachloride adducts. However, a second order rate law and large negative values for ΔS* (-15 to -24 cal K^?1 mol^?1) are found for the intermolecular neutral ligand exchange (measured by ¹H-NMR.) and for the intramolecular fluorine exchange (measured by ¹⁹F-NMR.) reactions on the pentafluoride adducts. The fluorine exchange is 2 to 5 times faster than the ligand exchange. The exchanges, on the pentachloride and on the pentafluoride adducts, are slowed down with increasing donor strength of the phosphoryl compound.     

An in-silico approach to find a peptidomimetic targeting extracellular domain of HER3 from a HER3 Nanobody

HER3 is an important therapeutic target in cancer treatments. HER3 Nanobodies (Nbs) are a novel class of antibodies with several competitive advantages over conventional antibodies. A peptidomimetic derived from these Nbs can be considered to be a small peptide mimicking some of the molecular recognition interactions of a natural peptide or protein in a three-dimensional (3D) space, with a receptor that has improved properties.In this study, we introduce a new approach to design a peptidomimetic derived from HER3 Nb through an in silico analysis. We propose that the complementarity determining region (CDR3) of HER3 Nb is large enough to effectively interact with HER3 antigen as well as with the entire Nb. A computational analysis has been performed using Nb models retrieved from SWISS-pdb Viewer 4.1.0 (spdbv) as a target spot and HER3 extracellular domain as its antigenic target to identify the interactions between them by the protein–protein docking method. Detailed analysis of selected models with docked complex help us to identify the interacting amino acid residues between the two molecules. The results of in silico analysis show that the CDR3 of HER3 Nb might be used by itself as a peptidomimetic drug instead of the full Nb. HER3 peptidomimetic-derived HER3 Nb may reduce Nb production costs and be used as a substitute for HER3 Nb after further experimental work. The paper demonstrates the feasibility of peptidomimetics designs using bioinformatic tools.     

Microfluidic paper-based multiplex colorimetric immunodevice based on the catalytic effect of Pd/Fe3O4@C peroxidase mimetics on multiple chromogenic reactions

In this report, a non-toxic method was proposed for the simple synthesis of palladium nanoparticles (Pd)/Fe₃O₄@C peroxidase mimetics by virtue of in situ growth of Pd nanoparticles on Fe₃O₄@C magnetic nanoparticles. And a microfluidic paper-based multiplex colorimetric immunodevice (named α-sheet) was developed by site-selectively immobilizing multiple antigens owing to its intrinsic high-efficiency catalytic activity of peroxidase mimetics to multiple chromogenic reactions. The immunosensor platform was prepared by growing a layer of flower-like gold nanoparticles which could entrap the primary antibodies onto paper sensing zones, and the as-prepared Pd/Fe₃O₄@C peroxidase mimetics was used to label secondary antibodies. In the presence of 3,3′,5,5′-tetramethylbenzidine and o-phenylenediamine chromogenic substrates, Pd/Fe₃O₄@C peroxidase mimetics catalyzed chromogenic reactions and showed different colors with respective intensity. To precisely identify the intensity, a piece of black wax printed chromatographic paper with three observing windows (named β-sheet) was flatted on α-sheet. Under the optimal condition, the proposed multiplex colorimetric immunodevice displayed wide linear ranges from 0.005 to 30 ng mL⁻¹ with low detection limits of 1.7 pg mL⁻¹ for carcinoembryonic antigen (CEA) and α-fetoprotein (α-AFP). Meanwhile, the proposed method provided provided a non-toxic, low-cost and promising tool for point-of-care diagnosis.     

Determination of impurities in niobium metal by a radiochemical neutron activation analysis

A radiochemical separation method using an anion exchange resin has been applied to 3N grade Nb for determining nine impurity elements. Five elements (Cr, Fe, Co, Zn and Se) were separated in 2M HF, three elements (Mo, W and Hf) in 32M HF, Nb in 0.5M HF/3M HCl, and Ta in 1M NH₄F/4M NH₄CCl. The contents of the elements were calculated by a single comparator method using two monitors of Au and Co. The main impurity was revealed to be Ta with a content of over 160 ppm.     

[Nb@Ge13/14]3−: New Family Members of Ge-Based Intermetalloid Clusters

During the past two decades, single-atom-centered medium-sized germanium clusters [M@Ge_n] (M=transition metals, n>12) have been extensively explored, both from theoretical perspectives and experimental gas-phase syntheses. However, the actual structural arrangements of the Ge₁₃ and Ge₁₄ endohedral cages are still ambiguous and have long remained an unresolved problem for experimental implementation. In this work, we successfully synthesize 13-/14-vertex Ge clusters [Nb@Ge₁₃]³⁻ ( 1 ) and [Nb@Ge₁₄]³⁻ ( 2 ), which are structurally characterized and exhibit unprecedented topologies, neither classical deltahedra nor 3-connected polyhedral structures. Theoretical analysis indicates that the major stabilization of the Ge backbones arises due to the substantial interaction of Ge 4p-AOs with the endohedral Nb 4d-AOs through three/four-center two-electron bonds with an enhanced electron density accumulated over the shortest Nb−Ge13 contact in 1 . Low occupancies of the direct two-center two-electron (2c–2e) Nb−Ge and Ge−Ge σ bonds point to a considerable degree of electron delocalization over the Ge cages revealing their electron deficiency.     

The crystal structures of strontium exchanged sodium titanosilicates in relation to selectivity for nuclear waste treatment

The exchange of Sr²⁺ into the proton form of the ion exchanger Na₂Ti₂O₃(SiO₄)·2H₂O was examined by means of X-ray powder diffractometry. This material has a sitinakite framework structure enclosing a tunnel parallel to the c-axis. At the 25% Sr²⁺ exchange level, the strontium ion was found near an oxo-framework oxygen midway between two adjacent faces of the tetragonal unit cell. It is bonded to five framework oxygen atoms and five water molecules. The Sr coordination number (CN) is reduced to nine in a sitinakite phase for which 16 mol% of the Ti (IV) was replaced by Nb (V). It has been previously shown that at a higher level of Nb substitution (25 mol%), the CN was further reduced to seven. This change in CN is opposite to what is observed for Cs⁺ where the CN is eight for the Ti phase and 12 for the Ti_1.5Nb_0.5 phase. The changes in CN are accompanied by a series of changes in the space group to accommodate occupancy of the exchange sites by the cations and water molecules. The selectivity of exchanger is governed by the strength and number of bonds formed by the exchange reactions.     

Isocratic anion exchange separations of Group V elements

Isocratic anion exchange separations of Group V elements from solutions containing HF have been considered for the development of Db aqueous phase chemistry experiments. Separation of Nb/Ta from an HF/NH₄F system has been demonstrated but has limited utility due to interferences with alpha and spontaneous fission (SF) source preparation. The physical parameters associated with ion exchange chromatography have been optimized for the separation and sequential isolation of Pa, Nb and Ta from mixed HF/HNO₃ solutions. A suitable procedure incorporating a series of successive chemical separation techniques, i.e. precipitation and ion exchange chromatography, has been suggested for off-line Db characterization studies.     

A Facile Route to Metal Nitride Clusterfullerenes by Using Guanidinium Salts: A Selective Organic Solid as the Nitrogen Source

Using guanidinium salts 1 and 2 as the new nitrogen sources, metal nitride clusterfullerenes (NCFs) based on a variety of metals (Dy, Sc, Y, Gd, Lu, and mixed metals Sc/Dy, Sc/Gd, Sc/Lu, and Lu/Ce) have been synthesized based on a new “selective organic solid” (SOS) route. The synthesis of Dy‐NCFs by using Dy/ 1 was studied in detail, and the optimum molar ratio of 1 /Dy/C has been determined to be 2.5:1:10. For several representative metals such as Sc, Y, Gd, Dy, and Sc/Dy, we quantitatively compared the yield of M₃N@C₈₀ synthesized by the SOS route with the reported “reactive gas atmosphere” route, thereby indicating that the yield of M₃N@C₈₀ by using 1 could be comparable to that obtained by the reactive gas atmosphere route. Three other nitrogen sources ( 3 – 5 ) were also studied for comparison, which were mixed with Dy metal but did not result in the formation of Dy‐NCF. A possible reaction scheme for the solid‐state reaction of 1 , metal, and graphite is proposed. The SOS route appears to be a general route for the synthesis of NCFs that promises both high selectivity of NCFs and high reproducibility of the fullerene yield. Another advantages of the SOS route compared to the reported “trimetallic nitride template” (TNT) process and the reactive gas atmosphere route is that no additional heating pretreatment is needed, thus simplifying the procedure and being much more facile.     

Deoxynivalenol-mimic nanobody isolated from a naïve phage display nanobody library and its application in immunoassay

In this study, using mycotoxin deoxynivalenol (DON) as a model hapten, we developed a nanobody-based environmental friendly immunoassay for sensitive detection of DON. Two nanobodies (N-28 and N-31) which bind to anti-DON monoclonal antibody (MAb) were isolated from a naive phage display library. These nanobodies are clonable, thermally stable and mycotoxin-free products and can be served as coating antigen mimetics in heterologous immunoassay. The half inhibition concentration (IC₅₀) of the immunoassay developed with N-28 and N-31 was 8.77 ± 0.41 ng mL⁻¹ and 19.97 ± 0.84 ng mL⁻¹, respectively, which were 18- and 8-fold more sensitive than the conventional coating antigen (DON-BSA) based immunoassay. In order to better understand the molecular mechanism of antigen mimicry by nanobody, the 3D structure of “nanobody (N-28) - anti-DON MAb” complex was presented and verified by molecular modeling and alanine-scanning mutagenesis. The results showed that hydrogen bond and hydrophobic interaction formed between Thr 102 – Ser 106 of N-28 and CDR H3 residues of anti-DON antibody may contribute to their binding. This novel concept of enhancing sensitivity of immunoassay for DON based on nanobody may provide potential applications in a general method for immunoassay of various food chemical contaminants.     

Ionic Liquid Stabilized Niobium Oxoclusters Catalyzing Oxidation of Sulfides with Exceptional Activity

We present here a new class of niobium oxoclusters that are stabilized effectively by carboxylate ionic liquids. These functionalized ILs are designated as [TBA][LA], [TBA][PA], and [TBA][HPA] in this work, in which TBA represents tetrabutylammonium and LA, PA, and HPA refer to lactate, propionate, 3-hydroxypropionate anions, respectively. The as-synthesized Nb oxoclusters have been characterized by use of elemental analysis, NMR, IR, XRD, TGA, HRTEM. It was found that [TBA][LA]-stabilized Nb oxoclusters (Nb−OC@[TBA][LA]) are uniformly dispersed with an average particle size of 2–3 nm and afforded exceptionally high catalytic activity for the selective oxidation of various thioethers. The turnover number with Nb−OC@[TBA][LA] catalyst was over 56 000 at catalyst loading as low as 0.0033 mol % (1 ppm). Meantime, the catalyst also showed the high activity for the epoxidation of olefins and allylic alcohols by using only 0.065 mol % of catalyst (50 ppm). The characterization of ⁹³Nb NMR spectra revealed that the Nb oxoclusters underwent structural transformation in the presence of H₂O₂ but regenerated to their initial state at the end of the reaction. In particular, the highly dispersed Nb oxoclusters can absorb a large amount of polar organic solvents and thus were swollen greatly, which exhibited “pseudo” liquid phase behavior, and enabled the substrate molecules to be highly accessible to the catalytic center of Nb oxocluster units.     

Novel soft chemical method for optically transparent Ru(bpy)3-K4Nb6O17 thin film

A unique guest-guest ion exchange method was developed for preparing a thin film of a nano-layered K(4)Nb(6)O(17).3H(2)O that possesses both (1) optical transparency and (2) ion-exchangeability under ambient conditions without calcination at high temperature. An optically transparent Ru(bpy)(3)(2+)-K(4)Nb(6)O(17) hybrid thin film, a photoresponsive electrode, was successfully prepared by the guest-guest exchange method by use of the intercalation compound MV(2+)-K(4)Nb(6)O(17) as a precursor. The optically transparent Ru(bpy)(3)(2+)-K(4)Nb(6)O(17) hybrid thin films have been characterized by X-ray diffraction, SEM, AFM, IR, and UV spectroscopies, as well as elemental analysis. The electrochemical behavior of the ITO/Ru(bpy)(3)(2+)-K(4)Nb(6)O(17) hybrid thin film electrode was studied; it also exhibits swift photoresponse in the visible region.     

Synthesis,molecular structures and PMR spectra of heteronuclear niobocene derivatives containing a niobium-tin bond

Treatment of niobocene carbonylhydride, Cp₂Nb(CO)H (I), with Ph_nSnCl_4?n and Et₂SnCl₂ in THF in the presence of Et₃N leads to the respective heteronuclear complexes Cp₂Nb(CO)SnR_nCl_3?n (R = Ph, n = 3 ÷ 1 (II–IV), R = Et, n = 2 (V)). Treatment of II with HCl in ether gives Cp₂Nb(CO)SnCl₃ (VI). Complex VI and its analog (MeC₅H₄)₂Nb(CO)SnCl₃ (VIII) were prepared by an alternative synthesis using direct reaction of I or (MeC₅H₄)₂Nb(CO)H with an equimolar quantity of SnCl₄ in THF in the presence of Et₃N. Complex VI is also generated by insertion of SnCl₂ into the NbCl bond in Cp₂Nb(CO)Cl (VII). X-Ray analysis of complexes II and VIII was performed: for II, space group P2₁/n, a = 10.1021(21), b = 17.4633(32), c= 14.2473(29) Å, β = 95.578(16)°, Z = 4; for VIII, space group. P2₁/n, a= 8.9369(15), b = 13.3589(12), c = 13.9292(20) Å, β = 99.490(14)°, Z = 4. The NbSn bond in VIII (2.764(9) Å) is shorter than that in II (2.825(2) Å). In both cases the NbSn bond is significantly shorter than the sum of Nb and Sn covalent radii (1.66 + 1.40 = 3.06 Å). It is probably partly multiple in character owing to an additional interaction of the lone electron pair of the Nb^III ion (d² configuration) with the antibonding Sn orbitals. The PMR spectra of II–VI exhibit two satellites of the singlet of C₅H₅ protons because of HSn¹¹⁷ and HSn¹¹⁹ spin-spin coupling (SSC). The SSC constant correlates with the number of electronegative chlorine atoms on the Sn atom.     

CsNb3Br7S: Synthese,Struktur und Bindungsverhältnisse

CsNb₃Br₇S: Synthesis, Structure, and Bonding States The reaction of NbBr₅ with Nb, Cs and S in a sealed Nb container affords CsNb₃Br₇S at 800°C (3 days). Further on isotypic compounds of the general formula ANb₃X₇Ch with A = Rb, Cs; X = Cl, Br and Ch = S, Se are obtained. CsNb₃Br₇S crystallizes monoclinic (space group P2₁/a, Z = 2), with the lattice parameters a = 707.4(2), b = 1 888.4(4), c = 994.1(2) pm and β = 98.59(2)°. The crystal structure contains Nb₃ clusters being linked by two additional Nb? Nb bonds to form infinite chains. Adjacent chains are bridged by Cs atoms in a cubeoctahedral coordination sphere of Br atoms. Similar with Nb₃Br₈ seven electrons occupy metal—metal bonding states.     

H2-D2 exchange reaction induced by interaction of Nb monomers with the SiO2 surface and the origins of catalytic activity studied by the DV-Xα cluster calculation

The SIO₂-attached Nb monomer catalyst was found to show catalytic activity for the H₂-D₂ exchange reaction, though almost no significant - or much less - activity was observed with the usual impregnated Nb₂O₅/SiO₂ catalyst or bulk Nb₂O₅. The catalysis activity of the Nb monomers with d^o states is contrary to the common rule that H₂ adsorption on transition metals or mononuclear metal complexes needs the back donation of electrons from metal d orbitals to hydrogen. To explain the unusual reactivity of the Nb monomers, the electronic structure of active Nb sites was calculated using the DV (discrete variational)-Xα cluster method. The calculated level structure for the attached Nb monomers showed a narrower band gap than that of unsupported Nbo₄³⁻ species or Si₃O₁₀⁸⁻ cluster. Furthermore, the component of Nb 4d orbitals in the SiO₂-attached Nb monomers was hybridized with the higher occupied O 2p levels, enabling the formation of Nb hydride species. On the other hand, in unsupported NbO₄³⁻, the Nb 4d in the lower unoccupied levels and the O 2p in the higher occupied levels were separate, with no mixing. The electronic change in Nb sites is discussed in relation to a metal-support interaction.     

Involvement of ��PIX in angiotensin II-induced migration of vascular smooth muscle cells

Angiotensin II (Ang II) stimulates migration of vascular smooth muscle cell (VSMC) in addition to its contribution to contraction and hypertrophy. It is well established that Rho GTPases regulate cellular contractility and migration by reorganizing the actin cytoskeleton. Ang II activates Rac1 GTPase, but its upstream guanine nucleotide exchange factor (GEF) remains elusive. Here, we show that Ang II-induced VSMC migration occurs in a βPIX GEF-dependent manner. βPIX-specific siRNA treatment significantly inhibited Ang II-induced VSMC migration. Ang II activated the catalytic activity of βPIX towards Rac1 in dose- and time-dependent manners. Activity reached a peak at 10 min and declined close to a basal level by 30 min following stimulation. Pharmacological inhibition with specific kinase inhibitors revealed the participation of protein kinase C, Src family kinase, and phosphatidylinositol 3-kinase (PI3-K) upstream of βPIX. Both p21-activated kinase and reactive oxygen species played key roles in cytoskeletal reorganization downstream of βPIX-Rac1. Taken together, our results suggest that βPIX is involved in Ang II-induced VSMC migration.     

Chemie der carbonylniobverbindungen: X. Neue hydridocarbonylkomplexe des vanadiums,niobs und tantals

Complexes of the general formula HM(CO)_n(oligophos) (M = V, n = 2; M = Nb, n = 3 and 2; M = Ta, n = 3) have been prepared by ion exchange on silica gel from their ionic precursors [Et₄N][M(CO)_4,3(oligophos)] (n = 3) or by UV irradiation of HM(CO)_n+1(oligophos) (n = 2). The new compounds, including fac-[Et₄N]-[Nb(CO)₃PPh(CH₂CH₂PPh₂)₂] and cis-[Et₄N][Ta(CO)₄PPh(CH₂CH₂PPh₂)₂], are characterized by their IR (ν(CO)), ¹H (hydride), ³¹P and metal (⁵¹V and ⁹³Nb) NMR spectra.     

Roles of the respective loops at complementarity determining region on the antigen-antibody recognition

For the rational design of antibody, it is important to clarify the characteristics of the interaction between antigen and antibody. In this study, we evaluated a contribution of the respective complementarity determining region (CDR) loops on the antibody recognition of antigen by performing molecular dynamics simulations for 20 kinds of antigen-antibody complexes. Ser and Tyr showed high appearance rates at CDR loops and the sum of averaged appearance rates of Ser and Tyr was about 20⿿30% at all the loops. For example, Ser and Tyr occupied 23.9% at the light chain first loop (L1) and 23.6% at the heavy chain third loop (H3). The direct hydrogen bonds between antigen and antibody were not equally distributed over heavy and light chains. That is, about 70% of the hydrogen bonds were observed at CDRs of the heavy chain and also the direct hydrogen bond with the shortest distance mainly existed at the loops of the heavy chain for all the complexes. It was revealed from the comparison in contribution to the binding free energy among CDR loops that the heavy chain (especially at H2 and H3) had significant influence on the binding between antigen and antibody because three CDR loops of the heavy chain showed the lowest binding free energy (οG_bind) in 19 complexes out of 20. Tyr in heavy chain (especially in H2 and H3) largely contributed to οG_bind whereas Ser hardly contributed to οG_bind even if the number of the direct hydrogen bond with Ser was the fourth largest and also the appearance rate at CDR was the highest among 20 kinds of amino acid residues. The contributions ofTrp and Phe, which bear aromatic ring in the side chain, were often observed in the heavy chain although the energetic contribution of these residues was not so high as Tyr. The present computational analysis suggests that Tyr plays an outstanding role for the antigen-antibody interaction and the CDR loops of the heavy chain is critically important for antibody recognition of antigen.     

An enrichment method of molybdenum on a cellulose nitrate resin for the determination by electrothermal atomic absorption spectrometry coupled with the resin suspension injection.

Cellulose derivative resin (CDR) suspensions containing resin particles of cellulose nitrate (CDR(CN)), cellulose acetate (CDR(CA)), or cellulose triacetate (CDR(CTA)) were prepared as the sorbent for resin suspension injection (RSI) electrothermal atomic absorption spectrometry (ETAAS), in which fine resin particles holding a desired trace element were directly injected into the graphite tube as the suspension. To compare the sorption ability, the distribution ratios of the Mo(VI)-phenylfluorone complex were measured between the aqueous phase and the sorbents, including the CDRs mentioned above and the finely divided anion exchange resin (AR). The results showed that the sorption ability decreases in the following order: CDR(CN) > or = AR > CDR(CA) > or = CDR(CTA). It was concluded that CDR(CN) was able to extract more than 98% of Mo(VI), and was suitable for RSI-ETAAS as well as AR. CDR(CN) was used for the determination of Mo in NIES certified reference materials, No. 10 Rice flour-unpolished; the results showed fairly good agreements between the analytical values and the certified values.     

Study of the Simultaneous Binding of ADP and ATP on Coupling Factor CF-1 by a Modification of the Hummel and Dreyer Method

Abstract

A modification of the Hummel and Dreyer method⁽¹⁾, based on anion exchange separation is used here for the study of the simultaneous binding of ADP and ATP on spinach coupling factor CF₁.

This method gives the same results as gel filtration (dissociation constant and number of sites) when ADP alone is present.

The extent of binding of ADP and ATP is approximately the same when mixed in equimolecular ratio, but since endogenous ADP is irreversible bound, this nucleotide is predominant on CF₁.

The binding of one nucleotide is partly prevented by prealable mixing of CF₁ with the other nucleotide. This phenomenon occurs likely at the level of high affinity sites, where binding would not be entirely reversible, contrarily to low affinity sites.

This method is of potential application for other ligands separable by anion exchange chromatography and for other types of chromatography (reversed phase).